Supplementary Figure 8: Identification and validation of Tbr1 target genes.

(a) Integrative Genomics Viewer plots showing alignment of Tbr1 ChIP-seq peaks³² to the Cdh8 (top panel) and Sorcs3 (bottom panel) genomic loci. For each gene, the top row represents viewing window in kilobases and the gene locus. Bottom two blue traces are peaks from n = 2 Tbr1 ChIP-seq replicates. Peaks associated with Cdh8 and Sorcs3, but not Jam2, Alcam or Smo, were within 50kb upstream of the annotated transcriptional start site, and may therefore be associated with regulatory regions. (b-c) Retinal cross-sections from control and Tbr1^ret/ret stained for Alcam and Neo1, showing no difference. Scale=25µm. (d) Expression of lacZ within the ganglion cell layer (GCL) of Cdh8^lacZ retinas from P3 to P7. Scale=50µm. (e) Retinal cross-section stained for Sorcs3 and Protein kinase C (PKC), a rod bipolar cell marker. Yellow arrows mark co-localization of Sorcs3 with dendrites of rod bipolar cells. Scale=25µm. (f) Expression of Sorcs3 in retinal cross-sections from P4 to P16. DR, animals dark-reared from birth. Upregulation of Sorcs3 in RGCs after eye-opening appears to be light-dependent. Scale=25µm. (g) Whole mounts from a Cdh8^lacZ; TYW7 retina. RGCs labeled in this line, including α-OFF-s-RGCs, do not express lacZ. Scale =25µm. Each experiment in b-g was repeated independently in three animals with similar results.