GEO DataSets

(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) We benchmarked deconvolution algorithms on human brain gene expression data. The data deposited here include A) mixtures on which algorithms were benchmarked, as well as B) signatures of pure brain cell-type expression

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676

17 Samples

Download data: CSV

(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) 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) By comparing blood mRNA responses of women with biopsy confimed Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (GC) induced pelvic inflammatory disease (PID) to those from women with CT and/or GC infection limited to their cervix and asymptomatic uninfected women determined via microarray, we discovered important pathogenic mechanisms in PID and response differences that provide a pathway to biomarker discovery. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

116 Samples

Download data: TXT

(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) Time course analysis series in Development of the transcriptome from Drosophila melanogaster using the Heidelberg FlyArray. All stages were hybridized against embryonic stage 0-4 h as reference control. Keywords: time-course

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL517

24 Samples

Download data

(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) 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:

GPL570

8 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) Next-generation sequencing of human BAL cells obtained from human patients with differing degrees of asthma in a search for variations in gene expressions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

39 Samples

Download data: TXT

(Submitter supplied) To generate this dataset in RNA-seq, we performed a mixing experiment, in which we mixed mRNAs from three cell lines: lung adenocarcinoma in humans (H1092), cancer-associated fibroblasts (CAFs) and tumor infiltrating lymphocytes (TIL), at different proportions to generate 32 samples, including 9 samples that correspond to three repeats of a pure cell line sample for three cell lines. The RNA amount of each tissue in the mixture samples was calculated on the basis of real RNA concentrations tested in the biologist’s lab. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

32 Samples

Download data: TXT

(Submitter supplied) Toxicogenomics databases are useful for understanding biological responses in individuals because they are derived from well-controlled experiments and include a diverse spectrum of biological responses. Although these databases contain no information regarding immune cells in the liver, which are important in the progression of liver injury, deconvolution that estimates cell-type proportions from bulk transcriptome could add information regarding immune cell trafficking to the database. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

61 Samples

Download data: TXT