|
| Status |
Public on Dec 06, 2017 |
| Title |
BRD4_IP_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
GM15850 LCLs (FRDA)
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: BRD4
cell line: GM15850 LCLs (FRDA)
treatment: 0.1% DMSO
treatment time: 24 h
|
| Treatment protocol |
GM15850 cells were treated with the indicated molecules for 24 h
|
| Growth protocol |
RPMI 1640 Medium with 2 mM L-glutamine and 15% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were chemically crosslinked by the addition of 4 mL of 1.5% formaldehyde in PBS per 10 cm2 dish for 15 min at room temperature. Cells were resusupended in Lysis Buffer 1 (50 mM HEPES , pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL, 0.25% Triton X-100, 1X HALT protease inhibitor) and 3T3 mouse embryonic fibroblast cells (formaldehyde fixed as above) equivalent to 10% GM15850 cells were added to each sample for downstream ChIP-RX analysis.
NGS libraries were generated with Thruplex DNAseq Single Index Kit (Rubicon) and sequenced (single end, 150 bp reads) via NextSeq 500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
n/a
Genome_build: Human: GRCh37 (hg19) Mouse: mm9
|
| |
|
| Submission date |
May 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Aseem Ansari |
| Organization name |
University of Wisconsin-Madison
|
| Department |
Biochemistry and The Genome Center
|
| Lab |
Ansari
|
| Street address |
440 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE99402 |
ChIP-RX of GM15850 cells treated with synthetic transcription elongation factors |
| GSE99403 |
Synthetic transcription elongation factors |
|
| Relations |
| BioSample |
SAMN07176164 |
| SRA |
SRX2867630 |
