refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 61 results
Sort by

Filters

Technology

Platform

accession-icon GSE26168
Type 2 Diabetes mellitus: mRNA and miRNA profiling
  • organism-icon Homo sapiens, Rattus norvegicus
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina HumanRef-8 v3.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

MicroRNA 144 impairs insulin signaling by inhibiting the expression of insulin receptor substrate 1 in type 2 diabetes mellitus.

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage

View Samples
accession-icon GSE21321
Blood microRNA profiles and upregulation of hsa-miR-144 in males with type 2 diabetes mellitus.
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina HumanRef-8 v3.0 expression beadchip

Description

In this study, we compared the expression profiles of miRNAs in blood samples from Impaired Fasting Glucose (IFG) and T2D male patients. Healthy adult males with no past history of T2D (n=158) and with desirable cholesterol and blood pressure profiles were enrolled in this study. They were then classified according to fasting glucose levels to have T2D, IFG or as healthy controls (CTL), for comparison of miRNA expression profiles. Employing miRNA microarray, we identified signature miRNAs in peripheral blood samples that distinguished IFG and T2D. Eight selected miRNAs were further validated using stem-loop real-time RT-PCR. miR-144 expression was found to be dysregulated in Type 2 Diabetes, wherein its expression was significantly higher than in healthy controls. Insulin receptor substrate 1 (IRS1) has been predicted to be a potential target of miR-144. Consistent with this observation, IRS1 mRNA and protein levels, verified by quantitative real-time PCR and western blotting respectively, were found to be down-regulated.

Publication Title

MicroRNA 144 impairs insulin signaling by inhibiting the expression of insulin receptor substrate 1 in type 2 diabetes mellitus.

Sample Metadata Fields

Sex

View Samples
accession-icon GSE7123
Gene profiling of responders and non-responders to antiviral therapies peg interferon and ribavirin against hepatitis C
  • organism-icon Homo sapiens
  • sample-icon 199 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Time series of gene expression arrays before and during treatment of Hepatitis C; days 0, 1, 2, 7, 14 and 28 for 69 participants (IDs 1 through 69 are used).

Publication Title

Changes in gene expression during pegylated interferon and ribavirin therapy of chronic hepatitis C virus distinguish responders from nonresponders to antiviral therapy.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP028570
Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells
  • organism-icon Homo sapiens
  • sample-icon 32 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity. Overall design: Cells were pulsed with 4-thiouridine for 2 hours and then RNA was extracted at 0, 2, 4, and 7 hr time-points in quadruplicate from each cell line. 4sU labeling followed by RNA-seq was then used to measure the abundance of transcripts in each population. A decay rate was estimated based on the rate at which transcript abundance was reduced at these time-points.

Publication Title

Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.

Sample Metadata Fields

Cell line, Subject, Time

View Samples
accession-icon SRP069873
Effect of Ppargc1a overexpression in mouse heart
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Ppargc1a overexpression in heart tissue measured using RNA sequencing Overall design: RNA expression profiles were generated using RNA-seq from control (N=3) and Ppargc1a overexpressing (N=3) mice

Publication Title

Peroxisome proliferator-activated receptor-γ coactivator 1 α1 induces a cardiac excitation-contraction coupling phenotype without metabolic remodelling.

Sample Metadata Fields

Specimen part, Treatment, Subject

View Samples
accession-icon GSE47420
Analysis of the effects of Bmx deficiency on Angiotensin II -induced cardiac hypertrophy
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

We show that Bmx-deficiency reduces angiotensin II -induced cardiac hypertrophy and pathological gene expression

Publication Title

Endothelial Bmx tyrosine kinase activity is essential for myocardial hypertrophy and remodeling.

