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accession-icon GSE76985
Genome-wide monitoring of gene expression in Saccharomyces cerevisiae upon KP1019 treatment
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

KP1019 (trans-[tetrachlorobis(1H-indazole) ruthenate(III)]) is a ruthenium complex that exhibited anti-cancer activity in several in vitro and in vivo studies. KP1019 was even efficient against cancer cells that were resistant to other chemotherapeutic agents and thus emerged as a promising anti-cancer drug without dose-limiting cytotoxicity. However, the molecular mechanisms of its action are elusive.

Publication Title

A systematic assessment of chemical, genetic, and epigenetic factors influencing the activity of anticancer drug KP1019 (FFC14A).

Alternate Accession IDs

E-GEOD-76985

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE25169
Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and their denucleation
  • organism-icon Mus musculus
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and its denucleation.

Alternate Accession IDs

E-GEOD-25169

Sample Metadata Fields

Specimen part

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accession-icon GSE22322
Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and their denucleation [lens tissue]
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

Genome-wide approach to identify the cell-autonomous role of Brg1 in lens fiber cell terminal differentiation.

Publication Title

Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and its denucleation.

Alternate Accession IDs

E-GEOD-22322

Sample Metadata Fields

Specimen part

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accession-icon GSE22362
HSF4 microarray gene expression analysis in the newborn mouse lens.
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

Differential expression of HSF4 in null newborn mouse and wildtype lenses was examined to identify putative downstream targets of HSF4.

Publication Title

Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and its denucleation.

Alternate Accession IDs

E-GEOD-22362

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE25168
Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and their denucleation [eyeball tissue]
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

Genome-wide approach to identify the cell-autonomous role of Brg1 in lens fiber cell terminal differentiation.

Publication Title

Chromatin remodeling enzyme Brg1 is required for mouse lens fiber cell terminal differentiation and its denucleation.

Alternate Accession IDs

E-GEOD-25168

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE13514
Targeting PKC: A Novel Role for beta-catenin in ER stress and Apoptotic Signaling
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

Targeting protein kinase C (PKC) isoforms by the small molecule inhibitor enzastaurin has shown promising pre-clinical activity in a wide range of tumor cells. In this study, we further delineated its mechanism of action in multiple myeloma (MM) cells and found a novel role of b-catenin in regulating growth and survival of tumor cells. Specifically, inhibition of PKC leads to rapid accumulation of b-catenin by preventing the phosphorylation required for its proteasomal degradation. Microarray analysis and siRNA-mediated gene silencing in MM cells revealed that accumulated b-catenin activates early ER stress signaling via eIF2a, CHOP and p21, leading to immediate growth inhibition. Furthermore, accumulated b-catenin contributes to enzastaurin-induced cell death. Both sequential knock-down of b-catenin, c-Jun, and p73, as well as overexpression of b-catenin or p73 confirmed that accumulated b-catenin triggers c-Jun-dependent induction of p73, thereby conferring MM cell apoptosis. In summary, our data reveal a novel role of b-catenin in ER stress-mediated growth inhibition, and a new pro-apoptotic mechanism triggered by b-catenin upon inhibition of PKC isoforms. Moreover, we identify p73 as a potential novel therapeutic target in MM. Based on these and previous data, enzastaurin is currently under clinical investigation in a variety of hematologic malignancies including MM.

Publication Title

Targeting PKC: a novel role for beta-catenin in ER stress and apoptotic signaling.

Alternate Accession IDs

E-GEOD-13514

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE64228
Expression data of leaves from transgenic barley expressing wheat Lr34 gene
  • organism-icon Hordeum vulgare
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Barley Genome Array (barley1)

Description

The wheat gene Lr34 (Yr18/Pm38/Sr57/Ltn1) encodes a putative ABCG-type of transporter and is a unique source of disease resistance providing durable and partial resistance against multiple fungal pathogens. Lr34 has been found to be functional as a transgene in barley.

Publication Title

The wheat resistance gene Lr34 results in the constitutive induction of multiple defense pathways in transgenic barley.

Alternate Accession IDs

E-GEOD-64228

Sample Metadata Fields

Specimen part

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accession-icon GSE16108
Transcription profiling of parental lines and bulked salt sensitive and salt tolerant RILs derived from 2 rice varieties
  • organism-icon Oryza sativa indica group
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

The aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively. The number of differentially expressed genes was drastically reduced to 70 and 30, by pooling the RNAs from ten extreme tolerant and ten extreme susceptible RILs due to normalization of irrelevant differentially expressed genes between the parents.

Publication Title

Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).

Alternate Accession IDs

E-GEOD-16108

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE6222
Genome-wide analysis of gene expression patterns in human liver cancers
  • organism-icon Homo sapiens
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

To investigate the mechanisms of liver cancer progression and metastasis, we did expression profiling of human liver cancer and benign tissues.

Publication Title

Identification of SOX4 target genes using phylogenetic footprinting-based prediction from expression microarrays suggests that overexpression of SOX4 potentiates metastasis in hepatocellular carcinoma.

Alternate Accession IDs

E-GEOD-6222

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP115218
Extracellular matrix (ECM) stiffness and collagen-1 (col-1) responsive genes in 3D cultured mammary epithelial cells
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

We report the expression profiles of MCF10A cells encapsulated in hydrogels of varying stiffness and composition. Cells were encapsulated for 7 days in either 1.) soft alginate and reconstituted basement membrane (rBM), 2.) stiff alginate and rBM, 3,) soft col-1 and rBM, or 4.) stiff col-1. We find global gene expression changes in response to enhanced ECM stiffness, independent of expression changes in response to col-1 exposure. These results provide a comprehensive study of the gene expression changes associated with increased ECM stiffness in addition to the gene expression changes associated with increased col-1 concentration in combination with, and independent of, ECM stiffness. Overall design: Expression profiling of MCF10A cells in four hydrogel conditions were sequenced in duplicate via Illumina HiSeq.

Publication Title

YAP-independent mechanotransduction drives breast cancer progression.

Alternate Accession IDs

GSE102506

Sample Metadata Fields

Specimen part, Cell line, Subject

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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