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Sample GSM1689881 Query DataSets for GSM1689881
Status Public on Jul 23, 2015
Title mdx 4 (375)
Sample type SRA
Source name P60 soleus whole muscle
Organism Mus musculus
Characteristics genotype: mdx 4 (375)
tissue: soleus
Treatment protocol None
Growth protocol None
Extracted molecule total RNA
Extraction protocol RNA extraction was perfoemd using the 5PRIME PerfectPure tissue RNA extraction kit, according to the Kit's manual
RNA libraries were prepared for sequencing using standard Truseq Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description 363
Data processing Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using tophat v2.0.10 with default parameters.
Reads per locus were quantified using the htseq-count software with the followng options: --stranded=no -t exon -m intersection-strict -q -i gene_id
The gtf file used for the quantification was prepared in-house based on the UCSC known genes.
Differential expression was calculated using DESeq2 version 1.6.3. The option "cooksCutoff=FALSE" was used when calculating the results.
Genome_build: mm9
Supplementary_files_format_and_content: DESeq2 results output. It contains raw htseq counts for each sample, DESeq2 normalized counts for each sample, baseMean expression intensity, log2FoldChange, lfcSE, stat, pvalue and padj.
Submission date May 18, 2015
Last update date May 15, 2019
Contact name kfir baruch Umansky
Phone 97289342318
Organization name Weizmann Institute
Street address POB 25
City Rehovot
State/province Rehovot
ZIP/Postal code 76100
Country Israel
Platform ID GPL17021
Series (2)
GSE56131 Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation
GSE68998 Runx1- responsive genes in mdx muscles
BioSample SAMN03700797
SRA SRX1032553

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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