Dernières modifications :

Correct tag.
diff --git a/biblio/8125298.mdwn b/biblio/8125298.mdwn
index da9cfad..455d62d 100644
--- a/biblio/8125298.mdwn
+++ b/biblio/8125298.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides."]]
-[[!tag cap method libraries]]
+[[!tag cap method library]]
 
 Gene. 1994 Jan 28;138(1-2):171-4.
 

Enhance.
diff --git a/biblio/23430654.mdwn b/biblio/23430654.mdwn
index 6bf463d..d38342a 100644
--- a/biblio/23430654.mdwn
+++ b/biblio/23430654.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Precise maps of RNA polymerase reveal how promoters direct initiation and pausing."]]
-[[!tag method sequence_tags transcriptome polymerase]]
+[[!tag method sequence_tags transcriptome polymerase oligo-capping]]
 
 Kwak H, Fuda NJ, Core LJ, Lis JT.
 
@@ -7,4 +7,4 @@ Science. 2013 Feb 22;339(6122):950-3. doi: 10.1126/science.1229386.
 
 Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.
 
-[[!pmid 23430654 desc="PRO-seq and PRO-cap."]]
+[[!pmid 23430654 desc="PRO-seq and PRO-cap (based on oligo-capping). Incorporation of biotin-NTPs cause the polymerase to stop, thus brings single-nucleotide resolution."]]

Pas lu.
diff --git a/biblio/28835501.mdwn b/biblio/28835501.mdwn
new file mode 100644
index 0000000..ae65218
--- /dev/null
+++ b/biblio/28835501.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres."]]
+[[!tag virus genome not_read]]
+
+J Virol. 2017 Oct 27;91(22). pii: e01137-17. doi:10.1128/JVI.01137-17
+
+Zhang E, Bell AJ, Wilkie GS, Suárez NM, Batini C, Veal CD, Armendáriz-Castillo I, Neumann R, Cotton VE, Huang Y, Porteous DJ, Jarrett RF, Davison AJ, Royle NJ.
+
+Inherited Chromosomally Integrated Human Herpesvirus 6 Genomes Are Ancient, Intact, and Potentially Able To Reactivate from Telomeres.
+
+[[!pmid 28835501 desc="Stable insertion in the telomeres of a single ancestor of Europeans 2.4 ± 1 ky ago."]]

Add primary paper.
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 89da0e5..d80e08e 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -4,6 +4,7 @@ Work in progress.
 
 On T4 RNL2:
 
+ - Primary paper: [[Ho et al., 2002|biblio/12228725]].
  - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
  - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
  - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]]).

Typographie.
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index d455a16..89da0e5 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -6,13 +6,13 @@ On T4 RNL2:
 
  - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
  - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
- - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]].
+ - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]]).
  - The RNA acceptor strand participates to its ligation by promoting
    adenylylation of the donor, and by promoting the formation of the
    phosphodiester bond.  With DNA, this step is 35 times slower
    ([[Nandakumar et al., 2005|biblio/15851476]]).
  - The K227Q mutation prevents transfer of the andenylyl residue from the
-   linker to RNA ends, thus prevents unwanted ligation products. 
-   [[Viollet et al., 2011|biblio/21722378]]
+   linker to RNA ends, thus prevents unwanted ligation products
+   ([[Viollet et al., 2011|biblio/21722378]]).
 
 [[!inline pages="tagged(ligase)" limit=0]]

Ligation to DNA.
diff --git a/biblio/14967495.mdwn b/biblio/14967495.mdwn
index bc7e2e5..2cea274 100644
--- a/biblio/14967495.mdwn
+++ b/biblio/14967495.mdwn
@@ -7,4 +7,5 @@ Yin S, Kiong Ho C, Miller ES, Shuman S.
 
 Characterization of bacteriophage KVP40 and T4 RNA ligase 2.
 
-[[!pmid 14967495 desc="One more tool in the box?"]]
+[[!pmid 14967495 desc="One more tool in the box? Ligation of RNA to an acceptor
+where the last base is DNA is stronlgy suppressed."]]
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 2490e33..d455a16 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -6,6 +6,11 @@ On T4 RNL2:
 
  - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
  - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
+ - Ligation of RNA to a DNA acceptor is very weak ([[Yin et al., 2004|biblio/14967495]].
+ - The RNA acceptor strand participates to its ligation by promoting
+   adenylylation of the donor, and by promoting the formation of the
+   phosphodiester bond.  With DNA, this step is 35 times slower
+   ([[Nandakumar et al., 2005|biblio/15851476]]).
  - The K227Q mutation prevents transfer of the andenylyl residue from the
    linker to RNA ends, thus prevents unwanted ligation products. 
    [[Viollet et al., 2011|biblio/21722378]]

RNL2 etc.
diff --git a/biblio/15205470.mdwn b/biblio/15205470.mdwn
index eae98df..e53f0f3 100644
--- a/biblio/15205470.mdwn
+++ b/biblio/15205470.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes."]]
-[[!tag ligation]]
+[[!tag ligase]]
 
 Nucleic Acids Res. 2004 Jun 17;32(11):e86 doi:10.1093/nar/gnh085
 
diff --git a/biblio/15247329.mdwn b/biblio/15247329.mdwn
index 449750a..5170fe6 100644
--- a/biblio/15247329.mdwn
+++ b/biblio/15247329.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry."]]
-[[!tag method library ligation]]
+[[!tag method library ligase]]
 
 So AP, Turner RF, Haynes CA.
 
diff --git a/biblio/17018278.mdwn b/biblio/17018278.mdwn
new file mode 100644
index 0000000..717d7bc
--- /dev/null
+++ b/biblio/17018278.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward."]]
+[[!tag ligase]]
+
+Nandakumar J, Shuman S, Lima CD.
+
+Cell. 2006 Oct 6;127(1):71-84
+
+RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.
+
+[[!pmid 17018278 desc="Structure-function analysis of sealing of nicked duplexes."]]
diff --git a/biblio/17510325.mdwn b/biblio/17510325.mdwn
index 4e77765..1e45767 100644
--- a/biblio/17510325.mdwn
+++ b/biblio/17510325.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="RNA maps reveal new RNA classes and a possible function for pervasive transcription."]]
-[[!tag ligation transcriptome small_RNA HepG2]]
+[[!tag ligase transcriptome small_RNA HepG2]]
 
 Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.
 
diff --git a/biblio/21722378.mdwn b/biblio/21722378.mdwn
new file mode 100644
index 0000000..f23d364
--- /dev/null
+++ b/biblio/21722378.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis"]]
+[[!tag ligase method enzyme]]
+
+Viollet S, Fuchs RT, Munafo DB, Zhuang F, Robb GB.
+
+BMC Biotechnol. 2011 Jul 1;11:72. doi: 10.1186/1472-6750-11-72.
+
+T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis
+
+[[!pmid 21722378 desc="The K227Q mutation prevents transfer of the adenylyl residue from the adapter to unwanted targets."]]
diff --git a/biblio/4000951.mdwn b/biblio/4000951.mdwn
index 7ea3887..5214692 100644
--- a/biblio/4000951.mdwn
+++ b/biblio/4000951.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Hexamine cobalt chloride promotes intermolecular ligation of blunt end DNA fragments by T4 DNA ligase."]]
-[[!tag ligation method]]
+[[!tag ligase method]]
 
 Nucleic Acids Res. 1985 Mar 25;13(6):1997-2008.
 
diff --git a/biblio/To_Do b/biblio/To_Do
index 20363d9..d845434 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -700,9 +700,6 @@ Reommends to use only dbSNP entries which have a phred score higher than 40.
 15693942 [mining]
 Uses a highly replicated experimental desigh to show that metabolic genes vary in their expresison between tissues, individuals and populations.
 
-17018278 [enzymes]
-Not Read
-
 16698958 [enhancers]
 Defines the concept of "maximal N-mers".
 
diff --git a/tags/ligase.mdwn b/tags/ligase.mdwn
index 90de02b..2490e33 100644
--- a/tags/ligase.mdwn
+++ b/tags/ligase.mdwn
@@ -1,4 +1,13 @@
 [[!meta title="pages tagged ligase"]]
 
-[[!inline pages="tagged(ligase)" actions="no" archive="yes"
-feedshow=10]]
+Work in progress.
+
+On T4 RNL2:
+
+ - Functional residues analysed by [[Yin et al., 2003|biblio/12611899]].
+ - The truncated Rnl2 was published by [[Ho et al., 2004|biblio/14962393]].
+ - The K227Q mutation prevents transfer of the andenylyl residue from the
+   linker to RNA ends, thus prevents unwanted ligation products. 
+   [[Viollet et al., 2011|biblio/21722378]]
+
+[[!inline pages="tagged(ligase)" limit=0]]

Old
diff --git a/biblio/16723398.mdwn b/biblio/16723398.mdwn
new file mode 100644
index 0000000..6d86193
--- /dev/null
+++ b/biblio/16723398.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Modularity and community structure in networks."]]
+[[!tag network]]
+
+Newman ME
+
+Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8577-82 doi:10.1073/pnas.0601602103
+
+Modularity and community structure in networks.
+
+[[!pmid 16723398 desc="Iterative division method with rules for stopping. Uses a "modularity matrix"."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index a1dddfe..20363d9 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -637,9 +637,6 @@ Few of them overlap FANTOM3 transcripts, but 32/36 can be detected by RT-PCR.
 16751773 [small RNAs]
 The mutation was found by quantitative trait locus (QTL) and single nucleotide polymorphism (SNP) analysis.
 
-16723398 [networks]
-Iterative division method with rules for stopping. Uses a "modularity matrix".
-
 16751776 [small RNAs]
 Loci encoding piRNAs are conserved, but not the piRNA themselves.
 

Old
diff --git a/biblio/17003135.mdwn b/biblio/17003135.mdwn
new file mode 100644
index 0000000..b6885b0
--- /dev/null
+++ b/biblio/17003135.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genomic analysis of the hierarchical structure of regulatory networks."]]
+[[!tag network]]
+
+Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14724-31 doi:10.1073/pnas.0508637103
+
+Yu H, Gerstein M.
+
+Genomic analysis of the hierarchical structure of regulatory networks.
+
+[[!pmid 17003135 desc="Breadth-first search: organises a network in a layered hierarchy. Highest nodes tend to be influencial, middle to have a high betweenness, and lowest to be essential."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 0457f8c..a1dddfe 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -688,9 +688,6 @@ Not read. 85 % of the fly genome is transcribed, and 30 % contributes to mature
 16930954 [enhancers]
 Not read. Human-mouse conserved enhancer in fgf15.
 
-17003135 [networks]
-Breadth-first search: organises a network in a layered hierarchy. Highest nodes tend to be influencial, middle to have a high betweenness, and lowest to be essential.
-
 16893951 [amplification]
 Combined use of T7 polymerase and helicase, strong strand displacement, and branched rolling circle isothermal amplification.
 

Old
diff --git a/biblio/17185604.mdwn b/biblio/17185604.mdwn
new file mode 100644
index 0000000..2ed2c80
--- /dev/null
+++ b/biblio/17185604.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Relating three-dimensional structures to protein networks provides evolutionary insights."]]
+[[!tag network]]
+
+Science. 2006 Dec 22;314(5807):1938-41 doi:10.1126/science.1136174
+
+Kim PM, Lu LJ, Xia Y, Gerstein MB.
+
+Relating three-dimensional structures to protein networks provides evolutionary insights.
+
+[[!pmid 17185604 desc="Mutually exclusive interactions defined by distinguishing interfaces on the nodes."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9fa531f..0457f8c 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -763,9 +763,6 @@ This sequence does not confer the cell cycle properties of mir-29b to siRNAs.
 16175253 [nanotechnologies]
 Continuous washing is necessary for efficient DDM coating.
 
-17185604 [networks]
-Mutually exclusive interactions defined by distinguishing interfaces on the nodes.
-
 17159156 [enhancers]
 Function of an enhancer lost in teleosts transferred to another one.
 

Old
diff --git a/biblio/17656717.mdwn b/biblio/17656717.mdwn
new file mode 100644
index 0000000..bb81e45
--- /dev/null
+++ b/biblio/17656717.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The product space conditions the development of nations."]]
+[[!tag network]]
+
+Science. 2007 Jul 27;317(5837):482-7 doi:10.1126/science.1144581
+
+Hidalgo CA, Klinger B, Barabási AL, Hausmann R.
+
+The product space conditions the development of nations.
+
+[[!pmid 17656717 desc="Derives a product network from per-country export data, and analyses how the countries evolve in time within this network."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 772cacd..9fa531f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -862,9 +862,6 @@ eQTL approach using bayesian statistics and Markoc chains.
 12671682 [normalisation]
 Global normalisation does not allow to survey broad increases or decreases of the total transcriptional activity. This method is more suited when this happens.
 
-17656717 [networks]
-Derives a product network from per-country export data, and analyses how the countries evolve in time within this network.
-
 17703193 [promoters]
 Some genes are up-regulated by the loss of TBP.
 

