GEO DataSets

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL25864

204 Samples

Download data: TXT

(Submitter supplied) Breast cancer validation study of CD4+ T cells in an independent group of 24 patients (median age [range], 61.5 [35–88] years) was recruited, based on the same inclusion criteria. All recruited patients were women. Additionally, 14 independent healthy controls were profiled.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL25864

38 Samples

Download data: TXT

(Submitter supplied) We conducted prospective clinical studies to validate the importance of CD4+ T cells in 13 diseases from the following ICD-10-CM chapters: Neoplasms (breast cancer, chronic lymphocytic leukemia); endocrine, nutritional and metabolic diseases (type I diabetes, obesity); diseases of the circulatory system (atherosclerosis); diseases of the respiratory system (acute tonsillitis, influenza, seasonal allergic rhinitis, asthma); diseases of the digestive system (Crohn’s disease [CD], ulcerative colitis [UC]); and diseases of the skin and subcutaneous tissue (atopic eczema, psoriatic diseases). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL25864

166 Samples

Download data: TXT

(Submitter supplied) A major health care problems today is that drug treatment is ineffective for many patients. This may depend on the involvement of thousands of genes, which vary between patients with the same diagnosis at different time points. Identification and prioritization of upstream regulatory (UR) genes for precision medicine are therefore great challenges. In this study, we present a framework to model dynamic cellulome- and genome-wide changes in digital twins, to prioritize UR genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

65 Samples

Download data: CSV

(Submitter supplied) The goal of this study is to discover fibroblast subpopulations relevant to recessive dystrophic epidermolysis bullosa

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

543 Samples

Download data: TXT

(Submitter supplied) We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

265 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; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

833 Samples

Download data

(Submitter supplied) We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

568 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) We used microfluidic single cell RNA-seq on mixed e16.5 mouse lung cells in order to determine the potential cell types present based on differential transcriptional profiles of the entire population using minimal cell selection bias.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

148 Samples

Download data: TXT

(Submitter supplied) To understand the molecular mechanisms of neural commitment from mouse ESCs, we selected very dense time points during neural differentiation based on qPCR results and performed mRNA-sequencing at both of cell population and single cell levels.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

113 Samples

Download data: TXT

(Submitter supplied) Abstract: The recently developed droplet-based single cell transcriptome sequencing (scRNA-seq) technology makes it feasible to perform a population-scale scRNA-seq study, in which the transcriptome is measured for tens of thousands of single cells from multiple individuals. Despite the advances of many clustering methods, there are few tailored methods for population-scale scRNA-seq studies. Here, we develop a BAyesian Mixture Model for Single Cell sequencing (BAMM-SC) method to cluster scRNA-seq data from multiple individuals simultaneously. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

11 Samples

Download data: MTX, TSV

(Submitter supplied) Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood using Ficoll-Paque density gradient centrifugation. Single-cell suspensions were stained with different antibody cocktails designed to enrich for particular immune cell populations, which were then single cell sorted in 96-well plates. Single cell RNA-sequencing libraries were subsequently generated for 2422 single cells using Smart-Seq2 (Picelli et al., Nature Methods, 2014). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15520 GPL16791

2384 Samples

Download data: TXT

(Submitter supplied) Dendritic cells (DC) are professional antigen-presenting cells that orchestrate immune responses. Important questions on the origins and differentiation paths of human DC populations remain elusive. Here we combined two high-dimensional technologies, single-cell mRNA sequencing and mass cytometry to define and characterize CD33+CD45RA+ DC precursors (pre-DC) present in human blood. In this study, we showed that a previously understimated pre-DC population shares surface markers with plasmacytoid DC (pDC), but has distinct functional properties that were previously attributed to pDC. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

18 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) The role of osteoblasts in peri-articular bone loss and bone erosion in rheumatoid arthritis (RA) has gained much attention, and microRNAs are hypothesized to play critical roles in the regulation of osteoblast function in RA. The aim of this study is to explore novel microRNAs differentially expressed in RA osteoblasts and to identify genes potentially involved in the dysregulated bone homeostasis in RA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: XLS, XLSX

(Submitter supplied) Single-cell RNA sequencing significantly deepened our insights into complex tissues and latest techniques are capable to analyze ten-thousands of cells simultaneously. With bigSCale, we provide an analytical framework being scalable to analyze millions of cells, addressing challenges of future large data sets. Unlike other methods, bigSCale does not constrain data to fit an a priori-defined distribution and instead uses an accurate numerical model of noise. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1847 Samples

Download data: CSV, H5, TXT, XLSX

(Submitter supplied) Evaluating the complex interplay of cell types in the tissue microenvironment is critical to understanding the origin and progression of diseases in the prostate and potential opportunities for intervention. Mouse models are an essential tool to investigate the molecular and cell-type-specific contributions of prostate disease at an organismal level. While there are well-documented differences in the extent, timing, and nature of disease development in various genetically engineered and exposure-based mouse models in different mouse strains and prostate lobes within each mouse strain, the underlying molecular phenotypic differences in cell types across mouse strains and prostate lobes are incompletely understood.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

20 Samples

Download data: MTX, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

78 Samples

Download data

(Submitter supplied) Prioratization of disease associated mechanisms in immune-mediated inflammatory diseases (IMIDs) is complicated by altered interactions across multiple organs and cell types. We have adressed these challenges by analyzing a multi-organ multicellular disease model (MO-MCDM) of a mouse IMID model, namely collagen-induced arthritis (CIA). In this pilot study, we sequenced at least one healthy and one CIA sample from each of the ten organs, joint, lung, muscle, skin, spleen, blood, draining lymph nodes, thymus, liver, and kidney. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

30 Samples

Download data: CSV