|
| Status |
Public on Mar 02, 2022 |
| Title |
PD-GW-2 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic tissue_KC/PD mice fed GW501516 diet
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: KC/PD
diet: GW501516 diet
tissue: pancreatic tissues
|
| Treatment protocol |
The KC and KC/Pd mice at 6-8 weeks were fed a GW diet (50 mg/kg) for 3 days and then euthanized (n=3 per group).
|
| Growth protocol |
The KC and KC/Pd mice on a GW501516 diet (50 mg/kg) were euthanized (n=3 per group). The pancreta were harvested in Trizol and then stored at -80C freezer till further analysis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the mouse pancreatic tissues using the RNeasy Mini/Micro Kit (Qiagen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500ng of total RNA for the construction of sequencing libraries.
Illumina-compatible mRNA libraries were constructed using the TruSeq RNA sample prep kit v2 (Illumina, Inc). 500ng of total RNA were enriched for Poly-A mRNA using Oligo-dT magnetic beads. The resulting Poly-A mRNA was fragmented to a median size of 150 bp using divalent cations. Randomly primed first- and second-strand synthesis was then performed to create double-stranded cDNA. The ends of the double-stranded cDNA fragments were repaired, 5′-phosphorylated, and 3′-A tailed, and then the Illumina-specific Y-shaped indexed adapters were ligated. The adaptor-ligated fragments were then purified and enriched by 7 cycles of PCR amplification. The amplified library was then quantified by quantitative PCR using a library quantification kit (KAPA Biosystems) and assessed for size distribution using the Bioanalyzer system (Agilent Technologies). Eight libraries were multiplexed and sequenced on an Illumina HiSeq3000 instrument using the 75-bp paired-end format. After sequencing, BCL files were converted into “.fastq.gz” files, and individual sample libraries were de-multiplexed using CASAVA 1.8.2 with no mismatches.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
PD_GW_2_S28_L005
|
| Data processing |
Sequenced reads were sligned to mm10 geome using STAR/2.6.0b.
Reads per gene were counted with HT-Seq/0.11.0.
Read counts were normalized with R package DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads for the genes
|
| |
|
| Submission date |
Jun 04, 2021 |
| Last update date |
Mar 02, 2022 |
| Contact name |
Xiaofeng Zheng |
| E-mail(s) |
xfzzxf@gmail.com
|
| Phone |
7137921077
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Bioinformatics & Computational Biology
|
| Street address |
1400 Pressler St.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE176135 |
Quantitative Analysis of PPARD mRNA-Seq Transcriptomes of Mouse KRAS Mutant Pancreatic Tissues by Next Generation Sequencing (NGS) |
|
| Relations |
| BioSample |
SAMN19555640 |
| SRA |
SRX11066107 |
