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Sample GSM921136 Query DataSets for GSM921136
Status Public on Dec 15, 2012
Title p300_MB_replicate3
Sample type SRA
 
Source name Growing C1C12 myoblasts
Organism Mus musculus
Characteristics cell type: C2C12
chromatin preparation method: Sonication
chip antibody: p300, SantaCruz: sc-585x
Treatment protocol Isolated chromatin was either sonicated to an average size of 250 bp or digested with MNAse to yield ~85% mono nucleososomal fragments.
Growth protocol C2C12 myoblasts were grown in DMEM containing 10% FBS and harvested at ~40% confluency for MB chromatin. For myotube differentiation, cells were allowed to grow to complete confluence at which point differentiation was induced by changing the media to DMEM containing 2% horse serum. Induced cells were incubated for 4 days with one change of media (DMEM/2% horse serum) after two days and myotubes were harvested after 4 days of differentiation.
Extracted molecule genomic DNA
Extraction protocol Libraries were generated from input chromatin or ChIP enriched chromatin according to Illumina's standard protocol but using reagents from other companies: DNA end-repair was performed using the End-It DNA repair kit, Epicentre (cat:ER81050). A-overhang generation was performed uising Klenow from NED (cat: M0212). Adapter ligation was performede using the LigaFast kit from Promega (cat:M8225). LM-PCR was performed using Phusion DNA pol master mix from NEB (cat:F-531S). Very stringent quality controls were applied to the libraries: 1. Enrichment of a given site had to be preserved in the libraries in a manner comparable to the original ChIP. 10-12 positive and negative sites were tested for library preparation. 2. The total yield of the LM-PCR had to be ~500 ng. 3. The size distribution had to be centred around 250 bp for libraries generated from MNAse chromatin and around 350 bp for sonicated with a variation no larger than +/- 75 bp. Libraries that did not pass these criteria were considered substandard and were not used for sequencing.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing Sequence reads within each individual replicate were filtered to remove identical sequence tags since those were likely generated by the LM-PCR amplification process while identical sequences present after the merging of replicates were retained. The sequence reads were aligned against the mouse mm9 genome build using the Illumina Pipeline and only tags locating to a single unique position were retained.
Peaks were identified using Qeseq, an algorithm developed in collaboration with Dr Klugers bioinformatics group. Setting for all MNAse libraries: sigma=50 and cut-off=15. For sonicated libraries the settings used were: sigma=100 and cut-off=12.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files: bed file format for enriched peaks; Processed files: cisg format for enriched tags, tab-delimited text files include chromosome, strand, starting position
 
Submission date Apr 23, 2012
Last update date May 15, 2019
Contact name Brian Dynlacht
E-mail(s) brian.dynlacht@nyumc.org
Organization name NYU Langone Medical Center
Street address 550 1st avenue
City New York
ZIP/Postal code 10016
Country USA
 
Platform ID GPL9250
Series (1)
GSE37525 Genome-wide identification of enhancers in skeletal muscle
Relations
SRA SRX144172
BioSample SAMN00862551

Supplementary file Size Download File type/resource
GSM921136_MB_p300_processed_replicate3.txt.gz 69.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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