Dernières modifications :

Old
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 5ccf4b1..a8ba77b 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -39,6 +39,7 @@ transcriptases have a TdT activity.
    transcriptase of the long terminal repeat retrotransposon Tf1, like other
    DNA polymerases, also adds non-templated As to blunt DNA duplexes.
 
+
 ### Templated TdT activity
 
 Surprisingly, reverse transcriptases can also extend cDNAs using a single
@@ -55,6 +56,12 @@ nucleotide as a template.
    2017b|biblio/28747695]]).
 
 
+### The 5′ cap enhances C-tailing
+
+ - [[Schmidt & Mueller, 1999|biblio/10518626]] showed that extra cytosine are
+   more frequently added in presence of the 5′ cap.
+
+
 ### The 5′ cap is reverse-transcribed
 
  - [[Hirzmann et al., 1993|biblio/8346046]] observed the presence of an extra G

Old
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 5c3a109..b78625d 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -45,7 +45,9 @@ as a replacement for RNA.
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
  - 3′ phosphate or biotin blocking groups abolish template-switching
-   ([[Turchinovich et al (2014)|biblio/24922482]] and others).
+   ([[Turchinovich et al (2014)|biblio/24922482]] and others).  However,
+   [[Pinto & Lindblad (2010)|biblio/19837043]] report the use of a
+   3′ C3 spacer (on all-DNA TSOs).
 
  - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
    of the TSO, and therefore blocks concatenation
@@ -62,10 +64,12 @@ as a replacement for RNA.
    magnesium concentration (to 6 mM) or adding manganese at the end of the
    reaction (1 or 2 mM) increased the frequency of dC addition (moderately
    for Mg<sup>2+</sup> and strongly for Mn<sup>2+</sup>).  Enzyme: SSII; dNTP
-   concentration: 1 mM each.
+   concentration: 1 mM each.  [[Pinto & Lindblad (2010)|biblio/19837043]] also
+   used manganese.
 
  - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
    switching non-capped molecules by increasing dNTPs to 2 mM and
    Mg<sup>2+</sup> to 9 mM.
 
+
 [[!inline pages="tagged(template_switching)" limit=0]]

Old.
diff --git a/biblio/19837043.mdwn b/biblio/19837043.mdwn
index 32875d4..045a852 100644
--- a/biblio/19837043.mdwn
+++ b/biblio/19837043.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="A guide for in-house design of template-switch-based 5′ rapid amplification of cDNA ends systems."]]
-[[!tag method template_switching]]
+[[!tag method template_switching manganese]]
+
+Anal Biochem. 2010 Feb 15;397(2):227-32. doi:10.1016/j.ab.2009.10.022
+
+Pinto FL, Lindblad P.
+
+A guide for in-house design of template-switch-based 5' rapid amplification of cDNA ends systems.
+
 [[!pmid 19837043 desc="Uses desoxyriboguanosine tails for template switching (but the last one is blocked by a propyl group (C3 spacer)."]]

Old.
diff --git a/biblio/21131977.mdwn b/biblio/21131977.mdwn
new file mode 100644
index 0000000..584c3e8
--- /dev/null
+++ b/biblio/21131977.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Transcription of functionally related constitutive genes is not coordinated."]]
+[[!tag yeast single_cell transcription]]
+
+Nat Struct Mol Biol. 2011 Jan;18(1):27-34. doi:10.1038/nsmb.1934
+
+Gandhi SJ, Zenklusen D, Lionnet T, Singer RH.
+
+Transcription of functionally related constitutive genes is not coordinated.
+
+[[!pmid 21131977 desc="Even two constitutively expressed alleles (MDN1) are not correlated.  Stoechoimetry is postulated to be acheived post-transcriptionally and post-traductionally."]]

strt
diff --git a/biblio/29180631.mdwn b/biblio/29180631.mdwn
new file mode 100644
index 0000000..85d3199
--- /dev/null
+++ b/biblio/29180631.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array."]]
+[[!tag tag library method template_switching]]
+
+Sci Rep. 2017 Nov 27;7(1):16327. doi:10.1038/s41598-017-16546-4
+
+Hochgerner H, Lönnerberg P, Hodge R, Mikes J, Heskol A, Hubschle H, Lin P, Picelli S, La Manno G, Ratz M, Dunne J, Husain S, Lein E, Srinivasan M, Zeisel A, Linnarsson S.
+
+STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.
+
+[[!pmid 29180631 desc="STRT for the icell8 platform.  SSIII better than SSIII with RNA TSO.  Optimum: ~2 μM."]]

sRNA.
diff --git a/biblio/28327113.mdwn b/biblio/28327113.mdwn
index a3dfc9d..ed6b575 100644
--- a/biblio/28327113.mdwn
+++ b/biblio/28327113.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium."]]
-[[!tag template_switching reverse_transcription]]
+[[!tag template_switching reverse_transcription sRNA]]
 
 Lee YH, Hsueh YW, Peng YH, Chang KC, Tsai KJ, Sun HS, Su IJ, Chiang PM.
 

Café
diff --git a/biblio/20598146.mdwn b/biblio/20598146.mdwn
new file mode 100644
index 0000000..9aa458f
--- /dev/null
+++ b/biblio/20598146.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples."]]
+[[!tag template_switching reverse_transcription]]
+
+BMC Genomics. 2010 Jul 2;11:413. doi:10.1186/1471-2164-11-413
+
+Kapteyn J, He R, McDowell ET, Gang DR.
+
+Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples.
+
+[[!pmid 20598146 desc="TSO starting with iCiGiC (iso-dC / iso-dG) does not form concatenates because the RTase is inhibited by these nucleotides, therefore it does not reach the end and no extra template switching occurs."]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index e7f8577..5c3a109 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -47,6 +47,10 @@ as a replacement for RNA.
  - 3′ phosphate or biotin blocking groups abolish template-switching
    ([[Turchinovich et al (2014)|biblio/24922482]] and others).
 
+ - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
+   of the TSO, and therefore blocks concatenation
+   ([[Kapteyn et al., 2010|biblio/20598146]]).
+
 ### Effect of TSO concentration
 
  - For the STRT method, [[Zajac et al (2013)|biblio/24392002]] concluded that

Corrections, simplifications.
diff --git a/biblio/15500255.mdwn b/biblio/15500255.mdwn
index abe68a2..28d781e 100644
--- a/biblio/15500255.mdwn
+++ b/biblio/15500255.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method."]]
-[[!tag cap enzyme]]
+[[!tag cap reverse_transcription]]
+
+DNA Res. 2004 Aug 31;11(4):305-9
+
+Ohtake H, Ohtoko K, Ishimaru Y, Kato S.
+
+Determination of the capped site sequence of mRNA based on the detection of cap-dependent nucleotide addition using an anchor ligation method.
+
 [[!pmid 15500255 desc="ADP cap templates extra T in the first strand cDNA."]]
diff --git a/biblio/15520289.mdwn b/biblio/15520289.mdwn
index 42fcc47..6a087f0 100644
--- a/biblio/15520289.mdwn
+++ b/biblio/15520289.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity."]]
-[[!tag cap enzyme]]
+[[!tag cap reverse_transcription]]
 
 Lavie L, Maldener E, Brouha B, Meese EU, Mayer J.
 
diff --git a/biblio/22035236.mdwn b/biblio/22035236.mdwn
index cc97666..0825b78 100644
--- a/biblio/22035236.mdwn
+++ b/biblio/22035236.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Template-independent DNA synthesis activity associated with the reverse transcriptase of the long terminal repeat retrotransposon Tf1."]]
-[[!tag enzyme reverse_transcription terminal_transferase]]
+[[!tag reverse_transcription]]
 
 Oz-Gleenberg I, Herzig E, Hizi A.
 
diff --git a/biblio/8346046.mdwn b/biblio/8346046.mdwn
index a4c8180..c350725 100644
--- a/biblio/8346046.mdwn
+++ b/biblio/8346046.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Determination of messenger RNA 5'-ends by reverse transcription of the cap structure."]]
-[[!tag cap enzyme]]
+[[!tag cap reverse_transcription]]
+
+Nucleic Acids Res. 1993 Jul 25;21(15):3597-8
+
+Hirzmann J, Luo D, Hahnen J, Hobom G.
+
+Determination of messenger RNA 5'-ends by reverse transcription of the cap structure.
+
 [[!pmid 8346046 desc="The mRNA cap can template an extra C in the first strand cDNA."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index b8914e0..5ccf4b1 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -71,7 +71,7 @@ nucleotide as a template.
    sequences of retrotransposons, showing that endogenous reverse-transcriptases
    also reverse-transcribe the cap.
 
- - [[Zhang et al, 2017|biblio/28673998] published a structure of an RNA-GpppG
+ - [[Zhang et al, 2017|biblio/28673998]] published a structure of an RNA-GpppG
    complex that suggests that a m7GpppNm / DNA duplex could form during the
    reverse-transcription of the cap
 
diff --git a/tags/terminal_transferase.mdwn b/tags/terminal_transferase.mdwn
deleted file mode 100644
index 23f3c37..0000000
--- a/tags/terminal_transferase.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged terminal transferase"]]
-
-[[!inline pages="tagged(terminal_transferase)" actions="no" archive="yes"
-feedshow=10]]

The cap is reverse-transcribed.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 8719370..b8914e0 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -35,6 +35,15 @@ transcriptases have a TdT activity.
    Activity increased with concentration for MMLV.  (High-concentration AMV was
    not available.)
 
+ - [[Oz-Gleenberg et al, 2011|biblio/22035236]] showed that the the reverse
+   transcriptase of the long terminal repeat retrotransposon Tf1, like other
+   DNA polymerases, also adds non-templated As to blunt DNA duplexes.
+
+### Templated TdT activity
+
+Surprisingly, reverse transcriptases can also extend cDNAs using a single
+nucleotide as a template.
+
  - Following an initial observation of [[Clark et al (1987)|biblio/3323527]] on
    the Klenow fragment, [[Ohtsubo et al, 2017a|biblio/28150748]] showed that
    specific tailing is enhanced by the complementary dNMP (C enhanced by dGMP,
@@ -45,6 +54,28 @@ transcriptases have a TdT activity.
    tailing when longer reaction times are allowed ([[Ohtsubo et al.,
    2017b|biblio/28747695]]).
 
+
+### The 5′ cap is reverse-transcribed
+
+ - [[Hirzmann et al., 1993|biblio/8346046]] observed the presence of an extra G
+   at the 5′ end of cDNA clones, and concluded that the cap can be
+   reverse-transcribed.  They supported their conclusion with molecular modelling.
+
+ - [[Volloch et al, 1995|biblio/8534373]] studied cap transcription (but I could
+   not access the article).
+
+ - [[Ohtake et al, 2004|biblio/15500255]] synthethised RNAs with A-caps and
+   showed that they are reverse-transcribed as Ts.
+
+ - [[Lavie et al, 2004|biblio/15520289]] found extra Gs at the ends of genomic
+   sequences of retrotransposons, showing that endogenous reverse-transcriptases
+   also reverse-transcribe the cap.
+
+ - [[Zhang et al, 2017|biblio/28673998] published a structure of an RNA-GpppG
+   complex that suggests that a m7GpppNm / DNA duplex could form during the
+   reverse-transcription of the cap
+
+
 ### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].