Old
diff --git a/biblio/15944704.mdwn b/biblio/15944704.mdwn
new file mode 100644
index 0000000..48cf541
--- /dev/null
+++ b/biblio/15944704.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Uncovering the overlapping community structure of complex networks in nature and society."]]
+[[!tag network]]
+
+Nature. 2005 Jun 9;435(7043):814-8.
+
+Palla G, Derényi I, Farkas I, Vicsek T.
+
+Uncovering the overlapping community structure of complex networks in nature and society.
+
+[[!pmid 15944704 desc="Adjascent k-clique communities can share nodes while staying distinct. This allows to create networks of communities."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index de718c3..772cacd 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -937,9 +937,6 @@ The buffer is dried on the lid of the tube, and one cell is deposited in a small
 17412706 [enzymes]
 An interesting protein that condensates DNA.
 
-15944704 [networks]
-Adjascent k-clique communities can share nodes while staying distinct. This allows to create networks of communitiest.
-
 15289330 [pcr]
 A method for selecting normalisation genes.
 

Old
diff --git a/biblio/15205470.mdwn b/biblio/15205470.mdwn
new file mode 100644
index 0000000..eae98df
--- /dev/null
+++ b/biblio/15205470.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes."]]
+[[!tag ligation]]
+
+Nucleic Acids Res. 2004 Jun 17;32(11):e86 doi:10.1093/nar/gnh085
+
+Cole K, Truong V, Barone D, McGall G.
+
+Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes.
+
+[[!pmid 15205470 desc="T4 RNA ligase reaction efficiency improved by PEG and pre-adenylation. Direct labelling method for big quantities: RNA fragmentation, then T4 RNA ligation of biotinylated oligos."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9f82fcf..de718c3 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -47,10 +47,6 @@ Single cell RT-PCR.
 12711698 [amplification] [tracked]
 Uses T3N9 instead of T7dT during all the RT reactions. No 3' bias. Efficient on degraded RNA. Independant of polyadenylation (useful for non-polyA genes, like histones).
 
-15205470 [libraries] [tracked]
-T4 RNA ligase reaction efficiency improved by PEG and pre-adenylation.
-direct labelling method for big quantities: RNA fragmentation, then T4 RNA ligation of biotinylated oligos.
-
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 

Old
diff --git a/biblio/12613261.mdwn b/biblio/12613261.mdwn
new file mode 100644
index 0000000..16d8677
--- /dev/null
+++ b/biblio/12613261.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Probe generation directly from small numbers of cells for DNA microarray studies."]]
+[[!tag random_priming amplification]]
+
+Biotechniques. 2003 Feb;34(2):386-8, 390, 392-3
+
+Xiang CC, Chen M, Kozhich OA, Phan QN, Inman JM, Chen Y, Brownstein MJ.
+
+Probe generation directly from small numbers of cells for DNA microarray studies.
+
+[[!pmid 12613261 desc="Uses T3N9 random nonamer amplification rounds (up to 5), after an initial T7dT RT."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e246214..9f82fcf 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -41,9 +41,6 @@ Aminoallyl UTP to labal cRNAs. In contrast to cDNAs, DMSO is required for subseq
 12161654 [misc]
 Fluorescent bar-coded oligos to monitor transcription in vivo.
 
-12613261 [amplification]
-Uses T3N9 random nonamer amplification rounds (up to 5), after an initial T7dT RT.
-
 10499525 [single cell]
 Single cell RT-PCR.
 

Old
diff --git a/biblio/11222780.mdwn b/biblio/11222780.mdwn
new file mode 100644
index 0000000..62d9aa8
--- /dev/null
+++ b/biblio/11222780.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Quantitative analysis of mRNA amplification by in vitro transcription."]]
+[[!tag ssbp reverse_transcription amplification]]
+
+Nucleic Acids Res. 2001 Mar 1;29(5):E29
+
+Baugh LR, Hill AA, Brown EL, Hunter CP.
+
+Quantitative analysis of mRNA amplification by in vitro transcription.
+
+[[!pmid 11222780 desc="T7 pol generates aberrant template-unrelated products. This is fixed by reducing the concentration of oligo dT primers, and of enzymes. Under these conditions, 2 rounds of RNA linear amplification is not generatng too much bias. Small-volume protocol. T4gp32, a single stranded protein, increases RT processivity."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 153377a..e246214 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -38,9 +38,6 @@ Noise due to RNA extraction is 40 times greater than noise due to replicate hybr
 12595569 [amplificaiton]
 Aminoallyl UTP to labal cRNAs. In contrast to cDNAs, DMSO is required for subsequent cyanine labelling.
 
-11222780 [amplification]
-T7 pol generates aberrant template-unrelated products. This is fixed by reducing the concentration of oligo dT primers, and of enzymes. Under these conditions, 2 rounds of RNA linear amplification is not generatng too much bias. Small-volume protocol. T4gp32, a single stranded protein, increases RT processivity.
-
 12161654 [misc]
 Fluorescent bar-coded oligos to monitor transcription in vivo.
 

Old
diff --git a/biblio/10748532.mdwn b/biblio/10748532.mdwn
index 6ab3a03..fe246d5 100644
--- a/biblio/10748532.mdwn
+++ b/biblio/10748532.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="High-fidelity mRNA amplification for gene profiling."]]
-[[!tag amplification]]
+[[!tag template_switching amplification]]
+
+Nat Biotechnol. 2000 Apr;18(4):457-9 doi:10.1038/74546
+
+Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM.
+
+High-fidelity mRNA amplification for gene profiling.
+
 [[!pmid 10748532 desc="Combines template switch with aRNA amplification"]]

Old
diff --git a/biblio/15560142.mdwn b/biblio/15560142.mdwn
new file mode 100644
index 0000000..3141d76
--- /dev/null
+++ b/biblio/15560142.mdwn
@@ -0,0 +1,9 @@
+[[!meta title="Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis."]]
+[[!tag amplification isothermal method]]
+
+Biotechniques. 2004 Nov;37(5):854-7
+
+Dafforn A, Chen P, Deng G, Herrler M, Iglehart D, Koritala S, Lato S, Pillarisetty S, Purohit R, Wang M, Wang S, Kurn N.
+
+Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis.
+[[!pmid 15560142 desc="Presentation of the Ribo-SPIA kit, which can replace T7 in vitro translation for linear amplification."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 99763d3..153377a 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -263,9 +263,6 @@ Two types of subgraphs are distinguished. Type I are abundant and form giant com
 15588312 [mining]
 Trains learning machines with a GO categor, and interrogates a 40 000 genes x 55 tissues matrix of microarray results.
 
-15560142 [amplification]
-Presentation of the Ribo-SPIA kit, which can replace T7 in vitro translation for linear amplification.
-
 7732590 [misc] [review]
 Reminds that in some organisms, most transcripts share their 5' end.
 

Expand.
diff --git a/biblio/17071717.mdwn b/biblio/17071717.mdwn
index 06041cf..7aa49cb 100644
--- a/biblio/17071717.mdwn
+++ b/biblio/17071717.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Gene expression profiling of single cells on large-scale oligonucleotide arrays."]]
-[[!tag single_cell amplification oligonucleotides]]
+[[!tag single_cell amplification oligonucleotides reverse_transcription]]
+
+Nucleic Acids Res. 2006;34(21):e143 doi:10.1093/nar/gkl740
+
+Hartmann CH, Klein CA.
+
+Gene expression profiling of single cells on large-scale oligonucleotide arrays.
+
 [[!pmid 17071717 desc="High concentration of a dT and random primers mix in reverse transcription."]]

Old
diff --git a/biblio/16542485.mdwn b/biblio/16542485.mdwn
new file mode 100644
index 0000000..4d53a75
--- /dev/null
+++ b/biblio/16542485.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level."]]
+[[!tag amplification template_switching]]
+
+Genome Biol. 2006;7(3):R18 doi:10.1186/gb-2006-7-3-r18
+
+Subkhankulova T, Livesey FJ.
+
+Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level.
+
+[[!pmid 16542485 desc="SMART has a much lower false discovery rate (FDR), but compresses the expression ratios."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 7fee431..99763d3 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -647,9 +647,6 @@ They are not found in other cell types.
 16751343 [non-coding RNA]
 Few of them overlap FANTOM3 transcripts, but 32/36 can be detected by RT-PCR.
 
-16542485 [amplification]
-SMART has a much lower false discovery rate (FDR), but compresses the expression ratios.
-
 16751773 [small RNAs]
 The mutation was found by quantitative trait locus (QTL) and single nucleotide polymorphism (SNP) analysis.
 

Old
diff --git a/biblio/16308152.mdwn b/biblio/16308152.mdwn
new file mode 100644
index 0000000..a64c86b
--- /dev/null
+++ b/biblio/16308152.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA amplification strategies for small sample populations."]]
+[[!tag method amplification template_switching]]
+
+Methods. 2005 Nov;37(3):229-37 doi:10.1016/j.ymeth.2005.09.003
+
+Ginsberg SD
+
+RNA amplification strategies for small sample populations.
+
+[[!pmid 16308152 desc="Detailed protocol for Terminal Continuation (TC)."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 51e4673..7fee431 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -32,9 +32,6 @@ ggcacgcga/cc => C-box for dro hairy.
 10537171
 Full in situ random priming cDNA synthesis
 
-9883850 [amplification]
-3 rounds of T7 RNA amplification (aRNA).
-
 12593794 [general]
 Noise due to RNA extraction is 40 times greater than noise due to replicate hybridisation
 
@@ -539,9 +536,6 @@ Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafis
 16280998 [patents]
 Perpetual-motion machines are not patentable.
 
-16308152 [amplification]
-Detailed protocol for Terminal Continuation (TC).
-
 16224006 [IP]
 20 % of the human coding genome is patented.
 
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 79fa05a..370aa19 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -2,7 +2,10 @@
 
 (work in progress)
 
- - In the "_terminal continuation_" method, [[Che et al., 2004|biblio/14647400]]
-   essentially do template switching with DNA oligonucleotides ending in `CCC`.
+ - The "_terminal continuation_" method ([[Ginsberg et al.,
+   2002|biblio/12462399]], [[Che et al., 2004|biblio/14647400]]) is essentially
+   a template switching with DNA oligonucleotides ending in `CCC` or `GGG`.  `AAA`
+   and `TTT` were also tested.  An extensive protocol was published in
+   [[Ginsberg, 2005|biblio/16308152]].
 
 [[!inline pages="tagged(template_switching)" limit=0]]

Expand.
diff --git a/biblio/15107803.mdwn b/biblio/15107803.mdwn
new file mode 100644
index 0000000..7f66640
--- /dev/null
+++ b/biblio/15107803.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Combined histochemical staining, RNA amplification, regional, and single cell cDNA analysis within the hippocampus."]]
+[[!tag template_switching single_cell not_read]]
+
+Lab Invest. 2004 Aug;84(8):952-62 doi:10.1038/labinvest.3700110
+
+Ginsberg SD, Che S.
+
+Combined histochemical staining, RNA amplification, regional, and single cell cDNA analysis within the hippocampus.
+
+[[!pmid 15107803 desc="Template switching in single cells, in 2004."]]

Expand.
diff --git a/biblio/12462399.mdwn b/biblio/12462399.mdwn
index 1b2ad8a..a1cf3a3 100644
--- a/biblio/12462399.mdwn
+++ b/biblio/12462399.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="RNA Amplification in Brain Tissues."]]
-[[!tag template_switching]]
-[[!pmid 12462399  desc="Comparison of template swithching oligos ending in -AAA, -CCC, -GGG or -TTT. No qualitative difference for the CCC and GGG variants were reported."]]
+[[!tag amplification template_switching]]
+
+Neurochem Res. 2002 Oct;27(10):981-92
+
+Ginsberg SD, Che S.
+
+RNA amplification in brain tissues.
+
+[[!pmid 12462399 desc="Comparison of template swithching oligos ending in -AAA, -CCC, -GGG or -TTT. No qualitative difference for the CCC and GGG variants were reported."]]

Expand.
diff --git a/biblio/14647400.mdwn b/biblio/14647400.mdwn
index 0e0259e..319fe50 100644
--- a/biblio/14647400.mdwn
+++ b/biblio/14647400.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Amplification of RNA transcripts using terminal continuation."]]
-[[!tag template_switching]]
-[[!pmid desc="Templates switching with an oligonucleotide ending in a mixture of Gs and Cs."]]
+[[!tag amplification template_switching]]
+
+Che S, Ginsberg SD.
+
+Lab Invest. 2004 Jan;84(1):131-7.
+
+Amplification of RNA transcripts using terminal continuation.
+
+[[!pmid 14647400 desc="Templates switching with a DNA oligonucleotide ending in a mixture of Gs and Cs."]]
diff --git a/tags/template-switching.mdwn b/tags/template-switching.mdwn
deleted file mode 100644
index abc760c..0000000
--- a/tags/template-switching.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged template-switching"]]
-
-[[!inline pages="tagged(template-switching)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 800093f..79fa05a 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged template_switching"]]
 
-[[!inline pages="tagged(template_switching)" actions="no" archive="yes"
-feedshow=10]]
+(work in progress)
+
+ - In the "_terminal continuation_" method, [[Che et al., 2004|biblio/14647400]]
+   essentially do template switching with DNA oligonucleotides ending in `CCC`.
+
+[[!inline pages="tagged(template_switching)" limit=0]]

Correct link.
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 206f832..7442037 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -17,8 +17,8 @@ Methods for enriching capped RNAs.
    single-strand (T)TTTGGG overhang, and prime second-strand synthesis.
 
