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accession-icon SRP183132
Defective zebrafish heart regeneration following depletion of let-7
  • organism-icon Danio rerio
  • sample-icon 48 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

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.

Publication Title

Modulation of TNFα Activity by the microRNA Let-7 Coordinates Zebrafish Heart Regeneration.

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon SRP124960
Timeseries of small RNA and mRNA expression during zebrafish heart regeneration
  • organism-icon Danio rerio
  • sample-icon 168 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Adult 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.

Publication Title

RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE7023
Renal Cell Carcinoma - Papillary types 1, and 2b, Normal Kidney Tissue
  • organism-icon Homo sapiens
  • sample-icon 47 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Myc oncogenic signature in Papillary type 2b

Publication Title

Detection of DNA copy number changes and oncogenic signaling abnormalities from gene expression data reveals MYC activation in high-grade papillary renal cell carcinoma.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE20874
Novel biomarkers for high grade T-cell lymphoma
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Mature 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.

Publication Title

Nuclear expression of MATK is a novel marker of type II enteropathy-associated T-cell lymphoma.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon SRP056153
RNA sequencing of SETD2 isogenic renal cell carcinoma cell lines
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

RNA sequencing of SETD2 isogenic renal cell carcinoma cell lines. Overall design: Examination of RNA expression in SETD2 isogenic cell lines

Publication Title

High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE21816
Gene expression profiling of BHDS-associated renal tumors
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Renal 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.

Publication Title

Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression.

Sample Metadata Fields

Disease, Disease stage

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accession-icon GSE39491
GLOBAL CHANGES IN GENE EXPRESSION OF BARRETT'S ESOPHAGUS COMPARED TO NORMAL SQUAMOUS ESOPHAGUS AND GASTRIC CARDIA TISSUES
  • organism-icon Homo sapiens
  • sample-icon 117 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

Barretts 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.

Publication Title

Global changes in gene expression of Barrett's esophagus compared to normal squamous esophagus and gastric cardia tissues.

Sample Metadata Fields

Specimen part

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accession-icon GSE106350
ZIC2 Is Required For Nodal Expression And The Establishment Of Left-Sided Identity
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

The 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.

Publication Title

A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity.

Sample Metadata Fields

Specimen part

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accession-icon GSE18877
Expression data from human triploid and diploid fibroblast cell cultures
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Dosage 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.

Publication Title

Dosage regulation of the active X chromosome in human triploid cells.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE18678
Expression data from ependymal layer of wild type and FoxJ1 null postnatal male mice
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

FoxJ1 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.

Publication Title

FoxJ1-dependent gene expression is required for differentiation of radial glia into ependymal cells and a subset of astrocytes in the postnatal brain.

Sample Metadata Fields

Specimen part

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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Developed by the Childhood Cancer Data Lab

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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