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Sample GSM4146881 Query DataSets for GSM4146881
Status Public on Nov 02, 2019
Title SCbeta_RNA-seq_rep1
Sample type SRA
 
Source name HUES 8 hESC line
Organism Homo sapiens
Characteristics cell line: HUES 8 hESC line
protocol: in vitro differentiated pluripotent stem cell
Stage: Stage 6 day 20
cell type: Scbeta hPSC-derived beta cell
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).
Primary islets were cultured in supplemented CRML-1066 medium +10% FBS in low-attachment plates (Corning).
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 HiSeq 2500 platform across multiple lanes.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description total RNA minus rRNA
Data processing Sequencing reads were mapped to the human hg19 reference genome assembly using TopHat2 (Kim et al., 2013) with default and “--min-anchor 5” parameters. Mapped reads from multiple sequencing lanes were merged using samtools (Li et al 2009). Gene expression based on GENCODE v19 annotations (Harrow et al., 2012) was determined using HTSeq (Anders et al. 2015) on “union” mode.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing Htseq output for each sample
 
Submission date Nov 01, 2019
Last update date Nov 06, 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 GPL16791
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 SAMN13176261
SRA SRX7085000

Supplementary file Size Download File type/resource
GSM4146881_SCbeta_RNA-seq_rep1_HTseq_byGencode.v19.htseq-count.out.txt.gz 237.8 Kb (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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