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Homo sapiens
32 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Intestinal perfusion of a 40-cm segment of the small intestine in 8 healthy volunteers. 2 test days, overnight fast. Gastroduodenoscopy for tissue sampling and positioning of perfusion catheter. Continuous injection of 0.055 M glutamine (10 ml/min) in saline at 10 cm distally from the pylorus for 4 h or continuous injection of 0.055 M glucose in saline. After the injection a second gastroduodenoscopy takes place for tissue sampling. In total we have 4 samples per individual (placebo-before; placebo-after; glutamine-before; and glutamine-after injection.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Subject, Compound, Time
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Left ventricular mass (LVM) and cardiac gene expression are complex traits regulated by factors both intrinsic and extrinsic to the heart. To dissect the major determinants of LVM, we combined expression quantitative trait locus1 and quantitative trait transcript (QTT) analyses of the cardiac transcriptome in the rat. Using these methods and in vitro functional assays, we identified osteoglycin (Ogn) as a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM. We also applied genome-wide QTT analysis to the human heart and observed that, out of 22,000 transcripts, OGN transcript abundance had the highest correlation with LVM. We further confirmed a role for Ogn in the in vivo regulation of LVM in Ogn knockout mice. Taken together, these data implicate Ogn as a key regulator of LVM in rats, mice and humans, and suggest that Ogn modifies the hypertrophic response to extrinsic factors such as hypertension and aortic stenosis.
Publication Title
Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Human intervention study with two doses of iron (as ferrous gluconate via intestinal perfusion) to study the effect on genome-wide gene expression in the small intestine, in order to obtain detailed information about intestinal transcriptomics in vivo.
Publication Title
Gene expression in human small intestinal mucosa in vivo is mediated by iron-induced oxidative stress.
Sample Metadata Fields
Sex, Disease, Disease stage, Subject
View Samples- Mus musculus
- 36 Downloadable Samples
Illumina HiSeq 2000
Description
Recent studies suggest vitamin D deficiency is associated with chronic lung diseases such as asthma and chronic obstructive pulmonary disease. Each of these are characterised by airway hyperresponsiveness (AHR) and airway remodeling, the latter characterized by increased airway smooth muscle (ASM) mass. In this study we investigated the biological mechanisms underlying increased ASM mass and AHR due to vitamin D deficiency via RNA-seq transcriptome analysis of female BALB/c mice at 8 weeks of age.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 36 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA expression in adipose and skin from women with polycystic ovary syndrome (PCOS) was examined using RNA sequencing (Illumina HiSeq 50 cycle single-read sequencing) as a function of the genotype at 16 PCOS genetic risk variants. We hypothesized that the tissue expression pattern in adipose and skin would help identify candidate genes and pathways that could provide insight into the underlying mechanism for risk at these loci.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples
SRP064894- Homo sapiens
- 30 Downloadable Samples
- IlluminaHiSeq2500
Description
High-throughput sequencing of RNA (RNA-Seq) in human cancer shows remarkable potential to simultaneously identify expression levels of protein-coding genes and long non-coding RNAs (lncRNAs). We performed RNA-Seq to investigate expression level of lncRNAs and protein-coding genes in 30 esophageal samples, including 15 esophageal squamous cell carcinoma (ESCC) tissue samples and 15 paired non-tumor tissues. We further developed an integrative bioinformatics method, denoted URW-LPE (for unsupervised random walk with each dysregulated lncRNA/PCG), to identify key functional lncRNAs that regulate expression of downstream protein-coding genes in ESCC. By this method, multiple known cancer and novel potentially functional lncRNAs were effectively identified. Quantitative reverse-transcription PCR was performed to confirm the lncRNA expression level of eight novel functional lncRNAs in an additional 120 paired ESCC patient samples. Finally, we characterized lncRNA625 as a novel ESCC regulator of cell proliferation, invasion and migration. Moreover, we identified E1A-binding protein p300 (EP300) as playing a key role in executing lncRNA625-induced transcriptional responses. These findings establish the utility of integrative bioinformatics analyses of RNA-Seq to identify cancer-associated functional lncRNAs.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 20 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a), Affymetrix Rat Genome U34 Array (rgu34b)
Description
We report a comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis and gametogenesis using High Density Oligonucleotide Microarrays and highly enriched cell populations. Among 11955 rat loci investigated, 1268 were identified as differentially transcribed in germ cells at subsequent developmental stages as compared to total testis, somatic Sertoli cells as well as brain and skeletal muscle controls. The loci were organized into four expression clusters that correspond to somatic, mitotic, meiotic and post-meiotic cell types. This work provides information about expression patterns of approximately 200 genes known to be important during male germ cell development. Approximately 40 of those are included in a group of 121 transcripts for which we report germ cell expression and lack of transcription in three somatic control cell types. Moreover, we demonstrate the testicular expression and transcriptional induction in mitotic, meiotic and/or post-meiotic germ cells of 293 as yet uncharacterized transcripts some of which are likely to encode factors involved in spermatogenesis and fertility. This group also contains numerous potential germ cell specific targets for innovative contraceptives. A graphical display of the data is conveniently accessible through the GermOnline database at <a href="http://www.germonline.org" target="_blank">http://www.germonline.org</a>.
Publication Title
Expression profiling of mammalian male meiosis and gametogenesis identifies novel candidate genes for roles in the regulation of fertility.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
CH causes perivascular inflammation, enhanced pulmonary arterial constriction and remodeling leading to the development of pulmonary hypertension. Pulmonary hypertension is a debilitating disease with a high mortality rate. CH develops in patients with chronic obstructive pulmonary disease (COPD), sleep apnea or people living at high altitude. Both COPD and sleep apnea are very prevalent and pulmonary hypertension develops in a large % of COPD and sleep apnea patients. The molecular mechanisms that underlie the development of CH-induced pulmonary hypertension are far from clear. We have previously demonstrated that CH activates the Ca2+/calcineurin-regulated transcription factor NFATc3 in PASMC and that NFATc3 is required for CH-induced pulmonary hypertension in mice. Although this work was the first to identify a role for this transcription factor in an experimental model of pulmonary hypertension, since a conventional whole animal KO was used it is unknown if PASMC NFATc3 contributes to CH-induced PH. Furthermore, the genes regulated by NFATc3 in PASMC under control and CH conditions are largely unknown.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 10 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The transcriptome of the three atino80 allelic mutants was compared to that of wild-type and 50B Arabidopsis plants (see Fritsch et al. 2004). Since the transcriptomes of 50B and wild-type plants were found to be identical, we compared expression in the mutant with 50B and with wild-type without distinction. Therefore, we had four replicates of the wild type condition (50B line, wild-type) and two replicates for each of the mutant alleles (atino80-1, atino80-2 and atino80-3), all ecotype Columbia. All lines were profiled in duplicate (grown independently at 2-week-intervals).
Publication Title
The INO80 protein controls homologous recombination in Arabidopsis thaliana.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- NextSeq 500
Description
Analysis of nuclear atrial gene expression in purified atrial cardiac myocyte nuclei isolated from right atrial appendages from adult patients undergoing open-heart surgery for coronary bypass or valve correction.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples