The adult zebrafish is capable of regenerating heart muscle, resolving collagen tissue and fully restoring heart function throughout its life. The goal of this study was to investigate how the highly upregulated, epicardium-enriched microRNA let-7i functions in wound closure and cardiomyocyte proliferation. We found that depletion of let-7 in adult zebrafish using locked-nucleic acid (LNA) antisense oligonucleotides results in defective heart regeneration. We assayed gene expression at 7 days post ventricular resection in LNA-scrambled and LNA-anti-let-7 treated adult zebrafish to determine the role of let-7 during heart regeneration. Overall design: mRNA gene expression profiling at 7 days post ventricular resection in LNA-scrambled and LNA-anti-let-7 treated zebrafish.
Modulation of TNFα Activity by the microRNA Let-7 Coordinates Zebrafish Heart Regeneration.
Specimen part, Treatment, Subject
View SamplesAdult zebrafish are capable of regenerating cardiac tissue following ventricular resection within 30 days. We profiled both small RNA and mRNA expression in uninjured (0dpa), 1, 3, 7, 14, 21 and 30 days post amputation to study biological processes orchestrate each stage of regeneration. Overall design: Small and mRNA gene expression profiling during 0, 1, 3, 7, 14, 21 and 30 days post ventricular resection.
RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa.
Specimen part, Cell line, Subject
View SamplesMyc oncogenic signature in Papillary type 2b
Detection of DNA copy number changes and oncogenic signaling abnormalities from gene expression data reveals MYC activation in high-grade papillary renal cell carcinoma.
No sample metadata fields
View SamplesMature NK and T-cell lymphomas are occasionally encountered in Asia but are very rare in Western populations. In part due to its rarity, little is known about this group of neoplasms, and despite being rather different disease entities, they are all treated similarly but with diverse clinical outcomes. Novel biomarkers (at both the genetic and protein levels) are needed to resolve diagnostic difficulties, improve prognostication and develop targeted therapies. To rectify this deficiency, we interrogated the transcriptome of several NK and mature T-cell lymphomas by whole-genome expression profiling for new markers that may further stratify this diverse group of conditions. Our initial efforts have identified a promising candidate marker that appears to differentiate NKTL lymphoma from other forms of T-cell neoplasms, and this finding has been validated by immunohistochemistry on archival material in a large number of patient cases.
Nuclear expression of MATK is a novel marker of type II enteropathy-associated T-cell lymphoma.
Specimen part, Cell line
View SamplesRNA sequencing of SETD2 isogenic renal cell carcinoma cell lines. Overall design: Examination of RNA expression in SETD2 isogenic cell lines
High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma.
No sample metadata fields
View SamplesRenal tumors that arise in individuals with BHD Syndrome represent a molecularly distinct form of renal cancer. In addition, BHD syndrome is due to a mutation the folliculin gene (FLCN). While the folliculin gene is an important tumor suppressor gene, the molecular function of this gene is not well defined. By analyzing tumor samples that contain FLCN mutations, we demonstrate that the FLCN gene is an important regulator of mitochondrial function.
Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression.
Disease, Disease stage
View SamplesBarretts esophagus (BE) is a metaplastic precursor lesion of esophageal adenocarcinoma (EA), the most rapidly increasing cancer in western societies. While the prevalence of BE is increasing, the vast majority of EA occurs in patients with undiagnosed BE. Thus, we sought to identify genes that are altered in BE compared to the normal mucosa of the esophagus, and which may be potential biomarkers for the development or diagnosis of BE.
Global changes in gene expression of Barrett's esophagus compared to normal squamous esophagus and gastric cardia tissues.
Specimen part
View SamplesThe purpose of this study was to identify putative downstream targets of the transcription factor ZIC2 in the mouse embryo. The results indicate loss of NODAL pathway expression, consistent with the observed phenotype of right isomerism in heart, lungs and viscera.
A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity.
Specimen part
View SamplesDosage compensation restores a balanced network of gene expression between autosomes and sex chromosomes in males (XY) and females (XX). In mammals, this is achieved by doubling the expression of X-linked genes in both sexes, together with X inactivation in females. X up-regulation may be controlled by DNA sequence based and/or epigenetic mechanisms that double the X output potentially in response to an autosomal counting factor. Human triploids with either one or two active X chromosomes (Xa) provide a mean to test X chromosome expression in the presence of three sets of autosomes, which will help understand the underlying mechanisms of X up-regulation.
Dosage regulation of the active X chromosome in human triploid cells.
Sex, Specimen part
View SamplesFoxJ1 dependent gene expression is required for establishment of ependymal cells in the postnatal brain. This data set compares gene expression profiles of wildtype and FoxJ1 null microdissected dissected tissues at multiple postnatal time points.
FoxJ1-dependent gene expression is required for differentiation of radial glia into ependymal cells and a subset of astrocytes in the postnatal brain.
Specimen part
View Samples