Onigiri.
diff --git a/biblio/28747695.mdwn b/biblio/28747695.mdwn
new file mode 100644
index 0000000..816248e
--- /dev/null
+++ b/biblio/28747695.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase."]]
+[[!tag reverse_transcription]]
+
+Sci Rep. 2017 Jul 26;7(1):6520. doi:10.1038/s41598-017-04765-8
+
+Ohtsubo Y, Nagata Y, Tsuda M.
+
+Compounds that enhance the tailing activity of Moloney murine leukemia virus reverse transcriptase.
+
+[[!pmid 28747695 desc="rA, r/dG, r/dC are potent enhancers of tailing.  In longer reactions, GMP, GDP or CDP promote continuous extension of the tail.  Reactions performed with 100 fmols of substrate DNA, 50 mM Tris-HCl pH 8.3, 75 mM KCl, 6 mM MgCl2, 2 mM DTT, 4 mM dATP, dCTP, dGTP, or dTTP, 4 mM MnCl2, and 50 U MMLV-RT, at 30 °C."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 6866b55..8719370 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -36,10 +36,15 @@ transcriptases have a TdT activity.
    not available.)
 
  - Following an initial observation of [[Clark et al (1987)|biblio/3323527]] on
-   the Klenow fragment, [[Ohtsubo et al, 2017|biblio/28150748]] showed that
+   the Klenow fragment, [[Ohtsubo et al, 2017a|biblio/28150748]] showed that
    specific tailing is enhanced by the complementary dNMP (C enhanced by dGMP,
    etc.), except for A-tailing, which is already the strongest.
 
+ - Other nucleotides than dNMPs can enhance tailing.  In particular, rA, dA, dG
+   and dC potently induce tailing, and GMP, GDP and CDP induce continuous
+   tailing when longer reaction times are allowed ([[Ohtsubo et al.,
+   2017b|biblio/28747695]]).
+
 ### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].

Normalisation.
diff --git a/biblio/28150748.mdwn b/biblio/28150748.mdwn
index 5023be5..38b0b49 100644
--- a/biblio/28150748.mdwn
+++ b/biblio/28150748.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase."]]
-[[!tag reverse-transcription]]
+[[!tag reverse_transcription]]
 
 Sci Rep. 2017 Feb 2;7:41769. doi:10.1038/srep41769
 

NMP
diff --git a/biblio/28150748.mdwn b/biblio/28150748.mdwn
new file mode 100644
index 0000000..5023be5
--- /dev/null
+++ b/biblio/28150748.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase."]]
+[[!tag reverse-transcription]]
+
+Sci Rep. 2017 Feb 2;7:41769. doi:10.1038/srep41769
+
+Ohtsubo Y, Nagata Y, Tsuda M.
+
+Efficient N-tailing of blunt DNA ends by Moloney murine leukemia virus reverse transcriptase.
+
+[[!pmid 28150748 desc="Specific tailing of first-strand cDNAs is robustly enhanced by the complementary dNMP (C enhanced by dGMP, etc.).  A-tailing is not enhanced, perhaps because it is already very strong.  Reactions made in presence of manganese; not tested with only magnesium."]]
diff --git a/biblio/3323527.mdwn b/biblio/3323527.mdwn
new file mode 100644
index 0000000..6570f75
--- /dev/null
+++ b/biblio/3323527.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli."]]
+[[!tag enzyme]]
+
+J Mol Biol. 1987 Nov 5;198(1):123-7.
+
+Clark JM, Joyce CM, Beardsley GP.
+
+Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli.
+
+[[!pmid 3323527 desc="Reports enhancement of +1 tailing by Klenow fragment with dNMPs."]]
diff --git a/biblio/7507249.mdwn b/biblio/7507249.mdwn
new file mode 100644
index 0000000..75611fe
--- /dev/null
+++ b/biblio/7507249.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Marked infidelity of human immunodeficiency virus type 1 reverse transcriptase at RNA and DNA template ends."]]
+[[!tag reverse_transcription]]
+
+Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):549-53 doi:10.1073/pnas.91.2.549
+
+Patel PH & Preston BD.
+
+Marked infidelity of human immunodeficiency virus type 1 reverse transcriptase at RNA and DNA template ends.
+
+[[!pmid 7507249 desc="On DNA/DNA blunt ends, adds a single nucleotide (A > G >> C|T).  On RNA/DNA blund ends, adds more nucleotides.  Addition is favoured by increased dNTP levels."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 696155c..6866b55 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -24,12 +24,22 @@ _(redaction in progress)_
 Like other DNA polymerases ([[Clark, 1988|biblio/2460825]]), reverse
 transcriptases have a TdT activity.
 
+ - [[Patel & Preston, 1994|biblio/7507249]] showed that HIV RT adds one
+   nucleotide (A > G >> T|C) on DNA/DNA duplexes, and more on DNA/RNA duplexes.
+   Addition is favoured by increased dNTP levels.  MMLV and AMV were also
+   reported (data not shown) to add multiple nucleotides.
+
  - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
    AMV, with a preference for adding As.  For MMLV, activity reduced abruptly
    between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.
    Activity increased with concentration for MMLV.  (High-concentration AMV was
    not available.)
 
+ - Following an initial observation of [[Clark et al (1987)|biblio/3323527]] on
+   the Klenow fragment, [[Ohtsubo et al, 2017|biblio/28150748]] showed that
+   specific tailing is enhanced by the complementary dNMP (C enhanced by dGMP,
+   etc.), except for A-tailing, which is already the strongest.
+
 ### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].

Café
diff --git a/biblio/28408603.mdwn b/biblio/28408603.mdwn
new file mode 100644
index 0000000..6de6c99
--- /dev/null
+++ b/biblio/28408603.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)."]]
+[[!tag single_cell amplification transposase genome method]]
+
+Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS.
+
+Science. 2017 Apr 14;356(6334):189-194. doi:10.1126/science.aak9787
+
+Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI).
+
+[[!pmid 28408603 desc="Tn5 tagmentation with custom adapters ending with T7 promoters, followed by linear amplification by transcription, followed by cDNA synthesis and sequencing."]]

slack
diff --git a/biblio/26152304.mdwn b/biblio/26152304.mdwn
new file mode 100644
index 0000000..41a1fb8
--- /dev/null
+++ b/biblio/26152304.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A new method to prevent carry-over contaminations in two-step PCR NGS library preparations."]]
+[[!tag library amplification method]]
+
+Seitz V, Schaper S, Dröge A, Lenze D, Hummel M, Hennig S.
+
+Nucleic Acids Res. 2015 Nov 16;43(20):e135. doi:10.1093/nar/gkv694
+
+A new method to prevent carry-over contaminations in two-step PCR NGS library preparations.
+
+[[!pmid 26152304 desc="Proposes to introduce indexes during the cDNA PCR, and to partially match them during Library PCR, so that 1) the PCR is more stringent and 2) contaminations can be detected by sequence analysis."]]

Dans le train.
diff --git a/biblio/29615780.mdwn b/biblio/29615780.mdwn
new file mode 100644
index 0000000..c0092c7
--- /dev/null
+++ b/biblio/29615780.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution."]]
+[[!tag evolution genome]]
+
+Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ.
+
+Sci Rep. 2018 Apr 3;8(1):5518. doi:10.1038/s41598-018-23749-w
+
+De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution.
+
+[[!pmid 29615780 desc="159 Mb assembly (82% of the predicted 194 Mb genome).  Comparison with other tunicates confirms extensive breakage of gene clusters."]]

Old
diff --git a/biblio/18426769.mdwn b/biblio/18426769.mdwn
new file mode 100644
index 0000000..4a9caef
--- /dev/null
+++ b/biblio/18426769.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Current techniques for single-cell lysis."]]
+[[!tag single_cell method lysis]]
+
+Brown RB, Audet J.
+
+J R Soc Interface. 2008 Oct 6;5 Suppl 2:S131-8. doi:10.1098/rsif.2008.0009.focus
+
+Current techniques for single-cell lysis.
+
+[[!pmid 18426769 desc="Does not cover lysis by heating."]]

Monophyletic chordates.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 5066380..2cd6d2d 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -7,4 +7,4 @@ Nature. 2006 Feb 23;439(7079):965-8.
 
 Tunicates and not cephalochordates are the closest living relatives of vertebrates.
 
-[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates."]]
+[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  This was refuted by Bourlat et al. in 2006.  Oikopleura is basal to other tunicates (and was not included in Bourlat et al)."]]
diff --git a/biblio/17051155.mdwn b/biblio/17051155.mdwn
new file mode 100644
index 0000000..8a0ced0
--- /dev/null
+++ b/biblio/17051155.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida."]]
+[[!tag evolution]]
+
+Bourlat SJ1, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES, Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ.
+
+Nature. 2006 Nov 2;444(7115):85-8 doi:10.1038/nature05241
+
+Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.
+
+[[!pmid 17051155 desc="Incorporation of a newly sequenced hemichordate produces a phylogenetic tree supporting the monophyly of chordates."]]

Encore.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 35f17ba..5066380 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -7,4 +7,4 @@ Nature. 2006 Feb 23;439(7079):965-8.
 
 Tunicates and not cephalochordates are the closest living relatives of vertebrates.
 
-[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]
+[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates."]]

Réparation.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 114bf48..35f17ba 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -7,4 +7,4 @@ Nature. 2006 Feb 23;439(7079):965-8.
 
 Tunicates and not cephalochordates are the closest living relatives of vertebrates.
 
-[[!pmid 16495997 desc='Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the "Olfactores" clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]
+[[!pmid 16495997 desc="Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]

Standardisation.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index ecaf314..114bf48 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Tunicates and not cephalochordates are the closest living relatives of vertebrates."]]
-[[!tag phylogeny Oikopleura]]
+[[!tag evolution Oikopleura]]
 
 Delsuc F, Brinkmann H, Chourrout D, Philippe H.
 
diff --git a/tags/phylogeny.mdwn b/tags/phylogeny.mdwn
deleted file mode 100644
index e0377da..0000000
--- a/tags/phylogeny.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged phylogeny"]]
-
-[[!inline pages="tagged(phylogeny)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/phylogeny
diff --git a/tags/phylogeny.mdwn b/tags/phylogeny.mdwn
new file mode 100644
index 0000000..e0377da
--- /dev/null
+++ b/tags/phylogeny.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged phylogeny"]]
+
+[[!inline pages="tagged(phylogeny)" actions="no" archive="yes"
+feedshow=10]]

Banane
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f132027..0a7822e 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -26,8 +26,9 @@ Evolution
    clade is sister of Stolidobranchia (that is, not basal in Tunicates).
    Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
- - Based on 258 orthologous proteins from 63 species, Oikopleuridae is basal to
-   all other tunicates ([[Delsuc et al., 2018|biblio/29653534]]).
+ - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]])
+   and then 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
+   show that Oikopleuridae is basal to all other tunicates.
 
 
 Genome

Onigiri.
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
new file mode 100644
index 0000000..ecaf314
--- /dev/null
+++ b/biblio/16495997.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tunicates and not cephalochordates are the closest living relatives of vertebrates."]]
+[[!tag phylogeny Oikopleura]]
+
+Delsuc F, Brinkmann H, Chourrout D, Philippe H.
+
+Nature. 2006 Feb 23;439(7079):965-8.
+
+Tunicates and not cephalochordates are the closest living relatives of vertebrates.
+
+[[!pmid 16495997 desc='Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the "Olfactores" clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates.  The euchordates clade is viewed as anthropcentric.  Oikopleura is basal to other tunicates.']]

