GEO DataSets

(Submitter supplied) To study cell heterogeneity and state transitions in the developing urinary tract we isolated renal cells (single cells or clusters) by Fluorescence-activated cell sorting (FACS) from the trunk of E8.75, E9.5 and E11.5 mouse embros and performed 10X Genomics single cell and Cluster RNA sequencing

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: H5

(Submitter supplied) To study cell heterogeneity and state transitions in the developing urinary tract we performed spatial transcriptomics from the trunk of E9.5 Pax2GFP mouse embryos using the 10X Genomics Visium Spatial Gene Expression protocol

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: CSV, H5, JSON, PNG

(Submitter supplied) To study cell heterogeneity and state transitions in the developing urinary tract we isolated Pax2-GFP positive single cells or clumps of cells by Fluorescence-activated cell sorting (FACS) from the trunk of E9.5 Pax2-GFP BAC transgenic embryos and performed 10X Genomics single cell and Clumps RNA sequencing

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: H5

(Submitter supplied) The goal of this study was to identify changes in gene expression within nephron progenitors and the whole embryonic kidney between Wnt11 mutants and wild type animals. Wnt11 mutant kidneys have disorganized nephron progenitor niches. Ultimately, nephron endowment is reduced by 50% in Wnt11 mutants. Gene expression changes are minimal between mutant and wild type samples, suggesting Wnt11 may act through non-canonical, non-transcritional mechanisms to regulate kidney development.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: TXT

(Submitter supplied) To delineate the epigenomic profile of the Six2+ mouse nephron progenitor cells, we mapped open chromatin using ATAC-Seq in Six2+ cells from E16.5 mouse kidneys.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BW, TXT

(Submitter supplied) The Six2 distal enhancer regulates expression of the 60 kb-downstream gene Six2, but does not regulate the Six3 gene which is 70 kb further downstream. CTCF ChIP-Seq and Hi-C data points to a chromatin domain boundary between Six2 and Six3 which may intervene interaction between Six2-DE and Six3. The irradiation-induced Brachyrrhine (Br) mutant allele was found to carry a 320 kb genomic inversion that includes Six2 and Six3, but not Six2DE. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

2 Samples

Download data: BEDGRAPH

(Submitter supplied) In developing mammalian kidney, nephron progenitor cells (NPC) give rise to all cells in mature nephrons. Several transcription factors, including Six2, Hoxd11, Osr1 and Wt1, are expressed in NPC and are essential for its maintenance and/or specification. In order to understand the regulatory functions of these factors, we mapped binding sites of Six2, Hoxd11 and Osr1 in NPC using a novel transgenic strategy, and of Wt1 in wild-type developing kidney.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

23 Samples

Download data: BW, TXT

(Submitter supplied) A platform for generating expandable, branching and gene-editable ureteric bud organoid from primary mouse and human ureteric bud progenitor cells and human pluripotent stem cells, and its maturation into collecting duct organoid.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

10 Samples

Download data: CSV

(Submitter supplied) In this study we identify molecules with highly restricted expression patterns during the initial stages of metanephric development, when the ureteric bud has entered the metanephric mesenchyme and initiated branching morphogenesis. Using the Affymetrix Mouse Genome 430 2.0 Array, we compare gene expression patterns in ureteric bud tips, stalks and metanephric mesenchymes from mouse E12.5 embryos. To identify conserved molecular pathways, we also analyze transcriptional profiles in rat E13.5 ureteric buds and metanephric mesenchymes using the Affymetrix Rat Genome U34 Set. more...

Organism:

Mus musculus; Rattus norvegicus

Type:

Expression profiling by array

Datasets:

GDS1572 GDS1581 GDS1582 GDS1583

4 related Platforms

18 Samples

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Analysis of ureteric bud (UB) tips and stalks and metanephric mesenchyme (MM) from E12.5 kidneys. UB-secreted factors induce conversion of adjacent MM cells into nephrons. Results identify as potential regulators a set of 20 secreted molecules specific to the UB and conserved between species.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 3 tissue sets

Platform:

GPL1261

Series:

GSE1983

6 Samples

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Analysis of ureteric buds (UBs) and metanephric mesenchyme (MM) from E13.5 kidneys. UB-secreted factors induce conversion of adjacent MM cells into nephrons. Results identify as potential regulators a set of 20 secreted molecules specific to the UB and conserved between species.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL87

Series:

GSE1983

4 Samples

Download data

Analysis of ureteric buds (UBs) and metanephric mesenchyme (MM) from E13.5 kidneys. UB-secreted factors induce conversion of adjacent MM cells into nephrons. Results identify as potential regulators a set of 20 secreted molecules specific to the UB and conserved between species.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL86

Series:

GSE1983

4 Samples

Download data

Analysis of ureteric buds (UBs) and metanephric mesenchyme (MM) from E13.5 kidneys. UB-secreted factors induce conversion of adjacent MM cells into nephrons. Results identify as potential regulators a set of 20 secreted molecules specific to the UB and conserved between species.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL85

Series:

GSE1983

4 Samples

Download data

(Submitter supplied) Morphogenesis of cellecting duct system within developing mouse kidney is driven by growth at the tips of ureteric epithelium. To characterize the transcription program within the tip compartment, here we performed mRNA-Seq of tip cells (Wnt11RFP+;Hoxb7+ cells) and stalk cells (Wnt11RFP-;Hoxb7GFP+ cells) obtained from mouse embryonic kidney through FACS. We identified tip-specific genes from these data, and verified with in situ hybridization and followed up with mechanistic study for some of the intersting targets.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) We report here bulk RNA sequencing results of control and MAPK/ERK-deficient ureteric bud (UB) epithelium and nephron progenitor cells (NP) in the developing mouse kidney. RNA isolated from 4 biological replicates for UB and 3 biological replicates for NP was subjected to the library preparation done using NuGen Ovation Solo. Sequencing with NextSeq was performed at BIDGEN DNA Sequencing, after data processing produced 1004 (UB) and 5053 (NP) differentially expressed genes with a statistical cutoff of Padj<0.05 and a magnitude threshold of │log2foldchange│≥1 .

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

14 Samples

Download data: XLSX

(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) To characterize the cellular diversity in the human kidney cortical nephrogenic niche we dissociated cells from the cortex and performed 10X Genomics single-cell RNA sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: TSV

(Submitter supplied) To characterize the expression profile of mouse nephron progenitors, we performed intracellular labeling of Six2 by antibody, followed by FACS and RNA-seq. To characterize the expression profile of mouse stromal progenitor cells, we isolated Tdt+ cells from Foxd1Cre;Tdt transgenic mice kidney by FACS followed by RNA-seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

19 Samples

Download data: TXT

(Submitter supplied) To characterize the molecular features of human and mouse nephron progenitors and stromal cells we performed intracellular labeling for SIX2 and/or MEIS1 antibodies, FACS, and RNA-seq. Mouse interstitial progenitors were isolated by Foxd1-Tdt transgenic line, FACS, and RNA-seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: TXT