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| Status |
Public on Apr 24, 2021 |
| Title |
S3 |
| Sample type |
SRA |
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| Source name |
Mus musculus CD8 TILs
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
cell type: CD8 tumor infiltrating lymphocytes (TIL)
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| Extracted molecule |
total RNA |
| Extraction protocol |
TILs were isolated by dissociating tumor tissue in the presence of collagenase D (2.5 mg/ml) for 20 min prior to centrifugation on a discontinuous Percoll gradient (GE Healthcare).
Smart-seq2 (Picelli et al., Nature Methods, 2014)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
single-cell RNA-Seq data
A3_S3
H5TJLBGX3_S3
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| Data processing |
Reads were aligned to a reference genome (mm10 Ensembl) using Bowtie
Expression levels were quantified using RSEM (inferred counts and tpm values), and log2(TPM+1) values generated.
cells were selected for subsequent analysis based on genecount and mapping rates to transcriptome (see manuscript)
Quality filtering parameters: (high-quality CD8 T) cells that had (1) 1,400-6,000 detected genes (defined by at least one mapped read), (2) at least 100,000 reads mapped to the transcriptome, (3) at least 20% of the reads mapped to the transcriptome, and (4) non-zero expression of either Cd3 or Cd8b1. Genes with non-zero expression in at least one cell were kept.
Genome_build: mm10
Supplementary_files_format_and_content: log2(TPM+1) values
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| Submission date |
Apr 24, 2018 |
| Last update date |
Apr 24, 2021 |
| Contact name |
Aviv Regev |
| E-mail(s) |
nmdespot@gmail.com
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| Organization name |
Broad Institute
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| Lab |
Regev Lab
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| Street address |
415 MAIN ST
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| City |
CAMBRIDGE |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
02142-1027 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE113602 |
Single-cell RNA-seq of sorted CD8+ T cells from B16 melanoma tumors |
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| Relations |
| BioSample |
SAMN08975977 |
| SRA |
SRX3990386 |
| 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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