Phylogénie.
diff --git a/biblio/19656395.mdwn b/biblio/19656395.mdwn
new file mode 100644
index 0000000..2fe9e0e
--- /dev/null
+++ b/biblio/19656395.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models."]]
+[[!tag Oikopleura evolution]]
+
+Tsagkogeorga G, Turon X, Hopcroft RR, Tilak MK, Feldstein T, Shenkar N, Loya Y, Huchon D, Douzery EJ, Delsuc F.
+
+BMC Evol Biol. 2009 Aug 5;9:187. doi:10.1186/1471-2148-9-187
+
+An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.
+
+[[!pmid 19656395 desc="Phylogenetic tree built with 18S rRNA sequences from 110 species including 4 Oikopleuridae places Oikopleuridae as sister group of Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or long-branch attraction.  Many other articles on the topic are cited in this paper."]]
diff --git a/biblio/29653534.mdwn b/biblio/29653534.mdwn
new file mode 100644
index 0000000..331833b
--- /dev/null
+++ b/biblio/29653534.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A phylogenomic framework and timescale for comparative studies of tunicates."]]
+[[!tag Oikopleura evolution]]
+
+Delsuc F, Philippe H, Tsagkogeorga G, Simion P, Tilak MK, Turon X, López-Legentil S, Piette J, Lemaire P, Douzery EJP.
+
+BMC Biol. 2018 Apr 13;16(1):39. doi:10.1186/s12915-018-0499-2
+
+A phylogenomic framework and timescale for comparative studies of tunicates.
+
+[[!pmid 29653534 desc="Phylogenetic tree based on 258 orthologous proteins from 63 species shows Oikopleura as a sister group of all other tunicates, with a split 447 ± 20 Mya ago.  A long-branch attraction artefact can nevertheless not be excluded."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index becb9e5..f132027 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -18,6 +18,18 @@ Some links:
  - Genoscope's genome browser: <http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/>
  - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/>
 
+
+Evolution
+---------
+
+ - Based on 18S rRNA sequences from 110 species including 4 Oikopleuridae, this
+   clade is sister of Stolidobranchia (that is, not basal in Tunicates).
+   Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or
+   long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
+ - Based on 258 orthologous proteins from 63 species, Oikopleuridae is basal to
+   all other tunicates ([[Delsuc et al., 2018|biblio/29653534]]).
+
+
 Genome
 ------
 
@@ -27,6 +39,7 @@ Genome
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
 
+
 Transcriptome
 -------------
 

Intron turnover.
diff --git a/biblio/15638456.mdwn b/biblio/15638456.mdwn
new file mode 100644
index 0000000..39190f5
--- /dev/null
+++ b/biblio/15638456.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica."]]
+[[!tag Oikopleura intron]]
+
+J Mol Evol. 2004 Oct;59(4):448-57 doi:10.1007/s00239-004-2636-5
+
+Edvardsen RB, Lerat E, Maeland AD, Flåt M, Tewari R, Jensen MF, Lehrach H, Reinhardt R, Seo HC, Chourrout D.
+
+Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica.
+
+[[!pmid 15638456 desc="Study on housekeeping genes suggests that “Most Oikopleura introns occupy nonconserved positions and probably originate from numerous late intron gains or sliding of ancient introns”.  Conservation within paralogs suggest possible gene conversion events."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 51f691d..becb9e5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -39,6 +39,9 @@ Transcriptome
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
+ - Introns are subjected to a large turnover: many ancestral introns are lost, and many
+   new species-specific introns found ([[Edvarsen et al., 2004|biblio/15638456]]).
+
 
 Tools
 -----

Length of O. dioica's SL.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8342708..51f691d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -31,7 +31,7 @@ Transcriptome
 -------------
 
  - O. dioica is the first chordate where gene operons have been described.  A
-   5′ splice leader (SL) bearing a trimethylated cap is found in some RNAs.
+   40-nt 5′ [[splice leader|tags/trans-splicing]] (SL) bearing a trimethylated cap is found in some RNAs.
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
    times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus
    ([[Ganot et al., 2004|biblio/15314184]]).

Normalise
diff --git a/biblio/26668163.mdwn b/biblio/26668163.mdwn
index a5f945d..873c1b0 100644
--- a/biblio/26668163.mdwn
+++ b/biblio/26668163.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis."]]
-[[!tag Ciona_intestinalis oligo_capping trans-splicing]]
+[[!tag Ciona_intestinalis oligo-capping trans-splicing]]
 
 Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K.
 
diff --git a/tags/oligo_capping.mdwn b/tags/oligo_capping.mdwn
deleted file mode 100644
index c314d3a..0000000
--- a/tags/oligo_capping.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged oligo capping"]]
-
-[[!inline pages="tagged(oligo_capping)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/oligo_capping
diff --git a/tags/oligo_capping.mdwn b/tags/oligo_capping.mdwn
new file mode 100644
index 0000000..c314d3a
--- /dev/null
+++ b/tags/oligo_capping.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged oligo capping"]]
+
+[[!inline pages="tagged(oligo_capping)" actions="no" archive="yes"
+feedshow=10]]

Trans-splicing again.
diff --git a/biblio/26668163.mdwn b/biblio/26668163.mdwn
new file mode 100644
index 0000000..a5f945d
--- /dev/null
+++ b/biblio/26668163.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis."]]
+[[!tag Ciona_intestinalis oligo_capping trans-splicing]]
+
+Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K.
+
+Genome Res. 2016 Jan;26(1):140-50. doi:10.1101/gr.184648.114
+
+Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.
+
+[[!pmid 26668163 desc="TSS-Seq libraries made of 200 µg of total RNA, sequenced on Illumina GA with a read length of 36, which is sufficient to go through the 16-nt splice leader."]]

creating tag page tags/Ciona_intestinalis
diff --git a/tags/Ciona_intestinalis.mdwn b/tags/Ciona_intestinalis.mdwn
new file mode 100644
index 0000000..84c7dee
--- /dev/null
+++ b/tags/Ciona_intestinalis.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Ciona intestinalis"]]
+
+[[!inline pages="tagged(Ciona_intestinalis)" actions="no" archive="yes"
+feedshow=10]]

Trans-splicing in C. intestinalis; size of splice leader.
diff --git a/biblio/16822859.mdwn b/biblio/16822859.mdwn
new file mode 100644
index 0000000..651deb5
--- /dev/null
+++ b/biblio/16822859.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis."]]
+[[!tag trans-splicing Ciona_intestinalis]]
+
+Nucleic Acids Res. 2006 Jul 5;34(11):3378-88 doi:10.1093/nar/gkl418
+
+Satou Y, Hamaguchi M, Takeuchi K, Hastings KE, Satoh N.
+
+Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis.
+
+[[!pmid 16822859 desc="Analysis of oligo-capped cDNAs reports a single splice leader (16 nt-long) in 27% of the cDNAs."]]
diff --git a/tags/trans-splicing.mdwn b/tags/trans-splicing.mdwn
index 22bf646..31411ab 100644
--- a/tags/trans-splicing.mdwn
+++ b/tags/trans-splicing.mdwn
@@ -1,4 +1,5 @@
 [[!meta title="pages tagged trans-splicing"]]
 
-[[!inline pages="tagged(trans-splicing)" actions="no" archive="yes"
-feedshow=10]]
+The splice leader is 16-nt in C. intestinalis ([[Satou et al, 2006|biblio/16822859]]) and 40-nt in O. dioica ([[Ganot et al., 2004|biblio/15314184]]).
+
+[[!inline pages="tagged(trans-splicing)" actions="no" limit=0]]

au bureau.
diff --git a/biblio/29449511.mdwn b/biblio/29449511.mdwn
new file mode 100644
index 0000000..343d94c
--- /dev/null
+++ b/biblio/29449511.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity."]]
+[[!tag CRISPR HPV method]]
+
+Science. 2018 Feb 15. pii: eaar6245. doi:10.1126/science.aar6245
+
+Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA.
+
+CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity.
+
+[[!pmid 29449511 desc="DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR).  Cas12a activates a single-strand nuclease after matching its target double-strand DNA.  A single-strand probe terminated by a fluorophore and a quencher signals the activation."]]

More background.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 18545b2..8342708 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -3,12 +3,14 @@
 Oikopleura
 ==========
 
-_Oikopleura dioica_ is a tunicate plankton.  Thus, it belongs to the same
-"chordate" phylum as us.  Its genome is very small, as each cell only contains
-70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
-Each animal secretes a mucus "house" that is used for feeding (and perhaps
-defending).  The main house proteins are called _oikosins_ and half or them
-are unique to Oikopleura and related animals ("_Appendicularia_").
+_Oikopleura dioica_ is a tunicate larvacean (synonym: urochordate
+appendicularian) plankton.  Thus, it belongs to the same "chordate" phylum as
+us.  As the name indicates, it is the only _dioecious_ species of _Oikopleura_
+(that is: male and female organisms are distinct).  Its reproduction is
+_semelparous_: the animals die afer releasing its gametes.  Each animal
+secretes a mucus "house" that is used for feeding (and perhaps defending).  The
+main house proteins are called _oikosins_ and half or them are unique to
+Oikopleura and related animals ("_Appendicularia_").
 
 Some links:
 
@@ -20,6 +22,7 @@ Genome
 ------
 
  - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
+ - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 

Expand.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index cd23cbc..18545b2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -27,9 +27,11 @@ Genome
 Transcriptome
 -------------
 
- - Some genes are organised in operons.  A 5′ splice leader (SL) is found in some RNAs.
+ - O. dioica is the first chordate where gene operons have been described.  A
+   5′ splice leader (SL) bearing a trimethylated cap is found in some RNAs.
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
-   times in the genome ([[Ganot et al., 2004|biblio/15314184]]).
+   times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus
+   ([[Ganot et al., 2004|biblio/15314184]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with

Correction.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 43de0f4..cd23cbc 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -48,7 +48,7 @@ Development
    _pax2/5/8_ is detected between the _otxa_ + _otxb_ and the _hox1_ territories.
    ([[Cañestro et al., 2005|biblio/16111672]]).
  - The _pum1_ and _vas4_ RNAs show localised expression during development. Prior
-   hatching, _pum1_ is found outside the embryo ([[|biblio/29486709]]).
+   hatching, _pum1_ is found outside the embryo ([[Olsen et al., 2018|biblio/29486709]]).
 
 
 Ecology

Extracellular RNA localisation !?
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c5e5eb0..43de0f4 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -47,6 +47,9 @@ Development
    hindbrain, and spinal cord, but not the midbrain.  No expression of
    _pax2/5/8_ is detected between the _otxa_ + _otxb_ and the _hox1_ territories.
    ([[Cañestro et al., 2005|biblio/16111672]]).
+ - The _pum1_ and _vas4_ RNAs show localised expression during development. Prior
+   hatching, _pum1_ is found outside the embryo ([[|biblio/29486709]]).
+
 
 Ecology
 -------

In the train
diff --git a/biblio/29486709.mdwn b/biblio/29486709.mdwn
new file mode 100644
index 0000000..1f0a06f
--- /dev/null
+++ b/biblio/29486709.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evidence for a centrosome-attracting body like structure in germ-soma segregation during early development, in the urochordate Oikopleura dioica."]]
+[[!tag Oikopleura localisation germ_line]]
+
+Olsen LC, Kourtesis I, Busengdal H, Jensen MF, Hausen H, Chourrout D.
+
+BMC Dev Biol. 2018 Feb 27;18(1):4. doi:10.1186/s12861-018-0165-5
+
+Evidence for a centrosome-attracting body like structure in germ-soma segregation during early development, in the urochordate Oikopleura dioica.
+
+[[!pmid 29486709 desc="Localised pumilio (pum1) and vasa (vas4) RNAs.  Prior hatching, pum1 is found outside the embryo!"]]

