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Sample GSM1499537 Query DataSets for GSM1499537
Status Public on Sep 09, 2014
Title IgG_ChIP-exo [rat]
Sample type SRA
 
Source name Primary cardiomyocytes
Organism Rattus norvegicus
Characteristics cell type: Primary rat cardiomyocytes
chip antibody: Normal Rabbit IgG
chip antibody vendor: Millipore
chip antibody cat. #: 12-370
Treatment protocol C2C12 were induced to differentiate in differentiation medium (DM) containing DMEM/High Glucose/L-Glutamine supplemented with 2% Horse Serum (Hyclone) and 1% Penicillin/Streptomycin for 48 hr.
Growth protocol Primary neonatal cardiomyocytes were prepared from 1 to 3 day old rats using the Neonatal Cardiomyocyte Isolation System (Worthington Biochemical Corp)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and MEF2A-DNA complexes were isolated with antibody.
Libraries were prepared according to Rhee and Pugh (2011). Briefly, after ChIP, P2 adapters were ligated to DNA fragments using T4 ligase. Lambda exonuclease was added to digest unbound DNA. Samples were eluted and sequences were extended with phi29 polymerase. P2 adapters, specific to the 5' end were added. Samples were purified, run on a gel, and samples between 120-160 bp were selcted for sequencing. Libraries were sequenced on the Illumina sequencer following the manufacturer's protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing library strategy: ChIP-exo
Basecalls performed using CASAVA 1.7.0
ChIP-exo reads were aligned to the mm10 or rn5 genome using BWA 0.5.9
Data were filtered using the following specifications: Picard (no duplicates) and samtools q37
peaks were called using MACS 1.4.2 (--nomodel --shiftsize=20 --to-large)
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: BED files were generated using MACS and contain chrom, chromstart, chromend, peak name and score (-10*log10pvalue of peak region) columns
 
Submission date Sep 08, 2014
Last update date May 15, 2019
Contact name John C McDermott
E-mail(s) jmcderm@yorku.ca
Organization name York University
Street address 4700 Keele Street
City Toronto
State/province ON
ZIP/Postal code M3J 1P3
Country Canada
 
Platform ID GPL14844
Series (2)
GSE61204 Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [ChIP-seq]
GSE61207 Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling
Relations
BioSample SAMN03023784
SRA SRX695945

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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