refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 2149 results
Sort by

Filters

Organism

Technology

Platform

accession-icon GSE68387
IMI MARCAR Project: towards novel biomarkers for cancer risk assessment
  • organism-icon Mus musculus, Rattus norvegicus, Homo sapiens
  • sample-icon 56 Downloadable Samples
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice.

Alternate Accession IDs

E-GEOD-68387

Sample Metadata Fields

Sex, Age, Specimen part, Treatment, Subject, Time

View Samples
accession-icon GSE113968
The induction and transcriptional regulation of the co-inhibitory gene module in T cells by IL-27
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Induction and transcriptional regulation of the co-inhibitory gene module in T cells.

Alternate Accession IDs

E-GEOD-113968

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE16716
MicroArray Quality Control Phase II (MAQC-II) Project
  • organism-icon Mus musculus, Rattus norvegicus, Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon

Description

The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models

Publication Title

Effect of training-sample size and classification difficulty on the accuracy of genomic predictors.

Alternate Accession IDs

E-GEOD-16716

Sample Metadata Fields

Sex, Age, Specimen part, Race, Compound

View Samples
accession-icon GSE99039
A blood-based gene signature characterizing Idiopathic Parkinson's disease
  • organism-icon Homo sapiens
  • sample-icon 558 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Establishing reliable biomarkers for assessing and validating clinical diagnosis at early prodromal stages of Parkinson’s disease is crucial for developing therapies to slow or halt disease progression. Here, we present the largest study to date using whole blood gene expression profiling from over 500 individuals to identify an 87-gene blood-based signature. Our gene signature effectively differentiates between idiopathic PD patients and controls in both a validation cohort and an independent test cohort, and further highlights mitochondrial metabolism and ubiquitination/proteasomal degradation as potential pathways disrupted in Parkinson’s disease.

Publication Title

Analysis of blood-based gene expression in idiopathic Parkinson disease.

Alternate Accession IDs

E-GEOD-99039

Sample Metadata Fields

Sex, Specimen part, Subject

View Samples
accession-icon GSE30140
Expression data from livers of F2 mice (C57BL/6 X DBA/2) deficient in leptin receptor (db/db)
  • organism-icon Mus musculus
  • sample-icon 435 Downloadable Samples
  • Technology Badge Icon

Description

In several models of obesity-induced diabetes, increased lipid accumulation in the liver has been associated with decreased diabetes susceptibility. For instance, deficiency in leptin receptor (db/db) leads to hyperphagia and obesity in both C57BL/6 and C57BLKS mice but, only on the C57BLKS background do the mice develop beta-cell loss leading to severe diabetes while C57BL/6 mice are relatively resistant. Liver triglyceride levels in the resistant C57BL/6 mice are 3 to 4 fold higher than in C57BLKS.

Publication Title

Systems genetics of susceptibility to obesity-induced diabetes in mice.

Alternate Accession IDs

E-GEOD-30140

Sample Metadata Fields

Sex, Age

View Samples
accession-icon GSE72088
Exploiting microRNA and mRNA profiles generated in vitro from carcinogen-exposed primary mouse hepatocytes for predicting in vivo genotoxicity and carcinogenicity
  • organism-icon Mus musculus
  • sample-icon 54 Downloadable Samples
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Exploiting microRNA and mRNA profiles generated in vitro from carcinogen-exposed primary mouse hepatocytes for predicting in vivo genotoxicity and carcinogenicity.

Alternate Accession IDs

E-GEOD-72088

Sample Metadata Fields

Specimen part, Compound

View Samples
accession-icon GSE21687
Comparative genomics matches mutations and cells to generate faithful ependymoma models
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon

Description

Genomic technologies have unmasked molecularly distinct subgroups among tumors of the same histological type; but understanding the biologic basis of these subgroups has proved difficult since their defining alterations are often numerous, and the cellular origins of most cancers remain unknown. We sought to decipher complex genomic data sets by matching the genetic alterations contained within these, with candidate cells of origin, to generate accurate disease models. Using an integrated genomic analysis we first identified subgroups of human ependymoma: a form of neural tumor that arises throughout the central nervous system (CNS). Validated alterations included amplifications and homozygous deletions of genes not yet implicated in ependymoma. Matching the transcriptomes of human ependymoma subgroups to those of distinct types of mouse radial glia (RG)neural stem cells (NSCs) that we identified previously to be a candidate cell of origin of ependymoma - allowed us to select RG types most likely to represent cells of origin of disease subgroups. The transcriptome of human cerebral ependymomas that amplify EPHB2 and delete INK4A/ARF matched most closely that of embryonic cerebral Ink4a/Arf-/- RG: remarkably, activation of EphB2 signaling in this RG type, but not others, generated highly penetrant ependymomas that modeled accurately the histology and transcriptome of one human cerebral tumor subgroup (subgroup D). Further comparative genomic analysis revealed selective alterations in the copy number and expression of genes that regulate neural differentiation, particularly synaptogenesis, in both mouse and human subgroup D ependymomas; pinpointing this pathway as a previously unknown target of ependymoma tumorigenesis. Our data demonstrate the power of comparative genomics to sift complex genetic data sets to identify key molecular alterations in cancer subgroups.

Publication Title

Cross-species genomics matches driver mutations and cell compartments to model ependymoma.

Alternate Accession IDs

E-GEOD-21687

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage

View Samples
accession-icon GSE27948
Pharmacology of PPAR isoform agonists on mouse
  • organism-icon Mus musculus
  • sample-icon 109 Downloadable Samples
  • Technology Badge Icon

Description

Transcriptional consequences of pharmacologic PPAR a, d, & g agonist administration in murine liver, heart, kidney, and skeletal muscle

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-27948

Sample Metadata Fields

Specimen part, Compound, Time

View Samples
accession-icon GSE37382
Subgroup specific somatic copy number aberrations in the medulloblastoma genome [mRNA]
  • organism-icon Homo sapiens
  • sample-icon 285 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.1 ST Array (hugene11st)

Description

Affymetrix Human Gene 1.1 ST Array profiling of 285 primary medulloblastoma samples.

Publication Title

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Alternate Accession IDs

E-GEOD-37382

Sample Metadata Fields

Sex, Age

View Samples
accession-icon ERP006948
Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages
  • organism-icon Danio rerio
  • sample-icon 276 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Paired-end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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
Version 1.42.67-hotfix - .0.0