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Sample GSM4802690 Query DataSets for GSM4802690
Status Public on Sep 15, 2022
Title ChIP_sgBRD8_H3K27ac
Sample type SRA
Source name glioblastoma
Organism Homo sapiens
Characteristics cell line: A382 expressing cas9 and sgBRD8
treatment: Stable cell line was generated by infecting A382 with FLAG-cas9 and sgBRD8 lentivirus
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
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
BioSample SAMN16261195
SRA SRX9187736

Supplementary file Size Download File type/resource 365.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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