|
| Status |
Public on Dec 18, 2019 |
| Title |
SCbeta_rep1_entrained_RNA-seq_CT36 |
| Sample type |
SRA |
| |
|
| Source name |
HUES 8 hESC line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUES 8 hESC line
tissue: hPSC-derived 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 |
SAMN13625119 |
| SRA |
SRX7411460 |
