GEO DataSets

(Submitter supplied) We characterized 57,979 cells from healthy mouse kidneys using unbiased single-cell RNA sequencing. We show that genetic mutations that present with similar phenotypes mostly affect genes that are expressed in a single unique differentiated cell type. On the other hand, we found unexpected cell plasticity of epithelial cells in the final segment of the kidney (collecting duct) that is responsible for final composition of the urine. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: TXT

(Submitter supplied) Notch signaling deficient kidney collecting ducts may serve as a useful resource to identify principal cell lineage and intercalated lineage specific factors since they develop a reduced number of principal cells and an increased number of intercalated cells compared with wild type kidney collecting ducts. We compared RNA from three E18.5 mouse kidneys per group: HoxB7Cre;RBPJf/-;Rosa+/Eyfp (Notch signaling deficient; mutant) versus RBPJf/f;Rosa+/Eyfp (wild type).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17543

6 Samples

Download data: IDAT, TXT

(Submitter supplied) Purpose: Transport processes in the renal collecting duct are responsible for precise regulation of blood pressure and body fluid composition. The collecting duct is composed of at least three cell types, type A intercalated cells (A-IC), type B intercalated cells (B-IC) and principal cells (PC). To identify the genes that are selectively expressed in each cell type, including cell-surface receptors, transcription factors, transporters and secreted proteins, we used cell surface markers necessary for isolation of each of the three cell types using fluorescence-activated cell sorting and carried out single-cell RNA-Seq to measure the mRNA species in each of these cell types. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21493

262 Samples

Download data: TXT

(Submitter supplied) Intercalated cells are known to be involved in acid-base homeostasis via vacuolar ATPase (H+-ATPase or V-ATPase) expression. Increasing evidence supports an innate immune role for ICs along with their traditional function of pH regulation. In this study, human kidney tissue was enriched for viable intercalated cells then exposed to uropathogenic E. coli versus saline control. Single cell transcriptomics was performed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: MTX, TSV

(Submitter supplied) Defining cellular and molecular identities within the kidney is necessary to understand its organization and function in health and disease. Here we demonstrate a reproducible method with minimal artifacts for single-nucleus Droplet-based RNA sequencing (snDrop-Seq) that we use to resolve thirty distinct cell populations in human adult kidney. We define molecular transition states along more than ten nephron segments spanning two major kidney regions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

47 Samples

Download data: CSV, TSV

(Submitter supplied) Kidneys are essential for acid-base homeostasis, especially when organisms cope with changes in acid or base dietary intake. Because collecting ducts constitute the final site for regulating urine acid-base balance, we undertook to identify the gene network involved in acid-base transport and regulation in the mouse outer medullary collecting duct (OMCD). For this purpose, we combined kidney functional studies and quantitative analysis of gene expression in OMCDs, by transcriptome and candidate gene approaches, during metabolic acidosis. more...

Organism:

Mus musculus

Type:

Expression profiling by SAGE

Platform:

GPL275

2 Samples

Download data

(Submitter supplied) We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development. Our data demonstrated the existence of two types of stem/progenitor cells with distinct molecular patterns during liver development. Both types of cells exhibit heterogeneity of transcriptional program within each cell population, suggesting they be in distinct status of self-renewal, cell proliferation and different sub-stages of differentiation and maturation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

507 Samples

Download data: FPKM_TRACKING

(Submitter supplied) The kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. De-fects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

1 Sample

Download data: H5, TAR

(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) We have applied single-cell RNA sequencing as an unbiased profiling strategy to interrogate and classify aortic macrophage heterogeneity at the single-cell level in atherosclerosis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

5 Samples

Download data: CSV, H5, TAR, TXT

(Submitter supplied) In many gene expression studies, cells are extracted by tissue dissociation and Fluorescence-Activated Cell Sorting (FACS), but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here, we applied single-cell mRNA sequencing (scRNA-seq) to muscle stem cells, and unexpectedly found a subpopulation that is strongly affected by the widely-used dissociation protocol that we employed. more...

Organism:

Mus musculus; Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL20828

21 Samples

Download data: CSV, FA, TSV, TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL13112

216 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Haematopoietic stem cells (HSCs) are derived early from embryonic precursor cells, such as haemogenic endothelial cells and pre-HSCs. However, the identity of precursor cells remains elusive due to their rareness, transience, and inability to be isolated efficiently. Here we employed potent surface markers to capture the nascent pre-HSCs at 30% purity, as rigorously validated by single-cell-initiated serial transplantation assay. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL17021

181 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Hematopoietic stem cells (HSCs) in adult are specified early from the endothelium-derived precursors (e.g., hemogenic endothelium, and pre-HSCs) in mouse mid-gestation embryos, the detailed process, however, is still largely unknown due to their rareness, transience, and current inability to prospectively isolate them efficiently . Here we developed a potent set of surface markers that could capture the earliest emerging HSCs, the CD45- pre-HSCs with high accuracy and purity, as rigorously and functionally verified by single-cell-initiated serial transplantation assays. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL17021

35 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Single cell RNA-seq is a powerful methodology, but with important limitations. In particular, the process of enzymatic separation of cells at 37O C can be expected to result in artifact changes in gene expression patterns. We here describe a dissociation method that uses protease from a psychrophilic microorganism with high activity in the cold. The entire procedure is carried out at 6O C or colder, where mammalian transcriptional machinery is largely inactive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) Pancreatic islet cells are critical for maintaining normal blood glucose levels and their malfunction underlies diabetes development and progression. We used single-cell RNA sequencing to determine the transcriptomes of 1,492 human pancreatic α-, β-, δ- and PP cells from non-diabetic and type 2 diabetes organ donors. We identified cell type specific genes and pathways as well as 245 genes with disturbed expression in type 2 diabetes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1600 Samples

Download data: TXT

(Submitter supplied) Background: The planarian, Schmidtea mediterranea, is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal have hindered the study of lineage progression and has made understanding the mechanisms of tissue replacement during regeneration a challenge. However, recent advances in single cell transcriptomics and analysis methods may allow for the discovery of novel cell lineages as differentiation progresses from stem cell to terminally differentiated cell. more...

Organism:

Schmidtea mediterranea

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21689 GPL20150

171 Samples

Download data: TXT

(Submitter supplied) Renal disease development is poorly understood, mostly because the kidney is made up of more than 20 different cell types, each of them with specific function and complex interaction. Here, we used single cell RNA sequencing to resolve cell-type specific and cell fraction changes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: H5

(Submitter supplied) To obtain new insight into the mammalian kidney, anatomy-guided, single cell RNA sequencing was performed on the adult male and female mouse kidney. Key observations were followed up through a variety of secondary studies including genetic lineage tracing. The data document novel cell diversity, unexpected origins to key cell types, and significant sex differences centered on proximal tubules segments of the nephron and principal cells of the collecting system. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

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