  - Cap-jumping ([[Efimov et al., 2001|biblio/11713326]]): oxidize diols,
-   covalently bind a 3′-amine oligonucleotide.  The [[reverse_transcriptase]]
-   ireads through the cap structure and chemical bond, and integrates the reverse
+   covalently bind a 3′-amine oligonucleotide.  The [[reverse transcriptase|reverse_transcription]]
+   reads through the cap structure and chemical bond, and integrates the reverse
    complement of the oligonucleotide to the first-strand cDNA.
 
  - [[Cleptet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4

Expand.
diff --git a/biblio/11713326.mdwn b/biblio/11713326.mdwn
index 1a698d9..7a677af 100644
--- a/biblio/11713326.mdwn
+++ b/biblio/11713326.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Detection of the 5'-cap structure of messenger RNAs with the use of the cap-jumping approach."]]
 [[!tag cap method]]
+
+Efimov VA, Chakhmakhcheva OG, Archdeacon J, Fernandez JM, Fedorkin ON, Dorokhov YL, Atabekov JG.Efimov VA1, Chakhmakhcheva OG, Archdeacon J, Fernandez JM, Fedorkin ON, Dorokhov YL, Atabekov JG.
+
+Nucleic Acids Res. 2001 Nov 15;29(22):4751-9.
+
+Detection of the 5'-cap structure of messenger RNAs with the use of the cap-jumping approach.
+
 [[!pmid 11713326 desc="Binds an oligonucleotide to the cap using its free diol group, and integrates its sequence to the full-length cDNA using template-switching."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 9a0c954..206f832 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -16,6 +16,11 @@ Methods for enriching capped RNAs.
    the first-strand cDNA, ligate a double-stranded adapter ending with a
    single-strand (T)TTTGGG overhang, and prime second-strand synthesis.
 
+ - Cap-jumping ([[Efimov et al., 2001|biblio/11713326]]): oxidize diols,
+   covalently bind a 3′-amine oligonucleotide.  The [[reverse_transcriptase]]
+   ireads through the cap structure and chemical bond, and integrates the reverse
+   complement of the oligonucleotide to the first-strand cDNA.
+
  - [[Cleptet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4
    DNA ligase and a double-stranded adapter with NNNNNN overhang instead of T4
    RNA ligase and a single-stranded linker.

Old
diff --git a/biblio/10471753.mdwn b/biblio/10471753.mdwn
new file mode 100644
index 0000000..495da5a
--- /dev/null
+++ b/biblio/10471753.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Regulation of average length of complex PCR product."]]
+[[!tag PCR amplification]]
+
+Nucleic Acids Res. 1999 Sep 15;27(18):e23.
+
+Shagin DA, Lukyanov KA, Vagner LL, Matz MV.
+
+Regulation of average length of complex PCR product.
+
+[[!pmid 10471753 desc="Amplify preferentially long PCR product with a single
+primer. Shorter molecules have a higher probability of undergoing
+inhibitory intramolecular interactions. (suppressive PCR)"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index c6266c0..51e4673 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -26,11 +26,6 @@ Review citing the 2 upper articles
 * Says that exponential (65+25 cycles) is more faithful than linear.
 * Limits [dNTP] to produce only 3' cDNA that are a few hundrer base pairs long.
 
-10471753
-Amplify preferentially long PCR product with a single
-primer. Shorter molecules have a higher probability of undergoing
-inhibitory intramolecular interactions.
-
 http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0020178
 ggcacgcga/cc => C-box for dro hairy.
 
@@ -61,15 +56,6 @@ Single cell RT-PCR.
 12711698 [amplification] [tracked]
 Uses T3N9 instead of T7dT during all the RT reactions. No 3' bias. Efficient on degraded RNA. Independant of polyadenylation (useful for non-polyA genes, like histones).
 
-12560512 [amplification] [tracked]
-«Semi-linear» Taq polymerase amplification used on the cDNA sample at the labelling step.
-
-14602935 [amplification] [tracked]
-Performs SMART, then exponential PCR, then random-primed klenow labelling.
-
-12398200 [amplification]
-Advocates a systematic round of RNA amplificatin, becaus it reduces interarray variability.
-
 15205470 [libraries] [tracked]
 T4 RNA ligase reaction efficiency improved by PEG and pre-adenylation.
 direct labelling method for big quantities: RNA fragmentation, then T4 RNA ligation of biotinylated oligos.
@@ -580,9 +566,6 @@ In this changing network, most parameters except the clustering coefficient depe
 15899964 [promoters]
 ChIP on chip focused on the preinitiation complexes of the ENCODE regions.
 
-10471753 [amplification]
-Single-primer PCR with a moderate suppressive effect can be used to regulate the product size.
-
 16407397 [enhancers]
 Idenification of conserved enhancers of shh hundreds of kp far of the coding sequence.
 

Old
diff --git a/biblio/8125298.mdwn b/biblio/8125298.mdwn
new file mode 100644
index 0000000..da9cfad
--- /dev/null
+++ b/biblio/8125298.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides."]]
+[[!tag cap method libraries]]
+
+Gene. 1994 Jan 28;138(1-2):171-4.
+
+Maruyama K, Sugano S.
+
+Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides.
+
+[[!pmid 8125298 desc="Oligo capping primary paper."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 8028f58..c6266c0 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -89,9 +89,6 @@ A method to amplify two distinguishable substrates in the same PCR tube, so that
 12582258 [misc]
 Direct labeling of 10µg total RNA.
 
-8125298 [libraries]
-Oligo capping primary paper.
-
 12902159 [networks]
 Correlating subnetwork topology, correlation or inverse collrelation, and phase.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 78ca0f3..9a0c954 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -6,11 +6,11 @@ Methods for enriching capped RNAs.
 
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
- - Oligo-capping ([[Suzuki et al., 1999|biblio/9373149]]): dephosphorylate,
+ - Oligo-capping ([[Maruyama et al., 1994|biblio/8125298]]): dephosphorylate,
    uncover functional phosphate with decapping enzyme, and ligate RNA adaptor
    with T4 RNA ligase.
 
-(wip: Fromont-racine et al., Maruyama et al.)
+(wip: Fromont-racine et al.)
 
  - CapSelect ([[Schmidt et al., 1999|biblio/10518626]]): Add a poly-A tail to
    the first-strand cDNA, ligate a double-stranded adapter ending with a

Minor edits.
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 27bfd58..78ca0f3 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -6,16 +6,18 @@ Methods for enriching capped RNAs.
 
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
- - Oligo-capping [[Suzuki et al., 1999|biblio/9373149]]: dephosphorylate, uncover functional
-   phosphate with decapping enzyme, and ligate RNA adaptor with T4 RNA ligase.
+ - Oligo-capping ([[Suzuki et al., 1999|biblio/9373149]]): dephosphorylate,
+   uncover functional phosphate with decapping enzyme, and ligate RNA adaptor
+   with T4 RNA ligase.
 
 (wip: Fromont-racine et al., Maruyama et al.)
 
- - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
-   cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
-   overhang, and prime second-strand synthesis.
+ - CapSelect ([[Schmidt et al., 1999|biblio/10518626]]): Add a poly-A tail to
+   the first-strand cDNA, ligate a double-stranded adapter ending with a
+   single-strand (T)TTTGGG overhang, and prime second-strand synthesis.
 
- - [[Cleptet et al., 2004|biblio/14704363]] used oligo-capping, but used T4 DNA ligase and a double-stranded
-   adapter with NNNNNN overhang instead of T4 RNA ligase and a single-stranded linker.
+ - [[Cleptet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4
+   DNA ligase and a double-stranded adapter with NNNNNN overhang instead of T4
+   RNA ligase and a single-stranded linker.
 
 [[!inline pages="tagged(cap)" limit=0]]

Old
diff --git a/biblio/163011.mdwn b/biblio/163011.mdwn
new file mode 100644
index 0000000..c0853f9
--- /dev/null
+++ b/biblio/163011.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A blocked structure at the 5' terminus of mRNA from cytoplasmic polyhedrosis virus."]]
+[[!tag cap not_read]]
+
+Nature. 1975 Jan 31;253(5490):374-5
+
+Furuichi Y, Miura K.
+
+A blocked structure at the 5' terminus of mRNA from cytoplasmic polyhedrosis virus.
+
+[[!pmid 163011 desc="Discovery of the cap."]]
diff --git a/biblio/9373149.mdwn b/biblio/9373149.mdwn
new file mode 100644
index 0000000..eff393a
--- /dev/null
+++ b/biblio/9373149.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library."]]
+[[!tag cap library method]]
+
+Gene. 1997 Oct 24;200(1-2):149-56.
+
+Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S.
+
+Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library.
+
+[[!pmid 9373149 desc="Oligo-capping to build 5′ or FL cDNA libraries."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 8db5444..8028f58 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -74,9 +74,6 @@ Advocates a systematic round of RNA amplificatin, becaus it reduces interarray v
 T4 RNA ligase reaction efficiency improved by PEG and pre-adenylation.
 direct labelling method for big quantities: RNA fragmentation, then T4 RNA ligation of biotinylated oligos.
 
-9373199 [libraries]
-Oligo-capping to build 5' ou FL cDNA libraries.
-
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 1ca3e1f..27bfd58 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -6,6 +6,11 @@ Methods for enriching capped RNAs.
 
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
+ - Oligo-capping [[Suzuki et al., 1999|biblio/9373149]]: dephosphorylate, uncover functional
+   phosphate with decapping enzyme, and ligate RNA adaptor with T4 RNA ligase.
+
+(wip: Fromont-racine et al., Maruyama et al.)
+
  - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.

Consolidation.
diff --git a/biblio/2020554.mdwn b/biblio/2020554.mdwn
index f11b3ad..a155d56 100644
--- a/biblio/2020554.mdwn
+++ b/biblio/2020554.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors."]]
-[[!tag libraries]]
+[[!tag library]]
 
 Nucleic Acids Res. 1991 Mar 11;19(5):1156 doi:10.1093/nar/19.5.1156
 
diff --git a/biblio/7760832.mdwn b/biblio/7760832.mdwn
index dc10fb3..ad0cce4 100644
--- a/biblio/7760832.mdwn
+++ b/biblio/7760832.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture)."]]
-[[!tag cap libraries]]
+[[!tag cap library]]
 
 Mol Cell Biol. 1995 Jun;15(6):3363-71.
 
diff --git a/tags/libraries.mdwn b/tags/libraries.mdwn
deleted file mode 100644
index f649073..0000000
--- a/tags/libraries.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged libraries"]]
-
-[[!inline pages="tagged(libraries)" actions="no" archive="yes"
-feedshow=10]]

Old
diff --git a/biblio/1923806.mdwn b/biblio/1923806.mdwn
new file mode 100644
index 0000000..84ef60b
--- /dev/null
+++ b/biblio/1923806.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Oligodeoxyribonucleotide ligation to single-stranded cDNAs: a new tool for cloning 5' ends of mRNAs and for constructing cDNA libraries by in vitro amplification."]]
+[[!tag library]]
+
+Nucleic Acids Res. 1991 Oct 11;19(19):5227-32
+
+Edwards JB, Delort J, Mallet J.
+
+Oligodeoxyribonucleotide ligation to single-stranded cDNAs: a new tool for cloning 5' ends of mRNAs and for constructing cDNA libraries by in vitro amplification.
+
+[[!pmid 1923806 desc="T4 RNA ligase to graft DNA linkers at the end of cDNAs."]]

Expand.
diff --git a/biblio/16708763.mdwn b/biblio/16708763.mdwn
index d9d1551..ab4171f 100644
--- a/biblio/16708763.mdwn
+++ b/biblio/16708763.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA."]]
-[[!tag protocols cDNA oligonucleotides hybridisation random_priming]]
+[[!tag protocols cDNA oligonucleotides hybridisation random_priming reverse_transcription]]
+
+Biotechniques. 2006 May;40(5):649-57.
+
+Stangegaard M, Dufva IH, Dufva M.
+
+Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA.
+
 [[!pmid 16708763 desc="Almost 100% of the RNA molecules are primed (using massive amounts of oligonucleotides)."]]

