Cargando…

Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data

Profiling T cell receptor (TCR) repertoire via short read transcriptome sequencing (RNA-Seq) has a unique advantage of probing simultaneously TCRs and the genome-wide RNA expression of other genes. However, compared to targeted amplicon approaches, the shorter read length is more prone to mapping er...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bai, Yu, Wang, David, Li, Wentian, Huang, Ying, Ye, Xuan, Waite, Janelle, Barry, Thomas, Edelmann, Kurt H., Levenkova, Natasha, Guo, Chunguang, Skokos, Dimitris, Wei, Yi, Macdonald, Lynn E., Fury, Wen
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2018
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237323/ https://www.ncbi.nlm.nih.gov/pubmed/30439982 http://dx.doi.org/10.1371/journal.pone.0207020

Ejemplares similares

Th17 Response and Inflammatory Autoimmune Diseases
por: Waite, Janelle C., et al.
Publicado: (2012)

Endogenous retroviral proteins provide an immunodominant but not requisite antigen in a murine immunotherapy tumor model
por: Ye, Xuan, et al.
Publicado: (2020)

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
por: David, Julianne K., et al.
Publicado: (2022)

Modeling non-uniformity in short-read rates in RNA-Seq data
por: Li, Jun, et al.
Publicado: (2010)

SeqEntropy: Genome-Wide Assessment of Repeats for Short Read Sequencing
por: Chu, Hsueh-Ting, et al.
Publicado: (2013)

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
por: Boratyn, Grzegorz M., et al.
Publicado: (2019)

pyTCR: A comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research
por: Peng, Kerui, et al.
Publicado: (2022)

NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data
por: Overbey, Eliah G., et al.
Publicado: (2021)

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
por: Yang, Ya, et al.
Publicado: (2013)

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
por: Zhao, Qiong-Yi, et al.
Publicado: (2011)

Mappability and read length
por: Li, Wentian, et al.
Publicado: (2014)

Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments
por: Ebrahimi, Ghazal, et al.
Publicado: (2022)

LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity
por: Xie, Juan, et al.
Publicado: (2023)

scReadSim: a single-cell RNA-seq and ATAC-seq read simulator
por: Yan, Guanao, et al.
Publicado: (2023)

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
por: Lefrançois, Philippe, et al.
Publicado: (2009)

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
por: Zhao, Shanrong
Publicado: (2014)

RNA-Seq Analysis and Gene Discovery of Andrias davidianus Using Illumina Short Read Sequencing
por: Li, Fenggang, et al.
Publicado: (2015)

CD8(−) DCs induce IL-12–independent Th1 differentiation through Delta 4 Notch-like ligand in response to bacterial LPS
por: Skokos, Dimitris, et al.
Publicado: (2007)

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data
por: Duan, Jialei, et al.
Publicado: (2012)

BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads
por: Hong, Lewis Z, et al.
Publicado: (2014)

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data
por: Ikegami, Tsutomu, et al.
Publicado: (2015)

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads
por: Bai, Yu, et al.
Publicado: (2014)

Handling multi-mapped reads in RNA-seq
por: Deschamps-Francoeur, Gabrielle, et al.
Publicado: (2020)

Read trimming is not required for mapping and quantification of RNA-seq reads at the gene level
por: Liao, Yang, et al.
Publicado: (2020)

scRNA-seq revealed the special TCR β & α V(D)J allelic inclusion rearrangement and the high proportion dual (or more) TCR-expressing cells
por: Zhu, Lanwei, et al.
Publicado: (2023)

BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
por: Videm, Pavankumar, et al.
Publicado: (2014)

De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
por: Hölzer, Martin, et al.
Publicado: (2019)

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
por: Lima, Leandro, et al.
Publicado: (2017)

Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform
por: Gerdemann, Ulrike, et al.
Publicado: (2022)

CoCo: RNA-seq read assignment correction for nested genes and multimapped reads
por: Deschamps-Francoeur, Gabrielle, et al.
Publicado: (2019)

Pre-TCRα and TCRα Are Not Interchangeable Partners of TCRβ during T Lymphocyte Development
por: Borowski, Christine, et al.
Publicado: (2004)

From RNA-seq reads to differential expression results
por: Oshlack, Alicia, et al.
Publicado: (2010)

CLASS: constrained transcript assembly of RNA-seq reads
por: Song, Li, et al.
Publicado: (2013)

CRAC: an integrated approach to the analysis of RNA-seq reads
por: Philippe, Nicolas, et al.
Publicado: (2013)

HLA typing from RNA-Seq sequence reads
por: Boegel, Sebastian, et al.
Publicado: (2012)

Shark: fishing relevant reads in an RNA-Seq sample
por: Denti, Luca, et al.
Publicado: (2020)

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
por: Zhao, Shanrong, et al.
Publicado: (2013)

Updates to the RMAP short-read mapping software
por: Smith, Andrew D., et al.
Publicado: (2009)

Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics
por: Tu, Min, et al.
Publicado: (2022)

Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads
por: Gohr, André, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_pn6hrmdoegc8u0ka420v64qt5t