|
| Status |
Public on Dec 22, 2016 |
| Title |
25 nM retinoic acid (2 hours), rep1 |
| Sample type |
SRA |
| |
|
| Source name |
neuromesodermal progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129 R1
tissue: embryonic stem cell
agent: 25 nM retinoic acid
|
| Treatment protocol |
Cells were treated with either DMSO control (2 hours), 25 nM retinoic acid (2 hours), or 1 µM retinoic acid (2 hours).
|
| Growth protocol |
Neuromesodermal progenitor cells were derived from mouse embryonic stem cells that were treated with bFGF for 2 days, then treated with bFGF and WNT agonist (CHIR99021) for 1 day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Ambion mirVana miRNA Isolation Kit.
1ug of Total RNA was used to construct multiplexed Libraries using Illumina's Truseq Stranded Total RNA Kit. First, the Total RNA was subjected to ribodepletion process to remove rRNA. The remaining RNA is purified, fragmented, Reverse transcribed, adapter ligated and finally PCR amplified to enrich the DNA fragments.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina’s Basespace was used to convert bcl files to FASTQ files and de-multiplex the samples
Sequenced reads were assessed with FastQC v0.11, then mapped to mm10 whole genome using TopHat2 v2.0.13 and Bowtie2 v2.2.5.0 with --b2-sensitive option and default parameters
Partek Genomics Suite v6.6 was applied for quantification based on RefSeq transcript model (2015-08-04)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count and RPKM values for each Sample
|
| |
|
| Submission date |
Jun 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregg Duester |
| E-mail(s) |
duester@sbpdiscovery.org
|
| Organization name |
Sanford Burnham Prebys Medical Discovery Institute
|
| Street address |
10901 N. Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE83251 |
RNA-seq analysis of retinoic acid treated mouse neuromesodermal progenitors |
|
| Relations |
| BioSample |
SAMN05231941 |
| SRA |
SRX1838103 |
