|
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 |