GEO DataSets

(Submitter supplied) 10X-based scRNA-seq data human fetal kidneys at 5 different ages

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: MTX, TSV

(Submitter supplied) Studies in mouse have led to enormous progress in our understanding of early human development. The identification of genes and the signaling pathways involved in mouse embryogenesis have helped us to better understand fertilization, morulation, gastrulation, organogenesis and embryonic development in mammals. We report a detailed analysis of the global gene expression profiles from oocyte to the end of organogenesis in mouse. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

36 Samples

Download data: CEL, TXT

(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) We performed single cell transcriptomic analysis on 17 urine samples obtained from five subjects at two different occasions using both spot and 24-hour urine collection. In addition, we used a combined spot urine samples of five healthy individuals as a control sample. We sequenced a total of 71,667 cells. After quality control and downstream analysis, we found that epithelial cells were the most common cell types in the urine. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

18 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL14663 GPL11670

229 Samples

Download data: CEL

(Submitter supplied) To identify genes with cell-lineage-specific expression not accessible by experimental micro-dissection, we developed a genome-scale iterative method, in-silico nano-dissection, which leverages high-throughput functional-genomics data from tissue homogenates using a machine-learning framework. This study applied nano-dissection to chronic kidney disease and identified transcripts specific to podocytes, key cells in the glomerular filter responsible for hereditary proteinuric syndromes and acquired CKD. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL11670 GPL14663

107 Samples

Download data: CEL

(Submitter supplied) To identify genes with cell-lineage-specific expression not accessible by experimental micro-dissection, we developed a genome-scale iterative method, in-silico nano-dissection, which leverages high-throughput functional-genomics data from tissue homogenates using a machine-learning framework. This study applied nano-dissection to chronic kidney disease and identified transcripts specific to podocytes, key cells in the glomerular filter responsible for hereditary proteinuric syndromes and acquired CKD. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL14663 GPL11670

122 Samples

Download data: CEL

(Submitter supplied) The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4- to 6-week human embryos when essentially all organs are just laid out. Based on over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 cell types that belong to 18 developmental systems, and identified hundreds of cell type specific markers. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL24676

111 Samples

Download data: MTX, TXT

(Submitter supplied) Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL21493

13 Samples

Download data: BIGWIG, CSV, RDS, TXT

(Submitter supplied) Human kidney is a major metabolic organ, which plays a crucial role in regulating homeostasis of human body. However, gene expression characterizations of human fetal kidney development is still not fully explored. Here, we used single-cell RNA-seq to analyze more than 3,000 individual renal cells of human fetal kidneys covering over four months of development in vivo.We found co-expression of self-renewal and differentiation genes in cap mesenchyme, progenitors differed from that of mouse as they persistently express SIX1 throughout the renal morphogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

70 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) The immune system of skin develops in stages in mice. However, the developmental dynamics of immune cells in human skin remains elusive. Here we perform transcriptome profiling of CD45+ hematopoietic cells in human fetal skin at an estimated gestational age of 10–17 weeks by single-cell RNA sequencing. A total of 13 immune cell types are identified. Skin macrophages show heterogeneity and dynamic over the course of skin development. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV

(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) 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) Single-cell RNA-seq (scRNA-seq) has greatly advanced the characterization of cellular heterogeneity in physiological and pathological conditions. However, since cells are lysed and can thus only be profiled once, it is currently impossible to perform downstream functional assays on the same cells and to obtain a direct scRNA-seq-based read-out of transcriptional dynamics. Here, we present Live-seq, a novel single cell transcriptomic biopsy approach based on fluidic force microscopy that differs from other scRNA-seq methods because the cells can be kept alive for further analysis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1012 Samples

Download data: CSV, XLS

(Submitter supplied) To investigate novel markers for snRNA seq and graft in-vivo snRNA seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: CSV

(Submitter supplied) A critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC-podocytes) have recently been generated in nephron-like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here, we show that hPSC-podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recapitulating key features of ultrastructure, gene expression, and mutant phenotype. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL19109 GPL19184

413 Samples

Download data: CEL