|
| Status |
Public on Dec 25, 2021 |
| Title |
Sample_4-HIF2-TAM-C5 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed background
tissue: Pancreatic tumor
genotype: FSF-KrasG12D/+; Trp53frt/frt; Pdx1-Flp; Hif2fl/fl; alphaSMACreERT2/+
treatment: normal chow
|
| Treatment protocol |
Once weaned, mice were fed with normal chow or tamoxifen chow to generate KPF CAF-HIF WT and KPF CAF-HIF KO mice
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
30mg Pancreatic tumor from KPF-CAF HIF2 WT and KO mice were homogenized and RNA was purified using an RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FSF-KrasG12D/+; Trp53frt/frt; Pdx1-Flp; Hif2fl/fl; αSMACreERT2/+
|
| Data processing |
bcl2fastq to demultiplex and generate fastq files
RSEM package was used to quantitate transcript abundance from RNA-seq fastq files.
RSEM expected counts were imported into DESeq2 and differential expression analysis was performed using DESeq2 package
Genome_build: mm9
Supplementary_files_format_and_content: csv file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: csv file with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Dec 22, 2021 |
| Last update date |
Dec 25, 2021 |
| Contact name |
Yanqing Huang |
| E-mail(s) |
YHuang10@mdanderson.org
|
| Phone |
7135630071
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Experimental Radiation Oncology
|
| Lab |
Cullen Taniguchi
|
| Street address |
6565 MD Anderson Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE192474 |
Stromal HIF2 Regulates Immune Suppression in the Pancreatic Cancer Microenvironment |
|
| Relations |
| BioSample |
SAMN24299326 |
| SRA |
SRX13487077 |
