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Validating single-cell genomics for the study of renal development.
- Source :
-
Kidney international [Kidney Int] 2014 Nov; Vol. 86 (5), pp. 1049-55. Date of Electronic Publication: 2014 Apr 23. - Publication Year :
- 2014
-
Abstract
- Single-cell genomics will enable studies of the earliest events in kidney development, although it is unclear if existing technologies are mature enough to generate accurate and reproducible data on kidney progenitors. Here we designed a pilot study to validate a high-throughput assay to measure the expression levels of key regulators of kidney development in single cells isolated from embryonic mice. Our experiment produced 4608 expression measurements of 22 genes, made in small cell pools, and 28 single cells purified from the RET-positive ureteric bud. There were remarkable levels of concordance with expression data generated by traditional microarray analysis on bulk ureteric bud tissue with the correlation between our average single-cell measurements and GUDMAP measurements for each gene of 0.82-0.85. Nonetheless, a major motivation for single-cell technology is to uncover dynamic biology hidden in population means. There was evidence for extensive and surprising variation in expression of Wnt11 and Etv5, both downstream targets of activated RET. The variation for all genes in the study was strongly consistent with burst-like promoter kinetics. Thus, our results can inform the design of future single-cell experiments, which are poised to provide important insights into kidney development and disease.
- Subjects :
- Animals
Cell Separation methods
Cluster Analysis
DNA-Binding Proteins genetics
DNA-Binding Proteins metabolism
Flow Cytometry
Gestational Age
High-Throughput Nucleotide Sequencing
Kidney embryology
Mice, Transgenic
Oligonucleotide Array Sequence Analysis
Organogenesis
Pilot Projects
Promoter Regions, Genetic
Proto-Oncogene Proteins c-ret genetics
Proto-Oncogene Proteins c-ret metabolism
Real-Time Polymerase Chain Reaction
Reproducibility of Results
Transcription Factors genetics
Transcription Factors metabolism
Ureter embryology
Wnt Proteins genetics
Wnt Proteins metabolism
Gene Expression Regulation, Developmental
Genomics methods
Kidney metabolism
Ureter metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1523-1755
- Volume :
- 86
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- Kidney international
- Publication Type :
- Academic Journal
- Accession number :
- 24759149
- Full Text :
- https://doi.org/10.1038/ki.2014.104