|
| Status |
Public on Nov 10, 2015 |
| Title |
Mouse islet polyA RNA-Seq biological replicate 1 CT16 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6 wild type mice
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Pancreatic islet cells
strain: C57BL/6
genotype: wild type
time (hours): 16
|
| Treatment protocol |
Synchronization by 1 hr forskolin pulse
For time series experiments circadian rhythms were entrained by a 1 hr forskolin pulse (10uM) and allowed to recover for 40 hrs prior to collecting the first time point
|
| Growth protocol |
Islet cells were cultured in RPMI 1640 supplemented with 1% pennicillin/streptomycin, 1% L-glutamine, and 10% FBS (mouse) or 10% human AB serum (human)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mouse islets were isolated by perfusing the pancreatic bile duct with collagenase
Illumina stranded LT kit for RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
M1CT16
|
| Data processing |
The data was analyzed by RNA Express v1.0 in BaseSpace
Reads were aligned to mm10 using STAR with the following parameters: readFilesCommand zcat outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical genomeLoad LoadAndKeep
Gene expression levels were computed by a proprietary alogorithm in BaseSpace
Differential expression was performed with DESeq2 using default parameters
Gene cycling data was computed with eJTK_Cycle
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files showing gene cycling data
|
| |
|
| Submission date |
Jun 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Perelis |
| E-mail(s) |
mperelis@u.northwestern.edu
|
| Organization name |
Northwestern University
|
| Street address |
303 E Superior Street Lurie Research Center Rm 7-220
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE69889 |
Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk |
| GSE70961 |
Pancreatic Beta Cell Enhancers Regulate Rhythmic Transcription of Exocyst Triggering and Diabetes |
|
| Relations |
| BioSample |
SAMN03775468 |
| SRA |
SRX1059061 |
