|
| Status |
Public on Jul 20, 2024 |
| Title |
MC38_tumor_HFD_anti-PD1_CD45pos_TCR |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
cell line: MC38
|
| Treatment protocol |
8-week-old C57BL/6 male mice were fed ad libitum a 10% kcal from fat (low fat) diet or a 45% kcal fat (high fat) diet (Research Diets D12450H and D12451, respectively). Following 28 weeks of diet treatment mice were injected subcutaneously with 2x105 MC38 cells. Tumors were collected on Day 20 post injection and mechanically and enzymatically digested using miltenyi mouse tumor digestion kit following manufacturer’s instructions. CD45+ and CD45- cells were separated from tumor suspensions using CD45+ microbeads (miltenyi) and enriched for live cells using a dead cell removal kit (miltenyi). Three samples from each diet treatment group were resuspended in PBS + 0.4% FBS and pooled together in equal number of live cells prior to submitting to single cell sequencing. Cell viability for all samples were >95% via trypan blue prior to submission
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
10X
10X Single Cell 5' PE
mRNA 5' capture
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
cellranger
Assembly: mm10
Supplementary files format and content: h5, csv
|
| |
|
| Submission date |
Jul 17, 2024 |
| Last update date |
Jul 20, 2024 |
| Contact name |
John Karijolich |
| E-mail(s) |
john.karijolich@vumc.org
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
PMI
|
| Lab |
John Karijolich Lab
|
| Street address |
1211 Medical Center Drive
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE179936 |
Single Cell RNA Sequencing reveals heterogenous tumor associated immune cell compartment in lean vs obese mice using an MC38 tumor model |
|
| Relations |
| BioSample |
SAMN42560438 |
| SRA |
SRX25362149 |
