|
| Status |
Public on Jun 14, 2018 |
| Title |
WT_12 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor B16F10 melanoma
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Tumor
genotype/variation: wild type
|
| Treatment protocol |
Tumor infiltrating CD8+ T cells were isolated from WT, Prdm1 cKO, c-Maf cKO, and Prdm1/c-Maf cDKO B16F10 melanoma bearing mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5uL of lysate from bulk CD8+ T cells as the input for each sample during RNA cleanup via SPRI beads (~2,000 cells lysed on average in RLT).
Tumor infiltrating CD8+ T cells were processed using an adaptation of the SMART-Seq 2 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were aligned using Tophat and RSEM-based quantification using known transcripts,
followed by further processing using the Bioconductor package DESeq in R.
Genome_build: mm9
Supplementary_files_format_and_content: The data was normalized using TMM normalization. The TMM method estimates scale factors between samples that can be incorporated into currently used statistical methods for DE analysis. Post-processing and statistical analysis was carried out in R. Differentially expressed genes were defined using the differential expression pipeline on the raw counts with a single call to the function DESeq (adjusted p value<0.1).
|
| |
|
| Submission date |
Apr 16, 2018 |
| Last update date |
Jun 14, 2018 |
| Contact name |
Asaf Madi |
| E-mail(s) |
asafmadi@gmail.com
|
| Organization name |
BWH
|
| Department |
Neurology
|
| Lab |
Ana Carrizosa Anderson
|
| Street address |
60 Fenwood Road, BTM 10016F
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE113221 |
RNAseq of Wild Type and Prdm1/c-Maf cDKO CD8+ Tumor infiltrating lymphocytes isolated from B16F10 melanoma |
| GSE113968 |
The induction and transcriptional regulation of the co-inhibitory gene module in T cells by IL-27 |
|
| Relations |
| BioSample |
SAMN08990384 |
| SRA |
SRX4006834 |
