GSE205941
GSE GEOSmall intestine and colon tissue-resident memory CD8+ T cells exhibit transcriptional, epigenetic, and functional heterogeneity in concert with differential dependence on Eomesodermin [CITE-seq]
Organism:
Mus musculus
Platform:
GPL24247
Samples:
16
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Other
Submitted:
Jun 12 2022
Last Updated:
Apr 11 2025
Status:
Public on Dec 28 2022
Contact:
John,,Chang (UC San Diego)
Relations
SubSeries of: GSE205942
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA848395
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 CITE-seq to unterstand look at heterogeneity
Analysis (5 steps)
View Data Processing
Processing steps for GSE205941
- Cell Ranger (v6.0.1) was used to process sequencing information and single cell barcodes.
- Gene and cell filtering, clustering, differential and average expression using Seurat (v4.1.1)
- Cell Ranger output was converted to .loom files with velocyto (v0.17.17) for velocity analysis.
- Velocity and latent time anlysis using scVelo (v0.2.4).
- Library strategy: CITE-seq
Supplementary Files (24)
GSE205941_3_19_NE_CIEL_CD45_1_2_barcodes.tsv.gz
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GSE205941_3_19_NE_CIEL_CD45_1_2_features.tsv.gz
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GSE205941_3_19_NE_CIEL_CD45_1_2_matrix.mtx.gz
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GSE205941_3_19_NE_CIEL_CD45_1_barcodes.tsv.gz
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GSE205941_3_19_NE_CIEL_CD45_1_features.tsv.gz
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GSE205941_3_19_NE_CIEL_CD45_1_matrix.mtx.gz
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GSE205941_3_19_NE_CLPL_CD45_1_2_barcodes.tsv.gz
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GSE205941_3_19_NE_CLPL_CD45_1_2_features.tsv.gz
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GSE205941_3_19_NE_CLPL_CD45_1_2_matrix.mtx.gz
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GSE205941_3_19_NE_CLPL_CD45_1_barcodes.tsv.gz
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GSE205941_3_19_NE_CLPL_CD45_1_features.tsv.gz
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GSE205941_3_19_NE_CLPL_CD45_1_matrix.mtx.gz
Download
GSE205941_3_19_NE_SIIEL_CD45_1_2_barcodes.tsv.gz
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GSE205941_3_19_NE_SIIEL_CD45_1_2_features.tsv.gz
Download
GSE205941_3_19_NE_SIIEL_CD45_1_2_matrix.mtx.gz
Download
GSE205941_3_19_NE_SIIEL_CD45_1_barcodes.tsv.gz
Download
GSE205941_3_19_NE_SIIEL_CD45_1_features.tsv.gz
Download
GSE205941_3_19_NE_SIIEL_CD45_1_matrix.mtx.gz
Download
GSE205941_3_19_NE_SILPL_CD45_1_2_barcodes.tsv.gz
Download
GSE205941_3_19_NE_SILPL_CD45_1_2_features.tsv.gz
Download
GSE205941_3_19_NE_SILPL_CD45_1_2_matrix.mtx.gz
Download
GSE205941_3_19_NE_SILPL_CD45_1_barcodes.tsv.gz
Download
GSE205941_3_19_NE_SILPL_CD45_1_features.tsv.gz
Download
GSE205941_3_19_NE_SILPL_CD45_1_matrix.mtx.gz
Download
Dataset Citations (1)
Small intestine and colon tissue-resident memory CD8<sup>+</sup> T cells exhibit molecular heterogeneity and differential dependence on Eomes.
