GEO DataSets

(Submitter supplied) A comprehensive cellular anatomy of normal human bladder is vital to address the cellular origins of benign bladder disease and bladder cancer. The physiological function and pathological changes of bladder are associated with its cell type. To investigate the classification and underlying function of bladder cells, we conducted single-cell RNA sequencing (scRNA seq) of 12,423 cells from human bladder and 12,884 cells from mouse bladder. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21273 GPL20795

5 Samples

Download data: MTX, TSV

(Submitter supplied) Objectives: Much of the information to date in terms of subtypes and function of bladder urothelial cells were derived from anatomical location or by the expression of a small number of marker genes. To have a comprehensive map of the cellular anatomy of bladder urothelial cells, we performed single-cell RNA-sequencing to thoroughly characterize mouse bladder urothelium. Materials and methods: A total of 18,917 single cells from mouse bladder urothelium was analyzed by unbiased single-cell RNA sequencing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1 Sample

Download data: MTX, TSV

(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) A key limitation in single cell genomics is generating a high-quality single cell suspension that contains rare or difficult to dissociate cell types and is free of RNA degradation or transcriptional stress responses. Samples with unpredictable availability or that must be collected at several timepoints present additional challenges. Using adult mouse kidney, we compared single-cell RNA sequencing (scRNA-seq) data generated using DropSeq with snRNA-seq data generated from nuclei using sNuc-DropSeq, DroNc-seq and 10X Chromium. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL21493

10 Samples

Download data: MTX, TSV

(Submitter supplied) Aging has multifaceted effects on the immune system, but how aging affects tissue-specific immunity is not well-defined. Bladder diseases characterized by chronic inflammation are highly prevalent in older women, but mechanisms by which aging promotes these pathologies remain unknown. Tissue transcriptomics of unperturbed, young, and aged bladders identified a highly altered immune landscape as a fundamental feature of the aging female bladder. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

8 Samples

Download data: TXT

(Submitter supplied) Aging has multifaceted effects on the immune system, but how aging affects tissue-specific immunity is not well-defined. Bladder diseases characterized by chronic inflammation are highly prevalent in older women, but mechanisms by which aging promotes these pathologies remain unknown. Tissue transcriptomics of unperturbed, young, and aged bladders identified a highly altered immune landscape as a fundamental feature of the aging female bladder. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV

(Submitter supplied) We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. more...

Organism:

Rattus norvegicus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL14844 GPL13112

137 Samples

Download data: TXT

(Submitter supplied) Analysis of gene expression changes during mouse salivary gland development using RNA-Seq

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

13 Samples

Download data: CSV

(Submitter supplied) We developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we constructed a basic scheme for the Mouse Cell Atlas. We reveal single cell hierarchy for many tissues that have not been well previously characterized. Our study demonstrates the wide applicability of the Microwell-seq technology and the Mouse Cell Atlas resource.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL22245

90 Samples

Download data: TAR, TXT

(Submitter supplied) Droplet-based single cell RNA sequencing (scRNA-seq) to classify molecularly distinct neuronal and non-neuronal cell types in the mouse ventral posterior hypothalamus. Cluster analysis of >16,000 single cells revealed 20 neuronal and 18 non-neuronal cell populations, defined by suites of discriminatory markers. We validated differentially expressed genes in a selection of neuronal populations through fluorescence in situ hybridization (FISH). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL21103

4 Samples

Download data: MTX, TSV

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease causing alveolar remodeling, inflammation, and fibrosis. We utilized single cell RNA-sequencing (scRNA-Seq) to identify epithelial cell types and associated biological processes involved in the pathogenesis of IPF. Transcriptomic analysis of epithelial cells from normal human lung defined gene expression patterns associated with highly differentiated alveolar type 2 (AT2) cells, indicated by enrichment of RNAs critical for surfactant homeostasis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: XLSX

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease causing alveolar remodeling, inflammation, and fibrosis. We utilized single cell RNA-sequencing (scRNA-Seq) to identify epithelial cell types and associated biological processes involved in the pathogenesis of IPF. Transcriptomic analysis of epithelial cells from normal human lung defined gene expression patterns associated with highly differentiated alveolar type 2 (AT2) cells, indicated by enrichment of RNAs critical for surfactant homeostasis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

540 Samples

Download data: TXT

(Submitter supplied) While the function of the mammalian pancreas hinges on complex interactions of distinct cell types, gene expression profiles have primarily been described with bulk mixtures of cells. Here, we invoked inDrop, a droplet-based single-cell RNA-Seq method, to determine the transcriptomes of over 12,000 individual pancreatic cells from four human donors and two strains of mice. Cells could be divided into 15 clusters that matched previously characterized cell types: all endocrine cell types, including rare ghrelin-expressing epsilon-cells, exocrine cell types, vascular cells, Schwann cells, quiescent and activated pancreatic stellate cells, and four types of immune cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

6 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

32 Samples

Download data

(Submitter supplied) Single-cell RNA-sequencing was conducted on specific cell types and heterogeneous viable cells (sorted by FACS) in order to determine a cellular atlas of the normal human prostate.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: MTX, TSV

(Submitter supplied) Differential expression of prostatic cell types were determined using RNA-sequencing of FACS sorted cell types from normal human prostates. The cell types sequenced were basal epithelia, luminal epithelia, a heterogeneous fibromuscular stroma and a poorly understood "other" epithelial population.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

13 Samples

Download data: JSON, TSV, TXT

(Submitter supplied) Tachykinins (TKs) are a family of peptides involved in the peripheral and central regulation of urinary functions through the stimulation of neurokinin (NK) NK1, NK2 and NK3 receptors. Recent evidence indicates that NK1 receptors are required in antigen-induced cystitis. Therefore, determining the regulatory network downstream NK1 receptor activation is a key step toward understanding the role of TKs in inflammation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL144

9 Samples

Download data

(Submitter supplied) We developed a method, CellDART, which estimates the spatial distribution of cells defined by single-cell level data using domain adaptation of neural networks, and applied to the spatial mapping of human lung tissue. The neural network that predicts the cell proportion in a pseudospot, a virtual mixture of cells from single-cell data, is translated to decompose the cell types in each spatial barcoded region. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

2 Samples

Download data: CSV, H5, JSON, PNG