refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
    0
github link
Showing
of 399 results
Sort by

Filters

Technology

Platform

accession-icon GSE27038
Expression data from the Ire1 null and control murine livers in the absence or presence of ER stress
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Ire1 conditional null or control mice of 3-months old were injected intraperitoneally with TM or vehicle.

Publication Title

The unfolded protein response transducer IRE1α prevents ER stress-induced hepatic steatosis.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE63362
Identification of sexually dimorphically expressed genes in rat tissues
  • organism-icon Rattus norvegicus
  • sample-icon 256 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

The sexually dimorphic expression of genes across 26 somatic rat tissues was using Affymetrix RAE-230 genechips. We considered probesets to be sexually dimorphically expressed (SDE) if they were measurably expressed above background in at least one sex, there was at least a two-fold difference in expression (dimorphism) between the sexes, and the differences were statistically significant after correcting for false discovery. 14.5% of expressed probesets were SDE in at least one tissue, with higher expression nearly twice as prevalent in males compared to females. Most were SDE in a single tissue. Surprisingly, nearly half of the probesets that were (SDE) in multiple tissues were oppositely sex biased in different tissues, and most SDE probesets were also expressed without sex bias in other tissues. Two genes were widely SDE: Xist (female-only) and Eif2s3y (male-only). The frequency of SDE probesets varied widely between tissues, and was highest in the duodenum (6.2%), whilst less than 0.05% in over half of the surveyed tissues. The occurrence of SDE probesets was not strongly correlated between tissues. Within individual tissues, however, relational networks of SDE genes were identified. In the liver, networks relating to differential metabolism between the sexes were seen. The estrogen receptor was implicated in differential gene expression in the duodenum. To conclude, sexually dimorphic gene expression is common, but highly tissue-dependent. Sexually dimorphic gene expression may provide insights into mechanisms underlying phenotypic sex differences.

Publication Title

The incidence of sexually dimorphic gene expression varies greatly between tissues in the rat.

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE31503
Exposure to Nickel, Chromium, or Cadmium Causes Distinct Changes in the Gene Expression Patterns of a Rat Liver Derived Cell Line
  • organism-icon Rattus norvegicus
  • sample-icon 44 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Many heavy metals, including nickel (Ni), cadmium (Cd), and chromium (Cr) are toxic industrial chemicals with an exposure risk in both occupational and environmental settings that may cause harmful outcomes. While these substances are known to produce adverse health effects leading to disease or health problems, the detailed mechanisms remain unclear. To elucidate the processes involved in the of toxicity of nickel, cadmium, and chromium at the molecular level and to perform a comparative analysis, H4-II-E-C3 rat liver-derived cell lines were treated with soluble salts of each metal using concentrations derived from viability assays, and gene expression patterns were determined with DNA microarrays.

Publication Title

Exposure to nickel, chromium, or cadmium causes distinct changes in the gene expression patterns of a rat liver derived cell line.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE41366
Alterations in gene expression in Caenorhabditis elegans associated with organophosphate pesticide intoxication and recovery
  • organism-icon Caenorhabditis elegans
  • sample-icon 146 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

The principal toxicity of acute organophosphate (OP) pesticides poisoning is the disruption of neurotransmission through inhibition of acetylcholinesterase (AChE). However, other mechanisms leading to persistent effects and neurodegeneration remain controversial and difficult to detect. Because Caenorhabditis elegans is relatively resistant to OP lethalityparticularly through the inhibition of AChEstudies in this nematode provide an opportunity to observe alterations in global gene expression following OP exposure that cannot be readily observed in less resistant organisms.

Publication Title

Alterations in gene expression in Caenorhabditis elegans associated with organophosphate pesticide intoxication and recovery.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE6420
Effect of LARK overexpression in CNS neurons
  • organism-icon Drosophila melanogaster
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome Array (drosgenome1)

Description

The goal of this study is to identify, in the head of adult flies, mRNA species whose expresson level are altered by overexpression of the Drosophila RNA-binding protein LARK in CNS neurons.

