|
| Status |
Public on Jun 26, 2024 |
| Title |
iKrasG12D; Trp53R172H/+ OT 2 weeks ON + 3 days OFF |
| Sample type |
SRA |
| |
|
| Source name |
Orthotopic pancreas tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Orthotopic pancreas tumor
cell line: A9993
number of_mice_pooled: 3
genotype: WT FVB/N
cell ranger_version: 2.2.0
genome: mm10
run date: Nov. 2018
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To prepare tissues for sequencing, samples were disrupted to single cell suspension by mechanically mincing the tissue, followed by enzymatic digestion with Collagenase V (1 mg/mL in RPMI, #C9263, Sigma-Aldrich) at 37°C for 30 min under constant shaking. After digestion, suspensions underwent serial filtration through 500 µm, 100 µm, and 40 µm mesh cell strainers. We then enriched for live cells using the MACS Dead Cell Removal Kit (#130-090-101, Miltenyi Biotec). The resulting single cell suspensions were brought to the University of Michigan Advanced Genomics Core for cDNA library preparation and sequencing.
Samples were run using 50-cycle paired-end reads on the HiSeq 4000 (Illumina) or NovaSeq 6000 (Illumina) to a depth of 100,000 reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
5 x 104 A9993 cells were implanted into syngeneic FVB/N mice. Mice were provided doxycycline chow for 2 weeks to maintain KrasG12D expression, and then randomly selected to return to regular diet for an additional 3 days (KrasG12D “OFF”) before tumor harvest. 1 female and 2 male mice were pooled in this submission.
|
| Data processing |
The University of Michigan Advanced Genomics Core performed processing and alignment of the raw data using Cell Ranger (versions 2.2.0-6.1.2 depending on date of sequencing) with default settings and an initial expected cell count of 10,000.
Assembly: mm10, mm10-2020-A, mm10-2020-A_EGFP, mm10-3.0.0, mm10-GFP-3.0.0
Supplementary files format and content: Raw and filtered Cell Ranger outputs
|
| |
|
| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Marina Pasca di Magliano |
| E-mail(s) |
marinapa@umich.edu
|
| Organization name |
University of Michigan Medical School
|
| Street address |
1500 E Medical Center Dr
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48103 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE269888 |
Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth [scRNA-seq] |
|
| Relations |
| BioSample |
SAMN41840763 |
| SRA |
SRX24931096 |
