|
| Status |
Public on Aug 04, 2022 |
| Title |
PD1lo TIL RNAseq 1 |
| Sample type |
SRA |
| |
|
| Source name |
B16 melanoma tumor
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cell
disease state: B16 melanoma
treatment: None
timepoint: Day 14 post-tumor
sorting scheme: CD8+CD44+PD1loTim3-
|
| Treatment protocol |
In immunotherapy experiments, when tumors were palpable (typically day 5), mice began anti-PD-1, anti-4-1BB, or isotype control therapy. Mice were treated with 200 μg of anti-PD-1, 200 μg of anti-4-1BB, or equivalent isotype control intraperitoneally three times per week for the duration of the experiment.
|
| Growth protocol |
Mice were injected intradermally with 2.5 × 105 B16 melanoma cells. Mice were sacrificed and dLN and TIL harvested on day 14, when tumors were typically 8-10 mm in diameter.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD8 T cells were isolated from tumors by surgical excision followed by flow sorting. cDNA was prepared from ~1,000 cells using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Libraries were prepared using the Nextera XT DNA Library Preparation kit. Libraries were denatured and diluted using the NextSeq 500 protocol Revision D.Cluster generation and 75-bp paired-end, dual-indexed sequencing were performed on the Illumina NextSeq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
TPM_TIL_LN_VVova.csv
TIL_PD1lo_rep1
|
| Data processing |
trimmed high quality reads were aligned to genome using HISAT2
Transcripts per Million (TPMs) calculated using Subread
Differentially expressed genes (DEG) determined using DEseq2 with cutoffs of 2 fold and padj<0.05
Genome_build: mm10 ensembl
Supplementary_files_format_and_content: Transcripts per Million (TPM) file, normalized counts
|
| |
|
| Submission date |
May 24, 2021 |
| Last update date |
Aug 04, 2022 |
| Contact name |
B. Rhodes Ford |
| E-mail(s) |
BRF56@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Department of Pediatrics
|
| Lab |
Poholek Lab
|
| Street address |
4401 Penn Ave.
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15224 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE175408 |
Altered costimulatory signaling and hypoxia support chromatin landscapes that limit the functional potential of exhausted T cells in cancer [RNA-seq] |
| GSE175443 |
Altered costimulatory signaling and hypoxia support chromatin landscapes that limit the functional potential of exhausted T cells in cancer |
|
| Relations |
| BioSample |
SAMN19316702 |
| SRA |
SRX10971148 |
