|
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 |