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accession-icon GSE38332
Identification of Nrf2-regulated genes in A549 lung cancer cells by oligonucleotide microarray
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

To elucidate the mechanisms by which Nrf2 regulates cell growth, we performed global gene expression profiling of A549 lung cancer cells with knockdown of Nrf2. Gene networks associated with carbohydrate metabolism and drug metabolism were significantly downregulated in Nrf2-depleted A549 cells. Gene Set Enrichment Analysis revealed significant enrichment of genes associated with carbohydrate catabolic processes, positive regulation of metabolic processes, PPP, and arachidonic acid metabolism. In summary, this analysis revealed that Nrf2 positively regulates transcription of genes that play key roles in central carbon metabolism.

Publication Title

Transcription factor NRF2 regulates miR-1 and miR-206 to drive tumorigenesis.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE113717
De novo lipogenesis represents a therapeutic target in Kras mutant NSCLC
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

We examine the potential of Kras as a metabolic target in lung cancer using the KrasLSL-G12D lung cancer model. We demonstrate that mutant Kras drives a lipogenic gene expression program, and that fatty acid synthesis is important in Kras-induced tumorigenesis.

Publication Title

De novo lipogenesis represents a therapeutic target in mutant Kras non-small cell lung cancer.

Sample Metadata Fields

Specimen part

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accession-icon GSE32328
Macrophage response to serum in culture medium
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Most cell culture experiments utilize media containing fetal calf serum. Results are often interpreted regarding importance to human pathways. We studied gene expression in mouse macrophages grown in the absence of serum, and in fetal calf serum, mouse serum, and human serum using genome wide expression systems in resting conditions and after stimulation with lipopolysaccharide.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE3583
Huntington's disease: Gene expression changes caused by Hdh CAG mutation or 3-nitropropionic acid in striatal cells
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Affymetrix MG430 2.0 expression levels of wild-type (STHdhQ7/Q7), 3NP-treated wild-type (STHdhQ7/Q7+3-NP), and mutant (STHdhQ111/Q111) striatal cells

Publication Title

Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE2210
Microarray-assisted Cloning of Mutants: Expression Profiling of tom-1 and unc-43
  • organism-icon Caenorhabditis elegans
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

Analysis of gene expression data in two C.elegans mutant strains: KP3293 tom-1(nu468) and KP3365 unc-43(n1186); hif-1(nu469). These results support the utility of microarray hybridizations to facilitate positional cloning.

Publication Title

Using microarrays to facilitate positional cloning: identification of tomosyn as an inhibitor of neurosecretion.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP125275
single cell RNA-seq raw reads of normal growing MCF7, T47D and MDA-MB-231
  • organism-icon Homo sapiens
  • sample-icon 134 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

NA

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

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accession-icon SRP125154
single cell RNA-seq raw reads of estrogen-stimulated breast cancer cell line T47D
  • organism-icon Homo sapiens
  • sample-icon 96 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Single-cell RNA-seq reveals dynamic estrogen-stimulated metabolic reprogramming in breast cancer cell lines

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon SRP125153
single cell RNA-seq raw reads of estrogen-stimulated breast cancer cell line MCF7
  • organism-icon Homo sapiens
  • sample-icon 93 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Single-cell RNA-seq reveals dynamic estrogen-stimulated metabolic reprogramming in breast cancer cell lines

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

View Samples
accession-icon GSE13367
Genome-wide gene expression analysis of mucosal colonic biopsies and isolated colonocytes...
  • organism-icon Homo sapiens
  • sample-icon 50 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Background & Aims: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. Methods: Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n=8), quiescent UC (n=9), and with irritable bowel syndrome (controls, n=10). After isolation of colonocytes and subsequent extraction of total RNA, GWGE data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P11 software (Umetrics, Ume, Sweden). Results: A clear separation between active UC, quiescent UC and control biopsies were found, whereas the model for the colonocytes was unable to distinguish between quiescent UC and controls. The differentiation between quiescent UC and control biopsies was governed by unique profiles containing gene expressions with significant fold changes. These primarily belonged to the family of homeostatic chemokines revealing a plausible explanation to the abnormal regulated innate immune response seen in patients with UC. Conclusion: This study has demonstrated the presence of a continuous inflammatory state in quiescent UC, which seems to reflect an altered gene expression profile of lamina propria cells.

Publication Title

Genome-wide gene expression analysis of mucosal colonic biopsies and isolated colonocytes suggests a continuous inflammatory state in the lamina propria of patients with quiescent ulcerative colitis.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP125274
single cell RNA-seq raw reads of normal growing MCF7
  • organism-icon Homo sapiens
  • sample-icon 30 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

NA

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

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

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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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