Literature DB >> 27140930

A synergistic combination: using RNAseq to decipher both T-cell receptor sequence and transcriptional profile of individual T cells.

Kilian Schober1, Dirk H Busch1,2,3.   

Abstract

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Year:  2016        PMID： 27140930     DOI： 10.1038/icb.2016.32

Source DB:  PubMed          Journal:  Immunol Cell Biol        ISSN： 0818-9641            Impact factor:   5.126


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  12 in total

1.  Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells.

Authors:  Auda A Eltahla; Simone Rizzetto; Mehdi R Pirozyan; Brigid D Betz-Stablein; Vanessa Venturi; Katherine Kedzierska; Andrew R Lloyd; Rowena A Bull; Fabio Luciani
Journal:  Immunol Cell Biol       Date:  2016-02-10       Impact factor: 5.126

2.  Linking T-cell receptor sequence to functional phenotype at the single-cell level.

Authors:  Arnold Han; Jacob Glanville; Leo Hansmann; Mark M Davis
Journal:  Nat Biotechnol       Date:  2014-06-22       Impact factor: 54.908

3.  High-throughput identification of antigen-specific TCRs by TCR gene capture.

Authors:  Carsten Linnemann; Bianca Heemskerk; Pia Kvistborg; Roelof J C Kluin; Dmitriy A Bolotin; Xiaojing Chen; Kaspar Bresser; Marja Nieuwland; Remko Schotte; Samira Michels; Raquel Gomez-Eerland; Lorenz Jahn; Pleun Hombrink; Nicolas Legrand; Chengyi Jenny Shu; Ilgar Z Mamedov; Arno Velds; Christian U Blank; John B A G Haanen; Maria A Turchaninova; Ron M Kerkhoven; Hergen Spits; Sine Reker Hadrup; Mirjam H M Heemskerk; Thomas Blankenstein; Dmitriy M Chudakov; Gavin M Bendle; Ton N M Schumacher
Journal:  Nat Med       Date:  2013-10-13       Impact factor: 53.440

4.  In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire.

Authors:  Brandon J DeKosky; Takaaki Kojima; Alexa Rodin; Wissam Charab; Gregory C Ippolito; Andrew D Ellington; George Georgiou
Journal:  Nat Med       Date:  2014-12-15       Impact factor: 53.440

5.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

6.  Paired analysis of TCRα and TCRβ chains at the single-cell level in mice.

Authors:  Pradyot Dash; Jennifer L McClaren; Thomas H Oguin; William Rothwell; Brandon Todd; Melissa Y Morris; Jared Becksfort; Cory Reynolds; Scott A Brown; Peter C Doherty; Paul G Thomas
Journal:  J Clin Invest       Date:  2010-12-06       Impact factor: 14.808

Review 7.  Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells.

Authors:  Evan W Newell; Mark M Davis
Journal:  Nat Biotechnol       Date:  2014-01-19       Impact factor: 54.908

8.  Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Authors:  Manfred G Grabherr; Brian J Haas; Moran Yassour; Joshua Z Levin; Dawn A Thompson; Ido Amit; Xian Adiconis; Lin Fan; Raktima Raychowdhury; Qiandong Zeng; Zehua Chen; Evan Mauceli; Nir Hacohen; Andreas Gnirke; Nicholas Rhind; Federica di Palma; Bruce W Birren; Chad Nusbaum; Kerstin Lindblad-Toh; Nir Friedman; Aviv Regev
Journal:  Nat Biotechnol       Date:  2011-05-15       Impact factor: 54.908

9.  IgBLAST: an immunoglobulin variable domain sequence analysis tool.

Authors:  Jian Ye; Ning Ma; Thomas L Madden; James M Ostell
Journal:  Nucleic Acids Res       Date:  2013-05-13       Impact factor: 16.971

10.  T cell fate and clonality inference from single-cell transcriptomes.

Authors:  Michael J T Stubbington; Tapio Lönnberg; Valentina Proserpio; Simon Clare; Anneliese O Speak; Gordon Dougan; Sarah A Teichmann
Journal:  Nat Methods       Date:  2016-03-07       Impact factor: 28.547
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  3 in total

1.  High CD8 T-Cell Receptor Clonality and Altered CDR3 Properties Are Associated With Elevated Isolevuglandins in Adipose Tissue During Diet-Induced Obesity.

Authors:  Wyatt J McDonnell; John R Koethe; Simon A Mallal; Mark A Pilkinton; Annet Kirabo; Magdalene K Ameka; Matthew A Cottam; Alyssa H Hasty; Arion J Kennedy
Journal:  Diabetes       Date:  2018-09-04       Impact factor: 9.461

2.  Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes.

Authors:  Howard R Seay; Erik Yusko; Stephanie J Rothweiler; Lin Zhang; Amanda L Posgai; Martha Campbell-Thompson; Marissa Vignali; Ryan O Emerson; John S Kaddis; Dave Ko; Maki Nakayama; Mia J Smith; John C Cambier; Alberto Pugliese; Mark A Atkinson; Harlan S Robins; Todd M Brusko
Journal:  JCI Insight       Date:  2016-12-08

3.  Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

Authors:  Simone Rizzetto; Auda A Eltahla; Peijie Lin; Rowena Bull; Andrew R Lloyd; Joshua W K Ho; Vanessa Venturi; Fabio Luciani
Journal:  Sci Rep       Date:  2017-10-06       Impact factor: 4.379
  3 in total

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