|
| Status |
Public on Jan 23, 2018 |
| Title |
mouse008_BL_M |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
group: baseline (non-injured)
gender: Male
tissue: Pancreas
|
| Treatment protocol |
Caerulein hyperstimulation was induced in both male and female mice by 8 hourly intra-peritoneal injections (50 µg/kg) for 2 consecutive days. The mice were maintained on a 12-hour light-dark cycle, and had free access to standard laboratory chow and water. All animal experiments were performed using a protocol approved by the University of Pittsburgh Institutional Animal Care and Use Committee.
|
| Growth protocol |
Caerulein hyperstimulation was performed on C57BL/6 mouse strain from Charles River Laboratories, 6- to 8-weeks of age, weighing 20 to 25 g.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was immediately extracted from the head of the pancreas using TRIzol (Ambion). RNA was treated with DNase I (Zymo Research) at room temperature for 20 minutes. The concentration of DNase I-treated RNA was measured using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific) and the integrity of the DNase I-treated RNA was analyzed on the Agilent TapeStation. All DNase I-treated RNA samples used for RNA library construction had RNA Integrity Numbers (RINs) above 6.4.
RNA libraries were prepared for sequencing using Illumina TruSeq Total Stranded RNA sample preparation kit with ribosomal depletion. Adaptor-ligated fragments were amplified by PCR for nine cycles. The quality and size of the final library preparations were analyzed on an Agilent TapeStation.
RNA-Seq using Illumina NextSeq 500 NGS platform, with approximately 40 million paired-end 75 bp reads for each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality control for raw fastq files were performed with FastQC
Low quality reads and 3’ adapters were trimmed with Trim Galore! and Cutadapt.
The trimmed reads were aligned to mm10 with the RNA-seq aligner STAR v2.5.2a
Gene expressions of every sample were quantified by counting the number of unique fragments mapped to genes using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts of genes for each sample.
|
| |
|
| Submission date |
Jun 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ting Wang |
| E-mail(s) |
wang9ting@gmail.com
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Clinical Research
|
| Street address |
1100 Fairview Ave. N.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE99774 |
Pancreatic gene expression during recovery after pancreatitis reveals unique transcriptome profiles |
|
| Relations |
| BioSample |
SAMN07203138 |
| SRA |
SRX2892807 |
