Illumina flowcell adaptors

Information extracted from the supplemental information of ?Bentley et al., 2008 (Accurate whole human genome sequencing using reversible terminator chemistry, Nature 456(7218):53–9)

Single read flowcell

5´-PSTTTTTTTTTT-(diol)3-AATGATACGGCGACCACCGA-3´
5´-PSTTTTTTTTTTCAAGCAGAAGACGGCATACGA-3´

Paired read flowcell

5´-PS-TTTTTTTTTTAATGATACGGCGACCACCGAGAUCTACAC-3´ (U = 2-deoxyuridine)
5´-PS-TTTTTTTTTTCAAGCAGAAGACGGCATACGAGoxoAT-3´  (Goxo = 8-oxoguanine)
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

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.

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

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.

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

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.

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

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”.

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

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

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

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.

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

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.

Posted
Genome sequencing in microfabricated high-density picolitre reactors.

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.

Posted