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| Status |
Public on Sep 19, 2023 |
| Title |
Pool3-RNA-multiome |
| Sample type |
SRA |
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| Source name |
tissue resident memory T cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver + Spleen
days p.i.: 14
replicate: 1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated from frozen, flow cytometry sorted CD8+ T cell subsets
scATAC-seq libraries were constructed using 10X genomics reagents and protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Multiome fastq files were processed using CellRanger-ARC pipeline v2
After read alignment with bwa for ATAC, fragment files were generated by offsetting Tn5 inserts and deduplicating
After read alignment with STAR for RNA, a cell x genes count matrix was generated using the featureCounts options
Assembly: mm10
Supplementary files format and content: fragments file containing trimmed, deduplicated, high quality atac-seq fragments and cell barcodes; h5 files containing the cell x feature matrices
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| Submission date |
Sep 19, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
lareauc@mskcc.org
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| Organization name |
Memorial Sloan Kettering
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| Street address |
417 E 68th St, Zuckerman - ZRC 1132
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE243593 |
A unique epigenomic landscape defines CD8+ tissue-resident memory T cells [multiome] |
| GSE243597 |
A unique epigenomic landscape defines CD8+ tissue-resident memory T cells |
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| Relations |
| BioSample |
SAMN37472244 |
| SRA |
SRX21828307 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7791670_pool3_filtered_feature_bc_matrix.h5 |
15.6 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
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