GEO DataSets

(Submitter supplied) Gene expression of 5 different Collaborative Cross mice strains and one C57BL/6 mouse

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Single-cell expression profiling is a rich resource of cellular heterogeneity. While profiling every sample under study is advantageous, such workflow is time consuming and costly. We devised CPM - a deconvolution algorithm in which cellular heterogeneity is inferred from bulk expression data based on pre-existing collection of single-cell RNA-seq profiles. We applied CPM to investigate individual variation in heterogeneity of murine lung cells during in vivo influenza virus infection, revealing that the relations between cell quantities and clinical outcomes varies in a gradual manner along the cellular activation process. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

74 Samples

Download data: TXT

(Submitter supplied) Tissue composition is a major determinant of phenotypic variation and a key factor influencing disease outcomes. Although scRNA-Seq has emerged as a powerful technique for characterizing cellular heterogeneity, it is currently impractical for large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. To overcome these challenges, we extended Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) into a new platform for in silico cytometry. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL570 GPL20301 GPL18573

315 Samples

Download data: CEL, MTX, TSV

(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) 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:

GPL18573 GPL19057

11 Samples

Download data: MTX, TSV

(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) Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

7 Samples

Download data: MTX, TSV

(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) HiChIP data generated for the retinoic acid-induced mESC differentiation at day 4.

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

17 Samples

Download data: BEDPE

(Submitter supplied) 464 scRNA-seq samples generated for the retinoic acid-induced mESC differenation at day 4.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

464 Samples

Download data: TXT

(Submitter supplied) 96 scATAC-seq samples generated for the retinoic acid-induced mESC differentiation at day 4.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

96 Samples

Download data: XLSX

(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) Here we compare the performance of these three approaches (inDrop, Drop-seq and 10x) using the same kind of sample with a unified data processing pipeline. We generated 2-3 replicates for each method using lymphoblastoid cell line GM12891. The average sequencing depth was around 50-60k reads per cell barcode. We also developed a versatile and rapid data processing workflow and applied it for all datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

7 Samples

Download data: TXT

(Submitter supplied) Single-cell profiling of wild type lungs was performed to delineate the expression profile of epithelial, endothelial, mesenchymal and immune cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: CLOUPE

(Submitter supplied) The Sendai virus infection model induces global changes involving multiple lung cell types. At 2 weeks post-infection, when the virus had been largely cleared and the lung is undergoing repair, proliferation of endothelial cells and alveolar type 2 (AT2) cells is observed, as well as aberrant appearance Trp63/Sox2-expressing basal-like cells reminiscent of pods or lineage-negative epithelial progenitors observed upon severe H1N1 virus infection.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: CLOUPE

(Submitter supplied) We have sequenced ovarian tumors in several different ways: 1) poly-A captured scRNA-seq, 2) poly-A captured pooled scRNA-seq in pools of 4 samples each 3) Bulk RNA-seq on ribo-depleted tumor chunks 4) Bulk RNA-seq on poly-A captured dissociated cells 5) Bulk RNA-seq on ribo-depleted dissociated cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

34 Samples

Download data: MTX, TSV

(Submitter supplied) During host-pathogen encounters, the complex interactions between different immune cell-types can determine the outcome of infection. Advances in single cell RNA-seq (scRNA-seq) allow to probe this complexity of immunity, and afforded the basis for deconvolution algorithms that infer cell-type compositions from bulk RNA-seq measurements. However, immune activation, an important aspect of immune surveillance, is not represented in current algorithms. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

1 Sample

Download data: TXT

(Submitter supplied) During host-pathogen encounters, the complex interactions between different immune cell-types can determine the outcome of infection. Advances in single cell RNA-seq (scRNA-seq) allow to probe this complexity of immunity, and afforded the basis for deconvolution algorithms that infer cell-type compositions from bulk RNA-seq measurements. However, immune activation, an important aspect of immune surveillance, is not represented in current algorithms. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

62 Samples

Download data: TXT

(Submitter supplied) During host-pathogen encounters, the complex interactions between different immune cell-types can determine the outcome of infection. Advances in single cell RNA-seq (scRNA-seq) allow to probe this complexity of immunity, and afforded the basis for deconvolution algorithms that infer cell-type compositions from bulk RNA-seq measurements. However, immune activation, an important aspect of immune surveillance, is not represented in current algorithms. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

13 Samples

Download data: TXT