GEO DataSets

(Submitter supplied) We used micro-dissection and trypsinization techniques to isolate single cells from the Embryonic day 12.5 (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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

86 Samples

Download data: TXT

(Submitter supplied) We used micro-dissection techniques and/or FACS to isolate cell types from the developing and adult kidney (E11.5 ureteric buds, E12.5, P1 and P4 cap mesenchyme, E15.5 collecting ducts, proximal tubules, ureter, Adult renal proximal tubules, podocytes, endothelial and mesangial cells). RNA-SEQ analysis was performed to determine the transcriptional profile of each cell type, identify component specific transcripts and isoforms and cell-type specific long-noncoding RNAs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

20 Samples

Download data: TXT

(Submitter supplied) We used micro-dissection with FACS sorting techniques to isolate renal vesicle single cell types from post natal day (P4) kidneys. 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

57 Samples

Download data: TXT

(Submitter supplied) We used micro-dissection with FACS sorting techniques to isolate single cells from the metanephric mesenchyme of the Embryonic day 11.5 (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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

49 Samples

Download data: TXT

(Submitter supplied) Kidneys from multiple litters of Six2GFP+ E14.5 mouse embryos were pooled into three replicate tubes and dissociated in parallel. Six2GFP+ cells were isolated and processed for single cell sequencing using 10x Genomics technology. This resulted in a dataset of 7844 single cells representing the nephron progenitor population of the mouse kidney.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

3 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from three biological replicates from the embryonic day (E)18.5 developing mouse kidney and three biological replicates of iPSC-derived human kidney organoids differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). When aggregated, the mouse data represents >6000 cells that passed our QC, containing most major cell types known to exist in the developing mouse kidney. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

7 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-seq, Chromium 10XGenomics and Fluidigm C1, to carry out single cell RNA-seq analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were able to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

3 Samples

Download data: TXT

(Submitter supplied) The kidney contains the functional units, the nephrons, surrounded by the renal interstitium. Previously, we discovered that, once Six2-expressing nephron progenitor cells and Foxd1-expressing renal interstitial progenitor cells form at the onset of kidney development, descendant cells from these populations contribute exclusively to the main body of nephrons and renal interstitial tissues, respectively, indicating a lineage boundary between the nephron and renal interstitial compartments. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

237 Samples

Download data: TXT

(Submitter supplied) Kidney development depends on a balance of nephron progenitor self-renewal and commitment. Here we examine how cells shift from a motile progenitor state to a static committed state during nephrogenesis. Cells that express Wnt4, an early marker of commitment, give rise to both the nephron lineage and a migrating sub-population that may re-enter the progenitor pool. Single cell transcriptional profiling reveals Wnt4-lineage cells across a range of transcriptional states, including cells that return to an uninduced progenitor state.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

3 Samples

Download data: MTX, TSV

(Submitter supplied) In order to shed light on human kidney development, we have used single-cell transcriptomics to characterize gene expression in different cell population, and to study individual cell dynamics and lineage trajectories during development

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL10787 GPL11202 GPL7202

14 Samples

Download data: TXT

(Submitter supplied) We have employed whole genome microarray expression profiling to identify genes regulated by Sall1 in the kidney.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

6 Samples

Download data: TXT

(Submitter supplied) We have employed whole genome microarray expression profiling to identify genes regulated by Sall1 in the kidney.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

4 Samples

Download data: TXT

(Submitter supplied) We have employed whole genome microarray expression profiling to identify genes regulated by Sall1 in the kidney.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

4 Samples

Download data: TXT

(Submitter supplied) To identify maturation-dependent genes, we here performed single cell RNA sequencing (scRNA-seq) analysis using developing kidneys at different stages in the mouse, followed by highly sensitive in situ hybridization. We identified multiple genes expressed abundantly in newborn kidneys, but minimally at embryonic day 15.5. We then applied these maturation markers to the transplanted embryonic kidneys and found that the maturation process did not occur equally throughout nephron segments upon transplantation: glomeruli and proximal renal tubules became more mature than the other nephron segments. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL21273

4 Samples

Download data: MTX, TSV

(Submitter supplied) Nephron number is a major determinant of long-term renal function. We hypothesized a link between epigenetic regulation and nephron formation. In support of this hypothesis, expression analysis evidenced high levels of DNA methyltransferases Dnmt1 and Dnmt3a in the nephrogenic zone of the developing mouse kidney. Using targeted loss-of-function manipulations in mice, we show that deletion of Dnmt1 in nephron progenitor cells results in a marked hypoplasia and reduction of nephron number at birth. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TSV

(Submitter supplied) We used R26R-tdTomato reporter mice activated by the Six2-TGC transgene to isolate cell populations co-expressing GFP and tdTomato by FACS from kidneys of control P0 mice. We observed two distinct populations of cells from control kidneys based on lower or higher tdTomato expression along with high GFP-expression from the Six2-TGC transgene. RNASeq experiment was conducted to analyze the transcriptome of these populations

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(Submitter supplied) p53 limits the self-renewing ability of a variety of stem cells. Here, contrary to its classical role in restraining cell proliferation, we demonstrate a divergent function of p53 in maintenance of self-renewal of the nephron progenitor population in the embryonic mouse kidney. p53-null nephron progenitor cells (NPC) exhibit progressive loss of the self-renewing progenitor niche in the cap mesenchyme, identified by Cited1 and Six2 expression, and loss of cap integrity. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of FACS-sorted Six2-positive nephron progenitor cells from Six2CreEGFP mice without (WT) or with (MUT) homozygously floxed HDAC1 and HDAC2 alleles at the age of embryonic day 15.5. This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of HDAC1&2 in the nephron progenitor population and successive changes to the series of events in kidney development.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

8 Samples

Download data: TXT

(Submitter supplied) Early human kidney development is poorly documented due to tissue inaccessibility and a lack of genetic tractability. Here we combine reprogramming, CRISPR/Cas9 gene-editing and organoid technologies to study the nephron lineage in a human context. We confirm the presence of a SIX2+ population in early kidney organoids with a transcriptional profile akin to human fetal nephron progenitors. Using lineage-tracing analyses, we show that SIX2-expressing cells contribute to nephron formation but not to the putative collecting duct epithelium. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: MTX, TSV