Old
diff --git a/biblio/14757812.mdwn b/biblio/14757812.mdwn
new file mode 100644
index 0000000..0000c97
--- /dev/null
+++ b/biblio/14757812.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome annotation by high-throughput 5' RNA end determination."]]
+[[!tag sequence_tags trans-splicing]]
+
+Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1650-5. doi:10.1073/pnas.0308384100
+
+Hwang BJ, Müller HM, Sternberg PW.
+
+Genome annotation by high-throughput 5' RNA end determination.
+
+[[!pmid 14757812 desc="TC-RED: primes with oligo-dT, amplifies primers complementary to the splice leader, cleaves tags with BpmI and sequences concatemers"]]

Au parc
diff --git a/biblio/29440632.mdwn b/biblio/29440632.mdwn
new file mode 100644
index 0000000..894a325
--- /dev/null
+++ b/biblio/29440632.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Detecting RNA base methylations in single cells by in situ hybridization"]]
+[[!tag methylation hybridisation]]
+
+Ranasinghe RT, Challand MR, Ganzinger KA, Lewis BW, Softley C, Schmied WH, Horrocks MH, Shivji N, Chin JW, Spencer J, Klenerman D
+
+Nat Commun. 2018 Feb 13;9(1):655. doi:10.1038/s41467-017-02714-7
+
+Detecting RNA base methylations in single cells by in situ hybridization
+
+[[!pmid 29440632 desc="“MR-FISH”: Molecular beacons designed against known bases known to be
+methylated on their Watson-Crick interface have reduced affinity or fail to
+hybridise."]]

creating tag page tags/DNAi
diff --git a/tags/DNAi.mdwn b/tags/DNAi.mdwn
new file mode 100644
index 0000000..a4b2096
--- /dev/null
+++ b/tags/DNAi.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged DNAi"]]
+
+[[!inline pages="tagged(DNAi)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/maternal
diff --git a/tags/maternal.mdwn b/tags/maternal.mdwn
new file mode 100644
index 0000000..567b6b5
--- /dev/null
+++ b/tags/maternal.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged maternal"]]
+
+[[!inline pages="tagged(maternal)" actions="no" archive="yes"
+feedshow=10]]

DNAi
diff --git a/biblio/28281645.mdwn b/biblio/28281645.mdwn
new file mode 100644
index 0000000..f9f25ba
--- /dev/null
+++ b/biblio/28281645.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica."]]
+[[!tag Oikopleura screen DNAi maternal]]
+
+Omotezako T, Matsuo M, Onuma TA, Nishida H
+
+Sci Rep. 2017 Mar 10;7:44226. doi:10.1038/srep44226
+
+DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica.
+
+[[!pmid 28281645 desc="A clone library was prepared by subtracting male to female cDNAs.  Clones were screened by pools of 5 and then resolved individually.  Identifies genes related to cell structure and adhesion."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 930c9e7..c5e5eb0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -35,6 +35,10 @@ Transcriptome
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
 
+Tools
+-----
+
+ - DNAi was used to screen for maternal genes ([[Omotezako et al., 2017|biblio/28281645]]).
 
 Development
 -----------

mraw
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index e10cf4a..e7f8577 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -21,6 +21,12 @@
    can extend a linker with the sequence of a small RNA via a template switching
    reaction.  (That is: a sRNA can play the same role as a TS oligonucleotide.)
 
+ - in _Capture and Amplification by Tailing and Switching_ (CATS,
+   [[Turchinovich et al (2014)|biblio/24922482]]), short and long RNAs are A-tailed,
+   oligo-dT-primed, and template swiched.  A PNK treatement is needed on
+   circulating RNAs, to remove phosphates or cyclophosphates that would
+   prevent the A-tailing.
+
 ### Effect of chemical composition of the TS oligonucleotide
 
 Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,
@@ -38,6 +44,9 @@ as a replacement for RNA.
  - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
+ - 3′ phosphate or biotin blocking groups abolish template-switching
+   ([[Turchinovich et al (2014)|biblio/24922482]] and others).
+
 ### Effect of TSO concentration
 
  - For the STRT method, [[Zajac et al (2013)|biblio/24392002]] concluded that

Tag.
diff --git a/biblio/24922482.mdwn b/biblio/24922482.mdwn
index 1e10e5c..c7cc9ad 100644
--- a/biblio/24922482.mdwn
+++ b/biblio/24922482.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA."]]
-[[!tag template_switching amplification method]]
+[[!tag sRNA template_switching amplification method]]
 
 RNA Biol. 2014;11(7):817-28. doi:10.4161/rna.29304
 

XbaI
diff --git a/biblio/29482522.mdwn b/biblio/29482522.mdwn
new file mode 100644
index 0000000..1b0cdc8
--- /dev/null
+++ b/biblio/29482522.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate."]]
+[[!tag Oikopleura CAGE promoter motif]]
+
+Danks GB, Navratilova P, Lenhard B, Thompson EM 
+
+BMC Genomics. 2018 Feb 26;19(1):164. doi:10.1186/s12864-018-4504-5
+
+Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.
+
+[[!pmid 29482522 desc="“369/502 (73.5%) of genes that are specifically expressed in the testis are associated with a TCTAGA promoter element, compared to 100/906 (11.0%) that are specific to the ovary and 7/275 (2.5%) that are specific to the trunk.” “Strong association of gene body DNA methylation with TATA-dependent promoters in O. dioica.” "]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ed52be9..930c9e7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -32,6 +32,9 @@ Transcriptome
    times in the genome ([[Ganot et al., 2004|biblio/15314184]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
+ - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
+   CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
+
 
 Development
 -----------

Minor
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index edae7db..e10cf4a 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -14,7 +14,7 @@
    [[Ginsberg, 2005|biblio/16308152]].
 
  - In the  single-cell tagged reverse transcription (STRT) method,
-   [[Islam et al, 2011|biblio/21543516]]) use template switching and unique
+   [[Islam et al, (2011)|biblio/21543516]] use template switching and unique
    molecular identifiers to sequence 5′ ends.  The method is oligo-dT-primed.
 
  - [[Mohr et al (2013)|biblio/23697550]] have shown (Fig 6) that retroviral RTs

tag
diff --git a/biblio/21543516.mdwn b/biblio/21543516.mdwn
index 8ead64b..15b323b 100644
--- a/biblio/21543516.mdwn
+++ b/biblio/21543516.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq."]]
-[[!tag template_switching single_cell method transcriptome tags]]
+[[!tag STRT template_switching single_cell method transcriptome tags]]
 
 Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.
 

STRT.
diff --git a/biblio/21543516.mdwn b/biblio/21543516.mdwn
new file mode 100644
index 0000000..8ead64b
--- /dev/null
+++ b/biblio/21543516.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq."]]
+[[!tag template_switching single_cell method transcriptome tags]]
+
+Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.
+
+Genome Res. 2011 Jul;21(7):1160-7. doi:10.1101/gr.110882.110
+
+Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.
+
+[[!pmid 21543516 desc="Single-cell Tagged Reverse Transcription (STRT)"]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 4619e75..edae7db 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -13,6 +13,10 @@
    and `TTT` were also tested.  An extensive protocol was published in
    [[Ginsberg, 2005|biblio/16308152]].
 
+ - In the  single-cell tagged reverse transcription (STRT) method,
+   [[Islam et al, 2011|biblio/21543516]]) use template switching and unique
+   molecular identifiers to sequence 5′ ends.  The method is oligo-dT-primed.
+
  - [[Mohr et al (2013)|biblio/23697550]] have shown (Fig 6) that retroviral RTs
    can extend a linker with the sequence of a small RNA via a template switching
    reaction.  (That is: a sRNA can play the same role as a TS oligonucleotide.)
@@ -34,6 +38,11 @@ as a replacement for RNA.
  - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
+### Effect of TSO concentration
+
+ - For the STRT method, [[Zajac et al (2013)|biblio/24392002]] concluded that
+   1 μM of TSO gave the highest yield.
+
 ### Effect of magnesium, manganese and dNTP concentrations
 
  - [[Schmidt and Mueller, 1999|biblio/10518626]] showed that increasing

CapSelect.
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index f24e517..4619e75 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -2,6 +2,11 @@
 
 (work in progress)
 
+ - In the "_CapSelect_" method, [[Schmidt and Mueller, 1999|biblio/10518626]]
+   stimulate template switching with manganese (see below), tail the first-strand
+   cDNAs with dA, and add 5′ linkers with T4 DNA ligase and duplex adapters
+   ending with a (T)TTTGGG overhang.
+
  - 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`

More details on Mg / Mn addition.
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 7af520c..f24e517 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -12,10 +12,6 @@
    can extend a linker with the sequence of a small RNA via a template switching
    reaction.  (That is: a sRNA can play the same role as a TS oligonucleotide.)
 
- - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
-   switching non-capped molecules by increasing dNTPs to 2 mM and
-   Mg<sup>2+</sup> to 9 mM.
-
 ### Effect of chemical composition of the TS oligonucleotide
 
 Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,
@@ -33,4 +29,16 @@ as a replacement for RNA.
  - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
+### Effect of magnesium, manganese and dNTP concentrations
+
+ - [[Schmidt and Mueller, 1999|biblio/10518626]] showed that increasing
+   magnesium concentration (to 6 mM) or adding manganese at the end of the
+   reaction (1 or 2 mM) increased the frequency of dC addition (moderately
+   for Mg<sup>2+</sup> and strongly for Mn<sup>2+</sup>).  Enzyme: SSII; dNTP
+   concentration: 1 mM each.
+
+ - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
+   switching non-capped molecules by increasing dNTPs to 2 mM and
+   Mg<sup>2+</sup> to 9 mM.
+
 [[!inline pages="tagged(template_switching)" limit=0]]

More details.
diff --git a/biblio/10518626.mdwn b/biblio/10518626.mdwn
index f69b0d8..7c7c1f6 100644
--- a/biblio/10518626.mdwn
+++ b/biblio/10518626.mdwn
@@ -1,5 +1,5 @@
 [[!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]]
+[[!tag cap method reverse_transcription manganese template_switching]]
 
 Nucleic Acids Res. 1999 Nov 1;27(21):e31.
 
@@ -7,4 +7,4 @@ 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."]]
+[[!pmid 10518626 desc="Extra cytosine are more frequently added in presence of the 5′ cap.  Increasing Mg2+ to 6 mM increases the frequency of addition of more than 1 C, but only moderately.  Instead, when adding BSA in the reaction, supplementing it with 1 or 2 mM Mn2+ after 1h, 3-4 extra dC residues are added to most of the first strand cDNAs.  Standard reaction: 0.75 μM oligo dT (or 0.25 μM gene-specific RT primer); 50 mM Tris-HCl (pH 8.3); 75 mM KCl; 3 mM MgCl2; 5 mM DTT; dNTPs 1mM each; 0.1 mg BSA; 20 U RNAse inhibitor (Roche), 200 U SuperScript II; 1h at 42 °C."]]

Oops, already had it.
diff --git a/biblio/2460825.mdwn b/biblio/2460825.mdwn
index 997b5cd..dfa2bcf 100644
--- a/biblio/2460825.mdwn
+++ b/biblio/2460825.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases."]]
-[[!tag reverse_transcription enzyme polymerase]]
+[[!tag reverse_transcription template_switching enzyme polymerase]]
 
 Nucleic Acids Res. 1988 Oct 25;16(20):9677-86
 
@@ -7,4 +7,7 @@ Clark JM
 
 Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases.
 
-[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Perference for adding As."]]
+[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Perference for adding As.  ‘We cannot exclude the formal possibility that some of these latter
++events, particularly the addition of dCMP by AMV reverse transcriptase, involve the use of coding
++information made available as a result of a transient misalignment of the primer/template
++substrate.’"]]

Earlier report.
diff --git a/biblio/2460825.mdwn b/biblio/2460825.mdwn
index 1e7faae..997b5cd 100644
--- a/biblio/2460825.mdwn
+++ b/biblio/2460825.mdwn
@@ -1,6 +1,10 @@
 [[!meta title="Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases."]]
-[[!tag template_switching enzyme]]
-[[!pmid 2460825 desc="‘we cannot exclude the formal possibility that some of these latter
-events, particularly the addition of dCMP by AMV reverse transcriptase, involve the use of coding
-information made available as a result of a transient misalignment of the primer/template
-substrate.’"]]
+[[!tag reverse_transcription enzyme polymerase]]
+
+Nucleic Acids Res. 1988 Oct 25;16(20):9677-86
+
+Clark JM
+
+Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases.
+
+[[!pmid 2460825 desc="Terminal desoxynucleotidyl transferase activity of DNA polymerases, including AMV reverse transcriptase.  Perference for adding As."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 2f7c195..696155c 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -21,6 +21,9 @@ _(redaction in progress)_
 
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 
+Like other DNA polymerases ([[Clark, 1988|biblio/2460825]]), reverse
+transcriptases have a TdT activity.
+
  - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
    AMV, with a preference for adding As.  For MMLV, activity reduced abruptly
    between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.

more
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 14fe42d..2f7c195 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -22,7 +22,10 @@ _(redaction in progress)_
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 
  - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
-   AMV, with a preference for adding As.
+   AMV, with a preference for adding As.  For MMLV, activity reduced abruptly
+   between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.
+   Activity increased with concentration for MMLV.  (High-concentration AMV was
+   not available.)
 
