|
| Status |
Public on Apr 09, 2022 |
| Title |
OCIAML2 Runx1R174*/wt 100nM HHT ChIP-Brd4 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured AML Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 100 nM HHT, 16hr
tissue: human Acute Myelogenous Leukemia (AML), M4
chip antibody: BRD4 rabbit monoclonal [ clone BL-149-2H5] (Bethyl Labs) catalog #A700-004 RRID:AB_2631885
|
| Treatment protocol |
1 x 10^7 Human AML cells were treated for 16 hours with DMSO or 100 nM of HHT.
|
| Growth protocol |
Culture human AML cells were cultured in 20% FBS containing alpha-MEM media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AML cells (10 million) were treated with 1% formaldehyde for 10 minutes with rotation. The crosslinking reaction was quenched with 2.5 M Glycine for 5 minutes. Chromatin lysates were clarified from ultra-sonicated nuclei and histone-DNA complexes or BRD4-containing complexes were isolated with H3K27Ac or BRD4 antibody, respectively. Following ChIP washes, the immunoprecipitated DNA fragments were treated with mutant Tn5 transposase for 10 minutes at 37°C to attach sequencing adapters to the DNA. Tagmented DNA was eluted and formaldehyde-induced crosslinks were reversed. Tagmented, eluted DNA was purified over a column and utilized for library preparation.
ChIP-Seq libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 12-15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
cut adapter by trim_galore (0.6.5)
aligment by bowtie2 (2.3.4.2)
remove duplicates by PICARD (2.9.0)
peak calling by MACS2 (2.1.2)
differential open region by diffReps.pl (5.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: macs2 called peaks
|
| |
|
| Submission date |
Aug 12, 2021 |
| Last update date |
Apr 10, 2022 |
| Contact name |
Yuan Qi |
| E-mail(s) |
yqi1@mdanderson.org
|
| Organization name |
University of Texas M.D. Anderson Cancer Center
|
| Department |
Bioinformatics & Computational Biology
|
| Street address |
1400 Pressler St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030-4008 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE182006 |
Effective therapy of AML with RUNX1 mutation by co-treatment with inhibitors of protein translation and BCL2 [ChIP-seq] |
| GSE182023 |
Effective therapy of AML with RUNX1 mutation by co-treatment with inhibitors of protein translation and BCL2 |
|
| Relations |
| BioSample |
SAMN20749710 |
| SRA |
SRX11730624 |
