The ChIP-seq data generated by this study are available for download from GEO under accession GSE47991.
We also used RNA-seq, DNase-seq, and MNase-seq data from previous studies, which can be downloaded from GEO under accessions: GSE19480, GSE31388 and GSE36979.
Note that GEO does not make the fastq files available for download. To obtain fastq files you will need to download the SRA files, and convert them using the fastq-dump utility from NCBI's SRA-toolkit.
A subset of the input files we used to run the combined haplotype test are here (includes read counts, genotypes, etc.). If you need the complete set of input files, please let us know (they are quite large).
Results from applying the combined haplotype test genome-wide are here (includes histone modification and Pol2 QTLs at different FDR thresholds).
For questions or to request code or additional data please contact
Graham McVicker (email@example.com), Bryce van de Geijn (firstname.lastname@example.org),
Yoav Gilad (email@example.com), or Jonathan Pritchard (firstname.lastname@example.org).