Expand/correct.
diff --git a/biblio/10037822.mdwn b/biblio/10037822.mdwn
index 1b4f93b..9c0a63a 100644
--- a/biblio/10037822.mdwn
+++ b/biblio/10037822.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Amplification of cDNA ends based on template-switching effect and step-out PCR."]]
 [[!tag template_switching PCR method ]]
+
+Nucleic Acids Res. 1999 Mar 15;27(6):1558-60.
+
+Matz M, Shagin D, Bogdanova E, Britanova O, Lukyanov S, Diatchenko L, Chenchik A.
+
+Amplification of cDNA ends based on template-switching effect and step-out PCR.
+
 [[!pmid 10037822 desc="To counter template-switching happening from inside the oligonucleotide instead of its tail."]]
diff --git a/biblio/12089562.mdwn b/biblio/12089562.mdwn
index 2e378cf..0bf567c 100644
--- a/biblio/12089562.mdwn
+++ b/biblio/12089562.mdwn
@@ -7,4 +7,4 @@ Nat Biotechnol. 2002 Jul;20(7):738-42.
 
 Amine-modified random primers to label probes for DNA microarrays.
 
-[[!pmid desc="Incorporates aminoallyl-dUTP instead of cy3/5dUTP. Uses priming hexamers with a amino C6dT in 5′. This allows to reduce by 10 folds the quantity of RNA as a starting material. Presence of amplification products of t/rRNAs is not a problem when « optimal » quantities of total RNA are used."]]
+[[!pmid 12089562 desc="Incorporates aminoallyl-dUTP instead of cy3/5dUTP. Uses priming hexamers with a amino C6dT in 5′. This allows to reduce by 10 folds the quantity of RNA as a starting material. Presence of amplification products of t/rRNAs is not a problem when « optimal » quantities of total RNA are used."]]

Text not available.
diff --git a/biblio/8247743.mdwn b/biblio/8247743.mdwn
new file mode 100644
index 0000000..b1d9844
--- /dev/null
+++ b/biblio/8247743.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Synthesis of full-length cDNA using DNA-capped mRNA."]]
+[[!tag cap method not_read]]
+
+Nucleic Acids Symp Ser. 1993;(29):143-4.
+
+Sekine S, Kato S.
+
+Synthesis of full-length cDNA using DNA-capped mRNA.
+
+[[!pmid 8247743 desc="Similar to oligo-capping."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index cc9b731..1ca3e1f 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -4,6 +4,8 @@ Methods for enriching capped RNAs.
 
 (work in progress)
 
+ - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
+
  - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.

Old
diff --git a/biblio/14704363.mdwn b/biblio/14704363.mdwn
new file mode 100644
index 0000000..6816e33
--- /dev/null
+++ b/biblio/14704363.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Improved full-length cDNA production based on RNA tagging by T4 DNA ligase."]]
+[[!tag cap method]]
+
+Nucleic Acids Res. 2004 Jan 2;32(1):e6 doi:10.1093/nar/gng158
+
+Clepet C, Le Clainche I, Caboche M.
+
+Improved full-length cDNA production based on RNA tagging by T4 DNA ligase.
+
+[[!pmid 14704363 desc="T4 DNA ligase used to ligate a double stranded cap-tag."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index fbc7431..8db5444 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -80,9 +80,6 @@ Oligo-capping to build 5' ou FL cDNA libraries.
 14606961 [libraries]
 The nuclease activity of T7 RNA pol could also show some transcript specificity.
 
-14704353 [libraries] [tracked]
-T4 DNA ligase used to ligate a double stranded cap-tag.
-
 3799962 [enzymes]
 Optimal : Donor/acceptor 5:1; hexammine cobalt chloride 5.0 mM, PEG8000 25%; ATP 100µM. Inhibitors: ATP > 100 µM, MN 2+ > 5mM, NaCl > 20 mM.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index b21b128..cc9b731 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -4,8 +4,11 @@ Methods for enriching capped RNAs.
 
 (work in progress)
 
- - [[CapSelect|biblio/10518626]]: Add a poly-A tail to the first-strand
+ - CapSelect [[Schmidt et al., 1999|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.
 
+ - [[Cleptet et al., 2004|biblio/14704363]] used oligo-capping, but used T4 DNA ligase and a double-stranded
+   adapter with NNNNNN overhang instead of T4 RNA ligase and a single-stranded linker.
+
 [[!inline pages="tagged(cap)" limit=0]]

Syntax
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index b41aee6..b21b128 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -4,7 +4,7 @@ Methods for enriching capped RNAs.
 
 (work in progress)
 
- - [[CapSelect|biblio/10518626.mdwn]]: Add a poly-A tail to the first-strand
+ - [[CapSelect|biblio/10518626]]: Add a poly-A tail to the first-strand
    cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
    overhang, and prime second-strand synthesis.
 

Cleanup.
diff --git a/tags/capi.mdwn b/tags/capi.mdwn
deleted file mode 100644
index c8d832d..0000000
--- a/tags/capi.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged capi"]]
-
-[[!inline pages="tagged(capi)" actions="no" archive="yes"
-feedshow=10]]

Expand.
diff --git a/biblio/10518626.mdwn b/biblio/10518626.mdwn
index f2e1e16..f69b0d8 100644
--- a/biblio/10518626.mdwn
+++ b/biblio/10518626.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs."]]
 [[!tag cap method enzyme manganese]]
+
+Nucleic Acids Res. 1999 Nov 1;27(21):e31.
+
+Schmidt WM, Mueller MW.
+
+CapSelect: a highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs.
+
 [[!pmid 10518626 desc="In presence of the 5' cap and Mn2+, the SuperScriptII enzyme adds 3-4 extra dC residues to the first strand cDNA."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 8c0c7c0..b41aee6 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -1,4 +1,11 @@
 [[!meta title="pages tagged cap"]]
 
-[[!inline pages="tagged(cap)" actions="no" archive="yes"
-feedshow=10]]
+Methods for enriching capped RNAs.
+
+(work in progress)
+
+ - [[CapSelect|biblio/10518626.mdwn]]: Add a poly-A tail to the first-strand
+   cDNA, ligate a double-stranded adapter ending with a single-strand (T)TTTGGG
+   overhang, and prime second-strand synthesis.
+
+[[!inline pages="tagged(cap)" limit=0]]

Old
diff --git a/biblio/11410683.mdwn b/biblio/11410683.mdwn
new file mode 100644
index 0000000..68a2277
--- /dev/null
+++ b/biblio/11410683.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Identification and prevention of a GC content bias in SAGE libraries."]]
+[[!tag method sequence_tags]]
+
+Nucleic Acids Res. 2001 Jun 15;29(12):E60-0.
+
+Margulies EH, Kardia SL, Innis JW.
+
+Identification and prevention of a GC content bias in SAGE libraries.
+
+[[!pmid 11410683 desc="Small changes in handling temperature can melt AT-rich tags and deplete them from the library."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index c5d97d1..fbc7431 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -778,9 +778,6 @@ SAGE libraries sequenced wiht 454 technology.
 17095694 [genome]
 Tiling arrays were designed with draft genome sequence; 11~13,000 genes detected.
 
-11410683 [tags]
-Small changes in handling temperature can melt AT-rich tags and deplete them from the library.
-
 16630818 [enhancers]
 Not read. Conserved developmental enhancers acting as silencers in ES cells.
 

Expand.
diff --git a/biblio/14676315.mdwn b/biblio/14676315.mdwn
index 03705a2..955d7e3 100644
--- a/biblio/14676315.mdwn
+++ b/biblio/14676315.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Gene expression analysis of plant host-pathogen interactions by SuperSAGE."]]
 [[!tag sequence_tags SAGE method EcoP15I enzyme]
+
+Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15718-23 doi:10.1073/pnas.2536670100
+
+Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Kruger DH, Terauchi R.
+
+Gene expression analysis of plant host-pathogen interactions by SuperSAGE.
+
 [[!pmid 14676315 desc="Uses the class III enzyme EcoP15I to get longer tags."]]

Old
diff --git a/biblio/9331369.mdwn b/biblio/9331369.mdwn
new file mode 100644
index 0000000..ca9fa8a
--- /dev/null
+++ b/biblio/9331369.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The significance of digital gene expression profiles."]]
+[[!tag sequence_tags statistics]]
+
+Genome Res. 1997 Oct;7(10):986-95
+
+Audic S, Claverie JM.
+
+The significance of digital gene expression profiles.
+
+[[!pmid 9331369 desc="Bayesian approach to identify differentially expressed genes in pairwise comparison."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 9f90110..c5d97d1 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -502,9 +502,6 @@ The distance between the EcoP15I sites can be as much as a few kilobasepairs.
 12429865 [tags]
 Provides an easy access to various statistical tests.
 
-9331369 [tags]
-Bayesian approach to identify differentially expressed genes in pairwise comparison.
-
 16059932 [enhancers] [not read]
 Small human-fugu conserved sequences (max 24 bp) in the promoter and intron 1 of a non-TF gene.
 

Old
diff --git a/biblio/11116099.mdwn b/biblio/11116099.mdwn
new file mode 100644
index 0000000..adc1ef2
--- /dev/null
+++ b/biblio/11116099.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The comparison of gene expression from multiple cDNA libraries."]]
+[[!tag sequence_tags statistics]]
+
+Genome Res. 2000 Dec;10(12):2055-61
+
+Stekel DJ, Git Y, Falciani F.
+
+The comparison of gene expression from multiple cDNA libraries.
+
+[[!pmid 11116099 desc="The distribution of the R statistic is exponential in randomized datasets. This could be used to determine a threshold."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 295b54f..9f90110 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -502,9 +502,6 @@ The distance between the EcoP15I sites can be as much as a few kilobasepairs.
 12429865 [tags]
 Provides an easy access to various statistical tests.
 
-1116099 [tags]
-The distribution of the R statistic is exponential in randomized datasets. This could be used to determine a threshold.
-
 9331369 [tags]
 Bayesian approach to identify differentially expressed genes in pairwise comparison.
 

Old
diff --git a/biblio/15371555.mdwn b/biblio/15371555.mdwn
new file mode 100644
index 0000000..2b94ebc
--- /dev/null
+++ b/biblio/15371555.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells."]]
+[[!tag random_priming sequence_tags]]
+
+Heidenblut AM, Lüttges J, Buchholz M, Heinitz C, Emmersen J, Nielsen KL, Schreiter P, Souquet M, Nowacki S, Herbrand U, Klöppel G, Schmiegel W, Gress T, Hahn SA.
+
+Nucleic Acids Res. 2004 Sep 15;32(16):e131 doi:10.1093/nar/gnh130
+
+aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells.
+
+[[!pmid 15371555 desc="Semi-random priming: the 5' oligo is N6-NlaIII."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 313a7f0..295b54f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -415,9 +415,6 @@ Repeat Associated siRNA (rasiRNA) were detected in zebrafish.
 15939778 [single cells]
 The cells were pulled out from midly digested ganglia with glass microelectrodes.
 
-15371555 [tags]
-Semi-random priming: the 5' oligo is N6-NlaIII.
-
 15911778 [networks]
 The muticommunauty structure of the air transortation network  explains why some cities with a high centrality are not hubs.
 

TS in the XXth.
diff --git a/biblio/10572191.mdwn b/biblio/10572191.mdwn
new file mode 100644
index 0000000..4dfc696
--- /dev/null
+++ b/biblio/10572191.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite."]]
+[[!tag template_switching sequence_tags]]
+
+Peters DG, Kassam AB, Yonas H, O'Hare EH, Ferrell RE, Brufsky AM.
+
+Nucleic Acids Res. 1999 Dec 15;27(24):e39
+
+Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite.
+
+[[!pmid 10572191 desc="Template-switching used to construct SAGE libaries."]]

Old
diff --git a/biblio/15781865.mdwn b/biblio/15781865.mdwn
new file mode 100644
index 0000000..8553a13
--- /dev/null
+++ b/biblio/15781865.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements."]]
+[[!tag sequence_tags ChIP epigenetic]]
+
+Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4813-8 doi:10.1073/pnas.0407069102
+
+Chen J, Sadowski I.
+
+Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements.
+
+[[!pmid 15781865 desc="Ancestor of ChIP-seq. Ditags without a spacer, separated by a 4-cutter (TalI)"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 7635d84..313a7f0 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -361,9 +361,6 @@ Future Nobel prize ? Maybe an explanation for the conservation of dev. enhancers
 15778292 [genome]
 2n species covered 1x would be more efficient than n covered 2x for the discovery of conserved elements, but the resulting genome assemblies would be of a much poorer qualities.
 
-15781865 [tags]
-Not tested on a large scale. Ditags without a spacer, separated by a 4-cutter (TalI)
-
 15564293 [misc]
 [not read] Normalisations based on uni/multivariate models, rather than substraction of the mean followed by divisoin by sd, are much more effective at detecting covariations.
 

Old
diff --git a/biblio/18032727.mdwn b/biblio/18032727.mdwn
new file mode 100644
index 0000000..e2340ef
--- /dev/null
+++ b/biblio/18032727.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A code for transcription initiation in mammalian genomes."]]
+[[!tag method promoter]]
+
+Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A.
+
+Genome Res. 2008 Jan;18(1):1-12. doi:10.1101/gr.6831208
+
+A code for transcription initiation in mammalian genomes.
+
+[[!pmid 18032727 desc="Primary paper for paraclu.  Local DNA sequence governs the selection of the TSS."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4a421b5..7635d84 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -970,9 +970,6 @@ Provides a R library
 10395892 [misc]
 [not read] Review on the "Kozak" sequence.
 
