|
| Status |
Public on Jun 06, 2024 |
| Title |
5817.PDXCre.AcutePanc RNA |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
cell line: C57Bl/6
genotype: PDX1-Cre (WT)
|
| Treatment protocol |
For induction of acute pancreatitis, cohorts of mice were fasted for 12 h before the first caerulein injection. Caerulein or saline control was administered via IP injection at a dose of 50 μg/kg once an hour for a total of eight injections. Food was returned after the first dose. Animals were euthanized 18 h after the initial dose.
|
| Growth protocol |
Standard mouse housing with controlled temperature, humidity and light cycles and provided with ad libitum standard rodent chow and water.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Pancreas was taken at time of euthanasia, minced in RNAlater and snap frozen with liquid nitrogen. RNA extraction was completed with ToTALLY RNA Kit (Ambion, Cat# AM1910) according to manufacturer’s protocols. Precipitated RNA was cleaned up according to Qiagen’s protocol on the miRNeasy column (Qiagen, Cat# 217004), with an on-column DNA digestion and RNaseOUT (Invitrogen, Cat# 10777019) added to final elution to reduce degradation during storage at -80°C.
Illumina TruSeq RNA v2 library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
DEAnalyses_acute panc PDX and P48; DEAnalyses_W_WO Acute Panc PDX
|
| Data processing |
Sequencing reads were processed through the MAP-Rseq version 3.0.0 workflow
Differential Expression Analysis using GLM model in edgeR (version 3.28.1)
Pathway analysis of DEGs using RITAN , R package
Assembly: Genome_build: Gencode vM23 (GRCm38.p6)
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include RAW and RPKM values for each Sample
|
| |
|
| Submission date |
Jun 06, 2024 |
| Last update date |
Jun 06, 2024 |
| Contact name |
Gwen Lomberk |
| E-mail(s) |
glomberk@mcw.edu
|
| Phone |
414-955-2440
|
| Organization name |
Medical College of Wisconsin
|
| Street address |
8701 W Watertown Plank Rd, Milwaukee, WI 53226
|
| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE269251 |
Ehmt2 Inactivation in Pancreatic Epithelial Cells Shapes the Transcriptional Landscape and Inflammation Response of the Whole Pancreas [RNA-seq] |
|
| Relations |
| BioSample |
SAMN41708918 |
| SRA |
SRX24824044 |
