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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 25, 2023 |
| Title |
Flexible and scalable control of T cell memory by a reversible epigenetic switch (ATAC-seq) |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| 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 ATAC-seq analysis.
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| Overall design |
Control naïve samples were sorted from splenoyctes as CD8+CD44-CD62L+Tcf7-YFP+ (1 replicate); antigen-experienced samples were sorted from splenocytes as CD8+CD44+CD62L+Tcf7-YFP+ (1 replicate); effector control samples were activated ex vivo for 3 days (1 replicate). 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 (3 replicates); Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3 , 1 (3 replicates).
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| Contributor(s) |
Abadie K, Clark EC, Daza RM, Shendure J, Kueh H |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 20, 2023 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Kathleen Abadie |
| E-mail(s) |
abadiek@uw.edu
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| Organization name |
University of Washington
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| Department |
Bioengineering
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| Lab |
Kueh Lab
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (11)
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| GSM7655043 |
Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3, 1 (ATAC-seq) |
| GSM7655044 |
Day9 Tcf7-YFP high, sorted Tcf7-YFP high at Day3, 2 (ATAC-seq) |
| GSM7655045 |
Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 1 (ATAC-seq) |
| GSM7655046 |
Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 2 (ATAC-seq) |
| GSM7655047 |
Day9 Tcf7-YFP low, sorted Tcf7-YFP low at Day3, 3 (ATAC-seq) |
| GSM7655048 |
Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 1 (ATAC-seq) |
| GSM7655049 |
Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 2 (ATAC-seq) |
| GSM7655050 |
Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 3 (ATAC-seq) |
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| This SubSeries is part of SuperSeries: |
| GSE237830 |
Flexible and scalable control of T cell memory by a reversible epigenetic switch |
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| Relations |
| BioProject |
PRJNA996893 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE237827_RAW.tar |
25.6 Gb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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