Journal article

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling

Rathi D Thiagarajan, Nicole Cloonan, Brooke B Gardiner, Tim R Mercer, Gabriel Kolle, Ehsan Nourbakhsh, Shivangi Wani, Dave Tang, Keerthana Krishnan, Kylie M Georgas, Bree A Rumballe, Han S Chiu, Jason A Steen, John S Mattick, Melissa H Little, Sean M Grimmond

BMC GENOMICS | BMC | Published : 2011

Abstract

BACKGROUND: 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. RESULTS: To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray dat..

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Grants

Awarded by National Health and Medical Research Council


Awarded by NIH NIDDK


Awarded by NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES


Funding Acknowledgements

We wish to thank all members from the Queensland Centre for Medical Genomics for computational resources, valuable feedback, and discussions. This work was supported by National Health and Medical Research Council grants to SMG [455857 to S. M. G. 456140, 631701] and NIH NIDDK grants to MHL and SMG (DK070136).