|
| Status |
Public on Dec 02, 2013 |
| Title |
ChIP_H3K27ac_RN2 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF9/NrasG12D murine cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MLL-AF9/NrasG12D AML cell line
treatment: none
chip antibody: anti-H3K27ac (Abcam, ab4729, GR104852-1)
|
| Treatment protocol |
Cells were treated with DMSO or nothing before crosslining. In brief, cells were crosslinked using 1% formaldehyde for 20 min at room temperature.
|
| Growth protocol |
Murine AML cell line was cultured in RPMI1640 supplement with 10% FBS and penicillin/streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. The chromatin extracts containing DNA fragments with an average size of 500 bp were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
All protocols for Illumina/Solexa sequence preparation, sequencing and quality control are provided by Illumina (http://www.illumina.com/pages.ilmn?ID=203).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all ChIP-Seq samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2 --best --sam. Seed length (-l) was set to read length for each dataset.
Genome_build: mm8
Supplementary_files_format_and_content: Supplementary_files_format_and_content: WIG files: For all ChIP-Seq samples, wiggle files were produced by MACS 1.4 with --space=50.
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher R Vakoc |
| Organization name |
Cold Spring Harbor Lab
|
| Lab |
Vakoc Lab
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE52277 |
Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation [ChIP-Seq] |
| GSE52279 |
Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation |
|
| Relations |
| BioSample |
SAMN02401329 |
| SRA |
SRX376586 |
