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Sample GSM2197666 Query DataSets for GSM2197666
Status Public on Dec 22, 2016
Title 1 µM 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: 1 µM 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 SAMN05231943
SRA SRX1838105

Supplementary file Size Download File type/resource
GSM2197666_RA3A.txt.gz 739.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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