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| Status |
Public on Jul 23, 2015 |
| Title |
mdx 3 (373) |
| Sample type |
SRA |
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| Source name |
P60 soleus whole muscle
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| Organism |
Mus musculus |
| Characteristics |
genotype: mdx 3 (373)
tissue: soleus
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| Treatment protocol |
None
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| Growth protocol |
None
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
361
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| 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.
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| Submission date |
May 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
kfir baruch Umansky |
| E-mail(s) |
kfirum@weizmann.ac.il
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| Phone |
97289342318
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| Organization name |
Weizmann Institute
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| Street address |
POB 25
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| City |
Rehovot |
| State/province |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| 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 |
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| Relations |
| BioSample |
SAMN03700796 |
| SRA |
SRX1032552 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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