Supplementary Information and Datafiles for  ChIP-Seq samples

ChIP-Seq Sample Information: 
We have performed a number of ChIP-Seq assays for blood transcription factors.  The relevant datafiles can be downloaded below:

Files for download (Wilson et al 2009):  
Supplementary Tables for Wilson et al 2009:              download

Files for download (Wilson et al 2010):  

Wig Files:

The files below can be used to display CHIP-Seq read density profiles in genome browsers.

ChIP-Seq density profile (wig file) for IgG  control:
     download

ChIP-Seq density profile (wig file) for H3Acet:             download

ChIP-Seq density profile (wig file) for Scl (Part1):        download

ChIP-Seq density profile (wig file) for Scl (part2):        download

ChIP-Seq density profile (wig file) for Lyl1:                  download

ChIP-Seq density profile (wig file) for Lmo2:                download

ChIP-Seq density profile (wig file) for Gata2:               download

ChIP-Seq density profile (wig file) for Runx1:               download

ChIP-Seq density profile (wig file) for Pu.1:                  download

ChIP-Seq density profile (wig file) for Erg:                    download

ChIP-Seq density profile (wig file) for Fli1:                    download

ChIP-Seq density profile (wig file) for Meis1:                download

ChIP-Seq density profile (wig file) for Gfi1b:                 download



ChIP-Seq Peak Table:

The table below contains ChIP-Seq peak coordinates that represent the intersection of 3 peak finding programs (MACS, PeakSeq and FindPeaks). All peak regions have been set to 399 bp centred around the peak summit called by MACS.  The control IgG ChIP-Seq sample was used by MACS and PeakSeq as negative control when scoring significant peaks.

Peak coordinates for all 10 transcription factors:
        download



Peak to Gene Mapping:

Entries in the following tables are not unique because a peak can "map" to more than one gene (if it is intergenic) and a gene locus can contain multiple peaks. The tables contain 7 columns (chromosome, peak start, peak end, gene start, gene end, Refseq gene identifier, Gene Name).

Scl complete peak to gene mapping:
                          download

Lyl1 complete peak to gene mapping:                         download

Lmo2 complete peak to gene mapping:                       download

Gata2 complete peak to gene mapping:                      download

Runx1 complete peak to gene mapping:                      download

Pu.1 complete peak to gene mapping:
                        download

Erg complete peak to gene mapping:                           download

Fli1 complete peak to gene mapping:                           download

Meis1 complete peak to gene mapping:                       download

Gfi1b complete peak to gene mapping:                        download



Candidate Target Genes:

The table below contains candidate target genes for all 10 TFs.  These lists were generated by simplifying information from the "Peak to Gene Mapping" tables above so that each gene is only represented once.

Candidate target gene list table:
                               download



Supplementary Tables:

Summary TF -> target gene list:
                                 download
(Gene names followed by 10 columns indicating
whether the gene locus has a TF ChIP-Seq peak)
 
Genes next to  heptad-bound peaks:                          download


Ontology analysis of genes with heptad peaks:          download


Genes next to peaks bound by Gata2 and Runx1:       download


Heptad-bound peaks lacking Runx/E-box motifs:
         download
(Peak coordinates and names of neighbouring 
genes for heptad peaks lacking Runx and E-box motifs)

Contact details:  for any further information, please contact:


Dr Nicola Wilson

Lab. 6.15, Department of Haematology, 
Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 0XY

Tel. 01223 336822

E-mail: nkw22@cam.ac.uk

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