Publication Title

The LARK RNA-binding protein selectively regulates the circadian eclosion rhythm by controlling E74 protein expression.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE51502
Use of an activated beta-catenin to identify Wnt/beta-catenin pathway target genes in C. elegans, including a subset of collagen genes expressed in late larval development
  • organism-icon Caenorhabditis elegans
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

The Wnt signaling pathway plays a fundamental role during the development of metazoans, where it functions in the regulation of diverse processes including cell fate specification, cell migration, and stem cell renewal. Activation of the beta-catenin dependent or canonical Wnt signaling pathway upregulates expression of Wnt target genes to mediate an appropriate cellular response. In the nematode C. elegans, a Wnt signaling pathway similar to the canonical pathway regulates several processes during larval development, however few target genes of this pathway have been identified. To address this deficit, we conditionally activated Wnt signaling in living animals during a defined stage of larval life by expressing a dominant, activated beta-catenin protein, then used microarray analysis to identify genes showing altered expression compared to control animals. In this way we identified 166 differentially expressed genes, of which 104 were upregulated. A subset of the upregulated genes were validated by qPCR and showed altered expression in Wnt pathway mutants with decreased or increased Wnt signaling; we consider these genes to be candidate Wnt pathway targets in the C. elegans hermaphrodite larva. Amongst these was a group of 6 genes, including the cuticular collagen genes, bli-1 col-38, col-49 and col-71, that show a peak of expression in the mid L4 stage during normal development. The L4 expression of these genes suggests they may be expressed for use in the adult cuticle, and consistent with this, reduction of function for several of the genes leads to phenotypes suggestive of defects in cuticle function or integrity. Therefore this work has identified a large number of putative Wnt pathway target genes during larval life, including a small subset of Wnt-regulated collagen genes that may function in synthesis of the adult cuticle.

Publication Title

Use of an activated beta-catenin to identify Wnt pathway target genes in caenorhabditis elegans, including a subset of collagen genes expressed in late larval development.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE6418
RNAs associated with LARK in Drosophila pharate adult brain
  • organism-icon Drosophila melanogaster
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome Array (drosgenome1)

Description

Circadian behaviors are regulated by intrinsic biological clocks consisting of central molecular oscillators and output pathways. Despite significant progress in elucidating the central timekeeping mechanisms, the molecular pathways coupling the circadian pacemaker to overt rhythmic behavior and physiology remain elusive. The Drosophila LARK RNA-binding protein is a candidate for such a coupling factor. Previous research indicates that LARK functions downstream of the clock to mediate behavioral outputs. To better understand the roles of LARK in the Drosophila circadian system, we sought to identify RNA molecules associated with LARK in vivo, using a novel strategy that involves capturing the RNA ligands by immunoprecipitation, visualizing the captured RNAs using whole gene microarrays, and identifying functionally relevant targets through genetic screens.

Publication Title

The LARK RNA-binding protein selectively regulates the circadian eclosion rhythm by controlling E74 protein expression.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE85359
Gene expression data from the sham and irradiated lungs of three murine strains with well-characterized phenotypic variation in pulmonary radiation response.
  • organism-icon Mus musculus
  • sample-icon 25 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Intrinsic variations in the development of lung injury among patients undergoing radiotherapy for tumors in the thoracic region suggest there are one or more genes that influence the development and severity of radiation pneumonitis and/or fibrosis.

Publication Title

Pathophysiological mechanisms underlying phenotypic differences in pulmonary radioresponse.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP049377
RNA-Seq data for five HER2 over-expressed samples with twelve green fluorescent protein control samples using human mammary epithelial cells
  • organism-icon Homo sapiens
  • sample-icon 17 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

Purpose: The goal was to capture the transcriptional activity due to over-expression of HER2 protein. We profiled this transcriptional activity using two different RNA-Seq alignment and quantification pipelines. We also used these samples to generate a gene expression signature of HER2 pathway activity. Over-expression was validated using Western blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in FPKM and TPM . Overall design: A profile of gene expression, downstream of ERBB2/HER2 over-expression, was generated in cells derived from breast and used to generate a gene-expression signature reflective of HER2 pathway activation status.

Publication Title

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP161807
Single cell RNA sequencing identifies unique inflammatory airspace macrophage subsets
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

In this study, we characterize transciprtional phenotypes of airway macrophagages (AMs) throughout homeostatsis, inflammation, and repair at single cell granularity. We confirm that cell origin is the major determinant of AM programing and describe two previously uncharacterized, transcriptionally distinct subdivisions of AMs based on proliferative capacity and inflammatory programing. Overall design: We stimulated mice with LPS and then sampled FACs sorted airway macrophage cells using BAL at Days 0, 3, and 6 and sequenced 1,134 cells from these three groups using RNA-seq

Publication Title

Single cell RNA sequencing identifies unique inflammatory airspace macrophage subsets.

Sample Metadata Fields

Specimen part, Cell line, Subject

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