 ### Reverse-transcriptases tolerate terminal mismatches
 

More on TdT.
diff --git a/biblio/11252793.mdwn b/biblio/11252793.mdwn
index d2c2f1e..ab611b9 100644
--- a/biblio/11252793.mdwn
+++ b/biblio/11252793.mdwn
@@ -7,4 +7,4 @@ Chen D, Patton JT.
 
 Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5'-RACE and primer extension.
 
-[[!pmid 11252793 desc="Terminal desoxynucleotidyl transferase activity of reverse transcriptases MMLV and AMV: preference for adding As."]]
+[[!pmid 11252793 desc="Terminal desoxynucleotidyl transferase activity on double-stranded substrates of reverse transcriptases MMLV and AMV: preference for adding As.  For MMLV, activity reduced abruptly between 45 and 50 °C.  For AMV, it decreased constantly from 25 to 50 °C.  Activity increased with concentration for MMLV.  (High-concentration AMV was not available.)"]]

Only two authors...
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 3c53de4..14fe42d 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -21,7 +21,7 @@ _(redaction in progress)_
 
 ### Terminal desoxynucleotidyl transferase (TdT) activity
 
- - [[Chen et al., 2001|biblio/11252793]] reported a TdT activity for MMLV and
+ - [[Chen & Patton, 2001|biblio/11252793]] reported a TdT activity for MMLV and
    AMV, with a preference for adding As.
 
 ### Reverse-transcriptases tolerate terminal mismatches

TdT.
diff --git a/biblio/11252793.mdwn b/biblio/11252793.mdwn
new file mode 100644
index 0000000..d2c2f1e
--- /dev/null
+++ b/biblio/11252793.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5'-RACE and primer extension."]]
+[[!tag reverse_transcription]]
+
+Biotechniques. 2001 Mar;30(3):574-80, 582
+
+Chen D, Patton JT.
+
+Reverse transcriptase adds nontemplated nucleotides to cDNAs during 5'-RACE and primer extension.
+
+[[!pmid 11252793 desc="Terminal desoxynucleotidyl transferase activity of reverse transcriptases MMLV and AMV: preference for adding As."]]
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index fcc0363..3c53de4 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -5,13 +5,13 @@ The reverse transcriptase
 
 _(redaction in progress)_
 
-## Additives that increase reaction performance:
+### Additives that increase reaction performance
 
  - Actinomycin D ([[Perocchi et al., 2007|biblio/17897965]]).
  - [[T4 bacteriophage gene 32 protein|ssbp]] (T4gp32, [[Kenzelmann _et al._, 2004|biblio/15028277]],
    [[Piché _et al._, 2005|biblio/16461948]]).
 
-## DNA-dependent DNA polymerase activity.
+### 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
@@ -19,17 +19,22 @@ _(redaction in progress)_
    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]]).
 
-## Reverse-transcriptases tolerate terminal mismatches:
+### Terminal desoxynucleotidyl transferase (TdT) activity
+
+ - [[Chen et al., 2001|biblio/11252793]] reported a TdT activity for MMLV and
+   AMV, with a preference for adding As.
+
+### Reverse-transcriptases tolerate terminal mismatches
 
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].
- - Utilised in [[Arnaud et al., 2015|biblio/27071605]] to reduce priming or
+ - Utilised in [[Arnaud et al., 2016|biblio/27071605]] to reduce priming or
    ribosomal or hemoglobin RNA.
 
-## Reverse-transcription primers:
+### Reverse-transcription primers
 
  - "N15" random pentadecamers: [[Stangegaard et al., 2006|biblio/16708763]].
  - Multi-targeted primers (MTP): [[Adomas et al., 2010|biblio/20716356]].
  - "Not-so random" (NSR) primers: [[Armour et al., 2009|biblio/19668204]].
- - "Pseudo-random" primers: [[Arnaud et al., 2015|biblio/27071605]].
+ - "Pseudo-random" primers: [[Arnaud et al., 2016|biblio/27071605]].
 
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

Reorganise and add pseudo-random primers.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index f6230ba..fcc0363 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -1,13 +1,17 @@
 [[!meta title="pages tagged reverse transcription"]]
 
-(redaction in progress)
+The reverse transcriptase
+=========================
 
-Additives that increase reaction performance:
+_(redaction in progress)_
+
+## Additives that increase reaction performance:
 
  - Actinomycin D ([[Perocchi et al., 2007|biblio/17897965]]).
- - T4 bacteriophage gene 32 protein (T4gp32, [[Kenzelmann _et al._, 2004|biblio/15028277]], [[Piché _et al._, 2005|biblio/16461948]]).
+ - [[T4 bacteriophage gene 32 protein|ssbp]] (T4gp32, [[Kenzelmann _et al._, 2004|biblio/15028277]],
+   [[Piché _et al._, 2005|biblio/16461948]]).
 
-Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
+## 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
@@ -15,16 +19,17 @@ Reverse-transcriptases have a DNA-dependent DNA polymerase activity.
    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]]).
 
-Reverse-transcriptases tolerate terminal mismatches: [[Mizuno et al., 1999|biblio/9973624]].
+## Reverse-transcriptases tolerate terminal mismatches:
+
+ - Reported by [[Mizuno et al., 1999|biblio/9973624]].
+ - Utilised in [[Arnaud et al., 2015|biblio/27071605]] to reduce priming or
+   ribosomal or hemoglobin RNA.
 
-Reverse-transcription primers:
+## Reverse-transcription primers:
 
  - "N15" random pentadecamers: [[Stangegaard et al., 2006|biblio/16708763]].
  - Multi-targeted primers (MTP): [[Adomas et al., 2010|biblio/20716356]].
  - "Not-so random" (NSR) primers: [[Armour et al., 2009|biblio/19668204]].
- - ... and many more (pseudo-random, ...)
-
-[[Single-strand binding proteins|ssbp]] are sometimes added to improve reverse
-transcriptions.
+ - "Pseudo-random" primers: [[Arnaud et al., 2015|biblio/27071605]].
 
 [[!inline pages="tagged(reverse_transcription)" actions="no" limit=0]]

The pseudo-random primers.
diff --git a/biblio/27071605.mdwn b/biblio/27071605.mdwn
new file mode 100644
index 0000000..79993aa
--- /dev/null
+++ b/biblio/27071605.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Targeted reduction of highly abundant transcripts using pseudo-random primers."]]
+[[!tag random_priming reverse_transcription method]]
+
+Arnaud O, Kato S, Poulain S, Plessy C.
+
+Biotechniques. 2016 Apr 1;60(4):169-74. doi:10.2144/000114400
+
+Targeted reduction of highly abundant transcripts using pseudo-random primers.
+
+[[!pmid 27071605 desc="Reduction of rRNA or hemoglobin with as few as 40 primers, while keepign whole-transcriptome coverage, at the cost of as systematic bias."]]

Add results.
diff --git a/biblio/15331507.mdwn b/biblio/15331507.mdwn
index a873ddb..3685eed 100644
--- a/biblio/15331507.mdwn
+++ b/biblio/15331507.mdwn
@@ -7,4 +7,4 @@ Ståhlberg A, Kubista M, Pfaffl M.
 
 Comparison of reverse transcriptases in gene expression analysis.
 
-[[!pmid 15331507 desc="Estimate yield by using reference DNA and RNA molecules of the same sequence."]]
+[[!pmid 15331507 desc="Estimate yield by using reference DNA and RNA molecules of the same sequence.  Best: SuperScript III; worst: AMV.  cDNAs were reverse-transcribed at the temperature recommended by the manufacturer, so this is probably a confounding factor."]]

tags
diff --git a/biblio/24056875.mdwn b/biblio/24056875.mdwn
index 313878a..870b78b 100644
--- a/biblio/24056875.mdwn
+++ b/biblio/24056875.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Smart-seq2 for sensitive full-length transcriptome profiling in single cells."]]
-[[!tag single_cell template_switching method]]
+[[!tag single_cell template_switching method LNA]]
 
 Picelli S, Björklund AK, Faridani OR, Sagasser S, Winberg G, Sandberg R.
 

Syntax
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 5712f8e..7af520c 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -22,15 +22,15 @@ Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,
 TSOs where only the last 3 bases are RNA became popular.   LNA was also tested
 as a replacement for RNA.
 
- - [Picelli et al (2013)|biblio/24056875] reported a higher performance for
+ - [[Picelli et al (2013)|biblio/24056875]] reported a higher performance for
    RRL compared to RRR, when preparing Smart-seq2 libraries.
 
- - [Harbers et al (2013)|biblio/24079827] used the nanoCAGE protocol to compare
+ - [[Harbers et al (2013)|biblio/24079827]] used the nanoCAGE protocol to compare
    TSOs ending in RRR, DDD, DDL, DLL or LLL, and reported that only the RRR
    TSOs had good efficiency (less PCR cycles needed to amplify the cDNAs) and had
    the lowest amount of strand invastion artefacts.
 
- - [Arguel et al (2017)|biblio/27940562] reported similar performance for
+ - [[Arguel et al (2017)|biblio/27940562]] reported similar performance for
    RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
 
 [[!inline pages="tagged(template_switching)" limit=0]]

RRL
diff --git a/biblio/27940562.mdwn b/biblio/27940562.mdwn
index 716c3e9..d853c3d 100644
--- a/biblio/27940562.mdwn
+++ b/biblio/27940562.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A cost effective 5' selective single cell transcriptome profiling approach with improved UMI design."]]
-[[!tag Fluidigm sequence_tags fingerprint method transcriptome LNA single_cell]]
+[[!tag Fluidigm sequence_tags fingerprint method transcriptome LNA single_cell template_switching]]
 
 Nucleic Acids Res. 2016 Dec 9. pii: gkw1242. doi:10.1093/nar/gkw1242
 
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 0e6b0d8..5712f8e 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -16,4 +16,21 @@
    switching non-capped molecules by increasing dNTPs to 2 mM and
    Mg<sup>2+</sup> to 9 mM.
 
+### Effect of chemical composition of the TS oligonucleotide
+
+Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,
+TSOs where only the last 3 bases are RNA became popular.   LNA was also tested
+as a replacement for RNA.
+
+ - [Picelli et al (2013)|biblio/24056875] reported a higher performance for
+   RRL compared to RRR, when preparing Smart-seq2 libraries.
+
+ - [Harbers et al (2013)|biblio/24079827] used the nanoCAGE protocol to compare
+   TSOs ending in RRR, DDD, DDL, DLL or LLL, and reported that only the RRR
+   TSOs had good efficiency (less PCR cycles needed to amplify the cDNAs) and had
+   the lowest amount of strand invastion artefacts.
+
+ - [Arguel et al (2017)|biblio/27940562] reported similar performance for
+   RRR and RRL, using a 5′-focused method similar to nanoCAGE or STRT.
+
 [[!inline pages="tagged(template_switching)" limit=0]]

Link to template-switching page.
diff --git a/tags/LNA.mdwn b/tags/LNA.mdwn
index 9a18dc9..54d4ab5 100644
--- a/tags/LNA.mdwn
+++ b/tags/LNA.mdwn
@@ -1,4 +1,10 @@
 [[!meta title="pages tagged LNA"]]
 
+Locked Nucleic Acids
+====================
+
+LNA bases have been reported by some to improve the efficiencly
+of [[template switching]], but it has been challenged by others.
+
 [[!inline pages="tagged(LNA)" actions="no" archive="yes"
 feedshow=10]]

More notes.
diff --git a/biblio/27940562.mdwn b/biblio/27940562.mdwn
index 31233de..716c3e9 100644
--- a/biblio/27940562.mdwn
+++ b/biblio/27940562.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A cost effective 5' selective single cell transcriptome profiling approach with improved UMI design."]]
-[[!tag Fluidigm sequence_tags fingerprint method transcriptome]]
+[[!tag Fluidigm sequence_tags fingerprint method transcriptome LNA single_cell]]
 
 Nucleic Acids Res. 2016 Dec 9. pii: gkw1242. doi:10.1093/nar/gkw1242
 
@@ -7,4 +7,5 @@ Arguel MJ, LeBrigand K, Paquet A, Ruiz García S, Zaragosi LE, Barbry P, Waldman
 
 A cost effective 5' selective single cell transcriptome profiling approach with improved UMI design.
 
