 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 24, 2017 |
| Title |
THP-1_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: AML cell line
translocation: MLL-AF9
|
| Growth protocol |
Cell lines were routinely cultured in RPMI 1640 supplemented with 10% FCS and 1% pen/strep at 37 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from cell lines was harvested and ChIPs were performed as described (Mandoli A, GDATA, 2014). Total RNA was extracted with TRIzol (Invitrogen) or RNAsol (GenDepot), treated with DNAse on column (Qiagen) and analyzed by strand specific sequencing.
ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, AF9, AF4, and RUNX1, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the Genome Analyzer (Illumina) or HiSeq 2000 (Illumina). For RNA-seq 250 ng of RNA was used for ribosomal RNA depletion with RiboZero (Illumina) and subsequent strand specific (USER) library preparation. 4C-seq libraries were prepared as previously described (Van de Werken, Nat. Meth., 2012)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Bases were called using the Illumina CASAVA 1.8.2
ChIP-seq: Tags were mapped using the Burrows-Wheeler Alignment Tool (BWA).
RNA-seq: Tags were mapped using TopHat2 (Bowtie2).
4C-seq: A reduced genome was generated by extracting the sequences flanking DpnII sites (30bp on each strand from the DpnII sites to downstream). Only uniquely mapped DpnII sites were considered for downstream analysis. Reads from each library were parsed based on the bait-specific primer sequence and mapped to the reduced genome using bwa (version 0.6.2) with the default parameters. 4C signal was calculated using a sliding window of 10Kb (±5Kb of a given DpnII site) and normalized to the total number uniquely mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 10 bp window. BedGraph files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 50 bp window
|
| |
|
| Submission date |
Apr 04, 2016 |
| Last update date |
Nov 11, 2021 |
| Contact name |
Joost Martens |
| E-mail(s) |
j.martens@science.ru.nl
|
| Phone |
0243780645
|
| Organization name |
Radboud University
|
| Department |
RIMLS
|
| Lab |
Molecular Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| State/province |
Nederland |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE79899 |
The MLL-AF9 and MLL-AF4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX1 program in MLLr AML |
|
| Relations |
| BioSample |
SAMN04606163 |
| SRA |
SRX1678068 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2108047_THP-1_H3K4me3.wig.gz |
56.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
