|
| Status |
Public on Jan 16, 2019 |
| Title |
Tim-3-PD-1- CD8+_iso rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor MC38-OVA
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Tumor MC38-OVA
genotype: wild type
cell type: Tim-3-PD-1- CD8+ TILs
treatment: isotype treated
|
| Treatment protocol |
On day 12 post tumor implantation, Tim-3+PD-1+ and Tim-3-PD-1- CD8+ TILs were isolated by cell sorting (BD FACS Aria II) from MC38-OVA tumor-bearing mice that were treated with anti-PD-1 and anti-Tim-3 antibodies or isotype controls.
|
| 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 |
| |
|
| Description |
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK3DN_iso
|
| 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.
|
| |
|
| Submission date |
Dec 26, 2018 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Asaf Madi |
| E-mail(s) |
[email protected]
|
| 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 (1) |
| GSE122969 |
Checkpoint blockade immunotherapy induces dynamic changes in PD-1-CD8+ tumor-infiltrating T cells |
|
| Relations |
| BioSample |
SAMN10644231 |
| SRA |
SRX5180081 |
