Embryonic Kidney RNA-seq
Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling
The developing mouse kidney is currently the best-characterized model of    organogenesis at a transcriptional level. Detailed spatial maps have been    generated for gene expression profiling combined with systematic in situ    screening. These studies, however, fall short of capturing the    transcriptional complexity arising from each locus due to the limited    scope of microarray-based technology, which is largely based on    gene-centric models.  To address this, the polyadenylated RNA and microRNA transcriptomes of the    15.5dpc mouse kidney were profiled using strand-specific RNA-sequencing    (RNA-Seq) to a depth sufficient to complement spatial maps from    pre-existing microarray datasets. The transcriptional complexity of RNAs    arising from mouse RefSeq loci was catalogued; including 3568    alternatively spliced transcripts and 532 uncharacterized alternate 3'    UTRs. Antisense expressions for 60% of RefSeq genes was also detected    including uncharacterized non-coding transcripts overlapping kidney    progenitor markers, Six2 and Sall1, and were validated by section in situ    hybridization. Analysis of genes known to be involved in kidney    development, particularly during mesenchymal-to-epithelial transition,    showed an enrichment of non-coding antisense transcripts extended along    protein-coding RNAs.  The resulting resource further refines the transcriptomic cartography of    kidney organogenesis by integrating deep RNA sequencing data with    locus-based information from previously published expression atlases. The    added resolution of RNA-Seq has provided the basis for a transition from    classical gene-centric models of kidney development towards more accurate    and detailed transcript-centric representations, which highlights the    extent of transcriptional complexity of genes that direct complex    development events.