|
| Status |
Public on May 15, 2018 |
| Title |
U87_BRD4_dBET6_500nM_24h |
| Sample type |
SRA |
| |
|
| Source name |
U87-MG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87 GBM
treatment: dBET6
antibody (catalog): BRD4 (Bethyl, A301-985A)
treatment_duration_in_hours: 24
|
| Growth protocol |
U87 cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw fastq files were aligned to human gneome using bowtie (VN:1.1.2) and duplicates were removed using picard. Alignent parameters and source code here: https://gist.github.com/PoisonAlien/f95e176ad9f2b07938bd36a37be32ebe
Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01 Source code here: https://gist.github.com/PoisonAlien/aeb9506d4cab20cbe11accb19feb9240Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01 Source code here: https://gist.github.com/PoisonAlien/aeb9506d4cab20cbe11accb19feb9240
Bedgraph files generated by MACS2 were converted to bigWig files using ucsc bedGraphToBigWig tool.
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million. NarrowPeak files indicating peaks detected by MACS2
|
| |
|
| Submission date |
May 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Phillip H Koeffler |
| E-mail(s) |
phillip_koeffler@nuhs.edu.sg
|
| Organization name |
Cancer Science Institute
|
| Lab |
H. Phillip Koeffler's lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE99171 |
Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [ChIP-seq] |
| GSE99183 |
Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy NA-seq (time course) May 15, 2018 approved TSV |
|
| Relations |
| BioSample |
SAMN07152408 |
| SRA |
SRX2841180 |
