refine.bio
  • Search
      • Normalized Compendia
      • RNA-seq Sample Compendia
  • Docs
  • About
  • My Dataset
github link
Showing
of 4476 results
Sort by

Filters

Organism

Technology

Platform

accession-icon GSE9018
IgA impact on distal small intestine after colonization with B. thetaiotaomicron
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Wildtype B6, Rag1-/- B6 and Rag1-/- B6 mice harboring the 225.4 IgA producing hybridoma were colonized for 10 days with Bacteroides thetaiotaomicron

Publication Title

IgA response to symbiotic bacteria as a mediator of gut homeostasis.

Alternate Accession IDs

E-GEOD-9018

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE17156
Gene expression signatures of symptomatic respiratory viral infection in adults
  • organism-icon Homo sapiens
  • sample-icon 113 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

Diagnosis of acute respiratory viral infection is currentlybased on clinical symptoms and pathogen detection. Use of host peripheral blood gene expression data to classify individuals with viral respiratory infection represents a novel means of infection diagnosis.

Publication Title

Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans.

Alternate Accession IDs

E-GEOD-17156

Sample Metadata Fields

Subject, Time

View Samples
accession-icon GSE1413
AKT_Prostate_RAD001_v_PLACEBO
  • organism-icon Mus musculus
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

Transgenic (Probasin driven Myr-AKT)or wild-type littermates were treated with RAD001 or placebo and sacrificed at 12 and 48 hours following the beginning of treatment

Publication Title

mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways.

Alternate Accession IDs

E-GEOD-1413

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE46403
Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.

Alternate Accession IDs

E-GEOD-46403

Sample Metadata Fields

Specimen part, Treatment, Time

View Samples
accession-icon GSE46319
Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome [Affymetrix]
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germline and may be mediated by Tet (ten-eleven-translocation) enzymes, which convert 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC). Tet enzymes have been extensively studied in mouse embryonic stem (ES) cells, which are generally cultured in the absence of Vitamin C, a potential co-factor for Fe(II) 2-oxoglutarate dioxygenase enzymes like Tets. Here we report that addition of Vitamin C to ES cells promotes Tet activity leading to a rapid and global increase in hmC. This is followed by DNA demethylation of numerous gene promoters and up-regulation of demethylated germline genes. Tet1 binding is enriched near the transcription start site (TSS) of genes affected by Vitamin C treatment. Importantly, Vitamin C, but not other antioxidants, enhances the activity of recombinant human Tet1 in a biochemical assay and the Vitamin C-induced changes in hmC and mC are entirely suppressed in Tet1/2 double knockout (Tet DKO) ES cells. Vitamin C has the strongest effects on regions that gain methylation in cultured ES cells compared to blastocysts and in vivo are methylated only after implantation. In contrast, imprinted regions and intracisternal A-particle (IAP) elements, which are resistant to demethylation in the early embryo, are resistant to Vitamin C-induced DNA demethylation. Collectively, this study establishes that Vitamin C is a direct regulator of Tet activity and DNA methylation fidelity in ES cells.

Publication Title

Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.

Alternate Accession IDs

E-GEOD-46319

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE8955
atmyc2_cop1_mutant_light_ABA_treatment
  • organism-icon Arabidopsis thaliana
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Although many regulatory components of light signaling have been functionally characterized, only a few of them have been reported to cross talk with other signaling cascades. In this study, we have analyzed the expression profiles of Arabidopsis genes in wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant seedlings grown under constant dark, constant blue-light, and constant blue-light along with abscisic acid (ABA) to illustrate the interplay of negative regulators, AtMYC2 and COP1, in light and ABA signaling

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-8955

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon E-MEXP-2714
Genome wide analysis of glucose brassinosteroid interaction in Arabidopsis
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Arabidopsis thaliana seeds after imbibition were inoculated in ½ MS medium supplemented with 0.8% agar and 1% sucrose. Once the plant material was uniformly germinated, the experimental conditions were applied. 5d old light-grown uniformly germinated seedlings were washed seven times with sterile water with last wash given by ½ MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ½ MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22oC for 24 h and then 3 h treatment was given with liquid ½ MS without glucose and liquid ½ MS supplemented with BR (0.1 ?M EBR), glucose (3%), glucose (3%) + BR (0.1 ?M EBR). Seedlings were harvested after 3h and preceded for RNA isolation and Microarray analysis.

Publication Title

Genome wide Analysis of Glucose and Brassinosteroid Signaling Interactions in Arabidopsis thaliana

Alternate Accession IDs

None

Sample Metadata Fields

Age, Time

View Samples
accession-icon GSE52845
Molecular pathways reflecting poor intrauterine growth are imprinted in Wharton's jelly derived Mesenchymal Stem Cells
  • organism-icon Homo sapiens
  • sample-icon 11 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Molecular pathways reflecting poor intrauterine growth are found in Wharton's jelly-derived mesenchymal stem cells.

Alternate Accession IDs

E-GEOD-52845

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE52843
Molecular pathways reflecting poor intrauterine growth are imprinted in Whartons jelly derived Mesenchymal Stem Cells [set3]
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

In order to identify gene-expression patterns in mesenchymal stem cells associated with different birth weights and intrauterine growth parameters,

Publication Title

Molecular pathways reflecting poor intrauterine growth are found in Wharton's jelly-derived mesenchymal stem cells.

Alternate Accession IDs

E-GEOD-52843

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE52844
Molecular pathways reflecting poor intrauterine growth are imprinted in Whartons jelly derived Mesenchymal Stem Cells [set4]
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

In order to identify gene-expression patterns in mesenchymal stem cells associated with different birth weights and intrauterine growth parameters,

Publication Title

Molecular pathways reflecting poor intrauterine growth are found in Wharton's jelly-derived mesenchymal stem cells.

Alternate Accession IDs

E-GEOD-52844

Sample Metadata Fields

Specimen part

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