NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2716693 Query DataSets for GSM2716693
Status Public on Mar 02, 2018
Title ChIPseq_MV-4-11-B_BRD4_BI00894999_1000nM_4h_NA_NA_NA_rep1_J3756
Sample type SRA
 
Source name MV-4-11-B cells
Organism Homo sapiens
Characteristics method: ChIP-seq
chip antibody: BRD4 (Bethyl, #A301-985A50)
treatment: BI00894999, 1000nM, 4h
replicate: rep1
internal id: J3756
Treatment protocol The corresponding compounds (dissolved in DMSO) were added directly into cell culture media, and cells were kept at normal growth conditions for the treatment duration.
Growth protocol The cell lines were cultured with the media suggested by ATCC at 37 degree Celsius incubators with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 10 ng of ChIP material per sample. NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB #E6240L) and for the quantity measurement KAPA Library Quantification Kit (KapaBiosystems, #KK4824) was used according to the manufacturer’s instructions. 2 nM samples were multiplexed for sequencing.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description ChIPseq_MV-4-11-B_BRD4_BI00894999_1000nM_4h_NA_NA_NA_NA_J3756-J2596-J2605_peaks.tsv.gz
Data processing Base calling was performed using Illumina RTA 1.18.64, afterwards multiplexed samples were converted to FASTQ files using CASAVA 1.8.2 allowing for 1 mismatch in the index sequence. Technical replicates were merged in a single FASTQ files.
ChIP-seq: Reads were mapped to hg19 (canoncial chromosomes) using bowtie2 version 2.2.9, peaks calls were perfomed with MACS2 version 2.1.0. and HOMER HOMER version 4.7 on uniquely mapping reads by using the intersection of calls. Parameters for calling super-enhancers were set as described in the HOMER manual. Note, biological replicates were merged for all analysis reported in the paper.
RNA-seq: Reads were mapped to hg19 (hs37d5) with gsnap version 2012-12-20. The ENSEMBL 70 gene annotation was used for further expression estimations. Raw counts were computed using HTSeq version 0.5.3p9, FPKM expression values were estimated using Cufflinks version 2.0.2. Differential gene expression was computed using DESeq filtering out genes with less than 10 reads across the tested samples.
Quant-seq: Reads were filtered using BBMap version 36.27 and mapped to hg38 (hs38d1) with STAR version 2.5.2b. Raw read counting over genes loci was also performed using STAR. Differential gene expression was computed using DESeq2 filtering out genes with less than 10 reads across the tested samples.
Genome_build: hg19/hg38
Supplementary_files_format_and_content: All processed data files contain tab-separated values. Peaks call files contain positions of all peaks with associated statistics from HOMER. Differential gene expression files list all genes and attach associated statistics from DESeq/DESeq2.
 
Submission date Jul 24, 2017
Last update date May 15, 2019
Contact name Daniel Gerlach
E-mail(s) daniel.gerlach@boehringer-ingelheim.com
Organization name Boehringer Ingelheim RCV GmbH & Co KG
Department Cancer Research
Lab Bioinformatics
Street address Dr.-Boehringer-Gasse 5-11
City Vienna
ZIP/Postal code 1121
Country Austria
 
Platform ID GPL18460
Series (1)
GSE101821 The novel BETi BI 894999 represses super-enhancer associated transcription and synergizes with CDK9 inhibition in AML by induction of apoptosis
Relations
BioSample SAMN07411166
SRA SRX3031981

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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