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Sample GSM3163891 Query DataSets for GSM3163891
Status Public on Oct 23, 2019
Title RNAseq_12hr_rep1
Sample type SRA
Source name Neural progenitor cells
Organism Homo sapiens
Characteristics cell type: H1 hESC-derived neural progenitor cells
Treatment protocol Neural induction was performed according to dual-Smad inhibition protocol (Chambers et al., 2009) for up to 72 hours.
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).
Library construction was done using Illumina TruSeq Stranded Total RNA Kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
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
Supplementary_files_format_and_content: featureCountsTable
Submission date May 29, 2018
Last update date Oct 23, 2019
Contact name Anat Kreimer
Organization name University of California, Berkeley
Street address 378 Stanley Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platform ID GPL18573
Series (2)
GSE115045 Massively parallel characterization of regulatory dynamics during neural induction [RNA-seq]
GSE115046 Massively parallel characterization of regulatory dynamics during neural induction
BioSample SAMN09276502
SRA SRX4136812

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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