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accession-icon GSE9234
Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

three replicates of HT29 cells per conditionwere grown under normoxic and hypoxic conditions. RNA and miRNA was extracted from each replicate and run on the GPL570 and GPL5106 arrays respectively.

Publication Title

Role of oxygen availability in CFTR expression and function.

Alternate Accession IDs

E-GEOD-9234

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE7570
ATR1_like_Clade_OE_and_miR
  • organism-icon Arabidopsis thaliana
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

check the effect of over expression and down regulation of this clade of TFs

Publication Title

The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators.

Alternate Accession IDs

E-GEOD-7570

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP183071
GOYA DLBCL clinical trial - RNASeq dataset
  • organism-icon Homo sapiens
  • sample-icon 502 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

This dataset contains collected RNASeq data of 552 samples from the GOYA clinical trial. Overall design: The GOYA trial tested the efficacy of Gazyva (GA101) compared with Rituxan (Rituximab) in first line, untreated DLBCL patients. Patients were randomized 1:1 to either G or R combined with a CHOP chemotherapy backbone. Tumor samples were collected at baseline, RNA was isolated using RNA-Access, and RNASeq was run with TruSeq (Illumina) RNASeq.

Publication Title

PD-L1 and tumor-associated macrophages in de novo DLBCL.

Alternate Accession IDs

GSE125966

Sample Metadata Fields

Treatment, Subject

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accession-icon GSE47744
Molecular mechanisms vascular smooth muscle cell (VSMC) acquisition of macrophage features in response to cholesterol loading
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

In this study, murine primary aortic smooth muscle cells (SMCs) were transcriptionally profiled at baseline, after 3 d of cholesterol loading, and after 3 d of subsequent cholesterol unloading with HDL treatment, to identify vascular SMC genes that are transcripionally dysregulated in response to cholesterol loading and/or unloading.

Publication Title

Cholesterol loading reprograms the microRNA-143/145-myocardin axis to convert aortic smooth muscle cells to a dysfunctional macrophage-like phenotype.

Alternate Accession IDs

E-GEOD-47744

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE72632
Licensing Delineates Helper and Effector NK Cell Subsets During Viral Infection
  • organism-icon Mus musculus
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Natural killer (NK) cells can be divided into phenotypic subsets based on the expression of receptors that bind self-MHC-I molecules with differing affinities; a concept termed licensing or education. Here we show that NK cell subsets exhibit markedly different migratory, effector, and immunoregulatory functions on dendritic cells and antigen-specific CD8+ T cell responses during influenza and murine cytomegalovirus infections. Shortly after infection, unlicensed NK cells preferentially trafficked to draining lymph nodes and produced GM-CSF, which promoted the expansion and activation of dendritic cells, and ultimately resulted in sustained antigen-specific CD8+ T cell responses. In contrast, licensed NK cells preferentially migrated to infected parenchymal tissues and produced greater levels of interferon- (IFN-). Importantly, human NK cell subsets exhibited similar phenotypic characteristics and patterns of cytokine production. Collectively, our studies demonstrate a critical demarcation between the functions of licensed and unlicensed NK cell subsets, with the former functioning as the classical effector subset in inflamed tissues and the latter as modulators of adaptive immunity helping to prime immune responses in draining lymph nodes.

Publication Title

Licensing delineates helper and effector NK cell subsets during viral infection.

Alternate Accession IDs

E-GEOD-72632

Sample Metadata Fields

Specimen part

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accession-icon GSE11703
Effect of v-erbA on RA-responsive genes in AML12 hepatocytes
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The v-erbA oncogene belongs to a superfamily of transcription factors called nuclear receptors, which includes the retinoic acid receptors (RARs) responsible for mediating the effects of retinoic acid (RA). Nuclear receptors bind to specific DNA sequences in the promoter region of target genes and v-erbA is known to exert a dominant negative effect on the activity of the RARs. The repressor activity of v-erbA has been linked to the development of hepatocellular carcinoma (HCC) in a mouse model. We have used microarray analysis to identify genes differentially expressed in hepatocytes in culture (AML12 cells) stably transfected with v-erbA and exposed to RA. We have found that v-erbA can affect expression of RA-responsive genes. We have also identified a number of v-erbA-responsive genes that are known to be involved in carcinogenesis and which may play a role in the development of HCC.

Publication Title

Modulation of expression of RA-regulated genes by the oncoprotein v-erbA.

Alternate Accession IDs

E-GEOD-11703

Sample Metadata Fields

Specimen part, Cell line

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accession-icon E-MEXP-153
Transcription profiling of prop-1 and Ghrhr mutations in gene expression during normal aging in mice (Ames dwarf and Little mice)
  • organism-icon Mus musculus
  • sample-icon 48 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

Effects of the prop-1 and Ghrhr mutations in gene expression during normal aging in mice.

Publication Title

Gene expression profile of long-lived Ames dwarf mice and Little mice.

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage

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accession-icon E-MEXP-347
Transcription profiling of long-lived Ames dwarf mice investigating the loss of liver sexual dimorphism
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice.

Publication Title

Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice.

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE8564
Analysis of Aire effects on individual mice of different genetic backgrounds
  • organism-icon Mus musculus
  • sample-icon 19 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We compared gene expression profiles of aire-deficient and wild-type littermate thymic medullary epithelial cells. This was done in order to determine whether Aire's effects differed among strains, and also among individuals of the same strain.

Publication Title

The variable immunological self: genetic variation and nongenetic noise in Aire-regulated transcription.

Alternate Accession IDs

E-GEOD-8564

Sample Metadata Fields

Sex

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accession-icon GSE8563
Lymphtoxin pathway effects on thymic medullary epithelial cells
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We compared gene expression profiles of lymphotoxin alpha- and lymphtoxin beta receptor-deficient thymic medullary epithelial cells with their wild-type littermates, as well as with Aire-deficient and wild-type littermates. This was done in order to determine whether there was overlap in the effects of lymphotoxin and aire.

Publication Title

Lymphotoxin pathway and Aire influences on thymic medullary epithelial cells are unconnected.

Alternate Accession IDs

E-GEOD-8563

Sample Metadata Fields

Sex

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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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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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