|
| Status |
Public on May 28, 2015 |
| Title |
NKX2.5:GFP+ RA |
| Sample type |
SRA |
| |
|
| Source name |
hESC-derived
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NKX2.5:GFP hESCs
treatment: Retinoic Acid
facs: NKX2.5-positive
|
| Treatment protocol |
hESCs differentiations were treated with 1 uM Retinoic Acid (Sigma) from day 4 to day 7 (Devalla et al., 2015; PMID: 2570017). Control differentiations were treated with DMSO from day 4 to day 7.
|
| Growth protocol |
Differentiation of hESCs to cardiac lineage was performed by Spin EB method. Cytokine cocktail is added on day 0 to the cells and refreshed on day 3. Beating EBs are observed on day 10.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with Macherey-Nagel Nucleospin Kit. DNAse treatment was performed on the column and quality of samples was asessed on Agilent bioanalyzer.
The strand-specific RNA-Seq libraries of the NKX2.5:GFP-positive and -negative cells were generated as described (Parkhomchuk et al., 2009; PMID: 19620212).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base quality trimming on the raw sequencing files was performed with SICKLE 1.33.
The sequences were aligned to a custom hg19 human genome using GSNAP (release 2014-12-06) with the following flags: --batch (set to 4), --novelsplicing (set to 1), --npaths (set to 1), and --quiet-if-excessive.
The SAM file was compressed into a BAM file, name-sorted, and indexed using SAMTOOLS 0.1.18.
The gene read count data were generated using HTSeq-count 0.6.1p1 using the Ensembl reference (http://genome.ucsc.edu), using the non-stranded and intersection-nonempty option flags (--stranded no and --m intersection-nonempty respectively).
Genome_build: hg19 reference genome
|
| |
|
| Submission date |
Apr 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Nannan He |
| E-mail(s) |
N.He@lumc.nl
|
| Organization name |
Leiden University Medical Center
|
| Street address |
Einthovenweg 20
|
| City |
Leiden |
| ZIP/Postal code |
2333 ZC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE67866 |
RNA sequencing of cells treated with DMSO or Retinoic acid during cardiac differentiation |
|
| Relations |
| BioSample |
SAMN03482415 |
| SRA |
SRX994792 |
