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Sample GSM3963283 Query DataSets for GSM3963283
Status Public on Oct 23, 2019
Title RNAseq_OTX1 rep 3
Sample type SRA
 
Source name H1 hESCs
Organism Homo sapiens
Characteristics treatment: Overexpressed with OTX1
Treatment protocol H1 hESCs were infected with transcription factor overexpression vectors via lentivirus and incubated for 14 days. As a control, hESC were induced by dual-Smad inhibition for 72 hours followed by further 72h-culture in N2B27 medium supplemented with FGF and EGF.
Growth protocol H1 hESCs were culture in mTeSR1 media on matrigel coated dishes.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy mini kit (Qiagen).
mRNA enrichment, cDNA synthesis, and library generation were performed by Novogene (https://en.novogene.com/).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were aligned to the hg19 human genome assembly with Tophat2 (Version 2.1.1; (Kim et al., 2013)), and low quality reads were removed with Trimmomatic (Version 0.3.2; (Bolger et al., 2014)). Reads that aligned to more than one gene as well as chimeric fragments were excluded.
We also removed genes that failed to be quantified in at least one sample by Cufflinks (Trapnell et al., 2010). We implemented a quality control (QC) pipeline that computes an extensive set of quality metrics, relying in part on FASTQC (Version 0.3.2; Babraham Bioinformatics) and the PICARD suite of alignment metrics (Version 2.5.0 with samtools 1.3.1).
Transcript levels were determined using RefSeq transcript annotations, and counting the number of reads aligning to every gene (defined as the union of all splice forms) with featureCounts (Version 1.5.0-p3; (Liao et al., 2014)).
Genome_build: hg19
 
Submission date Jul 22, 2019
Last update date Oct 23, 2019
Contact name Anat Kreimer
E-mail(s) anat.kreimer@berkeley.edu
Organization name University of California, Berkeley
Street address 378 Stanley Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL24676
Series (2)
GSE115046 Massively parallel characterization of regulatory dynamics during neural induction
GSE134678 Massively parallel characterization of regulatory dynamics during neural induction [RNA-seq II]
Relations
BioSample SAMN12339696
SRA SRX6489843

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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