Sample Metadata Fields

Sex

View Samples
accession-icon SRP058702
Genome wide transcriptional alterations during post-infarct remodeling in type 2 diabetic mice.
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The cellular and molecular aspects of post-infarct left-ventricle remodeling in presence of type-2 diabetes is poorly understood. In this study we have addressed the cellular and molecular aspects underlying post-infarct left-ventricle remodeling in type 2 diabetic (T2DM) mice using genome-wide mRNA-sequencing. Myocardial infarction was induced by ligating left-anterior descending artery (LAD) in 12-14 month old T2DM and control mice. Cardiac MRI was performed at baseline, day 7 and 14 post-LAD ligation. Blood and tissue samples were collected for biochemical and immunohistochemical, molecular biology analysis after sacrification at day 7 and 14. Genome-wide mRNA sequencing analysis was performed from left-ventricular tissues collected at day 7 post-LAD ligation. Mitochondrial dynamics, Leukocyte recruitment and Collagen I deposition were analyzed using electron microscopy, fluorescent assisted cell sorting (FACS) and fourier-transform infra-red (FTIR) spectroscopy from left ventricular tissues collected at day 7 and 14 post-LAD ligation. Cardiac ejection fraction (EF) and stroke volume (SV) were significantly reduced along with increased mortality in T2DM compared to controls. Ingenuity pathway analyses of differentially expressed genes were enriched for mitochondrial dysfunction, TCA cycle and fatty acid oxidation. Additionally, upstream transcription factor analysis showed inhibition of PGC1a, PGC1b, ESRRA, ESRRB and TFAM in infarcted myocardium of T2DM mice. Electron microscopy analysis showed an altered mitochondrial dynamics and cardiomyocyte death in ischemic myocardium of T2DM mice. Leukocytes exhibited an altered phenotype in ischemic myocardium of T2DM mice. Neovascularization was impaired and collagen deposition was increased in ischemic myocardium of T2DM mice. We conclude that an altered mitochondrial dynamics, cell death modalities, leukocyte phenotype, neovascularization responses and fibrosis may contribute to an increased mortality after myocardial infarction in T2DM. Modulation of mitochondrial dynamics and cardiomyocyte cell death modalities may offer a novel therapeutic target. Overall design: Myocardial infarction was induced by ligating left anterior descending artery (LAD). Total RNA was isolated from remote, Infarct and border zones at day 7 after myocardial infarction. Poly (A)+RNA fraction was subjected to RNA sequencing using Illumina HiSeq.

Publication Title

Aggravated Postinfarct Heart Failure in Type 2 Diabetes Is Associated with Impaired Mitophagy and Exaggerated Inflammasome Activation.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE14287
Expression data from precisely staged blastula wild-type and haploid Drosophila embryos
  • organism-icon Drosophila melanogaster
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

In most embryos, the mid-blastula transition is a complex process featuring maternal RNA degradation, cell cycle pause, zygotic transcriptional activation and morphological changes. The nucleocytoplasmic (N/C) ratio has been proposed to control the multiple events at MBT. To understand the global transcriptional response to the changes of the N/C ratio, we profiled wild type and haploid embryos using cDNA microarrays at three developmental stages.

Publication Title

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP070843
RNA sequencing of siSNRNP40 in breast cancer cells
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

To identify gene expression profile changes upon SNRNP40 depletion, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting SNRNP40. Overall design: Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina HiSeq 2500.

Publication Title

Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE28109
Cell type specific gene expression map of Arabidopsis thaliana SAM.
  • organism-icon Arabidopsis thaliana
  • sample-icon 19 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Shoot apical meristem (SAM) of higher plant composed of a few distinct cell types. All the cells in a mature plants SAM derived from 30~35 stem cells reservoir which are located at the tip of the apex. Plants ability to give rise diverse cell types from a pool of pluripotent stem cells requires orchestrated gene network that controls the cell fate commitment during the meristem development. To understand, how gene regulatory networks control cell identities switches during cell differentiation requires resolution in recording their gene expression pattern at single cell resolution. An earlier expression map involving three-cell population of stem cell niche revealed complex expression pattern among the cell types1. We developed this approach further and report here a gene expression map using cell-sorting methods for fluorescent protein marked cells in Arabidopsis shoot. The map covered 10 cell populations.

Publication Title

A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche.

Sample Metadata Fields

Specimen part, Disease

View Samples
...

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)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

Powered by Alex's Lemonade Stand Foundation

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.

BSD 3-Clause LicensePrivacyTerms of UseContact