Supplementary Captions and Legends

Supplementary captions and legends

Fig. S1. ChIP qPCR validation of FDR<10 Hoxa2-bound regions.

Fold enrichment of Hoxa2 over IgG negative control antibody (Neg Ab) is shown for each Hoxa2-bound region. Values represent the average of duplicate samples and are adjusted to the average enrichment of Pou6f2 from two independent experiments. Itih4 is a negative control (unbound region). For each sample the standard error of the mean is indicated by error bars. The dotted line represents a threshold of 2-fold or higher significant enrichment.

Fig. S2. Correlation between FDR and fold enrichment.

The FDR and fold enrichment values relative to the set of Hoxa2-bound regions analyzed by ChIP qPCR are displayed in a scatter plot. The trend line suggests a negative correlation between the increase of FDR and the fold enrichment in Hoxa2-bound regions.

Supplemental Table S3

Detailed information for the Hoxa2 binding regions identified by ChIP-seq analysis. The binding regions shown are FDR<10 and are ordered by P-value significance (transformed by -10log10 of P-value; highest number is most significant) and fold enrichment. Details generated by MACS are shown together with information on RefSeq genes that are associated with each binding region. A gene is associated with a binding region that overlaps with the body of its transcript (indicated in column V), its promoter region (-10 kb to +2.5 kb of the TSS; indicated in column U) or failing that, the closest gene (indicated in column N). Detailed figure legends are included in the Supplemental spreadsheet.

Fig. S4. De novo motif discovery in sequences flanking Hox and Pbx-Hox binding sites. Over-representation of motifs within the 100 nt flanking each TGATNNAT and TAAT (as indicated). The occurrence of TGACAG and AATTA in Hoxa2 bound regions was significantly higher than expected (P values= 1.80E-025 and 0.0286, respectively).

Supplemental Table S5

List of genes reported as regulated by Hoxa2 during embryonic development. For each gene, the embryonic area where regulation has been shown to occur, the relative reference, the coordinates of the Hoxa2-bound regions associated, and their relative distance to the gene are shown. The distance is expressed as a negative or a positive number to indicate the distance in nucleotides between the closest edge of the region and the transcription start site or the transcription stop site of the associated gene, respectively.

Supplemental Table S6

Up- and down regulated genes associated with Hoxa2-bound regions. For each class, genes are ranked alphabetically using gene symbols. The number of Hoxa2 bound regions associated with each gene are shown, along with the fold change for any corresponding probe sets. Differentially expressed genes were selected by applying the following cut-offs to the probe sets: average fold difference above 1.3; highest expression value above 20; P value below 0.05.

Supplemental Table S7

List of primer sequences used in ChIP qPCR.