Transcriptomics

Dataset Information

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RNA-SEQ analysis of single cells extracted from E12.5 embryonic kidneys.


ABSTRACT: We used micro-dissection and trypsinization techniques to isolate single cells from the E12.5 total 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. E12.5 kidneys are dissected; the kidneys are made into a single cell suspension via trypsinization. A subset of these cells is analysed individually via Fluidigm C1 single cell analysis. The long term goal is to generate a single cell resolution transcriptional atlas of the developing kidney.

ORGANISM(S): Mus musculus  

SUBMITTER: Eric W Brunskill   GUDMAP Developers  Steven Potter 

PROVIDER: E-GEOD-59127 | ArrayExpress | 2014-08-01

SECONDARY ACCESSION(S): SRP044133GSE59127PRJNA254486

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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