|
| Status |
Public on Jul 13, 2017 |
| Title |
K562_JQ1-TCO+JQ1 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
tissue: bone marrow
clickable molecule: JQ1–TCO
competitor molecule: JQ1
|
| Growth protocol |
MV4;11 cells were grown in RPMI-1640 supplemented with 20% FBS, penicillin (100 U/mL), streptomycin (100 µg/mL). K562 cells were grown in MEM medium supplemented with 1% pyruvate, 1% NAA and 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysate were isolated from formaldehybe cross-linked cells and digested with micrococcal nuclease to mononucleosomes, then incubated with the clickable molecule with/without competitor. Chem-precipitation was performed with pre-clicked biotin-tetrazine conjugated beads
NEBNext ChIP-seq library prep master mix set
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
K616-530
|
| Data processing |
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files from MACS2 for each sample
|
| |
|
| Submission date |
Oct 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE88749 |
Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [Click-Seq 2] |
| GSE88751 |
Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies |
|
| Relations |
| BioSample |
SAMN05908462 |
| SRA |
SRX2245528 |
