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Sample GSM2259143 Query DataSets for GSM2259143
Status Public on Apr 01, 2018
Title CTR D48 H3K4me1
Sample type SRA
 
Source name RMS cell line, mutant HRAS
Organism Homo sapiens
Characteristics antibody: H3K4me1, Active Motif (cat39141, lot01008001 pAb)
enrichment target: H3K4me1
target function: Poised enhancers and promoters
time: 48 hr
treatment: DMSO
Treatment protocol Cells were treated with either DMSO or Trametinib (100 nM) for 48 hours in complete media.
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
ChIP-seq and DNase-seq
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description DNA (ChIP-enriched)
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).
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 Aug 03, 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 GPL18573
Series (2)
GSE85169 MEK inhibition profoundly reprograms myogenic super enhancers in mutant-RAS driven Rhabdomyosarcoma
GSE85171 Epigenetic Reprogramming of mutant RAS-driven Rhabdomyosarcoma via MEK Inhibition
Relations
BioSample SAMN05510496
SRA SRX1998412

Supplementary file Size Download File type/resource
GSM2259143_Sample_CTR_H3K4me1_002_C_HCK7HBGXX_peaks.narrowPeak.nobl.bed.gz 362.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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