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| Status |
Public on Nov 30, 2016 |
| Title |
WT_OAsample1 |
| Sample type |
SRA |
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| Source name |
skeletal muscle from hindlimbs
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wildtype
tissue: satellite cells
age: 22-28 months
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| Treatment protocol |
Mice were anaesthetized using isoflurane in air and oxygen through a nose cone. For satellite cell activation, muscles were injured by injecting a total volume of 50 µl of 1.2% BaCl2 into approximately 20 sites in the hindlimb muscles
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| Growth protocol |
mice were kept in a pathogen-free environment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolted using the MagMAX 96 total RNA Isolation Kit (Ambion)
Libraries were generated with the TruSeq Stranded Total RNA (RiboZero Gold).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Gene expression 3 days after injury
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| Data processing |
Sequencing reads were filtered out for low quality sequences and trimmed of low quality bases by using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit
TopHat software (Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111, doi:10.1093/bioinformatics/btp120 (2009)) was used for mapping sequencing reads to mm9 genome.
Gene quantification was performed by using HT-Seq and differentially expressed genes (DEGs) were estimated by using DESEQ2 (Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169, doi:10.1093/bioinformatics/btu638 (2015); Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 15, 550, doi:10.1186/s13059-014-0550-8 (2014))
Genome_build: mm9
Supplementary_files_format_and_content: RefSeq genes were used for annotation. Tab-delimited text files include gene name and read numbers for each sample
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| Submission date |
Sep 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Friedrich Becker |
| E-mail(s) |
[email protected]
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| Phone |
+49 3641 656838
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| Organization name |
Leibniz Institute on Aging - Fritz Lipmann Institute
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| Department |
Stem cell aging
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| Lab |
Prof. Lenhard K. Rudolph
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| Street address |
Beutenberg Strasse 11
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| City |
Jena |
| State/province |
Thuringia |
| ZIP/Postal code |
07745 |
| Country |
Germany |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE87404 |
Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals [RNA-seq] |
| GSE87812 |
Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals |
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| Relations |
| BioSample |
SAMN05830363 |
| SRA |
SRX2193489 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2330253_OA_sample1.txt.gz |
92.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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