Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

被引：0

作者：

Igor Mandric

Jeremy Rotman

Harry Taegyun Yang

Nicolas Strauli

Dennis J. Montoya

William Van Der Wey

Jiem R. Ronas

Benjamin Statz

Douglas Yao

Velislava Petrova

Alex Zelikovsky

Roberto Spreafico

Sagiv Shifman

Noah Zaitlen

Maura Rossetti

K. Mark Ansel

Eleazar Eskin

Serghei Mangul

机构：

[1] University of California,Department of Computer Science

[2] Los Angeles,Department of Clinical Pharmacy

[3] School of Pharmacy,Bioinformatics Interdepartmental Ph.D. Program

[4] University of Southern California,Biomedical Sciences Graduate Program

[5] University of California,Department of Molecular, Cell, and Developmental Biology

[6] Los Angeles,Department of Microbiology, Immunology, and Molecular Genetics

[7] University of California,Program in Bioinformatics and Integrative Genomics

[8] San Francisco,Department of Computer Science

[9] University of California,The Laboratory of Bioinformatics

[10] Los Angeles,Department of Genetics

[11] University of California,Department of Medicine

[12] Los Angeles,Immunogenetics Center, Department of Pathology and Laboratory Medicine

[13] Harvard Medical School,Sandler Asthma Basic Research Center, Department of Microbiology and Immunology

[14] Wellcome Trust Sanger Institute,Department of Human Genetics

[15] Georgia State University,Department of Computational Medicine

[16] I.M. Sechenov First Moscow State Medical University,undefined

[17] Institute for Quantitative and Computational Biosciences,undefined

[18] University of California,undefined

[19] Los Angeles,undefined

[20] The Institute of Life Sciences,undefined

[21] The Hebrew University of Jerusalem,undefined

[22] University of California,undefined

[23] San Francisco,undefined

[24] David Geffen School of Medicine,undefined

[25] University of California,undefined

[26] Los Angeles,undefined

[27] University of California,undefined

[28] San Francisco,undefined

[29] David Geffen School of Medicine at UCLA,undefined

[30] David Geffen School of Medicine at UCLA,undefined

来源：

Nature Communications | / 11卷

关键词：

D O I：

暂无

中图分类号：

学科分类号：

摘要：

Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.6 million Ig sequences, termed the atlas of immunoglobulin repertoires (TAIR), across a broad range of tissue types that often do not have reported Ig repertoires information. Moreover, the flow of Ig clonotypes and inter-tissue repertoire similarities across immune-related tissues are also evaluated. In summary, TAIR is one of the largest collections of CDR3 sequences and tissue types, and should serve as an important resource for studying immunological diseases.

引用

共 50 条

[1] Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing
Mandric, Igor
Rotman, Jeremy
Yang, Harry Taegyun
Strauli, Nicolas
Montoya, Dennis J.
Van Der Wey, William
Ronas, Jiem R.
Statz, Benjamin
Yao, Douglas
Petrova, Velislava
Zelikovsky, Alex
Spreafico, Roberto
Shifman, Sagiv
Zaitlen, Noah
Rossetti, Maura
Ansel, K. Mark
Eskin, Eleazar
Mangul, Serghei
NATURE COMMUNICATIONS, 2020, 11 (01)
[2] Profiling tissue-resident T cell repertoires by RNA sequencing
Brown, Scott D.
Raeburn, Lisa A.
Holt, Robert A.
GENOME MEDICINE, 2015, 7
[3] Profiling tissue-resident T cell repertoires by RNA sequencing
Scott D. Brown
Lisa A. Raeburn
Robert A. Holt
Genome Medicine, 7
[4] Splicing factor and exon profiling across human tissues
de la Grange, Pierre
Gratadou, Lise
Delord, Marc
Dutertre, Martin
Auboeuf, Didier
NUCLEIC ACIDS RESEARCH, 2010, 38 (09) : 2825 - 2838
[5] Atlas of RNA sequencing profiles for normal human tissues
Suntsova, Maria
Gaifullin, Nurshat
Allina, Daria
Reshetun, Alexey
Li, Xinmin
Mendeleeva, Larisa
Surin, Varisa
Sergeeva, Anna
Spirin, Pavel
Prassolov, Vladimir
Morgan, Alexander
Garazha, Andrew
Sorokin, Maxim
Buzdin, Anton
SCIENTIFIC DATA, 2019, 6 (1)
[6] Atlas of RNA sequencing profiles for normal human tissues
Maria Suntsova
Nurshat Gaifullin
Daria Allina
Alexey Reshetun
Xinmin Li
Larisa Mendeleeva
Vadim Surin
Anna Sergeeva
Pavel Spirin
Vladimir Prassolov
Alexander Morgan
Andrew Garazha
Maxim Sorokin
Anton Buzdin
Scientific Data, 6
[7] Comparative transcriptome profiling in human bicuspid aortic valve disease using RNA sequencing
Padang, Ratnasari
Bagnall, Richard D.
Tsoutsman, Tatiana
Bannon, Paul G.
Semsarian, Christopher
PHYSIOLOGICAL GENOMICS, 2015, 47 (03) : 75 - 87
[8] Transcriptional profiling of bovine milk using RNA sequencing
Saumya Wickramasinghe
Gonzalo Rincon
Alma Islas-Trejo
Juan F Medrano
BMC Genomics, 13
[9] Transcriptional profiling of bovine milk using RNA sequencing
Wickramasinghe, Saumya
Rincon, Gonzalo
Islas-Trejo, Alma
Medrano, Juan F.
BMC GENOMICS, 2012, 13
[10] Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages
Bai, Jingyi
Lin, Yu
Zhang, Jiaman
Chen, Ziyu
Wang, Yujie
Li, Mingzhou
Li, Jing
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2023, 24 (13)

← 1 2 3 4 5 →