|
| Status |
Public on Aug 15, 2023 |
| Title |
TIM3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ TILs
|
| Organism |
Mus musculus |
| Characteristics |
treatment: E.G7 tumor
genotype: Bcl6-RFP
tissue: tumor
cell type: TIM-3+ CD8+ TILs
|
| Treatment protocol |
Tumor-infiltrating CD8+ T cells were isolated from E.G7 tumors on day 21 post tumor inoculation, then were FACS sorted for RNA-seq
|
| Growth protocol |
Bcl6-RFP mice were inoculated with E.G7 tumors (s.c.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 2fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (or read count) for each sample
|
| |
|
| Submission date |
Aug 13, 2021 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Chen Dong |
| Organization name |
Tsinghua University
|
| Department |
Institute for Immunology and School of Medicine
|
| Lab |
Dongchen's lab
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE182035 |
Bcl6 regulates CD8+ T cell fate decision in cancer [RNA-Seq] |
| GSE182036 |
Bcl6 mediates CD8+ T cell fate decision in cancer |
|
| Relations |
| BioSample |
SAMN20752393 |
| SRA |
SRX11740190 |
