Hirose Y, Shiozaki T, Hamano I, Yoshihara S, Tokumoto H, Eki T, Harada N.

DNA Res. 2020 Aug 1;27(4):dsaa017. doi:10.1093/dnares/dsaa017

A specific combination of dual index adaptors decreases the sensitivity of amplicon sequencing with the Illumina platform.

N704/S507 index pair considered harmful on MiSeq.

Genome Res. 2016 Mar;26(3):342-50. doi:10.1101/gr.193474.115

Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE.

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

“Chicago”: in vitro assembly of artificial chromosomes, followed by Hi-C. Sold as a kit by Dovetail genomics.

Genome Res. 1999 Jun;9(6):588-95

Korch C, Drabkin H.

Improved DNA sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators.

0.3 mM MnCl2 + 1:1 MnCit in absence of EDTA is optimal.

Kukimoto I, Maehama T, Sekizuka T, Ogasawara Y, Kondo K, Kusumoto-Matsuo R, Mori S, Ishii Y, Takeuchi T, Yamaji T, Takeuchi F, Hanada K, Kuroda M.

PLoS One. 2013 Nov 13;8(11):e80583. doi:10.1371/journal.pone.0080583

Genetic variation of human papillomavirus type 16 in individual clinical specimens revealed by deep sequencing.

Sequenced full-length circular DNA with only two primers. Within-host variablity was rarely more than 5% and most often less than 0.5 % per base pair.

Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ.

Nat Biotechnol. 2014 Jun;32(6):562-568. doi: 10.1038/nbt.2880

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.

Repurposed a GAIIx sequencer.

Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM.

Science. 2014 Feb 27. DOI: 10.1126/science.1250212

Highly Multiplexed Subcellular RNA Sequencing in Situ.

Fluorescent In Situ RNA SEQuencing (FISSEQ). Random-primed.

Lou DI, Hussmann JA, McBee RM, Acevedo A, Andino R, Press WH, Sawyer SL.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19872-7. doi: 10.1073/pnas.1319590110.

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.

Method to cancel PCR and sequencing noise. Needs long reads. Suggested for TCR sequencing.

Nat Biotechnol. 2013 Oct 13. doi: 10.1038/nbt.2705

A single-molecule long-read survey of the human transcriptome.

Sharon D, Tilgner H, Grubert F, Snyder M.

Starting material: 200 micrograms of total RNA.

Goldman N, Bertone P, Chen S, Dessimoz C, Leproust EM, Sipos B, Birney E.

Nature. 2013 Jan 23. doi: 10.1038/nature11875. [Epub ahead of print]

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.

On day, the meaning of 'my computer ate my data' will change.

Genome Res. 2012 Oct;22(10):2031-42. doi: 10.1101/gr.131847.111.

Windhager L, Bonfert T, Burger K, Ruzsics Z, Krebs S, Kaufmann S, Malterer G, L'hernault A, Schilhabel M, Schreiber S, Rosenstiel P, Zimmer R, Eick D, Friedel CC, Dölken L.

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.

60/5 min ratios “were highest for introns in a range of 300–400 nt”.

Genolet R, Stevenson BJ, Farinelli L, Osterås M, Luescher IF.

EMBO J. 2012 Feb 28;31(7):1666-78. doi: 10.1038/emboj.2012.48.

Highly diverse TCRα chain repertoire of pre-immune CD8⁺ T cells reveals new insights in gene recombination.

Synthethised aRNAs, ligated adaptors and sequenced paired-end on HiSeq 2000

Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R.

Nature. 2012 Jul 11;487(7406):190-5. doi: 10.1038/nature11236.

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.

Haplotype sequencing by pooling barcoded dillutions from the same sample.

Ding F, Manosas M, Spiering MM, Benkovic SJ, Bensimon D, Allemand JF, Croquette V.

Nat Methods. 2012 Mar 11;9(4):367-72. doi: 10.1038/nmeth.1925.

Single-molecule mechanical identification and sequencing.

Hybridization with unlabeled oligonucelotides of know sequence is detected as it prevents refolding of a hairpin structure.

He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ.

Neuron. 2012 Jan 12;73(1):35-48.

Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain.

AGO2-immunoprecipitated sRNAs are > 90% miRNAs, 50~80 % without precipitation.

Logan AC, Gao H, Wang C, Sahaf B, Jones CD, Marshall EL, Buño I, Armstrong R, Fire AZ, Weinberg KI, Mindrinos M, Zehnder JL, Boyd SD, Xiao W, Davis RW, Miklos DB.

Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21194-9.

High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment.

Application to diagnostics.

Lindner C, Wahl B, Föhse L, Suerbaum S, Macpherson AJ, Prinz I, Pabst O.

J Exp Med. 2012 Jan 16.

Age, microbiota, and T cells shape diverse individual IgA repertoires in the intestine.

Two-component clonotype distribution: power law, and tail.

β-fixed cells colonise hosts less efficiently than WT hosts.

Parallel study of antigen as self or non-self through transgenic expression.

Different receptoromes for regulatory and conventional T cells.

Estimates about one million different β chains in the blood.

Develops the concept of convergent recombination.

Confirms about one million different β chains in the blood.

Contains a description of sequencing by oligonucleotide ligation and detection (SOLiD).

Nature. 2005 Sep 15;437(7057):376-80. doi:10.1038/nature03959

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM.

Genome sequencing in microfabricated high-density picolitre reactors.

Primary reference for “454” sequencing.

Estimated a cost of $0.11 per kilobase.

A long tail (40 bp, for instance) increases the size of the fragments to separate on gel, and therefore resolution in 5′

Primary paper for Helicos sequencing.

Summarises 454, Solexa and SOLiD.

Uses microfluidic digital PCR for validation.

Nature. 2008 Nov 6;456(7218):53-9. doi: 10.1038/nature07517

Bentley DR, many co-authors, and Smith AJ.

Accurate whole human genome sequencing using reversible terminator chemistry.

Primary paper for Illumina-Solexa technology. The supplemental information contains the sequence of the oligonucleotides used on the flow cells.

“found evidence of convergence, in which different individuals made the same antibody”

Does not use quality values, and recommends to discard redundant reads.

Uses the Illumina Genome Analyzer to acheive high coverage, and compensates short read length with a shearing and assembly approach.

Genomics barcodes were amplified with PCR primers that were themselves barcoded, allowing multiplex analysis.

Under- or over-representation of insertion points in the sequenced library indicate if the insertion was deleterious or advantageous.

Basecalled RNA-seq reads to find SNPs and study allelic imbalance.

Uses six barcodes per subject.

Documents and clarifies the differences.

454 sequencing of α and β TCRs.

Uses 250 ng of polyadenlyated RNA.

Most enhancer bound by P300 in the mouse embryonnic heart at E11.5 are not strongly conserved.

78 % of the recombinant antibodies generated from the most abundant sequences were antigen-specific.