NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4802681 Query DataSets for GSM4802681
Status Public on Sep 15, 2022
Title ChIP_H3K27ac
Sample type SRA
 
Source name glioblastoma
Organism Homo sapiens
Characteristics cell line: A382
treatment: none
chip antibody: H3K27ac (Abcam, Ab4729)
Treatment protocol For BRD8 ChIP-seq, A382 cells were infected with BRD8 cDNA with fusion to triple FLAG
Growth protocol A382 cells were cultured in DMEM with 10% FBS and penicillin/streptomycin
Extracted molecule genomic DNA
Extraction protocol Cell lysates were clarified from sonicated nulcei; BRD8, p53, and histone-DNA complexes were isolated with Flag or histone antibody.
Libraries were constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, 50 µl of ChIP DNA was end-repaired, 3’-adenyl tailed, and then ligated with different index adaptors. The adaptor-ligated DNA was size selected (250-300 bp) using agarose gel electrophoresis, followed by PCR amplification. The amplified DNA was purified with AMPure XP beads (Beckman Coulter).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Sequence reads were mapped into reference human genome hg19 by using Bowtie2.
Peakcaling was done by using MACS2 FDR cutt off 5% with narrow peak and broad peak option for BRD8, p53, and histones seperately.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
 
Submission date Sep 24, 2020
Last update date Sep 15, 2022
Contact name Olaf Klingbeil
E-mail(s) klingbe@cshl.edu
Organization name Cold Spring Harbor Laboratory
Street address 1 Bungtown Road
City Cold Spring Harbor
State/province New York
ZIP/Postal code 11724
Country USA
 
Platform ID GPL18573
Series (2)
GSE158549 BRD8 maintains glioblastoma by epigenetic reprogramming of the P53 network [ChIP-seq]
GSE158551 BRD8 maintains glioblastoma by epigenetic reprogramming of the P53 network
Relations
BioSample SAMN16261204
SRA SRX9187727

Supplementary file Size Download File type/resource
GSM4802681_ChIP_H3K27ac.bw 128.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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