-18032727 [tags]
-Primary paper for paraclu
-
 17010214 [olfactory]
 Primary paper for CLICs (clusters in conservation).
 

Old
diff --git a/biblio/386284.mdwn b/biblio/386284.mdwn
new file mode 100644
index 0000000..6a78a5a
--- /dev/null
+++ b/biblio/386284.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The synthesis of oligodeoxyribonucleotides using RNA ligase."]]
+[[!tag ligase enzyme]]
+
+Nucleic Acids Res. 1979 Sep 25;7(2):453-64.
+
+Hinton DM, Gumport RI.
+
+The synthesis of oligodeoxyribonucleotides using RNA ligase.
+
+[[!pmid 386284 desc="A low ATP concentration contributes to the attainment of high yields. ATP regenerating systems allow to work at sub-stoechiometric concentrations. Rnase A can be used as a SSBP. Spermine enhances yield."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 8c864e3..4a421b5 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -661,9 +661,6 @@ The PPi produced during the PCR can be removed with the pyrosequencing enzymes t
 12448877 [protocols]
 Ligating a DNA adaptor 3' to the FScDNA using T4RNA ligase.
 
-386284 [protocols]
-A low ATP concentration contributes to the attainment of high yields. ATP regenerating systems allow to work at sub-stoechiometric concentrations. Rnase A can be used as a SSBP. Spermine enhances yield.
-
 9380524 [protocols]
 Concentrations as high as 1 M or 2.5 M can strongly improve the yield.
 

Old
diff --git a/biblio/1180897.mdwn b/biblio/1180897.mdwn
new file mode 100644
index 0000000..b83b9ad
--- /dev/null
+++ b/biblio/1180897.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The use of ammonium acetate in the precipitation of ribonucleic acid."]]
+[[!tag method purification]]
+
+Biochem J. 1975 May;147(2):367-8.
+
+Osterburg HH, Allen JK, Finch CE.
+
+The use of ammonium acetate in the precipitation of ribonucleic acid.
+
+[[!pmid 1180897 desc="Precipitation of RNA in 240 mM NH4OAc."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 6046c82..8c864e3 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -586,9 +586,6 @@ Estimates as 88% the frequency of full length cDNA produced by the oligo-capping
 16251272 [misc]
 Transcriptional repressor involved in splicing.
 
-1180897 [protocols]
-Precipitation of RNA in 240 mM NH4OAc.
-
 16418487 [enhancers]
 Not read. Deletion of an enhancer conserved in mouse and chicken and its phenotype.
 

creating tag page tags/LPA
diff --git a/tags/LPA.mdwn b/tags/LPA.mdwn
new file mode 100644
index 0000000..c444501
--- /dev/null
+++ b/tags/LPA.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged LPA"]]
+
+[[!inline pages="tagged(LPA)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/2326177.mdwn b/biblio/2326177.mdwn
new file mode 100644
index 0000000..8c5e9da
--- /dev/null
+++ b/biblio/2326177.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ethanol precipitation of DNA with linear polyacrylamide as carrier."]]
+[[!tag method purification LPA]]
+
+Nucleic Acids Res. 1990 Jan 25;18(2):378
+
+Gaillard C, Strauss F.
+
+Ethanol precipitation of DNA with linear polyacrylamide as carrier.
+
+[[!pmid 2326177 desc="More inert than glycogen."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index fa189bd..6046c82 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -661,9 +661,6 @@ Not read. An enhancer of Rpx/Hesx1 conserved between mouse and xenopus.
 16540077 [misc]
 The PPi produced during the PCR can be removed with the pyrosequencing enzymes themselves. The antarctic phosphatase from NEB was not very efficient at this task.
 
-2326177 [protocols]
-More inert than glycogen.
-
 12448877 [protocols]
 Ligating a DNA adaptor 3' to the FScDNA using T4RNA ligase.
 

Old
diff --git a/biblio/4000951.mdwn b/biblio/4000951.mdwn
new file mode 100644
index 0000000..7ea3887
--- /dev/null
+++ b/biblio/4000951.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hexamine cobalt chloride promotes intermolecular ligation of blunt end DNA fragments by T4 DNA ligase."]]
+[[!tag ligation method]]
+
+Nucleic Acids Res. 1985 Mar 25;13(6):1997-2008.
+
+Rusche JR, Howard-Flanders P.
+
+Hexamine cobalt chloride promotes intermolecular ligation of blunt end DNA fragments by T4 DNA ligase.
+
+[[!pmid 4000951 desc="HCC (1 mM) promotes intermolecular ligation. This effect is countered by monovalent cations."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index dffec3e..fa189bd 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -667,9 +667,6 @@ More inert than glycogen.
 12448877 [protocols]
 Ligating a DNA adaptor 3' to the FScDNA using T4RNA ligase.
 
-4000951 [protocols]
-HCC (1 mM) promotes intermolecular ligation. This effect is countered by monovalent cations.
-
 386284 [protocols]
 A low ATP concentration contributes to the attainment of high yields. ATP regenerating systems allow to work at sub-stoechiometric concentrations. Rnase A can be used as a SSBP. Spermine enhances yield.
 

Old
diff --git a/biblio/7479050.mdwn b/biblio/7479050.mdwn
new file mode 100644
index 0000000..6864c81
--- /dev/null
+++ b/biblio/7479050.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Protection of megabase DNA from shearing."]]
+[[!tag method]]
+
+Nucleic Acids Res. 1995 Oct 11;23(19):3999-4000.
+
+Kovacic RT1, Comai L, Bendich AJ
+
+Protection of megabase DNA from shearing.
+
+[[!pmid 7479050 desc="HCC protects DNA and enhances ligation at 1 mM. HCC is thought to condense DNA, similarly to spermine and spermidine."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 3d3f5f0..dffec3e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -667,9 +667,6 @@ More inert than glycogen.
 12448877 [protocols]
 Ligating a DNA adaptor 3' to the FScDNA using T4RNA ligase.
 
-7479050 [protocols]
-HCC protects DNA and enhances ligation at 1 mM. HCC is thought to condense DNA, similarly to spermine and spermidine.
-
 4000951 [protocols]
 HCC (1 mM) promotes intermolecular ligation. This effect is countered by monovalent cations.
 

Old
diff --git a/biblio/10400927.mdwn b/biblio/10400927.mdwn
new file mode 100644
index 0000000..961a01a
--- /dev/null
+++ b/biblio/10400927.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Improved DNA sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators."]]
+[[!tag sequencing manganese]]
+
+Genome Res. 1999 Jun;9(6):588-95
+
+Korch C, Drabkin H.
+
+Improved DNA sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators.
+
+[[!pmid 10400927 desc="0.3 mM MnCl2 + 1:1 MnCit in absence of EDTA is optimal."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index aaca0a6..3d3f5f0 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -781,9 +781,6 @@ Reommends to use only dbSNP entries which have a phred score higher than 40.
 15693942 [mining]
 Uses a highly replicated experimental desigh to show that metabolic genes vary in their expresison between tissues, individuals and populations.
 
-10400927 [protocol]
-0.3 mM MnCl2 + 1:1 MnCit in absence of EDTA is optimal.
-
 17018278 [enzymes]
 Not Read
 

T4gp32.
diff --git a/biblio/15028277.mdwn b/biblio/15028277.mdwn
index 829aa67..92c0f44 100644
--- a/biblio/15028277.mdwn
+++ b/biblio/15028277.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="High-accuracy amplification of nanogram total RNA amounts for gene profiling."]]
-[[!tag enzyme ssbp]]
+[[!tag reverse_transcription ssbp]]
+
+Kenzelmann M, Klären R, Hergenhahn M, Bonrouhi M, Gröne HJ, Schmid W, Schütz G.
+
+Genomics. 2004 Apr;83(4):550-8 doi:10.1016/j.ygeno.2003.09.026
+
+High-accuracy amplification of nanogram total RNA amounts for gene profiling.
+
 [[!pmid 15028277 desc="Augment temperature, lower primer concentration, and add T4gp32 to enhance reverse transcription."]]
diff --git a/biblio/16461948.mdwn b/biblio/16461948.mdwn
index 91c86d6..6155b26 100644
--- a/biblio/16461948.mdwn
+++ b/biblio/16461948.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Optimization of in vitro transcription and full-length cDNA synthesis using the T4 bacteriophage gene 32 protein."]]
-[[!tag reverse_transcription]]
+[[!tag reverse_transcription enzyme ssbp]]
 
 J Biomol Tech. 2005 Sep;16(3):239-47
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 62a3b8f..8f0d40b 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -5,7 +5,7 @@
 Additives that increase reaction performance:
 
  - Actinomycin D ([[Perocchi et al., 2007|biblio/17897965]]).
- - T4 bacteriophage gene 32 protein (T4gp32, [[Piché _et al._, 2005|biblio/16461948]]).
+ - T4 bacteriophage gene 32 protein (T4gp32, [[Kenzelmann _et al._, 2004|biblio/15028277]], [[Piché _et al._, 2005|biblio/16461948]]).
 
 Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
  - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.

ActD.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 2f8af9a..62a3b8f 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -4,6 +4,7 @@
 
 Additives that increase reaction performance:
 
+ - Actinomycin D ([[Perocchi et al., 2007|biblio/17897965]]).
  - T4 bacteriophage gene 32 protein (T4gp32, [[Piché _et al._, 2005|biblio/16461948]]).
 
 Reverse-transcriptases have a DNA-dependent DNA polymerase activity.

Cleanup.
diff --git a/tags/reverse-transcriptase.mdwn b/tags/reverse-transcriptase.mdwn
deleted file mode 100644
index 302204d..0000000
--- a/tags/reverse-transcriptase.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged reverse-transcriptase"]]
-
-[[!inline pages="tagged(reverse-transcriptase)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/reverse-transcription.mdwn b/tags/reverse-transcription.mdwn
deleted file mode 100644
index a6d340d..0000000
--- a/tags/reverse-transcription.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged reverse-transcription"]]
-
-[[!inline pages="tagged(reverse-transcription)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/reverse_transcriptase.mdwn b/tags/reverse_transcriptase.mdwn
deleted file mode 100644
index 73bd59d..0000000
--- a/tags/reverse_transcriptase.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged reverse transcriptase"]]
-
-[[!inline pages="tagged(reverse_transcriptase)" actions="no" archive="yes"
-feedshow=10]]

Old
diff --git a/biblio/16461948.mdwn b/biblio/16461948.mdwn
new file mode 100644
index 0000000..91c86d6
--- /dev/null
+++ b/biblio/16461948.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Optimization of in vitro transcription and full-length cDNA synthesis using the T4 bacteriophage gene 32 protein."]]
+[[!tag reverse_transcription]]
+
+J Biomol Tech. 2005 Sep;16(3):239-47
+
+Piché C, Schernthaner JP.
+
+Optimization of in vitro transcription and full-length cDNA synthesis using the T4 bacteriophage gene 32 protein.
+
+[[!pmid 16461948 desc="T4gp32 increases the yield of the smallest cDNAs by 10 %."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 833287f..aaca0a6 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -661,9 +661,6 @@ Not read. An enhancer of Rpx/Hesx1 conserved between mouse and xenopus.
 16540077 [misc]
 The PPi produced during the PCR can be removed with the pyrosequencing enzymes themselves. The antarctic phosphatase from NEB was not very efficient at this task.
 
-16461948 [protocols]
-T4gp32 increases the yield of the smallest cDNAs by 10 %.
-
 2326177 [protocols]
 More inert than glycogen.
 
