GEO DataSets

(Submitter supplied) The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

8 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL571 GPL570

12 Samples

Download data: CEL

(Submitter supplied) The cellular composition of heterogeneous samples can be predicted from reference gene expression profiles that represent the homogeneous, constituent populations of the heterogeneous samples. However, existing methods fail when the reference profiles are not representative of the constituent populations. We developed PERT, a new probabilistic expression deconvolution method, to address this limitation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

4 Samples

Download data: CEL

(Submitter supplied) Samples collected from human subjects in clinical trials possess a level of complexity, arising from multiple cell types, that can obfuscate the analysis of data derived from them. Blood, for example, contains many different cell types that are derived from a distinct lineage and carry out a different immunological purpose. Failure to identify, quantify, and incorporate sources of heterogeneity into an analysis can have widespread and detrimental effects on subsequent statistical studies. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

15 Samples

Download data: CEL

(Submitter supplied) Difference in RNA content of different cell types introduces bias to gene expression deconvolution methods. If ERCC spike-ins are introduced into samples, predicted proportions of deconvolution methods can be corrected

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

14 Samples

Download data: TSV, TXT

(Submitter supplied) The cell type composition of many biological tissues varies widely across samples. Such sample heterogeneity hampers efforts to probe the role of each cell type in the tissue microenvironment. Current approaches that address this issue have drawbacks. Cell sorting or single-cell based experimental techniques disrupt in situ interactions and alter physiological status of cells in tissues. Computational methods are flexible and promising; but they often estimate either sample-specific proportions of each cell type or cell-type-specific gene expression profiles, not both, by requiring the other as input. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

40 Samples

Download data: BW, TXT

(Submitter supplied) Inner uterine lining or endometrium is a unique constantly self-renewed adult tissue that is vital for embryo implantation. As the footrace for universal endometrial receptivity markers continues, RNA-seq remains the most powerful tool for transcriptomic marker discovery. In this study, we aimed to elucidate endometrial maturation mechanisms at transcriptomic level and identify novel robust biomarker candidates for endometrial receptivity in a multicentre study. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

70 Samples

Download data: CSV, TSV

(Submitter supplied) In addition to analyzing whole-genome methylation, we concomitantly evaluated sputum cell gene expression in the context of chronic inflammatory lung disease. Nucleic acids were purified from sputum samples of subjects with Asthma, COPD as well as healthy controls. Gene expression was analyzed on the Agilent Human GE 4x44k v2 platform.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13497

25 Samples

Download data: TXT

(Submitter supplied) We evaluated the applicability and usability of whole-genome methylomics of sputum samples in molecular profiling of chronic inflammatory lung diseases. Genomic DNA was purified from sputum samples of subjects with Asthma, COPD as well as healthy controls and analyzed on the Illumina Infinium HumanMethylation 450k platform.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

26 Samples

Download data: IDAT, TXT

(Submitter supplied) Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA methylation for deconvoluting the cellular mixture of heterogeneous biospecimens such as whole blood, offer a promising solution. However, their performance depends entirely on the library of DNA methylation markers being used as the basis for deconvolution. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

18 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

655 Samples

Download data

(Submitter supplied) Dense spatial gene expression profiling of a NSCLC tumor. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

376 Samples

Download data: TXT

(Submitter supplied) Gene expression profiling of mixed cell lines, used to evaluate the performance of deconvolution methods. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

56 Samples

Download data: CSV

(Submitter supplied) Dense spatial gene expression profiling of a NSCLC tumor. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

223 Samples

Download data: CSV

(Submitter supplied) Phenotypic heterogeneity has been observed among mesenchymal stem/stromal cell (MSC) populations, but specific genes associated with this variability have not been defined. To study this question, we analyzed two distinct MSC populations isolated from the same umbilical cord blood (UCB) sample. These populations (UCB1 and UCB2) are from a single donor, minimizing differences contributed by genetic background. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS3401 GDS3402

Platforms:

GPL97 GPL96

18 Samples

Download data: CEL

Comparison of UCB1 and UCB2 cells, two distinct isogenic mesenchymal stem/stromal cell (MSC) populations isolated from umbilical cord blood. UCB1 and UCB2 display phenotypic differences. Results provide insight into the molecular basis of the phenotypic heterogeneity among MSC populations.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 specimen sets

Platform:

GPL97

Series:

GSE6029

9 Samples

Download data: CEL

Comparison of UCB1 and UCB2 cells, two distinct isogenic mesenchymal stem/stromal cell (MSC) populations isolated from umbilical cord blood. UCB1 and UCB2 display phenotypic differences. Results provide insight into the molecular basis of the phenotypic heterogeneity among MSC populations.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 specimen sets

Platform:

GPL96

Series:

GSE6029

9 Samples

Download data: CEL

(Submitter supplied) Circadian rhythm study on transcriptional responses to i.v. administered 90 kBq iodine-131 after 24h in mouse kidney cortex and medulla, liver, lungs, spleen, and thyroid. Female BALB/c nude mice (n=4/group) were i.v. injected with 90 kBq 131I at three different times of day, i.e. at 9.00 am, at 12.00 pm, or at 3.00 pm, and killed under anesthesia after 24h following treatment for excision of organs. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

136 Samples

Download data: TXT

(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