|
| Status |
Public on Oct 06, 2021 |
| Title |
MC38_tumor_HFD |
| Sample type |
SRA |
| |
|
| Source name |
Mouse xenograft models
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: male
diet: 45% fat
tissue: tumor
|
| Treatment protocol |
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+ 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
|
| Growth 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).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X Single Cell 5' PE; mRNA 5' capture
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
4834-JB-3_S01_L005
|
| Data processing |
cellranger-4.0.0
scanpy-1.7.1
Genome_build: mm10
Supplementary_files_format_and_content: formatted hdf5 file containing mnn integrated matrix
|
| |
|
| Submission date |
Jul 12, 2021 |
| Last update date |
Oct 06, 2021 |
| Contact name |
Jeff Rathmell |
| E-mail(s) |
jeff.rathmell@vanderbilt.edu
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
PMI
|
| Lab |
Jeff Rathmell 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 |
SAMN20172563 |
| SRA |
SRX11412312 |
