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Sample GSM3565119 Query DataSets for GSM3565119
Status Public on Feb 26, 2019
Title RNAseq_Pax3_H9_1day_rep2
Sample type SRA
 
Source name differentiating hES cells
Organism Homo sapiens
Characteristics tissue: differentiating hES cells
differentiation protocol: serum
time: day6 of differentiation
purification: GFP-sorted
doxycycline-treatment: 1-day
Growth protocol Human ES cell differentiation was achieved by plating 10^6 cells in 6cm non-adherent Petri dishes and incubation at 37°C, 5% CO2 on a shaker at 60 RPM. After 2 days, mTeSR was replaced with EB Myogenic (EBM) Media supplemented with 10µM Y-27632 and 10µM GSK3 inhibitor (CHIR990217) [EB Myogenic media composition: IMDM supplemented with 15% FBS, 10% Horse Serum, 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol]. 2 days later, media was replaced to remove GSK3 inhibitor and the formed EBs were plated on gelatin-coated flasks using EBM + 10ng/ml human basic FGF (bFGF). 24h later, cultures were supplemented with 1µg/ml doxycycline (dox) for PAX3 induction. 24h later cells were harvested using Trypsin+EDTA solution and FACS sorted based on GFP expression.
Extracted molecule total RNA
Extraction protocol RNA-seq: sorted cells from murine and human differentiating ES cells were resuspended in Trizol. RNAs were extracted using the PureLink RNA mini prep kit following manufacturer's instruction (including in-column Dnase digestion).
RNA-seq libraries were generated using the TrueSeq stranded kit and dual-index adapter-barcodes following manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file:
RNAseq_human_iPAX3_1day.xlsx
RNAseq_H9_PAX3_1day_dox_02
Data processing Human RNA-seq analysis: each sample’s reads were then processed using RSEM version 1.2.3 (with bowtie-0.12.9 for the alignment step) [103, 104]. Genes were filtered to select only those with median-normalized TPM (Transcripts Per Million mapped reads) greater than 10 in at least one sample, log2fold change greater than 1 and p<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq: processed files contain tab-delimited expression values following analysis using EdgeR (mouse RNA-seq) and RSEM (human RNA-seq)
 
Submission date Jan 16, 2019
Last update date Feb 26, 2019
Contact name Alessandro Magli
E-mail(s) alemagli@gmail.com
Organization name University of Minnesota
Department Medicine
Street address 2231 6th St SE
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
 
Platform ID GPL16791
Series (1)
GSE125203 Chromatin accessibility landscape upon induction of Msgn1, Pax3 and Myf5 in mesodermal cells and identification of conserved Pax3 binding sites and target genes during skeletal myogenesis
Relations
BioSample SAMN10756580
SRA SRX5255406

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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