|
| Status |
Public on Oct 30, 2014 |
| Title |
MLL-AF9_UNC1999_H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF9-puro transformed murine leukemia cell line
|
| Organism |
Mus musculus |
| Characteristics |
treatment: UNC1999
chip antibody: H3K27ac (Abcam 4729)
|
| Treatment protocol |
Cells were treated with 3μM of the indicated compounds for 4 days, followed by ChIP-seq preparation.
|
| Growth protocol |
Transformed murine leukemia progenitor cell lines were cultured in Opti-MEM base medium supplemented with 10% FBS, 1% antibiotics, 50 μM mercaptoethanol, and stem cell factor (SCF)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone (or PRC2)-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP
|
| Data processing |
All reads were mapped to the mouse genome (mm9) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute) and the Integrative Genomics Browser (IGB, Affymetrix).
The MACS software was used for peak identification with data from input as controls and default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows
|
| |
|
| Submission date |
Oct 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bowen Xu |
| E-mail(s) |
bowenx@email.unc.edu
|
| Phone |
919-966-5953
|
| Organization name |
UNC-Chapel Hill
|
| Department |
Biochemistry and Biophysics
|
| Lab |
Wang
|
| Street address |
450 West Drive, CB7295, Lineberger Cancer Center, GREG WANG Lab, RM 31-331
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE62437 |
An Ezh2 and Ezh1 dual inhibitor, UNC1999, re-shapes the landscape of H3K27me3 versus H3K27ac in MLL-AF9-transformed murine leukemia |
|
| Relations |
| BioSample |
SAMN03113109 |
| SRA |
SRX734393 |
