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Sample GSM1711969 Query DataSets for GSM1711969
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
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
BioSample SAMN03775468
SRA SRX1059061

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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