|
| Status |
Public on Aug 15, 2022 |
| Title |
HL60_DMSO_H3K18ac |
| Sample type |
SRA |
| |
|
| Source name |
HL60
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HL60
cell type: acute myeloid leukemia
chip antibody: H3K18ac (EMD Millipore, #07-354)
|
| Treatment protocol |
Cells were treated with 3 µM A-485 or DMSO for 2 hours.
|
| Growth protocol |
MOLM-13 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin. HL-60 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fixed numbers of mouse or drosophila cells were spiked-in to treated cells. Cells were then lysed. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared with Takara ThruPLEX® DNA-Seq Kit (Cat. No. R400674) according to manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Sequenced reads were aligned to hg19 and either mm9 or dm3 reference genomes with bowtie2 using default parameters except for 'k -1'.
Alignment files were sorted and indexed with Samtools -sort and -index.
Peaks were called using MACS (1.4.2) with p-val = 1e-9 cutoff used.
Bedgraphs were made from bams using Bedtools genomecov with -bg option.
Read density was calculated using Bamliquidator (v1.0, http://github.com/BradnerLab/pipeline/wiki/bamliquidator) and were normalized by dividing by the number of reads that aligned to the spike-in (mm9 or dm3) genome.
Assembly: hg19
Supplementary files format and content: bedgraph files and bed files of MACS peaks
|
| |
|
| Submission date |
Aug 11, 2022 |
| Last update date |
Aug 15, 2022 |
| Contact name |
Michael Erb |
| E-mail(s) |
michaelerb@scripps.edu
|
| Phone |
858-784-7034
|
| Organization name |
The Scripps Research Institute
|
| Department |
Department of Chemistry
|
| Street address |
10650 N Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE211051 |
Metabolic adaptations underpin resistance to histone acetyltransferase inhibition [ChIP-seq] |
| GSE211054 |
Metabolic adaptations underpin resistance to histone acetyltransferase inhibition |
|
| Relations |
| BioSample |
SAMN30266046 |
| SRA |
SRX17033755 |
