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Series GSE89405 Query DataSets for GSE89405
Status Public on Feb 20, 2017
Title Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary During microbial infection, responding CD8+ T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA sequencing approach and analyzed individual CD8+ T lymphocytes sequentially throughout the course of a viral infection in vivo. Our analyses revealed a striking transcriptional divergence among cells that had undergone their first division and identified previously unknown molecular determinants controlling CD8+ T lymphocyte fate specification, including Ezh2, the catalytic component of the Polycomb Repressive Complex 2. Our data provide a revised model of terminal effector cell differentiation initiated by an early burst of transcriptional activity and subsequently refined by epigenetic silencing of transcripts associated with memory lymphocytes. These findings provide unexpected insights into tightly coupled transcriptional and epigenetic mechanisms underlying CD8+ T lymphocyte fate specification and highlight the power and necessity of single-cell approaches.
 
Overall design Gene expression profiles for key stages of T cell differentiation were derived from 256 single-cell RNAseq libraries prepared on Fluidigm C1 and sequenced on Illumina HiSeq2500 (with 224 unique sequencing samples and 64 duplicates). Epigenetic profiles of Ezh2 binding, its associated H3K27me3 mark, and PolII occupancy in invitro-activated T cells were derived from ChIP libraries prepared with NEB Next ChIP (4 Ezh2 fl/fl and 4 WT samples, each with a biological duplicate). These ChIPseq libraries and their matched IGG input DNA controls were sequenced on Illumina HiSeq 4000 together with bulk RNAseq libraries from T cells invivo-activated in either C57BL/6 wild-type or Ezh2-knockout mice (each with a biological duplicate).
 
Contributor(s) Kakaradov B, Arsenio J, Widjaja CE, He Z, Aigner S, Metz PJ, Yu B, Wehrens E, Lopez J, Kim SH, Zuniga EI, Goldrath AW, Chang JT, Yeo GW
Citation(s) 28218746
NIH grant(s)
Grant ID Grant title Affiliation Name
DP2 OD008469 Understanding the Basis for Cellular Diversity During Adaptive Immunity THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO John T Chang
R01 AI095277 Regulation and Function of Polarity and Asymmetric Cell Division in Immunity THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO John T Chang
R01 DK093507 Role of atypical Protein Kinase C in Inflammatory Bowel Disease THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO John T Chang
R01 AI072117 CD8 immunity to intracellular infection: Control by E-box transcription factors: Regulation of CD8 immunity to intracellular infections: Regulation of CD8 immunity to intracellular infections: CD8 immunity to intracellular infection: Control by E-box transcription factors: Regulation of CD8 immunity to intracellular infections: CD8 immunity to intracellular infection: Control by E-box transcription factors: Regulation of CD8 immunity to intracellular infections THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO Ananda W Goldrath
R01 AI096852 Metabolic Regulation of T cell Immunity THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO Ananda W Goldrath
R01 AI081923 Inhibitory Pathways Underlying Viral Persistance in vivo: Inhibitory Pathways Underlying Viral Persistence In Vivo: Inhibitory Pathways Underlying Viral Persistence In Vivo: Inhibitory Pathways Underlying Viral Persistance in vivo THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO Elina I Zuniga
R01 AI113923 Positive Immune-regulators During Chronic Viral Infections THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO Elina I Zuniga
U19 MH107367 Collaboration on preclinical autism cellular assays, biosignatures, and network analyses (Copacabana) THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO Eugene Wei-Ming Yeo
R01 HG004659 Functional RNA elements in the human genome THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO FU, Eugene Wei-Ming Yeo
Submission date Nov 01, 2016
Last update date Mar 21, 2019
Contact name Gene Yeo
E-mail geneyeo@ucsd.edu
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (304)
GSM2370654 H3K27me3_ChIPSeq WT rep1
GSM2370655 H3K27me3_ChIPSeq WT rep2
GSM2370656 H3K27me3_ChIPSeq KO rep1
Relations
BioProject PRJNA352070
SRA SRP092407

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE89405_Kakaradov_singlecell_expression_matrix.csv.gz 19.6 Mb (ftp)(http) CSV
GSE89405_RAW.tar 6.6 Mb (http)(custom) TAR (of BED)
GSE89405_bulkRNA_count.csv.gz 1.9 Mb (ftp)(http) CSV
Processed data is available on Series record
Raw data are available in SRA

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