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Sample GSM3712551 Query DataSets for GSM3712551
Status Public on Apr 30, 2019
Sample type SRA
Source name 293_HEK
Organism Homo sapiens
Characteristics cell line: 293 HEK
antibody: BRD4 (Abcam, 128874)
enrichment target: BRD4
target function: Acetylated Lysine Reader, Active Enhancers
treatment: 50nM CEM87, sgMYOD
Treatment protocol (dCas9 & ms2-FKBPx2)-infected cells were grown to 70% confluence, transfected with sgRNA using a PEI protocol. Media was changed 16 hours later, and cells were treated with 50 nM of CEM87 for 48 hours. Samples were then harvested after 1% formaldehyde fixation for 10 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.
Growth protocol Cell lines were grown in high-glucose DMEM supplemented with 10% FBS serum, 10 mM HEPES, NEAA, Pen/Strep, and 55 μM 2-Mercaptoethanol.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description DNA (ChIP-enriched)
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.
Enrichment of known and de novo motifs were found using HOMER version 4.8.2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.narrowPeak.nobl.GREAT.bed: Peak files are tab-delimited text files for each sample.
Submission date Apr 05, 2019
Last update date May 01, 2019
Contact name Javed Khan
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 (1)
GSE129407 Gene Specific Activation Driven by Small Molecules
BioSample SAMN11351205
SRA SRX5647963

Supplementary file Size Download File type/resource
GSM3712551_Sample_HEK_sgMYOD_CEM87_BRD4_037_C_HMJ2HBGX7_peaks.narrowPeak.nobl.GREAT.bed.gz 16.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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