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Series GSE237828 Query DataSets for GSE237828
Status Public on Jul 25, 2023
Title Flexible and scalable control of T cell memory by a reversible epigenetic switch (RNA-seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary In this study, we find that the Tcf7+ CD8 T cells present following acute challenge can form either from cells that maintain Tcf7 expression throughout activation or from cells that silence Tcf7 and reactivate it after stimulation removal. In this experiment, we asked whether both pathways can give rise to cells with genomic characteristics of memory. To do this, we activated naive CD8 T cells ex vivo for 2 days followed by 1 day of culture without TCR stimulation. On day 3, we sorted Tcf7-YFP high and low populations, all from a single CellTrace peak representing cells that had undergone the same number of divisions. The sorted populations were cultured for an additional 6 days and sorted again on day 9 by Tcf7-YFP levels. These samples, as well as control naive, antigen-experienced, and effector samples, were processed for RNA-seq analysis.
Overall design Control naïve samples were sorted from splenoyctes as CD8+CD44-CD62L+Tcf7-YFP+ (2 replicates); antigen-experienced samples were sorted from splenocytes as CD8+CD44+CD62L+Tcf7-YFP+ (2 replicates); effector control samples were activated ex vivo for 3 days (2 replicates). Cells sorted as Tcf7-YFP high and low at day 3 were recultured and sorted as Tcf7-YFP high or low at day 9: Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3 (2 replicates); Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3 (2 replicates); Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3 , 1 (2 replicates).
Contributor(s) Abadie K, Clark EC, Kueh H
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Submission date Jul 20, 2023
Last update date Jul 25, 2023
Contact name Kathleen Abadie
Organization name University of Washington
Department Bioengineering
Lab Kueh Lab
Street address 3720 15th Ave NE
City Seattle
State/province Washington
ZIP/Postal code 98195
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM7655051 Day3 effector, 1 (RNA-seq)
GSM7655052 Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3, 1 (RNA-seq)
GSM7655053 Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 1 (RNA-seq)
This SubSeries is part of SuperSeries:
GSE237830 Flexible and scalable control of T cell memory by a reversible epigenetic switch
BioProject PRJNA996894

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
GSE237828_RAW.tar 546.4 Mb (http)(custom) TAR (of H5, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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