-[[!pmid 27940562 desc="Backload of barcodes between RT and PCR."]]
+[[!pmid 27940562 desc="Backload of barcodes between RT and PCR.  Changing the terminal base of
+the template-switching oligonucleotide from RNA to LNA did not increase performance."]]

cafés
diff --git a/biblio/29618487.mdwn b/biblio/29618487.mdwn
new file mode 100644
index 0000000..58f7311
--- /dev/null
+++ b/biblio/29618487.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome."]]
+[[!tag repeat promoter evolution CAGE]]
+
+Li C, Lenhard B, Luscombe NM.
+
+Genome Res. 2018 Apr 4. pii: gr.231449.117. doi:10.1101/gr.231449.117
+
+Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome.
+
+[[!pmid 29618487 desc="Uses “sequence homology is a reasonable proxy for TSS age”.  Found polyA artefacts in the FANTOM5 HeliScopeCAGE libraries. Concludes that “1) new TSSs tend to have weaker transcription than old ones; 2) they tend to appear in repeat elements and associate with transcripts of uncertain functional status; 3) they are less likely to have a clear regulatory role, as demonstrated by the weaker regulatory potential from functional genomic data; 4) they also tend to appear in already active chromatin regions (e.g. near existing TSSs); and 5) new TSSs evolve more rapidly during their early phase of existence, which may be explained by the inherent instability of neighboring sequences or lack of a vital function”.  Suggests that new promoters first have a TATA box, and then may lose it: “We also found that ~50% of young LTR-associated TSSs contain a TATA-box motif 25~35 bp upstream (Supplemental Fig. S6) – a TATA-box motif upstream to the TSS is found in many, but not all LTR consensus sequences – whereas the proportion drops to ~30% for old LTR-associated TSSs. This suggests that a substantial fraction of TATA-less promoters may have originated as LTR- derived TATA-box containing promoters.”  Strong association between young TSS and repeat elements: “~70% of young TSSs have at least one repeat element within ±100 bp, but that only 24% of old TSSs do.”"]]

Add keyword.
diff --git a/biblio/29434199.mdwn b/biblio/29434199.mdwn
index 46e40f0..2dd301e 100644
--- a/biblio/29434199.mdwn
+++ b/biblio/29434199.mdwn
@@ -7,4 +7,4 @@ Hayashi T, Ozaki H, Sasagawa Y, Umeda M, Danno H, Nikaido I.
 
 Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
 
-[[!pmid 29434199 desc="First-strand cDNAs are synthesised with a RNAse H minus reverse-transcriptase.  DNAse I introduces nicks that prime synthesis of new cDNA molecules.  T4gp32 promotes the strand-displacement activity of the reverse-transcriptase.  Second-strand cDNAs are synthethised with Klenow fragment (3′ → 5′ exo-) primed with NSRs.  In single cells, genomic DNA needs to be removed because of the DNAseI digestion during RT and the low-complexity priming of the second-strand synthesis with NSRs.  The resulting DNA molecules are tagmented and sequenced with standard methods.  Thus, the method is non-stranded.  Despite the use of NSRs, the rRNA rate stays between 20 and 30 %."]]
+[[!pmid 29434199 desc="RamDA-seq.  First-strand cDNAs are synthesised with a RNAse H minus reverse-transcriptase.  DNAse I introduces nicks that prime synthesis of new cDNA molecules.  T4gp32 promotes the strand-displacement activity of the reverse-transcriptase.  Second-strand cDNAs are synthethised with Klenow fragment (3′ → 5′ exo-) primed with NSRs.  In single cells, genomic DNA needs to be removed because of the DNAseI digestion during RT and the low-complexity priming of the second-strand synthesis with NSRs.  The resulting DNA molecules are tagmented and sequenced with standard methods.  Thus, the method is non-stranded.  Despite the use of NSRs, the rRNA rate stays between 20 and 30 %."]]

Correct typo.
diff --git a/biblio/29434199.mdwn b/biblio/29434199.mdwn
index d9412a2..46e40f0 100644
--- a/biblio/29434199.mdwn
+++ b/biblio/29434199.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs."]]
-[[!tag single_cell method transcriptomei ssbp]]
+[[!tag single_cell method transcriptome ssbp]]
 
 Nat Commun. 2018 Feb 12;9(1):619. doi:10.1038/s41467-018-02866-0
 
diff --git a/tags/transcriptomei.mdwn b/tags/transcriptomei.mdwn
deleted file mode 100644
index 9b5a257..0000000
--- a/tags/transcriptomei.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged transcriptomei"]]
-
-[[!inline pages="tagged(transcriptomei)" actions="no" archive="yes"
-feedshow=10]]

creating tag page tags/transcriptomei
diff --git a/tags/transcriptomei.mdwn b/tags/transcriptomei.mdwn
new file mode 100644
index 0000000..9b5a257
--- /dev/null
+++ b/tags/transcriptomei.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged transcriptomei"]]
+
+[[!inline pages="tagged(transcriptomei)" actions="no" archive="yes"
+feedshow=10]]

nanda runda
diff --git a/biblio/29434199.mdwn b/biblio/29434199.mdwn
new file mode 100644
index 0000000..d9412a2
--- /dev/null
+++ b/biblio/29434199.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs."]]
+[[!tag single_cell method transcriptomei ssbp]]
+
+Nat Commun. 2018 Feb 12;9(1):619. doi:10.1038/s41467-018-02866-0
+
+Hayashi T, Ozaki H, Sasagawa Y, Umeda M, Danno H, Nikaido I.
+
+Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
+
+[[!pmid 29434199 desc="First-strand cDNAs are synthesised with a RNAse H minus reverse-transcriptase.  DNAse I introduces nicks that prime synthesis of new cDNA molecules.  T4gp32 promotes the strand-displacement activity of the reverse-transcriptase.  Second-strand cDNAs are synthethised with Klenow fragment (3′ → 5′ exo-) primed with NSRs.  In single cells, genomic DNA needs to be removed because of the DNAseI digestion during RT and the low-complexity priming of the second-strand synthesis with NSRs.  The resulting DNA molecules are tagmented and sequenced with standard methods.  Thus, the method is non-stranded.  Despite the use of NSRs, the rRNA rate stays between 20 and 30 %."]]

Normalisation.
diff --git a/biblio/15314184.mdwn b/biblio/15314184.mdwn
index e8a68e2..2ca7c3e 100644
--- a/biblio/15314184.mdwn
+++ b/biblio/15314184.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Spliced-Leader RNA trans Splicing in a Chordate, Oikopleura dioica, with a Compact Genome."]]
-[[!tag splice_leader Oikopleura operon]]
+[[!tag trans-splicing Oikopleura operon]]
 
 Ganot P, Kallesøe T, Reinhardt R, Chourrout D, Thompson EM.
 
diff --git a/tags/splice_leader.mdwn b/tags/splice_leader.mdwn
deleted file mode 100644
index bba447c..0000000
--- a/tags/splice_leader.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged splice leader"]]
-
-[[!inline pages="tagged(splice_leader)" actions="no" archive="yes"
-feedshow=10]]

Normalisation.
diff --git a/biblio/25525214.mdwn b/biblio/25525214.mdwn
index 7bf0070..c565a08 100644
--- a/biblio/25525214.mdwn
+++ b/biblio/25525214.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest."]]
-[[!tag Oikopleura trans_splicing CAGE]]
+[[!tag Oikopleura trans-splicing CAGE]]
 
 Danks GB, Raasholm M, Campsteijn C, Long AM, Manak JR, Lenhard B, Thompson EM.
 

Nettoyage.
diff --git "a/Debian/debi\303\242neries/courrielsSurNuage.en.po" "b/Debian/debi\303\242neries/courrielsSurNuage.en.po"
deleted file mode 100644
index d50d736..0000000
--- "a/Debian/debi\303\242neries/courrielsSurNuage.en.po"
+++ /dev/null
@@ -1,83 +0,0 @@
-# SOME DESCRIPTIVE TITLE
-# Copyright (C) YEAR Free Software Foundation, Inc.
-# This file is distributed under the same license as the PACKAGE package.
-# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
-#
-#, fuzzy
-msgid ""
-msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2018-04-06 13:09+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta date=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!tag Debian]]\n"
-msgstr ""
-
-#. type: Plain text
-#, no-wrap
-msgid "[[!meta title=\"Mon serveur de courriels dans les nuages\"]]\n"
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Mon serveur de courriels pour la zone _plessy.org_, hébergé à domicile "
-"pendant de longues années, est maintenant une instance virtuelle dans le "
-"[nuage Amazon](https://aws.amazon.com/fr/).  Bien qu'étant très satisfait de "
-"la fibre optique de NTT et de mon fournisseur [ASAHI "
-"Net](http://asahi-net.jp/en/), avec qui j'avais une adresse IP fixe, j'ai "
-"migré sur le câble ([YOUTV](http://www.netyou.jp/)), ce qui veut dire IP "
-"dynamique et port 25 bloqué.  Mais alors, pourquoi ? Pour déplacer le modem, "
-"le téléphone, la borne wifi et tous les câbles qui vont avec du salon vers "
-"le bureau.  Et si nous n'avions qu'une prise téléphone (NTT), nous avons une "
-"prise câble dans quasiment chaque pièce..."
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Pressé par le temps, et n'ayant pas trouvé un fournisseur à la fois bien "
-"connecté avec le Japon et utilisant une infrastructure Libre, j'ai choisi "
-"Amazon pour la proximité (zone « Asie-Pacifique (Tokyo) ») et parce que j'ai "
-"un peu d'[[awscli-et-vpc|expérience]] sur cette plate-forme via mes "
-"tentatives d'[[installeur-debian-dans-le-nuage-amazon|utiliser l'installeur "
-"Debian pour générer des images machine]].  Ceci dit, je peux encore changer; "
-"les suggestions sont les bienvenues."
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"La virtualisation s'est très bien passée.  La configuration de mon serveur "
-"était suivie par [etckeeper](http://etckeeper.branchable.com/).  J'ai "
-"démarré une [instance "
-"Stretch](https://wiki.debian.org/Cloud/AmazonEC2Image/Stretch) toute neuve, "
-"installé `postfix`, `postgrey`, et `dovecot-imapd`, et j'ai fusioné à la "
-"main les nouveaux fichiers de configuration dans les anciens.  J'ai ensuite "
-"mis à jour les enregistrements DNS.  Le tout tourne très bien avec une "
-"nano-instance de type `t2.nano` vu le peu de courriels à gérer."
-msgstr ""
-
-#. type: Plain text
-msgid ""
-"Bien entendu, ça me fait de la peine de perdre une partie de mon "
-"indépendance.  On peut supposer que les agences d'espionnage ayant un "
-"pouvoir légal sur Amazon et son centre de données au Japon peuvent lire mes "
-"courriels et leur archive si elles le souhaitent.  Si cela vous dérange, "
-"encryptez les messages que vous m'envoyez."
-msgstr ""

