|
| Status |
Public on Jul 11, 2014 |
| Title |
WT_pancreatic_islets_transcriptome 10 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wildtype
tissue: pancreatic islets
strain: C57BL/6 x 129S6
|
| Growth protocol |
All animals were maintained in a pathogen-free barrier facility on a 12-h light/12-h dark cycle with ad libitum access to water and food.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were sacrificed by cervical dislocation and the pancreas was inflated by intraductal injection of ice cold DMEM media containing 0.2 mg/ml Liberase TL Research Grade. Distended pancreas was digested by shaking in a 37 °C water bath for 17 minutes. Isolated islets were washed and picked under a stereomicroscope and incubated overnight at 37°C and 5% CO2 in RPMI-1640 media containing fetal bovine serum.
RNA libraries were prepared for sequencing using standard Illumina protocols TruSeq RNA Sample Preparation Kits v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Raw data was quality checked using FastQC software. It revealed low PHRED-scale scores at the 3’ end of the 101 bp long reverse reads. These reads were trimmed to a size of 80 bp. Then, reads were assigned to the individual animals using the ligated adapter indices. Further, the samples proceeded filtering to trim the adapter sequences and remove low-quality reads which were shorter than 60 bp or contained more than five bases with a quality score below 15 (PHRED-scale). The paired-end reads were mapped to the reference mouse genome (July 2007 NCBI37/mm9) with Ensembl v66 annotations using Tophat 1.3.3. with options -G -r 80 --library-type fr-unstranded and the aligner Bowtie (version 0.9.9).
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks 1.3.0 with options -G and --library-type fr-unstranded
Differential gene expression was assessed using DESeq version 1.16.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, tab-delimited text file with DESeq normalized read counts for all samples
|
| |
|
| Submission date |
Jul 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Torsten Schöneberg |
| E-mail(s) |
torsten.schoeneberg@medizin.uni-leipzig.de
|
| Organization name |
Leipzig University
|
| Department |
Medical Faculty
|
| Lab |
Molecular Biochemistry
|
| Street address |
Johannisallee 30
|
| City |
Leipzig |
| ZIP/Postal code |
04317 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE59285 |
The G Protein-coupled Receptor P2Y14 Influences Insulin Release and Smooth Muscle Function in Mice |
|
| Relations |
| BioSample |
SAMN02906738 |
| SRA |
SRX648739 |
