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Status |
Public on Mar 02, 2022 |
Title |
PD-GW-3 |
Sample type |
SRA |
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|
Source name |
pancreatic tissue_KC/PD mice fed GW501516 diet
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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).
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
|
Description |
PD_GW_3_S30_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
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|
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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 |
SAMN19555639 |
SRA |
SRX11066108 |