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| Status |
Public on Apr 30, 2019 |
| Title |
HEK sgMYOD CEM87 BRD4 |
| Sample type |
SRA |
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| Source name |
293_HEK
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| 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
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| 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.
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
DNA (ChIP-enriched)
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| 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.
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| Submission date |
Apr 05, 2019 |
| Last update date |
May 01, 2019 |
| Contact name |
Javed Khan |
| E-mail(s) |
khanjav@mail.nih.gov
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| Phone |
2407606135
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| Organization name |
NCI, NIH
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| Department |
Genetics Branch
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| Lab |
Javed Khan
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| Street address |
37 Convent Dr.
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE129407 |
Gene Specific Activation Driven by Small Molecules |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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