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| Status |
Public on Sep 07, 2016 |
| Title |
mtko2_dp_batch2 |
| Sample type |
SRA |
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| Source name |
Mus musculus CD8 TILs
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| Organism |
Mus musculus |
| Characteristics |
subpopulation: mtko2 dp
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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 HiSeq 2500 |
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| Description |
population RNA-Seq data
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| Data processing |
Reads were aligned to a reference genome (mm9 Ensembl) using Bowtie
Expression levels were quantified using RSEM (inferred counts and tpm values), and log2(TPM+1) values generated.
samples of low technical quality and/or extreme outliers were excluded (see manuscript)
data was batch-normalized using COMBAT and then quantile normalized
Genome_build: mm9
Supplementary_files_format_and_content: text file with tab delimiters
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| Submission date |
Aug 23, 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 |
GPL17021 |
| Series (2) |
| GSE85954 |
A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (part 2) |
| GSE86042 |
A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells |
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| Relations |
| BioSample |
SAMN05607815 |
| SRA |
SRX2039864 |
| 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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