updated PO files
diff --git "a/Debian/debi\303\242neries/courrielsSurNuage.en.po" "b/Debian/debi\303\242neries/courrielsSurNuage.en.po"
new file mode 100644
index 0000000..d50d736
--- /dev/null
+++ "b/Debian/debi\303\242neries/courrielsSurNuage.en.po"
@@ -0,0 +1,83 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2018-04-06 13:09+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sun, 10 Sep 2017 21:06:29 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"Mon serveur de courriels dans les nuages\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Mon serveur de courriels pour la zone _plessy.org_, hébergé à domicile "
+"pendant de longues années, est maintenant une instance virtuelle dans le "
+"[nuage Amazon](https://aws.amazon.com/fr/).  Bien qu'étant très satisfait de "
+"la fibre optique de NTT et de mon fournisseur [ASAHI "
+"Net](http://asahi-net.jp/en/), avec qui j'avais une adresse IP fixe, j'ai "
+"migré sur le câble ([YOUTV](http://www.netyou.jp/)), ce qui veut dire IP "
+"dynamique et port 25 bloqué.  Mais alors, pourquoi ? Pour déplacer le modem, "
+"le téléphone, la borne wifi et tous les câbles qui vont avec du salon vers "
+"le bureau.  Et si nous n'avions qu'une prise téléphone (NTT), nous avons une "
+"prise câble dans quasiment chaque pièce..."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Pressé par le temps, et n'ayant pas trouvé un fournisseur à la fois bien "
+"connecté avec le Japon et utilisant une infrastructure Libre, j'ai choisi "
+"Amazon pour la proximité (zone « Asie-Pacifique (Tokyo) ») et parce que j'ai "
+"un peu d'[[awscli-et-vpc|expérience]] sur cette plate-forme via mes "
+"tentatives d'[[installeur-debian-dans-le-nuage-amazon|utiliser l'installeur "
+"Debian pour générer des images machine]].  Ceci dit, je peux encore changer; "
+"les suggestions sont les bienvenues."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"La virtualisation s'est très bien passée.  La configuration de mon serveur "
+"était suivie par [etckeeper](http://etckeeper.branchable.com/).  J'ai "
+"démarré une [instance "
+"Stretch](https://wiki.debian.org/Cloud/AmazonEC2Image/Stretch) toute neuve, "
+"installé `postfix`, `postgrey`, et `dovecot-imapd`, et j'ai fusioné à la "
+"main les nouveaux fichiers de configuration dans les anciens.  J'ai ensuite "
+"mis à jour les enregistrements DNS.  Le tout tourne très bien avec une "
+"nano-instance de type `t2.nano` vu le peu de courriels à gérer."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Bien entendu, ça me fait de la peine de perdre une partie de mon "
+"indépendance.  On peut supposer que les agences d'espionnage ayant un "
+"pouvoir légal sur Amazon et son centre de données au Japon peuvent lire mes "
+"courriels et leur archive si elles le souhaitent.  Si cela vous dérange, "
+"encryptez les messages que vous m'envoyez."
+msgstr ""

creating tag page tags/trans_splicing
diff --git a/tags/trans_splicing.mdwn b/tags/trans_splicing.mdwn
new file mode 100644
index 0000000..20acafb
--- /dev/null
+++ b/tags/trans_splicing.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged trans splicing"]]
+
+[[!inline pages="tagged(trans_splicing)" actions="no" archive="yes"
+feedshow=10]]

Trans-splicing analysis using CAGE.
diff --git a/biblio/25525214.mdwn b/biblio/25525214.mdwn
new file mode 100644
index 0000000..7bf0070
--- /dev/null
+++ b/biblio/25525214.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest."]]
+[[!tag Oikopleura trans_splicing CAGE]]
+
+Danks GB, Raasholm M, Campsteijn C, Long AM, Manak JR, Lenhard B, Thompson EM.
+
+Mol Biol Evol. 2015 Mar;32(3):585-99. doi:10.1093/molbev/msu336
+
+Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest.
+
+[[!pmid 25525214 desc="“39% of annotated gene models are trans-spliced with the SL.” “42% of SL transcripts are monocistronic; in these cases SL trans-splicing has a function other than resolving polycistronic mRNA.” “A second wave of gene activation peaked at the metamorphic tailshift stage where 2,578 genes were switched on for the first time. Here, 80% of genes were non-trans-spliced nonoperon genes, only 4% were SL-trans-spliced operon genes, and 10% were SL-trans-spliced monocistronic genes.” “A Switch from Predominantly Trans-Spliced to Predominantly Non-trans-Spliced Transcripts Occurs at the Maternal to Zygotic Transition” Parallel study in O. dioica, C. elegans and C. intestinalis suggests that “trans-splicing itself, rather than the organization of genes into operons, is the common factor for maternal mRNA in these metazoans”.  The TOP motif of ribosomal protein genes is provided by the SL in O. dioica.  “We find that SL-trans-spliced mRNAs are enriched in the ovary and oocytes.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3d28395..ed52be9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -27,9 +27,11 @@ Genome
 Transcriptome
 -------------
 
- - Some genes are organised in operons.  A 5′ splice leader is found in some RNAs.
+ - Some genes are organised in operons.  A 5′ splice leader (SL) is found in some RNAs.
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
    times in the genome ([[Ganot et al., 2004|biblio/15314184]]).
+ - A study using CAGE found that 39% of annotated gene models are trans-spliced with the
+   SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
 
 Development
 -----------

Hopla hopla.
diff --git a/biblio/29481550.mdwn b/biblio/29481550.mdwn
new file mode 100644
index 0000000..f459f27
--- /dev/null
+++ b/biblio/29481550.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cell-type specific sequencing of microRNAs from complex animal tissues."]]
+[[!tag method sRNA]]
+
+Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L.
+
+Nat Methods. 2018 Apr;15(4):283-289. doi:10.1038/nmeth.4610
+
+Cell-type specific sequencing of microRNAs from complex animal tissues.
+
+[[!pmid 29481550 desc="Methylates the last base using the HEN1 methyltransferase from Arabidopsis thaliana, and inactivates unmethylated sRNAs with periodate oxydation (rendering them incompetent for ligation)."]]

Hopla
diff --git a/biblio/29512652.mdwn b/biblio/29512652.mdwn
new file mode 100644
index 0000000..8a135fa
--- /dev/null
+++ b/biblio/29512652.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolved Cas9 variants with broad PAM compatibility and high DNA specificity."]]
+[[!tag CRISPR]]
+
+Nature. 2018 Apr 5;556(7699):57-63. doi:10.1038/nature26155
+
+Hu JH, Miller SM, Geurts MH, Tang W, Chen L, Sun N, Zeina CM, Gao X, Rees HA, Lin Z, Liu DR.
+
+Evolved Cas9 variants with broad PAM compatibility and high DNA specificity.
+
+[[!pmid 29512652 desc="Screened using phage-assisted continuous evolution (PACE) in an assay where a catalytically inactive Cas9 protein fused to the ω subunit of bacterial RNA polymerase activates the promoter of an essential phage gene allowing for the reproduction of the phage and the transmission of advantageous mutations in the Cas protein.  The phage gene is provided through a library of constructs differing in their protospacer adjacent motif (PAM)."]]

Oikopleura
diff --git a/biblio/16111672.mdwn b/biblio/16111672.mdwn
new file mode 100644
index 0000000..6466be1
--- /dev/null
+++ b/biblio/16111672.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Development of the central nervous system in the larvacean Oikopleura dioica and the evolution of the chordate brain."]]
+[[!tag Oikopleura]]
+
+Cañestro C, Bassham S, Postlethwait J.
+
+Dev Biol. 2005 Sep 15;285(2):298-315 doi:10.1016/j.ydbio.2005.06.039
+
+Development of the central nervous system in the larvacean Oikopleura dioica and the evolution of the chordate brain.
+
+[[!pmid 16111672 desc="The Oikopleura CNS possesses homologs of the vertebrate forebrain, hindbrain, and spinal cord, but not the midbrain.  3 otx paralogs.  No expression of pax2/5/8 in the gap between otxa + otxb and hox1."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index dd9a5ab..3d28395 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -31,6 +31,14 @@ Transcriptome
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
    times in the genome ([[Ganot et al., 2004|biblio/15314184]]).
 
+Development
+-----------
+
+ - The Oikopleura CNS possesses homologs of the vertebrate forebrain,
+   hindbrain, and spinal cord, but not the midbrain.  No expression of
+   _pax2/5/8_ is detected between the _otxa_ + _otxb_ and the _hox1_ territories.
+   ([[Cañestro et al., 2005|biblio/16111672]]).
+
 Ecology
 -------
 

Hier.
diff --git a/biblio/29555762.mdwn b/biblio/29555762.mdwn
new file mode 100644
index 0000000..770335f
--- /dev/null
+++ b/biblio/29555762.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Precise Cas9 targeting enables genomic mutation prevention."]]
+[[!tag CRISPR]]
+
+Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):3669-3673 doi:10.1073/pnas.1718148115
+
+Alejandro Chavez, Benjamin W. Pruitt, Marcelle Tuttle, Rebecca S. Shapiro, Ryan J. Cecchi, Jordan Winston, Brian M. Turczyk, Michael Tung, James J. Collins and George M. Church.
+
+Precise Cas9 targeting enables genomic mutation prevention.
+
+[[!pmid 29555762 desc="Destabilising mutations in the guide RNA allow for discrimination of SNPs.  The targetted SNP is not in the host genome at the moment that the prevention system is inserted."]]

minor.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6b3bad4..dd9a5ab 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -21,7 +21,8 @@ Genome
 
  - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
- - ~80 "house proteins" have been identified and more than half lack similarity to known proteils ([[Hosp et al., 2012|biblio/22792236]]). 
+ - ~80 "house proteins" have been identified and more than half lack similarity
+   to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
 
 Transcriptome
 -------------

Oikosins.
diff --git a/biblio/22792236.mdwn b/biblio/22792236.mdwn
new file mode 100644
index 0000000..a9e7c5f
--- /dev/null
+++ b/biblio/22792236.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The evolving proteome of a complex extracellular matrix, the Oikopleura house."]]
+[[!tag Oikopleura]]
+
+PLoS One. 2012;7(7):e40172. doi:10.1371/journal.pone.0040172
+
+Hosp J, Sagane Y, Danks G, Thompson EM.
+
+The evolving proteome of a complex extracellular matrix, the Oikopleura house.
+
+[[!pmid 22792236 desc="“Almost half of the oikosin complement exhibit no known domain structures or other similarities to known proteins, suggesting de novo appearance in the appendicularian lineage. Known domains are implicated in cellulose binding, protein-protein interactions or sPLA2 activity. Production of the latter is concentrated in epithelial regions associated with construction of the fcf, suggesting a possible role of this structure in innate immune defence.” “The genomic organization of oikosin loci appears incompatible with common enhancers or locus control regions exerting [...] a coordinate regulatory role.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 20751ce..6b3bad4 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -6,6 +6,9 @@ Oikopleura
 _Oikopleura dioica_ is a tunicate plankton.  Thus, it belongs to the same
 "chordate" phylum as us.  Its genome is very small, as each cell only contains
 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
+Each animal secretes a mucus "house" that is used for feeding (and perhaps
+defending).  The main house proteins are called _oikosins_ and half or them
+are unique to Oikopleura and related animals ("_Appendicularia_").
 
 Some links:
 
@@ -18,6 +21,7 @@ Genome
 
  - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
+ - ~80 "house proteins" have been identified and more than half lack similarity to known proteils ([[Hosp et al., 2012|biblio/22792236]]). 
 
