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| Status |
Public on Sep 07, 2016 |
| Title |
AH3VMFBGXY_F4_S352 |
| Sample type |
SRA |
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| Source name |
Mus musculus CD8 TILs
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| Organism |
Mus musculus |
| Characteristics |
cell type: CD8 TILs
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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
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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)
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab delimiters
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| Submission date |
Aug 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Meromit Singer |
| E-mail(s) |
msinger@broadinstitute.org
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| Organization name |
Broad Institute of MIT and Harvard
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| Street address |
415 main st, ROOM 6031
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| City |
CAMBRIDGE |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE86028 |
A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (batch 1) |
| GSE86042 |
A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells |
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| Relations |
| BioSample |
SAMN05629541 |
| SRA |
SRX2051264 |
| 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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