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Sample GSM1714210 Query DataSets for GSM1714210
Status Public on Mar 22, 2016
Title WT_UTX_Female
Sample type SRA
 
Source name Satellite cells from muscle
Organism Mus musculus
Characteristics strain: B6/129
genotype: Pax7-CreER, Rosa26-Floxed-TdTomato
tissue: Differentiating Myoblasts
Sex: Female
Treatment protocol Sorted TdT+ SCs from UTXmKO/TdT or UTXWT/TdT mice were induced to differentiate for 24 h.
Growth protocol SCs from UTXmKO/TdT or UTXWT/TdT mice were grown in in Ham's F10 modified media supplemented with 20 % fetal calf serum, 4 mM L-Glutamine, 1.5 g/L sodium bicarbonate, 2.5 ng/mL of FGF, and 2.5 ┬ÁM of 4-OH-Tamoxifen.
Extracted molecule total RNA
Extraction protocol Total RNA was then isolated using RNAesay kit (Qiagen) using an on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequenced reads were initially mapped to the known mm9 transcripts (GTF file from the UCSC) using Bowtie version 2.2.4 / TopHat 2.0.12 using default values. Unmapped reads were then mapped to the mm9 genome.
Splice junctions were determined with TopHat version 2.0.12 using default values.
Transcript quantification was performed with Cufflinks version 2.2.1 and HT-Seq 0.6.1.
Identification of differentially expressed genes was performed with the CuffDiff from Cufflinks version 2.2.1 and EdgeR bioconductor package.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the read per million mapped reads coverage of the RNA-Seq across the genome. The files were generated using the BEDTools suite (version 2.16.2) and UCSC genome browser standalone tools for Unix from the aligned reads output of TopHat version 2.0.12 using default values.
Supplementary_files_format_and_content: Text file contains quantification for each gene in Fragments Per Million Kilobase (FPKM).
 
Submission date Jun 17, 2015
Last update date May 15, 2019
Contact name Marjorie Brand
E-mail(s) karthi.sivaraman@gmail.com, mbrand@ohri.ca
Organization name Ottawa Hospital Research Institute
Street address 501 Smyth Road
City Ottawa
State/province Ontario
ZIP/Postal code K1H 8L6
Country Canada
 
Platform ID GPL19057
Series (1)
GSE69968 RNA-Sequencing of primary myoblasts from mice with a satellite cell specific knockout of the histone demthylase UTX/KDM6A
Relations
BioSample SAMN03780055
SRA SRX1063696

Supplementary file Size Download File type/resource
GSM1714210_WT_UTX.bw 79.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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