 Transcriptome
 -------------

creating tag page tags/global_warming
diff --git a/tags/global_warming.mdwn b/tags/global_warming.mdwn
new file mode 100644
index 0000000..8934c67
--- /dev/null
+++ b/tags/global_warming.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged global warming"]]
+
+[[!inline pages="tagged(global_warming)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/pH
diff --git a/tags/pH.mdwn b/tags/pH.mdwn
new file mode 100644
index 0000000..419303e
--- /dev/null
+++ b/tags/pH.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged pH"]]
+
+[[!inline pages="tagged(pH)" actions="no" archive="yes"
+feedshow=10]]

creating tag page tags/temperature
diff --git a/tags/temperature.mdwn b/tags/temperature.mdwn
new file mode 100644
index 0000000..054e9f6
--- /dev/null
+++ b/tags/temperature.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged temperature"]]
+
+[[!inline pages="tagged(temperature)" actions="no" archive="yes"
+feedshow=10]]

Réchauffement.
diff --git a/biblio/29298334.mdwn b/biblio/29298334.mdwn
new file mode 100644
index 0000000..e81304d
--- /dev/null
+++ b/biblio/29298334.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Increased fitness of a key appendicularian zooplankton species under warmer, acidified seawater conditions."]]
+[[!tag Oikopleura global_warming temperature pH]]
+
+PLoS One. 2018 Jan 3;13(1):e0190625. doi:10.1371/journal.pone.0190625 
+
+Bouquet JM, Troedsson C, Novac A, Reeve M, Lechtenbörger AK, Massart W, Skaar KS, Aasjord A, Dupont S, Thompson EM. 
+
+Increased fitness of a key appendicularian zooplankton species under warmer, acidified seawater conditions. 
+
+[[!pmid 29298334 desc="Fertilty increases with acidity (tested values: 7.6, 8.0, 8.4), and generation time decreases with temperature (tested values: 12.0, 14.2, 14.5 and 17.2).  Survival decreases at higher pH and temperature values.  The gamete quality is not reduced.  In mesocosms, the increase of temperature of +3°C at pH 7.6 resulted in 2.5- and 5-fold increases in abundance."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 31ea315..20751ce 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -26,4 +26,10 @@ Transcriptome
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
    times in the genome ([[Ganot et al., 2004|biblio/15314184]]).
 
+Ecology
+-------
+
+ - O. dioica populations may have a higher fitness in warmer and more acid oceans
+   ([[Bouquet et al., 2018|biblio/29298334]]).
+
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

nucleus
diff --git a/biblio/8354698.mdwn b/biblio/8354698.mdwn
new file mode 100644
index 0000000..d2723a5
--- /dev/null
+++ b/biblio/8354698.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reversible effects of nuclear membrane permeabilization on DNA replication: evidence for a positive licensing factor."]]
+[[!tag nucleus]]
+
+J Cell Biol. 1993 Sep;122(5):985-92 doi:10.1083/jcb.122.5.985
+
+Coverley D, Downes CS, Romanowski P, Laskey RA.
+
+Reversible effects of nuclear membrane permeabilization on DNA replication: evidence for a positive licensing factor. 
+
+[[!pmid 8354698 desc="lysolecithin permeabilisation reversed by incubation with vesicles extracted from Xenopus eggs."]]

Minor changes.
diff --git a/biblio/29483654.mdwn b/biblio/29483654.mdwn
index bdaea0f..81509e0 100644
--- a/biblio/29483654.mdwn
+++ b/biblio/29483654.mdwn
@@ -7,4 +7,4 @@ di Iulio J, Bartha I, Wong EHM, Yu HC, Lavrenko V, Yang D, Jung I, Hicks MA, Sha
 
 The human noncoding genome defined by genetic diversity.
 
-[[!pmid 29483654 desc="Study of the variation of on the 4th base of all possible heptamers in the human genome.  Defined “context-dependent tolerance score (CDTS)” as “the absolute difference of the observed variation from the expected variation” in genomic windows, using  7,794 unrelated genomes.  Identifies non-conserved, non-protein regions with human-specific sequence constraints."]]
+[[!pmid 29483654 desc="Study of the variation on the 4<sup>th</sup> base of all possible heptamers in the human genome.  Defined “context-dependent tolerance score (CDTS)” as “the absolute difference of the observed variation from the expected variation” in genomic windows, using  7,794 unrelated genomes.  Identifies non-conserved, non-protein regions with human-specific sequence constraints."]]

Ce matin.
diff --git a/biblio/29483654.mdwn b/biblio/29483654.mdwn
new file mode 100644
index 0000000..bdaea0f
--- /dev/null
+++ b/biblio/29483654.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The human noncoding genome defined by genetic diversity."]]
+[[!tag non_coding variability]]
+
+Nat Genet. 2018 Mar;50(3):333-337. doi:10.1038/s41588-018-0062-7
+
+di Iulio J, Bartha I, Wong EHM, Yu HC, Lavrenko V, Yang D, Jung I, Hicks MA, Shah N, Kirkness EF, Fabani MM, Biggs WH, Ren B, Venter JC, Telenti A.
+
+The human noncoding genome defined by genetic diversity.
+
+[[!pmid 29483654 desc="Study of the variation of on the 4th base of all possible heptamers in the human genome.  Defined “context-dependent tolerance score (CDTS)” as “the absolute difference of the observed variation from the expected variation” in genomic windows, using  7,794 unrelated genomes.  Identifies non-conserved, non-protein regions with human-specific sequence constraints."]]

Oikopleura
diff --git a/biblio/22300585.mdwn b/biblio/22300585.mdwn
new file mode 100644
index 0000000..31271a5
--- /dev/null
+++ b/biblio/22300585.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics."]]
+[[!tag Oikopleura pharmacology]]
+
+BMC Genomics. 2012 Feb 2;13:55. doi:10.1186/1471-2164-13-55
+
+Yadetie F, Butcher S, Førde HE, Campsteijn C, Bouquet JM, Karlsen OA, Denoeud F, Metpally R, Thompson EM, Manak JR, Goksøyr A, Chourrout D.
+
+Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics.
+
+[[!pmid 22300585 desc="“Oikopleura appears to have the smallest CYP complement of sequenced animal genomes and has no detectable CYP1 family genes. AhR, which is the transcriptional regulator of CYP1 family genes in vertebrates, is also undetectable in Oikopleura. Thus, the AhR signaling pathway may not exist in Oikopleura. Components of the Nrf2 signaling pathway appear to be conserved in Oikopleura.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 780987a..31ea315 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -17,6 +17,7 @@ Genome
 ------
 
  - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
+ - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
 
 Transcriptome
 -------------

Midi.
diff --git a/biblio/22205972.mdwn b/biblio/22205972.mdwn
new file mode 100644
index 0000000..cc4d364
--- /dev/null
+++ b/biblio/22205972.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gentle masking of low-complexity sequences improves homology search."]]
+[[!tag alignment]]
+
+Frith MC
+
+PLoS One. 2011;6(12):e28819. doi:10.1371/journal.pone.0028819
+
+Gentle masking of low-complexity sequences improves homology search.
+
+[[!pmid 22205972 desc="In the case of DNA, score 1 for same letter and same case, 0 for same letter but different case, and -1 for different letter."]]

Corrected.
diff --git a/biblio/18305863.mdwn b/biblio/18305863.mdwn
index 878acd2..41c0f3f 100644
--- a/biblio/18305863.mdwn
+++ b/biblio/18305863.mdwn
@@ -7,4 +7,4 @@ Lab Chip. 2008 Mar;8(3):443-50
 
 Integrating whole transcriptome assays on a lab-on-a-chip for single cell gene profiling.
 
-[[!pmid 18305863 desc="For simple RT-PCR, cDNAs were pre-amplified 40× on chip.  Template-switching did not work, probably as the TS primers, which were not removed after reaction, inhibited the PCR."]]
+[[!pmid 18305863 desc="For simple RT-PCR, cDNAs were pre-amplified 40× on chip.  cDNAs must be dilluted at least 500× before amplification, otherwise TS-PCR is inhibited by leftovers of the RT."]]

Oikopleura
diff --git a/biblio/11752568.mdwn b/biblio/11752568.mdwn
new file mode 100644
index 0000000..a1f7e70
--- /dev/null
+++ b/biblio/11752568.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Miniature genome in the marine chordate Oikopleura dioica."]]
+[[!tag Oikopleura genome]]
+
+Science. 2001 Dec 21;294(5551):2506 doi:10.1126/science.294.5551.2506
+
+Seo HC, Kube M, Edvardsen RB, Jensen MF, Beck A, Spriet E, Gorsky G, Thompson EM, Lehrach H, Reinhardt R, Chourrout D.
+
+Miniature genome in the marine chordate Oikopleura dioica.
+
+[[!pmid 11752568 desc="Genome size estimated to 72 ± 13 Mb by DNA contents and comparison to Ciona.  A large-scale shotgun sequencing of 128,386 short reads lead to a lower-bound estimate of 65 Mb and 15,000 genes."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 43a61a9..780987a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -13,6 +13,11 @@ Some links:
  - Genoscope's genome browser: <http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/>
  - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/>
 
+Genome
+------
+
+ - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
+
 Transcriptome
 -------------
 

Old
diff --git a/biblio/18974218.mdwn b/biblio/18974218.mdwn
new file mode 100644
index 0000000..e568142
--- /dev/null
+++ b/biblio/18974218.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The chemistrode: a droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution."]]
+[[!tag microfluidic]]
+
+Chen D, Du W, Liu Y, Liu W, Kuznetsov A, Mendez FE, Philipson LH, Ismagilov RF.
+
+Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):16843-8. doi:10.1073/pnas.0807916105
+
+The chemistrode: a droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution.
+
+[[!pmid 18974218 desc="Sampling with a stream of droplets contacting a surface."]]

Old
diff --git a/biblio/19606291.mdwn b/biblio/19606291.mdwn
new file mode 100644
index 0000000..39c8d33
--- /dev/null
+++ b/biblio/19606291.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Isolation, incubation, and parallel functional testing and identification by FISH of rare microbial single-copy cells from multi-species mixtures using the combination of chemistrode and stochastic confinement."]]
+[[!tag single_cell microfluidic]]
+
+Lab Chip. 2009 Aug 7;9(15):2153-62. doi:10.1039/b904958d
+
+Liu W, Kim HJ, Lucchetta EM, Du W, Ismagilov RF.
+
+Isolation, incubation, and parallel functional testing and identification by FISH of rare microbial single-copy cells from multi-species mixtures using the combination of chemistrode and stochastic confinement.
+
+[[!pmid 19606291 desc="Stochastic isolation of single cells into 'plugs' separated by carrier fluid (not emulsions) using a 'chemistrode'."]]

About Oikopleura.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7394947..43a61a9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -1,4 +1,23 @@
 [[!meta title="pages tagged Oikopleura"]]
 
-[[!inline pages="tagged(Oikopleura)" actions="no" archive="yes"
-feedshow=10]]
+Oikopleura
+==========
+
+_Oikopleura dioica_ is a tunicate plankton.  Thus, it belongs to the same
+"chordate" phylum as us.  Its genome is very small, as each cell only contains
+70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
+
+Some links:
+
+ - Oikopleura Histone Database: <http://apps.cbu.uib.no/oikohistonedb>
+ - Genoscope's genome browser: <http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/>
+ - OikoBase: <http://oikoarrays.biology.uiowa.edu/Oiko/>
+
+Transcriptome
+-------------
+
+ - Some genes are organised in operons.  A 5′ splice leader is found in some RNAs.
+   The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
+   times in the genome ([[Ganot et al., 2004|biblio/15314184]]).
+
+[[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

creating tag page tags/splice_leader
diff --git a/tags/splice_leader.mdwn b/tags/splice_leader.mdwn
new file mode 100644
index 0000000..bba447c
--- /dev/null
+++ b/tags/splice_leader.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged splice leader"]]
+
+[[!inline pages="tagged(splice_leader)" actions="no" archive="yes"
+feedshow=10]]