|
| Status |
Public on Jan 08, 2018 |
| Title |
TAF2-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
murine MLL-AF9/NrasG12D AML
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RN2
cell types: wt cells
chip antibodies: A302-131, Behtyl
strain: C57BL/6
|
| Treatment protocol |
For FLAG-TAF12 ChIP-seq in dox-regulated shREN and shMYB.2652 cells, cells were treated with doxycycline for 24 hrs. Cell cultures were collected and cross-likned with formaldehyde at room temperature for 15 mins.
|
| Growth protocol |
RN2 cells derived from MLL-AF9/NrasG12D AML mouse model were cultured in RPMI with 10%FBS and P/S.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cross-link, cells were incubated with cell lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40) and then resuspended and sonicated in nuclei lysis buffer (50mM Tris pH8.0, 10mM EDTA, 1%SDS) for 15mins, followed by ChIP
Library was constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture’s protocol. Briefly, ChIP DNA was end repaired, followed by A tailing and size selection (250-500 bp) by gel electrophoresis. 15 PCR cycles were used for final library amplification and the library was analyzed on Bioanalyzer using high sensitivity DNA chip (Agilent) on Bio-analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
50bp single end sequencing reads were mapped to mm9 genome using Bowtie with 2 mismatches allowed
PCR duplicates were removed from sequencing reads using SAMTools.
MACS 1.4.2 was used to call peaks with input genomic DNA as control with other default parameters: 1e-05 Pvalue cutoff for peak detection, 10-30 within MFOLD range
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files converted from wiggle file generated from MACS peaks calling
|
| |
|
| Submission date |
Sep 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yali XU |
| E-mail(s) |
yxu@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE104307 |
A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia (ChIP-seq) |
| GSE104309 |
A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN07709334 |
| SRA |
SRX3219121 |
