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Sample GSM3814486 Query DataSets for GSM3814486
Status Public on May 05, 2021
Title H3K27Ac contol
Sample type SRA
 
Source name Head and neck squamous cell carcinoma cells
Organism Homo sapiens
Characteristics agent: contol
cell line: SCC1
chip antibody: H3K27Ac rabbit antibody (Abacm, cat#ab4729)
Treatment protocol SCC1 cells were treated with 500nM JQ1 or with control for 24 hours.
Growth protocol 10% FBS in DMEM
Extracted molecule genomic DNA
Extraction protocol ChIP was performed uing EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Sigma, Cat#17-10086). 10–50 ng of ChIP DNA for each sample was sonicated and used for the ligation of barcoded Kapa adapters.
Sequencing libraries were generated using a KAPA Hyper DNA Kit (KAPA Biosystems, Cat# KK8503)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Description H3K27Ac contol
Data processing Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.2.0.
The unique mapped reads was used for peak calling by MACS2 with default setting
Supplementary_files_format_and_content: bedGraph files and big wig files
 
Submission date May 23, 2019
Last update date May 06, 2021
Contact name Jiong Li
E-mail(s) jli29@vcu.edu
Phone 3105617186
Organization name VCU
Street address 800 E Leigh Street, suite 212
City Richmond
State/province Virginia
ZIP/Postal code 23298
Country USA
 
Platform ID GPL21290
Series (1)
GSE131710 ChIP-seq analysis of BRD4, MED1 and P65 in SCC1 cells after JQ1 treatment
Relations
BioSample SAMN11841053
SRA SRX5888988

Supplementary file Size Download File type/resource
GSM3814486_H3K27Ac-con.bw 200.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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