PMID 36580919
· 2023
· Immunity
Yun Hsuan Lin, Han G Duong, Abigail E Limary, Eleanor S Kim, Paul Hsu, Shefali A Patel, William H Wong, Cynthia S Indralingam, Yi Chia Liu, Priscilla Yao, Natalie R Chiang, Sara A Vandenburgh, Taylor R Anderson, Jocelyn G Olvera, Amir Ferry, Kennidy K Takehara, Wenhao Jin, Matthew S Tsai, Gene W Yeo, Ananda W Goldrath, John T Chang
SRA Experiments (16) and Runs (16)
Total: 47335 MBGSM6235873: Control siIEL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380823
BioProject: PRJNA848395
BioSample: SAMN29005091
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine intraepithelial lymphocytes
tissue: Small intestine intraepithelial lymphocytes
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine intraepithelial lymphocytes
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632543 | 72753375 | 14696181750 | 5489.66 | 3_19_NE_SIIEL_CD45_1_RNA_S61_L003_R1_001.fastq.gz, 3_19_NE_SIIEL_CD45… | SRA |
GSM6235874: Control siIEL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380822
BioProject: PRJNA848395
BioSample: SAMN29005090
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine intraepithelial lymphocytes
tissue: Small intestine intraepithelial lymphocytes
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine intraepithelial lymphocytes
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632542 | 62585901 | 12642352002 | 5326.09 | 3_19_NE_SIIEL_CD45_1_ADT_S61_L002_R1_001.fastq.gz, 3_19_NE_SIIEL_CD45… | SRA |
GSM6235875: Eomes iKO siIEL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380824
BioProject: PRJNA848395
BioSample: SAMN29005089
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine intraepithelial lymphocytes
tissue: Small intestine intraepithelial lymphocytes
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine intraepithelial lymphocytes
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632541 | 65787988 | 13289173576 | 4952.01 | 3_19_NE_SIIEL_CD45_1_2_RNA_S62_L003_R1_001.fastq.gz, 3_19_NE_SIIEL_CD… | SRA |
GSM6235876: Eomes iKO siIEL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380826
BioProject: PRJNA848395
BioSample: SAMN29005088
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine intraepithelial lymphocytes
tissue: Small intestine intraepithelial lymphocytes
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine intraepithelial lymphocytes
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632540 | 47347203 | 9564135006 | 4028.31 | 3_19_NE_SIIEL_CD45_1_2_ADT_S62_L002_R1_001.fastq.gz, 3_19_NE_SIIEL_CD… | SRA |
GSM6235877: Control siLPL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380825
BioProject: PRJNA848395
BioSample: SAMN29005087
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine LPL
tissue: Small intestine LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632539 | 52522801 | 10609605802 | 3959.65 | 3_19_NE_SILPL_CD45_1_RNA_S63_L003_R1_001.fastq.gz, 3_19_NE_SILPL_CD45… | SRA |
GSM6235878: Control siLPL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380827
BioProject: PRJNA848395
BioSample: SAMN29005086
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine LPL
tissue: Small intestine LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632538 | 36365913 | 7345914426 | 3094.83 | 3_19_NE_SILPL_CD45_1_ADT_S63_L002_R1_001.fastq.gz, 3_19_NE_SILPL_CD45… | SRA |
GSM6235879: Eomes iKO si LPL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380829
BioProject: PRJNA848395
BioSample: SAMN29005085
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine LPL
tissue: Small intestine LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632537 | 29933311 | 6046528822 | 2252.32 | 3_19_NE_SILPL_CD45_1_2_RNA_S64_L003_R1_001.fastq.gz, 3_19_NE_SILPL_CD… | SRA |
GSM6235880: Eomes iKO si LPL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380828
BioProject: PRJNA848395
BioSample: SAMN29005084
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Small intestine LPL
tissue: Small intestine LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Small intestine LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632536 | 8391079 | 1694997958 | 715.32 | 3_19_NE_SILPL_CD45_1_2_ADT_S64_L002_R1_001.fastq.gz, 3_19_NE_SILPL_CD… | SRA |
GSM6235881: Control cIEL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380830
BioProject: PRJNA848395
BioSample: SAMN29005083
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon IEL
tissue: Colon IEL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon IEL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632535 | 56713758 | 11456179116 | 4281.58 | 3_19_NE_CIEL_CD45_1_RNA_S67_L003_R1_001.fastq.gz, 3_19_NE_CIEL_CD45_1… | SRA |
