GEO DataSets

Gene atlas of human protein-encoding transcriptome. Examined gene expression profiles from 79 physiologically normal tissues obtained from various sources.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 79 tissue sets

Platform:

GPL96

Series:

GSE1133

158 Samples

Download data: CEL

(Submitter supplied) The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS592 GDS596

Platforms:

GPL1074 GPL96 GPL1073

438 Samples

Download data: CEL

Gene atlas of mouse protein-encoding transcriptome. Gene expression profiles from 61 physiologically normal tissues. Samples generated from adult (10-12 week old) C57BL/6 mice (4 male, 3 female) by dissection.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 61 tissue sets

Platform:

GPL1073

Series:

GSE1133

122 Samples

Download data: CEL

(Submitter supplied) Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we perform allele-specific RNA-Seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic stages and in pluripotent cell lines. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos or from embryos obtained after nuclear transfer (NT), as well as B6D2F1 ESCs and EpiSCs derived after parthenogenetic activation (PGA). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112 GPL11002

22 Samples

Download data: WIG

(Submitter supplied) During early mammalian development transient pools of pluripotent cells emerge that can be immortalised upon stem cell derivation. The pluripotent state, "naïve" or "primed", depends on the embryonic stage and derivation conditions used. Here we analyse the temporal gene expression patterns of mouse, cattle and porcine embryos at stages that harbour different types of pluripotent cells. We document conserved and divergent traits in gene expression, and identify predictor genes shared across the species that are associated with pluripotent states in vivo and in vitro Amongst these are the pluripotency-linked genes Klf4 and Lin28b The novel genes discovered include naïve- (Spic, Scpep1 and Gjb5) and primed-associated (Sema6a and Jakmip2) genes as well as naïve-to primed transition genes (Dusp6 and Trip6). more...

Organism:

Mus musculus; Sus scrofa; Bos taurus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

34 Samples

Download data: BEDGRAPH, WIG

(Submitter supplied) In this study, we screened human placental samples for allele-specific methylation and subsequently novel imprinted genes associated with these regions. We used reduced representation bisulfite sequencing to identify partially methylated CpG islands (CGIs) in the human placental genome. We were able to delineate potential candidates for allele-specific methylation based on the calculation of a concordance statistic. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL10999

10 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array

5 related Platforms

10 Samples

Download data: CEL, CHP

(Submitter supplied) Comparison of gene expression levels between matUPD18 and patUPD18 8.5 dpc whole embryo samples (maternal versus paternal uniparental disomy of Chr 18). Identification of highly differentially expressed transcripts. Keywords: genetic modification

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

2 Samples

Download data: CEL, CHP

(Submitter supplied) Comparison of gene expression levels between matUPD12 and patUPD12 15.5 dpc whole embryo or placenta samples (maternal versus paternal uniparental disomy of Chr 12). Identification of highly differentially expressed transcripts. Keywords: genetic modification

Organism:

Mus musculus

Type:

Expression profiling by array

4 related Platforms

8 Samples

Download data: CEL, CHP

(Submitter supplied) During oogenesis, DNA methyltransferase 3-like (Dnmt3l) is required for the establishment of the maternal germline DNA methylation imprints that in the offspring, govern the parent-of-origin-specific expression of most known imprinted genes (Science 2001, 294:2536-9). Dnmt3l-deficient dams were crossed with wildtype sires to obtain Dnmt3l-/+ embryos that lack maternal methylation imprints. Gene expression was measured in Dnmt3l-/+ and wildtype embryos and is expected to differ for imprinted genes that are under the control of a maternal methylation mark. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

3 Samples

Download data: CEL, CHP

(Submitter supplied) ChIP-seq for CTCF and Rad21 in 3 week old mouse brain from reciprocal BxC and CxB crosses. One biological replicate of each.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

8 Samples

Download data: BAM

(Submitter supplied) An oligonucleotide microarray study of 42,000 new and predicted mouse genes across a comprehensive set of 55 tissues Keywords: other

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1537

55 Samples

Download data

(Submitter supplied) RNA Polymerase-II active regions were mapped comparing mouse neural retina tissue at age P25 and P2 to find novel gene activation predictions during maturation of photoreceptors. Over 800 predictions of increased activation were novel compared to previous mRNA expression array studies.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

3 Samples

Download data: BED, CEL

(Submitter supplied) Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on E17.5 mouse placenta cDNA samples from reciprocal cross F1 progeny of AKR and PWD mouse strains, and quantified the allele-specific expression and the degree of parent-of-origin effect transcriptome-wide. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9185

2 Samples

Download data: SAM

(Submitter supplied) Mouse embryo fibroblasts (MEFs) closely resemble mouse embryos and are convenient sources for biochemical studies when cell number may be limiting from mouse embryos. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we characterized them using strand- and allele-specific RNA deep sequencing. We used Sequenom allelotyping in embryo and adult organs to verify parental allele-specific expression patterns. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: GFF

(Submitter supplied) Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. Here we have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. more...

Organism:

Candida albicans

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10637 GPL10636

12 Samples

Download data: TXT

(Submitter supplied) Background: DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

70 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Expression profiling by RT-PCR

Platforms:

GPL10331 GPL18234

32 Samples

Download data

(Submitter supplied) RNA samples were prepared from freshly sorted mammary cell subpopulations (MaSC/basal-enriched, luminal progenitor, mature luminal and stromal) from five sets of adult mice. High throughput RT-PCR was used to measure the global microRNA expression profiles of each cell subpopulation. The expression profiles were compared between cell subpopulations to gain insight into the regulation of lineage-restricted genes.

Organism:

Rattus norvegicus; Mus musculus

Type:

Expression profiling by RT-PCR

Platform:

GPL10331

14 Samples

Download data: XLS

(Submitter supplied) RNA samples were prepared from freshly sorted mammary cell subpopulations (MaSC/basal-enriched, luminal progenitor, mature luminal and stromal) from five human donors. High throughput RT-PCR was used to measure the global microRNA expression profiles of each cell subpopulation. The expression profiles were compared between cell subpopulations to gain insight into the regulation of lineage-restricted genes.

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL18234

18 Samples

Download data: XLS