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 0410921..2f8af9a 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -2,6 +2,10 @@
 
 (redaction in progress)
 
+Additives that increase reaction performance:
+
+ - T4 bacteriophage gene 32 protein (T4gp32, [[Piché _et al._, 2005|biblio/16461948]]).
+
 Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
  - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.
  - It is also a source of antisense artefacts when the RT makes a second-strand cDNA

ActD.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 7d2e930..0410921 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -1,4 +1,12 @@
 [[!meta title="pages tagged reverse transcription"]]
 
-[[!inline pages="tagged(reverse_transcription)" actions="no" archive="yes"
-feedshow=10]]
+(redaction in progress)
+
+Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
+ - It is utilised in [[template_switching]] methods to add linkers to first-strand cDNAs.
+ - It is also a source of antisense artefacts when the RT makes a second-strand cDNA
+   that is mistaken for a first-strand cDNA.  ActinomycinD inhibits DNA-dependent,
+   but not RNA-dependent polymerase activity and is used to suppress these
+   artefacts ([[Perocchi et al., 2007|biblio/17897965]], [[Kanamori-Katayama et al., 2011|biblio/21596820]]).
+
+[[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

Normalise.
diff --git a/biblio/10632587.mdwn b/biblio/10632587.mdwn
index 7338f2e..ac48bc0 100644
--- a/biblio/10632587.mdwn
+++ b/biblio/10632587.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Kv4.2 mRNA abundance and A-type K(+) current amplitude are linearly related in basal ganglia and basal forebrain neurons."]]
-[[!tag single_cell qPCR reverse-transcriptase]]
+[[!tag single_cell qPCR reverse_transcription]]
 
 J Neurosci. 2000 Jan 15;20(2):579-88.
 
diff --git a/biblio/16963776.mdwn b/biblio/16963776.mdwn
index 63fa0ec..9266027 100644
--- a/biblio/16963776.mdwn
+++ b/biblio/16963776.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Dynamic assembly of primers on nucleic acid templates."]]
-[[!tag enzyme reverse-transcriptase]]
+[[!tag enzyme reverse_transcription]]
 
 Nucleic Acids Res. 2006;34(17):4702-10. doi:10.1093/nar/gkl625
 
diff --git a/biblio/17897965.mdwn b/biblio/17897965.mdwn
index 60c5302..02fce7a 100644
--- a/biblio/17897965.mdwn
+++ b/biblio/17897965.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D."]]
-[[!tag reverse-transcription method]]
+[[!tag reverse_transcription method]]
 
 Nucleic Acids Res. 2007;35(19):e128 doi:10.1093/nar/gkm683
 

Old
diff --git a/biblio/17897965.mdwn b/biblio/17897965.mdwn
new file mode 100644
index 0000000..60c5302
--- /dev/null
+++ b/biblio/17897965.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D."]]
+[[!tag reverse-transcription method]]
+
+Nucleic Acids Res. 2007;35(19):e128 doi:10.1093/nar/gkm683
+
+Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM.
+
+Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D.
+
+[[!pmid 17897965 desc="Adding actinomycin D suppresse self-priming."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 5dc8477..833287f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -970,9 +970,6 @@ Digests single-stranded 5' phosphorylated DNA or RNA molecules
 12136033 [tags]
 The distribution of the SAGE tags follow a power law.
 
-17897965 [protocols]
-Adding actinomycin D suppresse self-priming.
-
 17936740 [enhancers]
 Another conserved enhancer in a developmental regulator that is not a transcription factor.
 

Spelling.
diff --git a/biblio/14990785.mdwn b/biblio/14990785.mdwn
index 482deef..f9ae203 100644
--- a/biblio/14990785.mdwn
+++ b/biblio/14990785.mdwn
@@ -7,4 +7,4 @@ Ghadessy FJ, Holliger P.
 
 A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system.
 
-[[!pmid 14990785 desc="Primary paper for the use of ABIL EM90.  Span/Tween superfactants oxydise the reagents.  DTT partly prevents oxydisation but inhibits reactions above 20 mM."]]
+[[!pmid 14990785 desc="Primary paper for the use of ABIL EM90.  Span/Tween surfactants oxydise the reagents.  DTT partly prevents oxydisation but inhibits reactions above 20 mM."]]

Old
diff --git a/biblio/9661199.mdwn b/biblio/9661199.mdwn
new file mode 100644
index 0000000..00516bb
--- /dev/null
+++ b/biblio/9661199.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Man-made cell-like compartments for molecular evolution."]]
+[[!tag emulsion]]
+
+Nat Biotechnol. 1998 Jul;16(7):652-6 doi:10.1038/nbt0798-652
+
+Tawfik DS, Griffiths AD.
+
+Man-made cell-like compartments for molecular evolution.
+
+[[!pmid 9661199 desc="Only the constructs encoding methylases escape degradation."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e4a5d1f..5dc8477 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -574,9 +574,6 @@ Unlike mouse ngn3, zebrafish ngn3 is not expressed in the pancreas (but zebrafis
 16280998 [patents]
 Perpetual-motion machines are not patentable.
 
-99661199 [emulsion]
-Only the constructs encoding methylases escape degradation.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 3de02b1..b72e5ee 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -7,16 +7,16 @@ How to add contents to droplets ?
 
 How to break the droplets ?
 
- - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
- - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
+ - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; surfactant: Triton X-100 0.1%).
+ - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; surfactant: Triton X-100 0.1% and Span 80 4.5%).
  - High salt:
-   - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
-   - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
- - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
+   - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % Triton X-100 and Tris (oil: mineral, surfactant: ABIL WE09).
+   - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; surfactant: Sun Soft No. 818SK).
+ - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, surfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % Triton X-100).
 
-Different kinds of superfactants:
+Different kinds of surfactants:
 
- - TritonX-100, Span 80, Tween 80 (many articles),
+ - Span 80 4.5 % and Tween 80 0.5 % (oil: mineral; primary paper: [[Tawfik _et al._, 1998|biblio/9661199]], followed by many others, sometimes adding Triton X-100 and changing the concentrations).
  - ABIL WE09 (polysiloxane–polycetyl–polyethylene glycol copolymer; primary paper: [[Dielh _et al._, 2004|biblio/14990785]])
  - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])
  - DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]]

Old
diff --git a/biblio/10471784.mdwn b/biblio/10471784.mdwn
new file mode 100644
index 0000000..235f8e2
--- /dev/null
+++ b/biblio/10471784.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="STABLE: protein-DNA fusion system for screening of combinatorial protein libraries in vitro."]]
+[[!tag emulsion selection]]
+
+FEBS Lett. 1999 Aug 27;457(2):227-30.
+
+Doi N, Yanagawa H.
+
+STABLE: protein-DNA fusion system for screening of combinatorial protein libraries in vitro.
+
+[[!pmid 10471784 desc="The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e76008f..e4a5d1f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -577,9 +577,6 @@ Perpetual-motion machines are not patentable.
 99661199 [emulsion]
 Only the constructs encoding methylases escape degradation.
 
-10471784 [emulsion]
-The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

No no, no no no no, no no no no limit !
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index d45975f..3de02b1 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -21,4 +21,4 @@ Different kinds of superfactants:
  - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])
  - DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]]
 
-[[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]
+[[!inline pages="tagged(emulsion)" actions="no" limit=0]]

Old
diff --git a/biblio/11274352.mdwn b/biblio/11274352.mdwn
new file mode 100644
index 0000000..33a39fe
--- /dev/null
+++ b/biblio/11274352.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Directed evolution of polymerase function by compartmentalized self-replication."]]
+[[!tag selection polymerase emulsion]]
+
+Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4552-7 doi:10.1073/pnas.071052198
+
+Ghadessy FJ, Ong JL, Holliger P.
+
+Directed evolution of polymerase function by compartmentalized self-replication.
+
+[[!pmid 11274352 desc="No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 1bfc85c..e76008f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -580,12 +580,6 @@ Only the constructs encoding methylases escape degradation.
 10471784 [emulsion]
 The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
 
-12433997 [emulsion]
-Random primers were used to introduce mutations.
-
-11274352 [emulsion]
-No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/12482612.mdwn b/biblio/12482612.mdwn
new file mode 100644
index 0000000..e927a3e
--- /dev/null
+++ b/biblio/12482612.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry."]]
+[[!tag selection emulsion]]
+
+FEBS Lett. 2002 Dec 18;532(3):455-8
+
+Sepp A, Tawfik DS, Griffiths AD.
+
+Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry.
+
+[[!pmid 12482612 desc="As tyramide is converted to a free radical which reacts with neighbouring proteins, only beads displaying the epitope become fluorescent."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 5040d54..1bfc85c 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -580,9 +580,6 @@ Only the constructs encoding methylases escape degradation.
 10471784 [emulsion]
 The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
 
-12482612 [emulsion]
-As tyramide is converted to a free radical which reacts with neighbouring proteins, only beads displaying the epitope become fluorescent.
-
 12433997 [emulsion]
 Random primers were used to introduce mutations.
 

Old
diff --git a/biblio/12697388.mdwn b/biblio/12697388.mdwn
new file mode 100644
index 0000000..df12ac4
--- /dev/null
+++ b/biblio/12697388.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-molecule PCR using water-in-oil emulsion."]]
+[[!tag emulsion PCR]]
+
+Nakano M, Komatsu J, Matsuura S, Takashima K, Katsura S, Mizuno A.
+
+J Biotechnol. 2003 Apr 24;102(2):117-24.
+
+Single-molecule PCR using water-in-oil emulsion.
+
+[[!pmid 12697388 desc="Uses the Triton X-100 contained in the PCR buffer as a surfactant."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index e47098e..5040d54 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -589,12 +589,6 @@ Random primers were used to introduce mutations.
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
-14990785 [emulsion]
-Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
-
-12697388 [emulsion]
-Uses the Triton X-100 contained in the PCR buffer as a surfactant.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/14500846.mdwn b/biblio/14500846.mdwn
new file mode 100644
index 0000000..d1eae5c
--- /dev/null
+++ b/biblio/14500846.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA display for in vitro selection of diverse peptide libraries."]]
+[[!tag emulsion selection]]
+
+Nucleic Acids Res. 2003 Oct 1;31(19):e118
+
+Yonezawa M, Doi N, Kawahashi Y, Higashinakagawa T, Yanagawa H.
+
+DNA display for in vitro selection of diverse peptide libraries.
+
+[[!pmid 14500846 desc="Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index ae9947d..e47098e 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -595,12 +595,6 @@ Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
 12697388 [emulsion]
 Uses the Triton X-100 contained in the PCR buffer as a surfactant.
 
-14715296 [emulsion]
-Oil droplets containing water droplets can be FACS sorted.
-
-14500846 [emulsion]
-Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/14715296.mdwn b/biblio/14715296.mdwn
new file mode 100644
index 0000000..53056e1
--- /dev/null
+++ b/biblio/14715296.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting."]]
+[[!tag emulsion]]
+
+Bernath K, Hai M, Mastrobattista E, Griffiths AD, Magdassi S, Tawfik DS.
+
+Anal Biochem. 2004 Feb 1;325(1):151-7
+
+In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting.
+
+[[!pmid 14715296 desc="Oil droplets containing water droplets (w/o/w) can be FACS sorted."]]

Old
diff --git a/biblio/14985532.mdwn b/biblio/14985532.mdwn
new file mode 100644
index 0000000..1115e05
--- /dev/null
+++ b/biblio/14985532.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization."]]
+[[!tag emulsion selection enzyme]]
+
+Protein Eng Des Sel. 2004 Jan;17(1):3-11 doi:10.1093/protein/gzh001
+
+Cohen HM, Tawfik DS, Griffiths AD
+
+Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization.
+
+[[!pmid 14985532 desc="Uses 16% glycerol to promote star activity."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 2ec868b..ae9947d 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -592,9 +592,6 @@ No beads. A bacterial cel is used as a subcompartment maintaining gene and prote
 14990785 [emulsion]
 Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
 
-14985532 [emulsion]
-Uses 16% glycerol to promote star activity.
-
 12697388 [emulsion]
 Uses the Triton X-100 contained in the PCR buffer as a surfactant.
 

Old
diff --git a/biblio/15156154.mdwn b/biblio/15156154.mdwn
new file mode 100644
index 0000000..a8c1d03
--- /dev/null
+++ b/biblio/15156154.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution."]]
+[[!tag selection polymerase]]
+
+Nat Biotechnol. 2004 Jun;22(6):755-9 doi:10.1038/nbt974
+
+Ghadessy FJ, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, Vaisman A, Woodgate R, Holliger P.
+
+Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution.
+
+[[!pmid 15156154 desc="Polymerases selected on the ability to amplify their gene despite a 3' mismach in the primers were shown to be able to incorporate a broad range of nucleotide analogs."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 5e926ce..2ec868b 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -604,9 +604,6 @@ Oil droplets containing water droplets can be FACS sorted.
 14500846 [emulsion]
 Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR.
 
-15156154 [emulsion]
-Polymerases selected on the ability to amplify their gene despite a 3' mismach in the primers were shown to be able to incorporate a broad range of nucleotide analogs.
-
 16308152 [amplification]
 Detailed protocol for Terminal Continuation (TC).
 

Old
diff --git a/biblio/15247328.mdwn b/biblio/15247328.mdwn
new file mode 100644
index 0000000..2ba3941
--- /dev/null
+++ b/biblio/15247328.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="In vitro selection of restriction endonucleases by in vitro compartmentalization."]]
+[[!tag emulsion selection enzyme]]
+
+Nucleic Acids Res. 2004 Jul 6;32(12):e95 doi:10.1093/nar/gnh096
+
+Doi N, Kumadaki S, Oishi Y, Matsumura N, Yanagawa H.
+
+In vitro selection of restriction endonucleases by in vitro compartmentalization.
+
+[[!pmid 15247328 desc="The cleaved DNA molecules are selected by filling of their ends with biotin-dUTP"]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4d867e2..5e926ce 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -604,9 +604,6 @@ Oil droplets containing water droplets can be FACS sorted.
 14500846 [emulsion]
 Improvement of STABLE by addtion of one biotinylated end, usage of wheat germ extract for translation, and reduction of the GC content of the streptavidin gene to facilitate PCR.
 
