|
| Status |
Public on Feb 14, 2015 |
| Title |
wt1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pancreatic islets
strain: Wfs1tm1Koks
genotype: wild-type
|
| Growth protocol |
Pancreatic islets were isolated as previously described by Shimomura et al. (2009) from 6 mice in each genotype. Briefly, mice were executed by cervical dislocation and the islets isolated by collagenase digestion (Sigma, final concentration 1 mg/mL). The inflated pancreas was dissected out and incubated in a 37°C water bath for 13 minutes. The tissue was washed twice with 0.2% BSA (Sigma) and HBSS (Sigma) solution. The islets were handpicked under stereomicroscope in 0.2% BSA and HBSS solution. Finally, the islets were picked into high glucose (4.5 g/L) DMEM/Ham's F12 media (PAA), containing 10% FBS (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco) and 20 mM L-glutamine (Invitrogen). Islets were incubated overnight at 37°C before insulin secretion assay or RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit
RNA-sequencing was used for transcriptome analysis. Pancreatic islets from 4 animals were used in each genotype group. Total RNA was isolated from islets using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol and cDNA for sequencing was synthesized using Ovation RNA-Seq System V2 (NuGEN Technologies, Inc.), 10 ng of total RNA was used. SOLiD DNA Fragment library kit (cDNA input 2 µg) was used to generate libraries and quality was controlled with the Agilent Bioanalyzer 2100 (Agilent Technologies) before sequencing. The libraries were marked with different barcodes and pooled together for the following template preparation. The automated SOLiD EZ Bead System and SOLiD EZ Bead E80 System Consumables (Life Technologies) were applied for the template preparation. For sequencing the SOLiD 5500xl System and paired end (75 bp forward and 35 bp reverse) chemistry for DNA sequencing was applied (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: mm10
Supplementary_files_format_and_content: counts data
|
| |
|
| Submission date |
Feb 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sulev Koks |
| E-mail(s) |
sulev.koks@murdoch.edu.au
|
| Phone |
+61864570313
|
| Organization name |
Murdoch University
|
| Department |
Centre for Molecular Medicine and Innovative Therapeutics
|
| Street address |
90 South Street
|
| City |
Perth |
| State/province |
Western Australia |
| ZIP/Postal code |
6150 |
| Country |
Australia |
| |
|
| Platform ID |
GPL15907 |
| Series (1) |
| GSE65929 |
Reduced insulin secretion in WFS1-deficient mice may be related to downregulation of Trpm5 |
|
| Relations |
| BioSample |
SAMN03344740 |
| SRA |
SRX877832 |
