|
Status |
Public on Aug 15, 2022 |
Title |
MOLM13_DMSO_ENL |
Sample type |
SRA |
|
|
Source name |
MOLM-13
|
Organism |
Homo sapiens |
Characteristics |
cell line: MOLM-13 cell type: acute myeloid leukemia chip antibody: ENL (Cell Signaling Technology, #14893)
|
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.
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|
|
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
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|
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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 |
SAMN30266054 |
SRA |
SRX17033747 |