Allday Lab ChIP-seq data

FLAG-tagged EBNA3 ChIP experiments (Acc No: GSE59181).

The first set of ChIP-seq data were generated by the Allday laboratory, published in Paschos et al NAR 45:2368-83 (2017). Original read data and called peaks are available from GEO (accession GSE88729). The Experimental approach is to use LCLs established with viruses encoding C-terminally FLAG-tagged EBNA3A or EBNA3C or N-terminally FLAG-tagged EBNA3B to ChIP with the anti-FLAG antibody. This same antibody ChIPped in untagged LCLs is used as a negative control. BAM files were not held on GEO so the Donor 11 BAM files can be accessed here. In order to view them on UCSC viewer, please copy the entire link shown in green below to upload the tracks into the genome browser. Please note that the tracks are aligned to human genome version 19 (hg19) so set the viewer up accordingly. The tracks are best viewed with display mode: full; select display as density graph (type: bar). Use either auto-scale or a viewing range maximum of 50 (higher for regions with tall peaks) to best view the data.

EBNA3A-FLAG-D11: track type=bam name=“EBNA3A-FLAG" description=“EBNA3A-FLAG-D11” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA3A-FLAG.bam
FLAG-EBNA3B-D11: track type=bam name=“EBNA3B-FLAG" description=“EBNA3B-FLAG-D11” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA3B-FLAG-merged.bam
EBNA3C-FLAG-D11: track type=bam name=“EBNA3C-FLAG" description=“EBNA3C-FLAG-D11” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA3C-FLAG.bam
Untagged EBV D11: track type=bam name=“WT-D11" description=“WT-D11-FLAG_-ve-ctrl” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/WT-D11.bam
Processed files with significant peaks called can be viewed by pasting the following URLs into the custom track window:
http://www.epstein-barrvirus.org.uk/ChIPseq2/3A-D11-peaks.txt
http://www.epstein-barrvirus.org.uk/ChIPseq2/3A-D13-peaks.txt
http://www.epstein-barrvirus.org.uk/ChIPseq2/3B-D11-peaks.txt
http://www.epstein-barrvirus.org.uk/ChIPseq2/3C-D11-peaks.txt
http://www.epstein-barrvirus.org.uk/ChIPseq2/3C-D13-peaks.txt

West Lab ChIP-seq data
These next ChIP-seq data files were generated by Michelle West's lab (University of Sussex) using shep anti_EBNA3C antibody that cross reacts with all the EBNA3s (panEBNA3), anti-EBNA2 and anti-RBPJ antibodies.
http://www.epstein-barrvirus.org.uk/ChIPseq2/panEBNA3-West.txt
http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA2-WestPeaks.txt
http://www.epstein-barrvirus.org.uk/ChIPseq2/rbpj_peaks.txt

Kieff Lab ChIP-seq data
These next ChIP-seq data files were generated from data produced in Elliott Kieff's laboratory (For EBNA3A data cite: Schmidt et al. PNAS 112:554(2014) and for EBNAC data cite: Jiang et al. PNAS 111:421 (2014)) using HA-tagged EBNA-3A or EBNA3C expressed from the viral genome in LCLs. The files are bigWig (3A) or bam (3C) files. In order to view them on UCSC viewer, please copy the entire link shown in green below to upload the tracks into the genome browser. Please note that the tracks are aligned to human genome version 18 (hg18) so set the viewer up accordingly.

EBNA3A-HA experiments (Acc No: GSE59181).
3A-Replicate 1 (GSM1429820): track type=bigWig name=“EBNA3A-HA_Rep1" description=“EBNA3A-HA_Rep1” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA3A_Rep1.bw
3A-Replicate 2 (GSM1429821): track type=bigWig name=“EBNA3A-HA_Rep2" description=“EBNA3A-HA_Rep2” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA3A_Rep2.bw

EBNA3C-HA experiments (Acc No: GSE52632).
3C-Replicate 1 (SRR1035616): track type=bam name=“EBNA3C-HA_Rep1" description=“EBNA3C-HA_Rep1” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA3C_Rep1.sorted.bam
3C-Replicate 2 (GSM1429821): track type=bam name=“EBNA3C-HA_Rep2" description=“EBNA3C-HA_Rep2” bigDataUrl=http://www.epstein-barrvirus.org.uk/ChIPseq2/EBNA3C_Rep2.sorted.bam

If any other researchers would like to send tracks (or links to those tracks) here, so that I can expand this resource, please contact me..


Other resources:

Click to access our 2015 review of the EBNA3 proteins and our EBNA3 review in memory of Martin Allday.
You will be able to find EBV ChIP-seq data here. The range of tracks will be expanded as development time allows.
You will be able to browse our EBV microarray data here.
The EBV genome annotation map is maintained by Prof Paul Farrell.