|
| Status |
Public on Apr 17, 2018 |
| Title |
BRD4_ChIPseq_1b |
| Sample type |
SRA |
| |
|
| Source name |
B-Chronic Lymphocytic Leukemia (CLL) cels
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary B-CLL cells
protocol: 4 hours stimulation with 3.2uM of CpG oligonucleotide
chip-antibody: BRD4 (Active Motif #A301-985A1)
|
| Treatment protocol |
a=baseline; b=4 hours stimulation with 3.2uM of CpG oligonucleotide; c=4 hours stimulation with 3.2uM of CpG oligonucleotide + 1 uM of BET inhibitor (PLX51107)
|
| Growth protocol |
RPMI 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
extract_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
0007Ohio_CLL_BRD4_2nd_actregs.xlsx
02_0007Ohio_CLL_Patient_1b_BRD4_hs_i82
|
| Data processing |
ChIP-seq reads from samples 1 and 2 were mapped to the human reference genome (GRCh37/hg19) using the bwa-0.6.1 with default parameters. Aligned and unaligned reads and their quality strings are contained in resulting bam files. Therefore, bam files are provided as raw data
ChIP seq reads from samples 3 and 4 were mapped to the human reference genome (GRCh37/hg19) using the bwa-0.7.12 with default parameters. Aligned and unaligned reads and their quality strings are contained in resulting bam files. Therefore, bam files are provided as raw data
Peak locations for BRD4 and H3K27 ChIP experiments were determined using the MACS -1.4.2 with a cutoff p-value of 1E-7 for narrow peaks and 1E-1 for broad peaks
Enriched regions for Pol2 ChIP experiments were identified using the SICER algorithm with a cutoff FDR of 1E-10 and gap parameter of 600bp
ChIP peak regions from multiple samples (of the same ChIP type) were merged, and aligned reads for these newly defined regions were caluclated (even for those where no peak was called). Then the resulting regions were annotated with gene information by calculating distances from RefSeq gene starts and ends to the center of the newly defined peak regions.
ATAC-seq reads were mapped to the human reference genome (GRCh37/hg19) using the Bowtie2-2.2.6 with maximum fragment length of 1000 and no-mixed mode. Duplicates marked with Picard-1.140.
DNase2hotspots software package (https://sourceforge.net/projects/dnase2hotspots) was used to identify hotspots (enriched regions) from ATAC-seq
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Combined peak regions and scores of ChIP data are in Microsoft Excel files
Supplementary_files_format_and_content: ATAC-seq hotspots are reported in form of bedgraphs
|
| |
|
| Submission date |
Jan 19, 2018 |
| Last update date |
Apr 17, 2018 |
| Contact name |
Hatice Gulcin Ozer |
| E-mail(s) |
ozer.9@osu.edu
|
| Phone |
614-366-1538
|
| Organization name |
The Ohio State University
|
| Department |
Biomedical Informatics
|
| Street address |
1800 Cannon Dr
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE109411 |
BRD4 profiling identifies critical Chronic Lymphocytic Leukemia oncogenic circuits and reveals sensitivity to PLX51107, a novel structurally distinct BET inhibitor [ChIP-seq] |
| GSE109593 |
BRD4 profiling identifies critical Chronic Lymphocytic Leukemia oncogenic circuits and reveals sensitivity to PLX51107, a novel structurally distinct BET inhibitor |
|
| Relations |
| BioSample |
SAMN08378917 |
| SRA |
SRX3591429 |
