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accession-icon GSE71695
Characterization of RA839, a non-covalent small-molecule binder to Keap1 and selective activator of Nrf2 signalling
  • organism-icon Mus musculus
  • sample-icon 28 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The activation of the transcription factor NF-E2-related factor 2 (Nrf2) maintains cellular homeostasis in response to oxidative stress by the regulation of multiple cytoprotective genes. Without stressors the activity of Nrf2 is inhibited by its interaction with the kelch-like ECH-associated protein 1 (Keap1). Here, we describe RA839, a small molecule that binds non-covalently to the Nrf2-interacting kelch domain of Keap1 with a Kd of approximately 6 M, as demonstrated by X-ray co-crystallization and isothermal titration calorimetry. Whole-genome DNA arrays showed that at 10 M RA839 significantly regulated 105 genes in bone marrow-derived macrophages. Canonical pathway mapping of these genes revealed an activation of pathways linked with Nrf2 signalling. These pathways were also activated after the activation of Nrf2 by the silencing of Keap1 expression. RA839 regulated only two genes in Nrf2 knockout macrophages. Similar to the activation of Nrf2 by either silencing of Keap1 expression or by the reactive compound CDDO-Me, RA839 prevented the induction of both inducible nitric oxide synthase expression and nitric oxide release in response to lipopolysaccharides in macrophages. In mice RA839 acutely induced Nrf2-target gene expression in liver. RA839 is a selective inhibitor of the Keap1/Nrf2 interaction and a useful tool compound to study the biology of Nrf2.

Publication Title

Characterization of RA839, a Noncovalent Small Molecule Binder to Keap1 and Selective Activator of Nrf2 Signaling.

Sample Metadata Fields

Specimen part, Treatment

View Samples
accession-icon GSE41568
A Molecular Profile of Colorectal Cancer to Guide Therapy [PDCCEs]
  • organism-icon Homo sapiens
  • sample-icon 132 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The ability to dissect heterogeneity in colorectal cancer (CRC) is a critical step in developing predictive biomarkers. The goal of this study was to develop a gene expression based molecular subgrouping model, which predicts the likelihood that patients will respond to specific therapies.

Publication Title

Activation of the mTOR Pathway by Oxaliplatin in the Treatment of Colorectal Cancer Liver Metastasis.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP148556
Placental transcriptome in pregnancies complicated by Intrauterine growth restriction (IUGR) and preeclampsia (PE)
  • organism-icon Homo sapiens
  • sample-icon 66 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Purpose: Identify differentially expressed genes in placental samples from early-onset (EO) IUGR, EO-PE, as well as pregnancies complicated by both EO-PE and EO-IUGR Overall design: Methods: Isolated total RNA from human placenta at birth and used it for RNA-sequencing on the Hiseq2000. Sequences were aligned to the human transcriptome (hg19/genome_build37) . Aligned sequences were then used to obtain abundance measurements and conduct differential expression analysis.

Publication Title

Placental microRNAs in pregnancies with early onset intrauterine growth restriction and preeclampsia: potential impact on gene expression and pathophysiology.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE7681
Grape berry expression profiling: developmental series and treatment effects
  • organism-icon Vitis vinifera
  • sample-icon 174 Downloadable Samples
  • Technology Badge Icon Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE34748
Intragraft Gene Expression in Positive Crossmatch Kidney Allografts: Ongoing Inflammation Mediates Chronic Antibody-Mediated Injury
  • organism-icon Homo sapiens
  • sample-icon 53 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We studied intragraft gene expression profiles of positive crossmatch (+XM) kidney transplant recipients who develop transplant glomerulopathy (TG) and those who do not. Whole genome microarray analysis and quantitative rt-PCR for 30 transcripts were performed on RNA from protocol renal allograft biopsies in 3 groups: 1) +XM/TG+ biopsies before and after TG; 2) +XM/NoTG; and 3) negative crossmatch kidney transplants (control). Microarray comparisons showed few differentially expressed genes between paired biopsies from +XM/TG+ recipients before and after the diagnosis of TG. Comparing +XM/TG+ and control groups, significantly altered expression was seen for 2,447 genes (18%) and 3,200 genes (24%) at early and late time points, respectively. Canonical pathway analyses of differentially expressed genes showed inflammatory genes associated with innate and adaptive immune responses. Comparing +XM/TG+ and +XM/NoTG groups, 3,718 probe sets were differentially expressed but these were over-represented in only 4 pathways. A classic accommodation phenotype was not identified. Using rt-PCR, the expression of inflammatory genes was significantly increased in +XM/TG+ recipients compared to control biopsies and to +XM/NoTG biopsies. In conclusion, pre-transplant DSA results in a gene expression profile characterized by inflammation and cellular infiltration and the majority of XM+ grafts are exposed to chronic injury.

Publication Title

Intragraft gene expression in positive crossmatch kidney allografts: ongoing inflammation mediates chronic antibody-mediated injury.

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE7677
Grape berry developmental series from a vineyard in Willunga, South Australia (WIL-04)
  • organism-icon Vitis vinifera
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)

Description

Changes in gene expression during berry development during a grape growing season were analysed.

Publication Title

Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE8445
A comparison of gene expression between the skin and flesh tissue of grape berries (CLAsf_05)
  • organism-icon Vitis vinifera
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)

Description

Differences in gene expression were compared for grape berry flesh and skin.

Publication Title

Alignment of time course gene expression data and the classification of developmentally driven genes with hidden Markov models.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE43811
CD109 plays a role in osteoclastogenesis.
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

The primary aim of this project was to identify novel factors, in particular the cell-surface protein CD109, which regulate osteoclastogenesis. Microarray analysis was performed comparing two pre-osteoclast cell lines generated from the RAW 264.7 osteoclast cell line: one that has the capacity to fuse forming large multinucleated cells and one that does not fuse. It was found that CD109 was up-regulated by > 17-fold in the osteoclast forming cell line when compared to the cell line that does not fuse.

Publication Title

CD109 plays a role in osteoclastogenesis.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE54779
Transcriptional profiles of genes in the early stage of osteoclastogenesis
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Osteoclast (OC) differentiation undergoes a two-step process: commitment of hematopoietic progenitor cells to tartrate-resistant acid phosphatase (TRAcP) positive OC precursors (OCPs), and fusion of OCPs into multinucleated OCs. In order to identify transcriptional profiles of genes in the transitional phase between OC commitment and fusion in OCG, Affymetrix Mouse Gene 1.0 ST arrays were performed on total RNA extracted from mouse (SV129/BL6 ) monocytes and pre-osteoclasts (pre-OCs), primed with macrophage colony-stimulated factor (M-CSF) or M-CSF and soluble recombinant receptor activator of NF-B ligand (sRANKL), respectively. The analysis identified 656 RANKL-up or down-regulated in the early stage of osteoclastogenesis.

Publication Title

The actin binding protein adseverin regulates osteoclastogenesis.

Sample Metadata Fields

Specimen part

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accession-icon E-MEXP-412
Transcription profiling of R1 embryonic stem cells treated with :to DMSO and retinoic acid vs control
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430B Array (moe430b), Affymetrix Mouse Expression 430A Array (moe430a)

Description

Comparison of R1 embryonic stem cells response to DMSO and retinoic acid and control

Publication Title

Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set.

Sample Metadata Fields

Specimen part, Cell line, Compound

View Samples
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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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