Figure 2

Visualization of RNA-Seq and kidney subcompartments microarray data on UCSC Genome Browser of Lhx1 long 3'UTR. Representation of the 3' end of the mouse Lhx1 gene (chr11:84330068-84335347) (mm9) is shown within the genome browser along with default and custom tracks. A: Affymetrix mouse 430.2 microarray platform probesets 1421951_at localized to the canonical 3' untranslated region (UTR) and 1450428_at ~500 bp downstream; and corresponding probeset expression heatmap across kidney subcompartments (microarray data from [5]) microarray compartments from top to bottom of heatmap: ureteric tip; s-shaped body; proximal tubule; cortical, and medullary interstitium; medullary, and cortical collecting duct; renal corpuscle; cap mesenchyme; loop of Henle; renal vesicle. B: RNA-Seq exon junction tags are represented as UCSC Genome Browser BED data tracks (top) spanning exons, and 'wiggle' plots showing coverage of negative strand tags corresponding to Lhx1 expression (bottom). C: Riboprobes used for in situ hybridization (ISH): i) overlapping the canonical region as represented by Affymetrix probeset 1421951_at and ii) overlapping extended 3' signal captured by RNA-Seq and probeset 1450428_at, which also contains a microRNA binding site for miR-30 [28]. D: Histological 15.5 dpc mouse kidney section ISH (SISH) of canonical 3'UTR (i) and extended 3'UTR (ii) both detected in distal compartments of the renal vesicle. E: Pre-built UCSC genome browser data tracks of: (top-bottom) mouse RefSeq genes, Ensembl gene model predictions, mouse expressed sequence tags (ESTs). Green tags represent EST tags derived from kidney cDNA libraries, and evolutionarily conserved regions (black).