Supplementary Data for Cheng et al. (Genome Research)


qPCR validation results & qPCR primers

Quantitative real-time PCR assays were conducted with the un-amplifed ChIP DNA to test the quality of the GATA-1 binding hits generated by the ChIP-chip. All the primers and the corresponding q_PCR results for the tested GHPs are shown in the attachment.


Browser view of the Data

Custom tracks for data mentioned in the paper were uploaded onto UCSC genome browser. A list of all the GHPs (both high and low stringent sets) with the corresponding "Phastcon score","RP score" are shown on the left column.


Enhancer activity assay results

This sorted box plot shows the enhancer activity distribution of all the GHPs in the high stringent threshold set. For each GHPs, each individual measurement of the enhancer activity are shown in the supplementary data file.


Phylogenetic depth of conservation

The multiz alignments of each region were drawn using R. For each species, a diagram of the aligned sequence shows thin lines for internal gaps, represented by '-' in the alignment text, thick rectangles for the sequence, and empty space in blocks where the species does not align. Alignment blocks are drawn consecutively by position of the mouse (mm8) sequence; the x-axis shows the text position within the concatenated blocks. Alignment blocks are colored with a grey scale in proportion to the relative alignment score per column in each image. The grey scale is intended to highlight distinction between blocks by relative conservation, but is scaled for each alignment and may not be comparable between images. Sequence matches to the motif WGATAR are highlighted in gold, and are generally considered conserved if they share the same position on the x-axis between species.