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Sample GSM4224893 Query DataSets for GSM4224893
Status Public on Dec 18, 2019
Title HI_entrained_RNA-seq_CT24
Sample type SRA
 
Source name Primary human adult islets
Organism Homo sapiens
Characteristics tissue: Primary human adult islet
treatment: entrained to circadian metabolic rhythms
Growth protocol Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from total RNA using the Ribo-Zero Gold Kit (Epicentre, Madison, WI).
Directional cDNA libraries were prepared using a KAPA Biosystems Stranded RNA-seq Library Preparation kit, pooled, and sequenced on an Illumina HiSeq2000 platform across multiple lanes.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequencing reads were mapped to the human hg38 reference genome assembly using STAR (Dobin et al., 2013) with default parameters. Gene expression based on GENCODE annotations (Harrow et al., 2012) was determined using RSEM (Li and Dewey 2011). Genes with expected count values >=10 across all samples were retained, normalized by library scaling using DESeq2 (Love, et al. 2014), and used for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing RSEM output for each sample
 
Submission date Dec 18, 2019
Last update date Dec 19, 2019
Contact name Juan R Alvarez-Dominguez
Organization name Harvard University
Department Stem Cell and Regenerative Biology
Street address 7 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL18573
Series (2)
GSE139816 Chromatin dynamics reveal circadian control of human in vitro islet maturation [RNA-seq]
GSE139817 Chromatin dynamics reveal circadian control of human in vitro islet maturation
Relations
BioSample SAMN13625052
SRA SRX7411435

Supplementary file Size Download File type/resource
GSM4224893_LIB034352_TRA00123486_S3_L001234.genes.results.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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