GSM6235882: Control cIEL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380832
BioProject: PRJNA848395
BioSample: SAMN29005082
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon IEL
tissue: Colon IEL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon IEL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632534 | 7672171 | 1549778542 | 653.78 | 3_19_NE_CIEL_CD45_1_ADT_S67_L002_R1_001.fastq.gz, 3_19_NE_CIEL_CD45_1… | SRA |
GSM6235883: Eomes iKO cIEL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380831
BioProject: PRJNA848395
BioSample: SAMN29005081
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon IEL
tissue: Colon IEL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon IEL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632533 | 35853461 | 7242399122 | 2718.53 | 3_19_NE_CIEL_CD45_1_2_RNA_S68_L003_R1_001.fastq.gz, 3_19_NE_CIEL_CD45… | SRA |
GSM6235884: Eomes iKO cIEL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380833
BioProject: PRJNA848395
BioSample: SAMN29005080
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon IEL
tissue: Colon IEL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon IEL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632532 | 4867014 | 983136828 | 415.0 | 3_19_NE_CIEL_CD45_1_2_ADT_S68_L002_R1_001.fastq.gz, 3_19_NE_CIEL_CD45… | SRA |
GSM6235885: Control cLPL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380834
BioProject: PRJNA848395
BioSample: SAMN29005079
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon LPL
tissue: Colon LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632531 | 41117584 | 8305751968 | 3097.52 | 3_19_NE_CLPL_CD45_1_RNA_S65_L003_R1_001.fastq.gz, 3_19_NE_CLPL_CD45_1… | SRA |
GSM6235886: Control cLPL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380835
BioProject: PRJNA848395
BioSample: SAMN29005078
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon LPL
tissue: Colon LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632530 | 17808849 | 3597387498 | 1517.08 | 3_19_NE_CLPL_CD45_1_2_ADT_S66_L002_R1_001.fastq.gz, 3_19_NE_CLPL_CD45… | SRA |
GSM6235887: Eomes iKO cLPL P14 CD8+ T cells RNA; Mus musculus; OTHER
Sample: SRS13380836
BioProject: PRJNA848395
BioSample: SAMN29005077
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon LPL
tissue: Colon LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632529 | 59764230 | 12072374460 | 4496.3 | 3_19_NE_CLPL_CD45_1_2_RNA_S66_L003_R1_001.fastq.gz, 3_19_NE_CLPL_CD45… | SRA |
GSM6235888: Eomes iKO cLPL P14 CD8+ T cells ADT; Mus musculus; OTHER
Sample: SRS13380837
BioProject: PRJNA848395
BioSample: SAMN29005076
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Colon LPL
tissue: Colon LPL
cell type: T cells
genotype: CD8+
geo_loc_name: missing
collection_date: missing
Original files (1)
Colon LPL
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19632528 | 3949978 | 797895556 | 336.56 | 3_19_NE_CLPL_CD45_1_ADT_S65_L002_R1_001.fastq.gz, 3_19_NE_CLPL_CD45_1… | SRA |
Linked Publications (1)
Data Files (16)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | 3_19_NE_CIEL_CD45_1_2_ADT_S68_L002_R1_001.fastq.gz | OTHER | 415.0 MB | link | |||
| — | 3_19_NE_CIEL_CD45_1_2_RNA_S68_L003_R1_001.fastq.gz | OTHER | 2.7 GB | link | |||
| — | 3_19_NE_CIEL_CD45_1_ADT_S67_L002_R1_001.fastq.gz | OTHER | 653.8 MB | link | |||
| — | 3_19_NE_CIEL_CD45_1_RNA_S67_L003_R1_001.fastq.gz | OTHER | 4.2 GB | link | |||
| — | 3_19_NE_CLPL_CD45_1_2_ADT_S66_L002_R1_001.fastq.gz | OTHER | 1.5 GB | link | |||
| — | 3_19_NE_CLPL_CD45_1_2_RNA_S66_L003_R1_001.fastq.gz | OTHER | 4.4 GB | link | |||
| — | 3_19_NE_CLPL_CD45_1_ADT_S65_L002_R1_001.fastq.gz | OTHER | 336.6 MB | link | |||
| — | 3_19_NE_CLPL_CD45_1_RNA_S65_L003_R1_001.fastq.gz | OTHER | 3.0 GB | link | |||
| — | 3_19_NE_SIIEL_CD45_1_2_ADT_S62_L002_R1_001.fastq.gz | OTHER | 3.9 GB | link | |||
| — | 3_19_NE_SIIEL_CD45_1_2_RNA_S62_L003_R1_001.fastq.gz | OTHER | 4.8 GB | link | |||
| — | 3_19_NE_SIIEL_CD45_1_ADT_S61_L002_R1_001.fastq.gz | OTHER | 5.2 GB | link | |||
| — | 3_19_NE_SIIEL_CD45_1_RNA_S61_L003_R1_001.fastq.gz | OTHER | 5.4 GB | link | |||
| — | 3_19_NE_SILPL_CD45_1_2_ADT_S64_L002_R1_001.fastq.gz | OTHER | 715.3 MB | link | |||
| — | 3_19_NE_SILPL_CD45_1_2_RNA_S64_L003_R1_001.fastq.gz | OTHER | 2.2 GB | link | |||
| — | 3_19_NE_SILPL_CD45_1_ADT_S63_L002_R1_001.fastq.gz | OTHER | 3.0 GB | link | |||
| — | 3_19_NE_SILPL_CD45_1_RNA_S63_L003_R1_001.fastq.gz | OTHER | 3.9 GB | link |