|
| Status |
Public on Jan 01, 2016 |
| Title |
KO3 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Pancreatic islets
age: 10-14 weeks
genotype: Ffar3-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted from isolated islets that were selected from pooled islet isolations from two pancreata using an RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapters were removed and reads were removed that had either more than 5% unknown bases, or more than 50% of the reads had a phred score less than 10
The remaining reads were aligned to mm10 (UCSC) with TopHat v2.0.8b with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa. FPKM values were extracted from the cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Apr 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Layden |
| E-mail(s) |
b-layden@northwestern.edu
|
| Organization name |
Northwestern
|
| Street address |
303 E Chicago
|
| City |
Chicago |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE67991 |
RNA seq of pancreatic islets isolated from free fatty acid receptor 3 knockout (Ffar3 KO) and wildtype (Ffar3 WT) male mice |
|
| Relations |
| BioSample |
SAMN03490234 |
| SRA |
SRX998558 |
