|
Status |
Public on Oct 23, 2019 |
Title |
RNAseq_dSi rep 1 |
Sample type |
SRA |
|
|
Source name |
H1 hESCs
|
Organism |
Homo sapiens |
Characteristics |
treatment: hESC-derived neural progenitors that were induced by dual-Smad inhibition for 72 hours followed by further 72h-culture in N2B27 medium supplemented with FGF and EGF
|
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 |
SAMN12339686 |
SRA |
SRX6489853 |