-15247328 [emulsion]
-The cleaved DNA molecules are selected by filling of their ends with biotin-dUTP
-
 15156154 [emulsion]
 Polymerases selected on the ability to amplify their gene despite a 3' mismach in the primers were shown to be able to incorporate a broad range of nucleotide analogs.
 

Syntax.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 41f66a5..d45975f 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -15,6 +15,7 @@ How to break the droplets ?
  - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
 Different kinds of superfactants:
+
  - TritonX-100, Span 80, Tween 80 (many articles),
  - ABIL WE09 (polysiloxane–polycetyl–polyethylene glycol copolymer; primary paper: [[Dielh _et al._, 2004|biblio/14990785]])
  - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])

Expand.
diff --git a/biblio/14990785.mdwn b/biblio/14990785.mdwn
index 9b987ab..482deef 100644
--- a/biblio/14990785.mdwn
+++ b/biblio/14990785.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system."]]
-[[!tag emulsion product not_read]]
-[[!pmid 14990785 desc="Uses ABIL EM90"]]
+[[!tag emulsion DTT]]
+
+Protein Eng Des Sel. 2004 Mar;17(3):201-4 doi:10.1093/protein/gzh025
+
+Ghadessy FJ, Holliger P.
+
+A novel emulsion mixture for in vitro compartmentalization of transcription and translation in the rabbit reticulocyte system.
+
+[[!pmid 14990785 desc="Primary paper for the use of ABIL EM90.  Span/Tween superfactants oxydise the reagents.  DTT partly prevents oxydisation but inhibits reactions above 20 mM."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index bb76020..41f66a5 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -14,6 +14,10 @@ How to break the droplets ?
    - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
  - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
-Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]), DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]].
+Different kinds of superfactants:
+ - TritonX-100, Span 80, Tween 80 (many articles),
+ - ABIL WE09 (polysiloxane–polycetyl–polyethylene glycol copolymer; primary paper: [[Dielh _et al._, 2004|biblio/14990785]])
+ - Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid; primary paper: [[Kojima _et al._, 2005|biblio/16214800]])
+ - DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]]
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/15522920.mdwn b/biblio/15522920.mdwn
new file mode 100644
index 0000000..8e2c16d
--- /dev/null
+++ b/biblio/15522920.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Covalent DNA display as a novel tool for directed evolution of proteins in vitro."]]
+[[!tag emulsion selection]]
+
+Protein Eng Des Sel. 2004 Sep;17(9):699-707. Epub 2004 Nov 2.
+
+Bertschinger J, Neri D.
+
+Covalent DNA display as a novel tool for directed evolution of proteins in vitro.
+
+[[!pmid 15522920 desc="A methyl transferase fusion protein which binds covalently 5-fluorodesoxycytosine, gets linked to the constructs in which it is encoded."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index f0aa4da..4d867e2 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -580,9 +580,6 @@ Only the constructs encoding methylases escape degradation.
 10471784 [emulsion]
 The gene product, fused to streptavidin, is bound to a biotinylated molecule in which it is encoded.
 
-15522920 [emulsion]
-A methyl transferase fusion protein which binds covalently 5-fluorodesoxycytosine, gets linked to the constructs in which it is encoded.
-
 12482612 [emulsion]
 As tyramide is converted to a free radical which reacts with neighbouring proteins, only beads displaying the epitope become fluorescent.
 

Expand.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index c0b6ced..bb76020 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -3,6 +3,7 @@
 How to add contents to droplets ?
 
  - In [[Agresti et al., 2005|biblio/16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
+ - In [[Bernath _et al._, 2005|biblio/15644201]], nanodroplets were prepared with mineral oil, 7.5 % Span 80 and 2.5 % Tween 80, and incupated with the emulsion, with gentle mixing.
 
 How to break the droplets ?
 

Old
diff --git a/biblio/15644201.mdwn b/biblio/15644201.mdwn
new file mode 100644
index 0000000..644f9d4
--- /dev/null
+++ b/biblio/15644201.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery."]]
+[[!tag emulsion selection]]
+
+J Mol Biol. 2005 Feb 4;345(5):1015-26. doi:10.1016/j.jmb.2004.11.017
+
+Bernath K, Magdassi S, Tawfik DS.
+
+Directed evolution of protein inhibitors of DNA-nucleases by in vitro compartmentalization (IVC) and nano-droplet delivery.
+
+[[!pmid 15644201 desc="Selection pressure can be increased by reducing the volume of the spheres."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 4984443..f0aa4da 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -592,9 +592,6 @@ Random primers were used to introduce mutations.
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
-15644201 [emulsion]
-Selection pressure can be increased by reducing the volume of the spheres.
-
 14990785 [emulsion]
 Abil EM90 oil is inert enough to allow protein experssion in the RRL system.
 

454 superfactant.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 65071cf..c0b6ced 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -13,6 +13,6 @@ How to break the droplets ?
    - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
  - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
-Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]).
+Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]), DC 5225C Formulation Aid / DC 749 Fluid (Dow Chemical Co.) [[Margulies _et al._, 2005|biblio/16056220]].
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Expand.
diff --git a/biblio/16056220.mdwn b/biblio/16056220.mdwn
index a54a5bc..4f26806 100644
--- a/biblio/16056220.mdwn
+++ b/biblio/16056220.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Genome sequencing in microfabricated high-density picolitre reactors."]]
-[[!tag emulsion sequencing]]
+[[!tag emulsion sequencing 454]]
+
+Nature. 2005 Sep 15;437(7057):376-80. doi:10.1038/nature03959
+
+Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM.
+
+Genome sequencing in microfabricated high-density picolitre reactors.
+
 [[!pmid 16056220 desc="Primary reference for “454” sequencing."]]

Old
diff --git a/biblio/16131588.mdwn b/biblio/16131588.mdwn
new file mode 100644
index 0000000..6f5f73f
--- /dev/null
+++ b/biblio/16131588.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization."]]
+[[!tag emulsion biotin selection ribozyme]]
+
+RNA. 2005 Oct;11(10):1555-62. doi:10.1261/rna.2121705
+
+Levy M, Griswold KE, Ellington AD.
+
+Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization.
+
+[[!pmid 16131588 desc="During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead if no blocking of biotin is added."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 2bb9c61..4984443 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -589,9 +589,6 @@ As tyramide is converted to a free radical which reacts with neighbouring protei
 12433997 [emulsion]
 Random primers were used to introduce mutations.
 
-16131588 [emulsion]
-During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead in no excess of biotin is added.
-
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index b263477..65071cf 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -11,6 +11,7 @@ How to break the droplets ?
  - High salt:
    - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
    - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
+ - Extraction of beads with hexane:oil 1:1, in [[Levy _et al._, 2005|biblio/16131588]] (oil: mineral, superfactant: 5.5% Span 80, 0.5% Tween 80, 0.1 % TritonX-100).
 
 Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]).
 

Typo.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 50b4ace..b263477 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -10,8 +10,8 @@ How to break the droplets ?
  - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
  - High salt:
    - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
-   - In [[Kojima _et al._, 2005|biblio|16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
+   - In [[Kojima _et al._, 2005|biblio/16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
 
-Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio|16214800]]).
+Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio/16214800]]).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16214800.mdwn b/biblio/16214800.mdwn
index bc960cc..5bfec57 100644
--- a/biblio/16214800.mdwn
+++ b/biblio/16214800.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets."]]
-[[!tag emulsion]]
+[[!tag emulsion PCR]]
+
+Nucleic Acids Res. 2005 Oct 6;33(17):e150 doi:10.1093/nar/gni143
+
+Kojima T, Takei Y, Ohtsuka M, Kawarasaki Y, Yamane T, Nakano H.
+
+PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets.
+
 [[!pmid 16214800 desc="The composition of the mixture has been modified so that it stays stable in a PCR of 55 cycles of 10 minutes. Uses Sun Soft N° 818SK."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 4771a2c..50b4ace 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -8,6 +8,10 @@ How to break the droplets ?
 
  - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
  - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
- - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in presence of high salt (100 mM NaCl), SDS (1%), TritonX-100 (1%) (oil: mineral, superfactant: ABIL WE09).
+ - High salt:
+   - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in 100 mM NaCl, 1 % SDS, 1 % TritonX-100 and Tris (oil: mineral, superfactant: ABIL WE09).
+   - In [[Kojima _et al._, 2005|biblio|16214800]], by mixing with 1M NaCl, 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA (oil: mineral; superfactant: Sun Soft No. 818SK).
+
+Different kinds of superfactants: TritonX-100, Span 80, Tween 80 (many articles), ABIL WE09 ([[Dielh _et al._, 2006|biblio/16791214]] and others), Sun Soft No. 818SK (polyglycerol esters of intersesterified ricinoleic acid [[Kojima _et al._, 2005|biblio|16214800]]).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16791213.mdwn b/biblio/16791213.mdwn
index 1fe192e..25fa521 100644
--- a/biblio/16791213.mdwn
+++ b/biblio/16791213.mdwn
@@ -1,3 +1,9 @@
 [[!meta title="Amplification of complex gene libraries by emulsion PCR."]]
-[[!tag emulsion]]
+[[!tag emulsion PCR]]
+
+Nat Methods. 2006 Jul;3(7):545-50 doi:10.1038/nmeth896
+
+Williams R, Peisajovich SG, Miller OJ, Magdassi S, Tawfik DS, Griffiths AD.
+
+Amplification of complex gene libraries by emulsion PCR.
 [[!pmid 16791213 desc="Protects the templates frome size bias by isolating them from each other."]]
diff --git a/biblio/16791214.mdwn b/biblio/16791214.mdwn
index 437bfcf..8099627 100644
--- a/biblio/16791214.mdwn
+++ b/biblio/16791214.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="BEAMing: single-molecule PCR on microparticles in water-in-oil emulsion."]]
 [[!tag emulsion biotin]]
+
+Nat Methods. 2006 Jul;3(7):551-9 doi:10.1038/nmeth898
+
+Diehl F, Li M, He Y, Kinzler KW, Vogelstein B, Dressman D
+
+BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions.
+
 [[!pmid 16791214 desc="Recommends (in Box 1) a double-biotin to avoid breaking the complexes at high temperatures."]]
diff --git a/biblio/16791215.mdwn b/biblio/16791215.mdwn
index 791dd70..7dfc274 100644
--- a/biblio/16791215.mdwn
+++ b/biblio/16791215.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Directed evolution by in vitro compartmentalization."]]
 [[!tag emulsion]]
+
+Nat Methods. 2006 Jul;3(7):561-70 doi:10.1038/nmeth897
+
+Miller OJ, Bernath K, Agresti JJ, Amitai G, Kelly BT, Mastrobattista E, Taly V, Magdassi S, Tawfik DS, Griffiths AD.
+
+Directed evolution by in vitro compartmentalization.
+
 [[!pmid 16791215 desc="Method for water in oil in water emulsion (w/o/w)."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 5e2895f..4771a2c 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -8,5 +8,6 @@ How to break the droplets ?
 
  - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
  - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
+ - In [[Dielh _et al._, 2006|biblio/16791214]], by pipetting up and down in presence of high salt (100 mM NaCl), SDS (1%), TritonX-100 (1%) (oil: mineral, superfactant: ABIL WE09).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Expand.
diff --git a/biblio/16233792.mdwn b/biblio/16233792.mdwn
index 454035d..e0edd5a 100644
--- a/biblio/16233792.mdwn
+++ b/biblio/16233792.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Single-molecule reverse transcription polymerase chain reaction using water-in-oil emulsion."]]
-[[!tag emulsion]]
+[[!tag emulsion reverse_transcription]]
+
+J Biosci Bioeng. 2005 Mar;99(3):293-5. doi:10.1263/jbb.99.293
+
+Nakano M, Nakai N, Kurita H, Komatsu J, Takashima K, Katsura S, Mizuno A.
+
+Single-molecule reverse transcription polymerase chain reaction using water-in-oil emulsion.
+
 [[!pmid 16233792 desc="The emulsion is destroyed by centrifugation after 13 cycles, and then the PCR is restarted for 30 cycles."]]
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index df1139e..5e2895f 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -4,5 +4,9 @@ How to add contents to droplets ?
 
  - In [[Agresti et al., 2005|biblio/16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
 
+How to break the droplets ?
+
+ - In [[Nakano _et al._, 2005|biblio/16233792]], by centrifugation (oil: silicone; superfactant: TritonX-100 0.1%).
+ - In [[Agresti et al., 2005|biblio/16260754]], by centrifugation in presence of diethyl ether (oil: mineral; superfactant: TritonX-100 0.1% and Span 80 4.5%).
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16432518.mdwn b/biblio/16432518.mdwn
new file mode 100644
index 0000000..640daae
--- /dev/null
+++ b/biblio/16432518.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="BEAMing up for detection and quantification of rare sequence variants."]]
+[[!tag emulsion]]
+
+Li M, Diehl F, Dressman D, Vogelstein B, Kinzler KW.
+
+Nat Methods. 2006 Feb;3(2):95-7. doi:10.1038/nmeth850
+
+BEAMing up for detection and quantification of rare sequence variants.
+
+[[!pmid 16432518 desc="RCA amplification of DNA coupled to beads, followed by single-base extension and flow sorting."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index aa4e6be..2bb9c61 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -1060,9 +1060,6 @@ After 10 weeks, elevated DNA strand break levels are detected in the sperm DNA o
 16902134 [networks]
 Behavioral graph coloring
 
-16432518 [emulsions]
-RCA amplification of DNA coupled to beads, followed by single-base extension and flow sorting.
-
 16449203 [enzymes]
 2'OMe RNAs can not be polyadenylated in vitro.
 

