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| Status |
Public on Dec 28, 2022 |
| Title |
Control cLPL P14 CD8+ T cells RNA |
| Sample type |
SRA |
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| Source name |
Colon LPL
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| Organism |
Mus musculus |
| Characteristics |
tissue: Colon LPL
cell type: T cells
genotype: CD8+
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Control and Eomes iKO P14 CD8+T cells were harvested from the siIEL, siLPL, cIEL, and cLPL tissue compartments from recipient mice infected more than 21 days prior, FACS-isolated, and prepared for single-cell libraries.
Libaries were constructed using the Chromium Next GEM Single Cell 3’Kit v3.1 (10xGenomics).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
3_19_NE_CLPL_CD45_1_2_barcodes.tsv.gz
3_19_NE_CLPL_CD45_1_2_features.tsv.gz
3_19_NE_CLPL_CD45_1_2_matrix.mtx.gz
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| Data processing |
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).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq
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| Submission date |
Jun 12, 2022 |
| Last update date |
Dec 28, 2022 |
| Contact name |
John Chang |
| E-mail(s) |
jtc007@health.ucsd.edu
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| Organization name |
UC San Diego Health
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| Street address |
200 W Arbor Dr
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92103 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE205941 |
Small intestine and colon tissue-resident memory CD8+ T cells exhibit transcriptional, epigenetic, and functional heterogeneity in concert with differential dependence on Eomesodermin [CITE-seq] |
| GSE205942 |
Small intestine and colon tissue-resident memory CD8+ T cells exhibit transcriptional, epigenetic, and functional heterogeneity in concert with differential dependence on Eomesodermin |
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| Relations |
| BioSample |
SAMN29005079 |
| SRA |
SRX15683016 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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