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Sample GSM3611922 Query DataSets for GSM3611922
Status Public on Aug 22, 2019
Title MondoA_KD_ChIP-seq
Sample type SRA
 
Source name Primary skeletal myotube
Organism Homo sapiens
Characteristics cell type: Primary human myocytes
genotype: MondoA KD
passages: P7
chip antibody: MondoA (ProteinTech, catalog # 13614-1-AP, lot # 00042515)
Treatment protocol siRNA against MondoA or control was transfected on day 6 following differentiaiton. The cells were harvested 3days after transfection.
Growth protocol Primary human skeletal myoblasts are cultured in low glucose DMEM supplemented with 10% fetal bovine serum. When the cells reach 80-90% confluency, the cells are switched to differentiation media composed of alpha-MEM with 2% fetal bovine serum. This media is replaced every other day.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and MondoA or Histione-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using OvationĀ® Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN, Catalog # 0344)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing reads alignment by STAR 2.5.0c with parameters "--runMode alignReads --runThreadN 4 --genomeDir %s --readFilesIn %s --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outReadsUnmapped None --alignIntronMax 1 --genomeLoad LoadAndKeep --readFilesCommand zcat --limitBAMsortRAM 10000000000 --outFileNamePrefix %s" with "--genomeDir" for your reference genome, "--readFilesIn" for your input raw data and "--outFileNamePrefix" for the output prefix
tag directory made by Homer 5.10 for each Sample and only unique mapped reads were used
Peak calling by the "findPeaks" command in Homer 5.10 using the default setting
Bigwig files were generated by Homer and bedGraphToBigWig command
motif analysis by the "findMotifsGenome" command in Homer 5.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig
 
Submission date Feb 19, 2019
Last update date Aug 22, 2019
Contact name Byungyong Ahn
E-mail(s) byahn@pennmedicine.upenn.edu
Phone 2158982374
Organization name University of Pennsylvania
Department Penn Cardiovascular Institute
Street address 3400 Civic Center Blvd Bldg 421
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platform ID GPL20301
Series (2)
GSE126733 Genomic profiling of MondoA and H3K27ac in primary human skeletal myotubes
GSE126767 MondoA Links Muscle Lipid Accumulation and Insulin Resistance Driven by Nutrient Overload
Relations
BioSample SAMN10964862
SRA SRX5391035

Supplementary file Size Download File type/resource
GSM3611922_Combine_MondoA_KD.homer.bw 376.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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