|
| 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.
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| |
|
| 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 |
Global Computational Biology and Digital Sciences
|
| 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 |
