|
| Status |
Public on Oct 23, 2019 |
| Title |
RNAseq_3hr_rep2 |
| 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 |
| 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 |
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 |
|
| Relations |
| BioSample |
SAMN09276340 |
| SRA |
SRX4136817 |
