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Sample GSM1240212 Query DataSets for GSM1240212
Status Public on Jun 16, 2014
Title IP flag PGC-1alpha rep.2
Sample type SRA
 
Source name C2C12 myotubes, IP flag PGC-1alpha
Organism Mus musculus
Characteristics cell type: C2C12 myotubes
chip antibody: Monoclonal ANTI-FLAG® M2 Antibody, Sigma
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.
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
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
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
 
Submission date Sep 25, 2013
Last update date May 15, 2019
Contact name Christoph Handschin
Organization name Biozentrum, University of Basel
Street address Klingelbergstrasse 50/70
City Basel
ZIP/Postal code 4056
Country Switzerland
 
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
Relations
BioSample SAMN02364117
SRA SRX360389

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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