Figure 1

Embryonic kidney RNA-Seq coverage, depth and sensitivity. A: Tag distribution across active genes with varying levels of expression in the 15.5 dpc mouse kidney. Genes are grouped into reads per kilobases per million (RPKM) (y-axis) bins according to expression abundance based on tag coverage (x-axis). Low abundance genes are considered to have RPKM values between, 1-10 RPKM, moderate expression at 10-100 RPKM, and highly expressed at above 100 RPKM. B: Box-plot representation of embryonic kidney subcompartments captured by whole-kidney RNA-Seq profiling. Transcripts with the most subcompartment-specific expression from each structured identified from the embryonic kidney subcompartment microarray atlas (Brunskill et al. [5]) were represented by RPKM values (log 10) as detected by RNA-Seq to gauge sensitivity of detecting specific embryonic kidney cell-types. Each box represents kidney subcompartment-specific transcripts with corresponding RPKM values; The boxes extend from the 25^th percentile (lower hinge) to the 75^th percentile (upper hinge) of RPKM values. The line across the box represents the median. The lengths of the lines above and below the box are defined by the maximum and minimum RPKM values (respectively). Subcompartments: CI: cortical interstitium; Cap: cap mesenchyme; MI: medullary interstitium; Utip: ureteric tip; CCD: cortical collecting duct; MCD: medullary collecting duct; RV: renal vesicle; SSB: s-shaped body; RC: renal corpuscle; PT: proximal tubule; LOH: loop of Henle.