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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 16, 2014 |
Title |
IP flag PGC-1alpha rep.2 |
Sample type |
SRA |
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Source name |
C2C12 myotubes, IP flag PGC-1alpha
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Organism |
Mus musculus |
Characteristics |
cell type: C2C12 myotubes chip antibody: Monoclonal ANTI-FLAG® M2 Antibody, Sigma
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Growth protocol |
C2C12 cells were grown to 90% confluence in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 Units/ml penicillin and 100ug/ml streptomycin. The differentiation to myotubes was induced by changing the medium to DMEM supplemented with 2% horse serum for 72h. Follwing differentiation, the cells were cultivated in the presence of Flag-PGC-1alpha adenovirus.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Starting with approximately 1x10^8 C2C12 cells (crosslinked with formaldehyde), the chromatin immunoprecipitation was performed according to the Agilent Mammalian ChIP-on-chip Protocol version 10.0 using magnetic beads (Dynabeads® Protein G, Invitrogen), which were previously coated with monoclonal anti-flag antibodies (Monoclonal ANTI-FLAG® M2 Antibody, Sigma). ChIP DNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
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Data processing |
The sequenced reads were filtered based on the quality score of each read and its alignments. Read were retained when Phred score >= 20, read length >= 25 bps and number of wrongly called nucleotides (Ns) <= 2. Those reads that passed the filter were aligned to the mouse genome, UCSC mm9 assembly, using Bowtie version 0.12.7 (Langmead et al., 2009) using parameters --best --strata -a --m 100. We used a peak calling algorithm as described in more detail in the manuscript. To identify regions that were significantly enriched in the ChIP, we passed a 200 bps long sliding window along the genome, sliding by 25 bps between consecutive windows, and estimated the fraction of all ChIP reads fIP that fall within the window, as well as the fraction fWCE of reads from the WCE that fall in the same window (which we estimate from a 2000 bps long window centered on the same genomic location). All regions with a Z-statistic larger than 4.5 as significantly enriched were defined as "peaks" and used for further analysis. Genome_build: mm9
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Submission date |
Sep 25, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Christoph Handschin |
Organization name |
Biozentrum, University of Basel
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Street address |
Spitalstrasse 41
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City |
Basel |
ZIP/Postal code |
4056 |
Country |
Switzerland |
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Platform ID |
GPL11002 |
Series (2) |
GSE51178 |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program [ChIP-Seq] |
GSE51191 |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program |
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Relations |
BioSample |
SAMN02364117 |
SRA |
SRX360389 |
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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