Try again.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 543069a..df1139e 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -2,7 +2,7 @@
 
 How to add contents to droplets ?
 
- - In [[Agresti et al., 2005|16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
+ - In [[Agresti et al., 2005|biblio/16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
 
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Syntax.
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 711c7e3..543069a 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -2,7 +2,7 @@
 
 How to add contents to droplets ?
 
- - In [[16260754|Agresti et al., 2005]], small molecules mixed with EtOH or DMSO were added by vortexing.
+ - In [[Agresti et al., 2005|16260754]], small molecules mixed with EtOH or DMSO were added by vortexing.
 
 
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

Old
diff --git a/biblio/16260754.mdwn b/biblio/16260754.mdwn
new file mode 100644
index 0000000..a5de437
--- /dev/null
+++ b/biblio/16260754.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization."]]
+[[!tag emulsion selection ribozyme]]
+
+Agresti JJ, Kelly BT, Jäschke A, Griffiths AD.
+
+Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16170-5 doi:10.1073/pnas.0503733102
+
+Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization.
+
+[[!pmid 16260754 desc="Small molecules mixed with EtOH or DMSO were added by vortexing."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 339766f..aa4e6be 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -595,9 +595,6 @@ During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead
 11274352 [emulsion]
 No beads. A bacterial cel is used as a subcompartment maintaining gene and proteins together. Evidence for leakage of small molecules at high compartment density.
 
-16260754 [emulsion]
-Small molecules mixed with EtOH or DMSO were added by vortexing.
-
 15644201 [emulsion]
 Selection pressure can be increased by reducing the volume of the spheres.
 
diff --git a/tags/emulsion.mdwn b/tags/emulsion.mdwn
index 7861ff2..711c7e3 100644
--- a/tags/emulsion.mdwn
+++ b/tags/emulsion.mdwn
@@ -1,3 +1,8 @@
 [[!meta title="pages tagged emulsion"]]
 
+How to add contents to droplets ?
+
+ - In [[16260754|Agresti et al., 2005]], small molecules mixed with EtOH or DMSO were added by vortexing.
+
+
 [[!inline pages="tagged(emulsion)" actions="no" feedshow=0]]

creating tag page tags/selection
diff --git a/tags/selection.mdwn b/tags/selection.mdwn
new file mode 100644
index 0000000..1ee4e9d
--- /dev/null
+++ b/tags/selection.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged selection"]]
+
+[[!inline pages="tagged(selection)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/16242713.mdwn b/biblio/16242713.mdwn
new file mode 100644
index 0000000..6b0af64
--- /dev/null
+++ b/biblio/16242713.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization."]]
+[[!tag emulsion selection]]
+
+J Mol Biol. 2005 Nov 25;354(2):212-9. Epub 2005 Oct 3 doi:10.1016/j.jmb.2005.09.051
+
+Sepp A, Choo Y.
+
+Cell-free selection of zinc finger DNA-binding proteins using in vitro compartmentalization.
+
+[[!pmid 16242713 desc="With their Kd of 3pM, zinc finger protein fusions could be used instead of streptavitin or M.HaeIII to bind the DNA molecule in which they are encoded."]]
diff --git a/biblio/To_Do b/biblio/To_Do
index 584dd85..339766f 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -589,9 +589,6 @@ As tyramide is converted to a free radical which reacts with neighbouring protei
 12433997 [emulsion]
 Random primers were used to introduce mutations.
 
-16242713 [emulsion]
-With their Kd of 3pM, zinc finger protein fusions could be used instead of streptavitin or M.HaeIII to bind the DNA molecule in which they are encoded.
-
 16131588 [emulsion]
 During immunolabelling, biotinylated nucleic acids can diffuse from bead to bead in no excess of biotin is added.
 

Expansion.
diff --git a/biblio/15289471.mdwn b/biblio/15289471.mdwn
index 6097d7e..df2443d 100644
--- a/biblio/15289471.mdwn
+++ b/biblio/15289471.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Regional patterns of gene expression in human and chimpanzee brains."]]
-[[!tag chimpanzee brain visual_cortex variability]]
+[[!tag chimpanzee brain visual_cortex variability transcriptome]]
+
+Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do HH, Weiss G, Enard W, Heissig F, Arendt T, Nieselt-Struwe K, Eichler EE, Pääbo S.
+
+Genome Res. 2004 Aug;14(8):1462-73 doi:10.1101/gr.2538704
+
+Regional patterns of gene expression in human and chimpanzee brains.
+
 [[!pmid 15289471 desc="Individual variations are stronger than regional variations in cortex. Developmental genes are implicated in inter-reigonal, but not inter-species variations. Differential interspecific variation correlates with recent chromosomal duplications."]]

Nettoyage.
diff --git a/biblio/To_Do b/biblio/To_Do
index ed0970e..584dd85 100644
--- a/biblio/To_Do
+++ b/biblio/To_Do
@@ -46,9 +46,6 @@ Noise due to RNA extraction is 40 times greater than noise due to replicate hybr
 12595569 [amplificaiton]
 Aminoallyl UTP to labal cRNAs. In contrast to cDNAs, DMSO is required for subsequent cyanine labelling.
 
-11955710 [visual cortex]
-Cat visual cortex cDNAs hybridized to human macroarrays to study critical period mechanism
-
 11222780 [amplification]
 T7 pol generates aberrant template-unrelated products. This is fixed by reducing the concentration of oligo dT primers, and of enzymes. Under these conditions, 2 rounds of RNA linear amplification is not generatng too much bias. Small-volume protocol. T4gp32, a single stranded protein, increases RT processivity.
 
@@ -154,9 +151,6 @@ Apical localisation increases the robustness of development (more segmenatal def
 14732405 [promoters]
 Pax6 has at least two transcription start sites.
 
-15345244 [visual cortex]
-Differential display. Age-dependant variations account for 6.5% of the variations.
-
 15196954 [enhancers] [review]
 Gene networks.
 
@@ -169,9 +163,6 @@ Dual strategy using full length cDNAs and whole genome tiling arrays to annotate
 15001784 [networks] [tracked]
 Distribution of triads and tetrads in networks can cluster them in functional classes.
 
-15295028 [visual cortex] [tracked]
-Synaptic changes in dark-reared animals stimulated by 6 hours of light before sacrifice.
-
 15208707 [networks]
 
 4599081 [crick]
@@ -277,9 +268,6 @@ Alternative promoters which transcribe variants with different translational eff
 15342556 [genome]
 These blocks contain most validated and predicted transcription factor binding sites.
 
-15509747 [visual cortex]
-Another slightly different critical period, and another PV:GFP transgene.
-
 15849325 [genome]
 Proteomics to demonstrate that some short ORFs are translated.
 
@@ -394,9 +382,6 @@ Coordinated expression of e and y is necessary for spot formation. Ancestral pat
 15282333 [networks]
 CDS, 3'UTRs, but not 5'UTRs of highly connected genes of  the human and mouse coexpression networks evolve more slowly
 
-15009647 [visual cortex]
-Identifies immediate early genes that are upregulated in visual cortex after monocular enucleation.
-
 15860629 [networks]
 Model of network growth which takes into account the propension to link to newcommers or to good old friends.
 
@@ -436,9 +421,6 @@ The cells were pulled out from midly digested ganglia with glass microelectrodes
 15371555 [tags]
 Semi-random priming: the 5' oligo is N6-NlaIII.
 
-15901564 [visual cortex]
-OBCAM RNA and protein levels are higher juvenile and dark reared adults, compared to light reared adults.
-
 15911778 [networks]
 The muticommunauty structure of the air transortation network  explains why some cities with a high centrality are not hubs.
 
@@ -541,9 +523,6 @@ Usage of "Bayes Error Rate" instead of a cutoff on p-values. R packaged availabl
 16103215 [misc]
 Supports the idea that the only function of some RNA is to have been transcribed.
 
-16107646 [visual cortex]
-Substracted library spotted on microarrays.
-
 16094371 [networks]
 Functional validation.
 
@@ -565,9 +544,6 @@ Sequence surrounding UCRs might regulate negatively their activity.
 16141073 [genome]
 S/AS pairs usually show positive correlation of their expression.
 
-16195464 [visual cortex]
-Loss of function delays the closure of the critical period.
-
 16168087 [networks]
 Different collaboration network in different research consortiums.
 
@@ -670,15 +646,6 @@ Not read. Deletion of an enhancer conserved in mouse and chicken and its phenoty
 14701942 [enhancers]
 Not read. A pdx-1 enhancer conserved in human, mouse and chicken.
 
-10408598 [visual cortex]
-Not read. egr1 is down-regulated in dark-reared rats.
-
-11739581 [visual cortex]
-Not read. Phenotype of the egr1 KO for the activity-dependant plasticity in the visual cortex.
-
-8656291 [visual cortex]
-not read. Nuclear extracts from dark reared rats have a lesser binding activity to an egr1 probe.
-
 16314298 [protocols]
 Adding gold in PCR tubes enhances the yield when the cycling is quick.
 
@@ -742,9 +709,6 @@ Not read. Enhancers of Krox-20, conserved between chicken and mouse.
 16527264 [enhancers]
 Not read. An enhancer of Rpx/Hesx1 conserved between mouse and xenopus.
 
-16540572 [visual cortex]
-Not read. Monocular deprivation can lead to shifts in ocular dominance in adults if they are deprived of visual stumuli 10 days before the experiment...
-
 16540077 [misc]
 The PPi produced during the PCR can be removed with the pyrosequencing enzymes themselves. The antarctic phosphatase from NEB was not very efficient at this task.
 
@@ -781,12 +745,6 @@ By weakening the DNA-protein interaction, the authors acheived the suppression o
 16618967 [enzymes]
 The combined use of a complementary DNA oligo and DNA ligase suppresses the artifacts seen in RNA ligase adenylation.
 
-16709670 [visual cortex]
-Weakening the extracellular matrix influences the plasticity process.
-
-16723524 [visual cortex]
-Publicly available cell-type-specific expression patterns were used to analyse the results of whole-tissue microarray experiments.
-
 16344560 [alternative promoters]
 Detected an average of 3.1 promoters per gene.
 
@@ -1096,9 +1054,6 @@ Primary paper for CLICs (clusters in conservation).
 17284453 [misc]
 [not read] The 3' end of RefSeq protein-coding genes is enriched in putative binding sites (the 5' as well).
 
-17510325 [transcriptome]
-Small RNAs were directly labelled with pCpBiotin.
-
 18024554 [tags]
 A sort of Superverylong 3'SAGE.
 

creating tag page tags/HepG2
diff --git a/tags/HepG2.mdwn b/tags/HepG2.mdwn
new file mode 100644
index 0000000..a56fbc9
--- /dev/null
+++ b/tags/HepG2.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged HepG2"]]
+
+[[!inline pages="tagged(HepG2)" actions="no" archive="yes"
+feedshow=10]]

Old
diff --git a/biblio/17510325.mdwn b/biblio/17510325.mdwn
new file mode 100644
index 0000000..4e77765
--- /dev/null
+++ b/biblio/17510325.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA maps reveal new RNA classes and a possible function for pervasive transcription."]]
+[[!tag ligation transcriptome small_RNA HepG2]]
+
+Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.
+
+Science. 2007 Jun 8;316(5830):1484-8 doi:10.1126/science.1138341
+
+RNA maps reveal new RNA classes and a possible function for pervasive transcription.
+
+[[!pmid 17510325 desc="Small RNAs were directly labelled with pCpBiotin.  Defines PASRs and PALRs as promoter-associated long or short RNAs."]]

Normalisation.
diff --git a/biblio/28911121.mdwn b/biblio/28911121.mdwn
index 143f947..b30a1ab 100644
--- a/biblio/28911121.mdwn
+++ b/biblio/28911121.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase."]]
-[[!tag enzyme reverse-transcription]]
+[[!tag enzyme reverse_transcription]]
 
 Nucleic Acids Res. 2017 Sep 6;45(15):9046-9058. doi:10.1093/nar/gkx633
 

Pas lu.
diff --git a/biblio/26000487.mdwn b/biblio/26000487.mdwn
new file mode 100644
index 0000000..6f7ddda
--- /dev/null
+++ b/biblio/26000487.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells."]]
+[[!tag emulsion single_cell]]
+
+Cell. 2015 May 21;161(5):1187-1201. doi:10.1016/j.cell.2015.04.044
+
+Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L,
+Weitz DA, Kirschner MW.
+
+Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
+
+[[!pmid 26000487 desc="inDrop.  Uses photo-cleavable oligonucleotides."]]