|
| Status |
Public on Aug 10, 2022 |
| Title |
LN_CD8_Ramp1 WT..B16_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
cell type: CD8
genotype: RAMP1wt (CD45.1+)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total CD8+ T-cells were isolated from the spleen of wild-type (CD45.1+) or RAMP1-/- (CD45.2+) mice, expanded and amplified in vitro using a mouse T-cell Activation/Expansion Kit (Miltenyi cat #130-093-627). CD8+ cells from RAMP1-/- and RAMP1wt were injected separately or 1:1 mix through tail vein of Rag1-/- mice. One week after, the mice were inoculated with B16F10-OVA-mCherry cancer cells (5 × 105), and tumor growth was measured daily using a handheld digital caliper. On day 14, tumor and draining lymph node were harvested, and RAMP1-/- (CD45.2+) and RAMP1wt (CD45.1+) CD8+ T-cells were FACS-purified using a FACSAria IIu cell sorter (Becton Dickinson).
For FACS-purified cells, RAMP1-/- and RAMP1wt CD8+ T-cells RNA-seq libraries were constructed using KAPA Hyperprep RNA (1x75bp) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
peformed by FULGENT (temple, CA)
|
| Data processing |
Nextseq500 (0.5 Flowcell High Output; 200 M de fragments; 75 cycles Single-End read) sequencing was performed onsite at the IRIC (Institute for Research in Immunology and Cancer) genomic center. Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M23, based on Ensembl 98) using STAR v2.5.1b32.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in TPM (Transcripts Per Kilobase Million) values, for these stranded RNA libraries. DESeq2 version 1.18.134 was then used to normalize gene readcounts. Sample clustering based on normalized log readcounts produces the following hierarchy of samples.
Supplementary files format and content: Individual cell data are shown as a log10 of (transcript per million x 1000).
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Aug 10, 2022 |
| Contact name |
sebastien Talbot |
| E-mail(s) |
sebastien.Talbot@umontreal.ca
|
| Organization name |
university of Montreal
|
| Department |
pharmacology
|
| Street address |
2900 Boulevard Edouard-Montpetit,
|
| City |
montreal |
| State/province |
quebec |
| ZIP/Postal code |
H3T 1J4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE205863 |
Nociceptor neurons affect cancer immunosurveillance [RNA-seq 1] |
| GSE205866 |
Nociceptor neurons affect cancer immunosurveillance |
|
| Relations |
| BioSample |
SAMN28968160 |
| SRA |
SRX15670529 |
