|
| Status |
Public on Mar 24, 2021 |
| Title |
Control_Panc_A |
| Sample type |
SRA |
| |
|
| Source name |
Healthy pancreas
|
| Organism |
Mus musculus |
| Characteristics |
doxycycline treatment duration: 3 weeks
condition: Healthy control
genotype: p48Cre; R26rtTa/rtTa
|
| Treatment protocol |
iKras* and iKras* p53*mice were administered doxycycline chow (BioServ, F3949) to induce expression of KrasG12D for 72 hours, followed by two days of 8 intraperitoneal injections of caerulein (Sigma, 75 ?g/kg) to induce pancreatitis. Doxycycline chow was continuously administered until experiment endpoint.
|
| Growth protocol |
7940b cells were grown in DMEM supplemented with 10% FBS and 1% Pen-Strep. Mouse tumors were harvested after three weeks. Biomaterial scaffolds were harvested three weeks after tumor cell implantation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were mechanically and enzymatically (Collagenase P; 1mg/mL in DMEM) digested under constant agitation. Single cell suspension was obtained by filtering through a 40 µm mesh. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.).
Single-cell cDNA libraries were prepared and sequenced using the 10x Genomics Platform at the University of Michigan Advanced Genomics Core.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Samples OT_Tumor_1, Control_Scaff_B and iKras_p53_Scaff were run on HiSeq 4000. All other samples were run on the NovaSeq 6000 (Illumina). All samples were run using paired end 50 cycle reads to a depth of 100,000 reads.
The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 2.2.0, 3.0.0, or 3.1.0 with default settings was used, with an initial expected cell count of 10,000.
Genome_build: Mouse samples were aligned to the mouse genome mm10-3.0.0 using Cell Ranger. Human samples were aligned to the human genome hg19-3.0.0.
Supplementary_files_format_and_content: Zipped GZ archive file containing barcodes.tsv, genes.tsv/features.tsv, and matrix.mtx files, and .h5 files for reading into R using the Seurat Pipeline.
|
| |
|
| Submission date |
Jan 08, 2021 |
| Last update date |
Mar 24, 2021 |
| Contact name |
Marina Pasca di Magliano |
| Organization name |
University of Michigan
|
| Department |
Surgery
|
| Street address |
1500 E Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE158356 |
Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages |
|
| Relations |
| BioSample |
SAMN17264862 |
| SRA |
SRX9808471 |
