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Sample GSM2214074 Query DataSets for GSM2214074
Status Public on Apr 27, 2017
Title 7250-PAX3-FOXO1 DNase rep1
Sample type SRA
 
Source name Fibroblast cell line, PAX3-FOXO1 vector added
Organism Homo sapiens
Characteristics cell line: 7250
cell type: fibroblast
antibody: NA
enrichment target: DNase-sensitivity
target function: Open Chromatin
Treatment protocol ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies. DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C. The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use). Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).
Growth protocol Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol. DNase DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation
 
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina HiSeq 2000
 
Description DNA (DNase sensitive regions)
Data processing ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0. DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Chromatin states were learned using ChromeHMM version 1.10
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.
 
Submission date Jun 26, 2016
Last update date May 15, 2019
Contact name Javed Khan
E-mail(s) khanjav@mail.nih.gov
Phone 2407606135
Organization name NCI, NIH
Department Genetics Branch
Lab Javed Khan
Street address 37 Convent Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL11154
Series (2)
GSE83725 PAX3-FOXO1 establishes myogenic super enhancers and recruits BRD4 de novo [7250 ChIP-seq]
GSE83728 Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma
Relations
BioSample SAMN05293614
SRA SRX1878940

Supplementary file Size Download File type/resource
GSM2214074_Sample_7250_PF19_20X_D_C6FEFANXX_peaks.narrowPeak.nobl.bed.gz 332.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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