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| Status |
Public on Feb 05, 2016 |
| Title |
M-BRPF3 |
| Sample type |
SRA |
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| Source name |
human colon carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: RKO
synchronisation: mimosine 0.5mM for 22h
chip antibody: homemade rabbit BRPF3 (from X-J Yang, McGill univ)
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| Treatment protocol |
no treatment (AS), synchronisation: mimosin 0.5mM 22h (M), cells released 3h and HU 3mM treated 1h30 (M+HU)
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| Growth protocol |
DMEM, 10% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . 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 library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
BRPF1/2 ChIP-seq in RKO cells
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| Data processing |
Raw sequences were mapped using Bowtie version 0.12.8 on build hg18 or hg19 of the human genome . BPRF1/2 and input data were previously deposited under accession numbers GSE47190 and GSE33221 (Avvakumov et al. 2012; Lalonde et al. 2013). Read alignments in sam format were converted to bam files using samtools [PMID : 19261174]. Samtools was then successively applied to remove duplicated reads, sort, and index bam files. Peak calling was performed using MACS version 1.4.0 by comparing AS-Brpf3, HU-Brpf3 and M-Brpf3 to M-HU IgG and Brpf1/2 to the signal from the input[PMID : 18798982]. We identified intersection between two sets of significant peaks in hg19 coordinates using bedtools “intersect” function [PMID : 20110278]. In case where we needed to compare hg18 and hg19 peaks, we used the liftover tool from the UCSC genome browser to convert hg18 into hg19 coordinates [PMID 12045153]. The ORC1 ChIP-seq data used for comparison was obtained from Dellino et al. Genome Res 2013 (GSE37583). We used the Bioconductor package VennDiagram [PMID:21269502] to display the overlaps between the different experiments and IGV for ChIP-seq signal visualization in genomic context [PMID:22517427].
genome build: hg19
processed data files format and content: bw, bed
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| Submission date |
Dec 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric R Paquet |
| Organization name |
EPFL
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| Department |
Life sciences
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| Lab |
Naef lab
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| Street address |
Station 15 CH - 1015
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| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE63722 |
ChIP-seq of MYST acetyltransferases in RKO cell line |
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| Relations |
| BioSample |
SAMN03252684 |
| SRA |
SRX796085 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1556188_HI.2080.001.Index_5.M-BRPF3.bam.hg19.rpm.bw |
279.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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