GSE205549
GSE GEOSmall intestine and colon tissue-resident memory CD8+ T cells exhibit transcriptional, epigenetic, and functional heterogeneity in concert with differential dependence on Eomesodermin [scATAC-seq]
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Summary
Tissue-resident memory CD8+T (TRM) cells are a distinct component of the memory T cell armamentarium found in many tissues. Recent studies have shown disparities among TRM cells across tissues, but it is unknown whether there is heterogeneity among TRM cells from differentanatomic compartments of the small intestine and colon. Herewe show that intestinal TRM cells exhibit distinctive patterns of cytokine and granzyme expression, along with substantial transcriptional, epigenetic, and functional heterogeneity. We elucidate unexpected tissue- and context-specific regulatory roles for the T-box transcription factor Eomesodermin (Eomes), previously described to repressskin, liver, and kidney TRM cell formation, in promoting the maintenance of established TRM cells in the small intestine, but not in the colon. Taken together, these data provide previously unappreciated insights into the heterogeneity and differential requirements for the formation vs. maintenance of TRMcells from the small intestine and colon.
Overall Design
Performed scATAC-seq to unterstand look at heterogeneity
Analysis (3 steps)
View Data Processing- Cell Ranger ATAC (v6.0.1) was used to process sequencing information and single cell barcodes.
- Cellranger outputs were analyzed in R using Signac (v1.6.0)
- Annotation, quality control, dimensional reduction, and UMAPcreationwerecompleted using the standard Signac workflow.
Supplementary Files (1)
GEO Samples (4)
Dataset Citations (1)
SRA Experiments (4) and Runs (4)
Total: 72463 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19560830 | 275486594 | 62259970244 | 19843.93 | 1_CIEL_S1_L001_R1_001.fastq.gz, 1_CIEL_S1_L001_R2_001.fastq.gz, 1_CIE… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19560829 | 232243344 | 52486995744 | 16906.26 | 2_CLPL_S2_L001_R1_001.fastq.gz, 2_CLPL_S2_L001_R2_001.fastq.gz, 2_CLP… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19560828 | 313310984 | 70808282384 | 22613.19 | 4_SI_IEL_S4_L001_R1_001.fastq.gz, 4_SI_IEL_S4_L001_R2_001.fastq.gz, 4… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19560827 | 177621356 | 40142426456 | 13099.91 | 6_SI_LPL_S6_L001_R1_001.fastq.gz, 6_SI_LPL_S6_L001_R2_001.fastq.gz, 6… | SRA |
Linked Publications (1)
Data Files (5)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | 1_CIEL_S1_L001_R1_001.fastq.gz | ATAC-seq | 19.4 GB | link | |||
| — | 2_CLPL_S2_L001_R1_001.fastq.gz | ATAC-seq | 16.5 GB | link | |||
| — | 4_SI_IEL_S4_L001_R1_001.fastq.gz | ATAC-seq | 22.1 GB | link | |||
| — | 6_SI_LPL_S6_L001_R1_001.fastq.gz | ATAC-seq | 12.8 GB | link | |||
| — | SRR19560828.lite | ATAC-seq | 22.1 GB | link |