|
Status |
Public on Nov 10, 2015 |
Title |
Mouse islet polyA RNA-Seq biological replicate 3 CT0 |
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): 0
|
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 |
M3CT00
|
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
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|
|
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 |
SAMN03775560 |
SRA |
SRX1059081 |