GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3814478 Query DataSets for GSM3814478
Status Public on May 05, 2021
Title Input control
Sample type SRA
Source name Head and neck squamous cell carcinoma cells
Organism Homo sapiens
Characteristics agent: control
cell line: SCC1
chip antibody: none
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 Input control
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 05, 2021
Contact name Jiong Li
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
BioSample SAMN11841047
SRA SRX5888980

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap