Transcriptomics

Dataset Information

61

RNA-SEQ analysis of single cells extracted from the metanephric mesenchyme of Embryonic day 11.5 (E11.5) Crym-EGFP transgenic mice.


ABSTRACT: We used micro-dissection with FACS sorting techniques to isolate single cells from the metanephric mesenchyme of the E11.5 developing kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. Kidneys are harvested from Tg(Crym-EGFP)GF82Gsat mice. Single cells are extracted from E11.5 metanephric mesenchyme using manual micro-dissection techniques. A subset of these cells is analyzed individually via Fluidigm single cell analysis. The long term goal is to generate a transcriptional atlas of the developing kidney.

ORGANISM(S): Mus musculus  

SUBMITTER: Eric W Brunskill  GUDMAP Developers   Steven Potter    

PROVIDER: E-GEOD-59129 | ArrayExpress | 2014-12-10

SECONDARY ACCESSION(S): SRP044134GSE59129PRJNA254485

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Single cell dissection of early kidney development: multilineage priming.

Brunskill Eric W EW   Park Joo-Seop JS   Chung Eunah E   Chen Feng F   Magella Bliss B   Potter S Steven SS  

Development (Cambridge, England) 20140801 15


We used a single cell RNA-seq strategy to create an atlas of gene expression patterns in the developing kidney. At several stages of kidney development, histologically uniform populations of cells give rise to multiple distinct lineages. We performed single cell RNA-seq analysis of total mouse kidneys at E11.5 and E12.5, as well as the renal vesicles at P4. We define an early stage of progenitor cell induction driven primarily by gene repression. Surprising stochastic expression of marker genes  ...[more]

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