|
| Status |
Public on Mar 27, 2012 |
| Title |
RUNX1_non-t(8;21)_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood MNC CD34+ from non-t(8;21)AML patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood MNC CD34+
target: RUNX1
antibody: ab23980 (lot number728911)
|
| Treatment protocol |
Mononuclear cells were prepared from samples by differential centrifugation using Lymphoprep (Axis-Shield UK, Cambridgeshire, UK), and CD34+ blast cells were then isolated using MACS Micro Beads staining and separation on magnetic columns according to the manufacturer's guidelines. Purity of CD34+ cells was >85%.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries of DNA fragments from chromatin immunoprecipitation or DNase I treatment were prepared from approximately 10ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer's guidelines). "A" bases were added to 3' ends of fragments using Klenow Fragment (3' - 5' exo- ), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18 cycle PCR reaction using adapter-specific primers The libraries were purified and adapter dimers removed by running PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Peaks: Peak finding analysis was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) using hg18
|
| |
|
| Submission date |
May 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Salam Adli Assi |
| E-mail(s) |
s.a.assi@bham.ac.uk
|
| Organization name |
University of Birmingham
|
| Department |
Institute for Cancer and Genomic Sciences
|
| Street address |
IBR
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE29222 |
Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding [ChIP-Seq and DNAse-Hypersensitivity data] |
| GSE29225 |
Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding |
|
| Relations |
| SRA |
SRX062339 |
| BioSample |
SAMN00265093 |
