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accession-icon GSE46873
Dual targeting of MYC and CYCLON by BET bromodomain inhibition optimizes Rituximab response in lymphoma.
  • organism-icon Homo sapiens
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Immuno-chemotherapy regimens elicit high response rates in B-cell non-Hodgkin lymphoma but heterogeneity in response duration is observed, with some patients achieving cure and others showing refractory disease or relapse. Using a transcriptome-powered targeted proteomics screen, we discovered a gene regulatory circuit involving the nuclear factor CYCLON which characterizes aggressive disease and resistance to the anti-CD20 monoclonal antibody, Rituximab, in high-risk B-cell lymphoma. CYCLON knockdown was found to inhibit the aggressivity of MYC-overexpressing tumors in mice and to modulate gene expression programs of biological relevance to lymphoma. Furthermore, CYCLON knockdown increased the sensitivity of human lymphoma B cells to Rituximab in vitro and in vivo. Strikingly, this effect could be mimicked by in vitro treatment of lymphoma B cells with a small molecule inhibitor for BET bromodomain proteins (JQ1). In summary, this work has identified CYCLON as a new MYC cooperating factor that drives aggressive tumor growth and Rituximab resistance in lymphoma. This resistance mechanism is amenable to next-generation epigenetic therapy by BET bromodomain inhibition, thereby providing a new combination therapy rationale for high-risk lymphoma.

Publication Title

Identification of a novel BET bromodomain inhibitor-sensitive, gene regulatory circuit that controls Rituximab response and tumour growth in aggressive lymphoid cancers.

Alternate Accession IDs

E-GEOD-46873

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE84733
FGFR3 knock-down
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2), Affymetrix Human Exon 1.0 ST Array [CDF: Brainarray Version 12.1.0 (huex10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

An FGFR3/MYC positive feedback loop provides new opportunities for targeted therapies in bladder cancers.

Alternate Accession IDs

E-GEOD-84733

Sample Metadata Fields

Cell line

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accession-icon GSE84732
Gene expression data from RT112 following FGFR3 knock-down using FGFR3 siRNAs
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

To better understand the molecular mechanisms underlying altered-FGFR3 oncogenic activity in bladder carcinomas, we made use of RT112 cell lines, which were derived from a human bladder tumor and endogenously expressed the FGFR3-TACC3 fusion protein, the growth and transformation of these cell lines being dependent on activated-FGFR3 activity. We conducted a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not with FGFR3 siRNAs.

Publication Title

An FGFR3/MYC positive feedback loop provides new opportunities for targeted therapies in bladder cancers.

Alternate Accession IDs

E-GEOD-84732

Sample Metadata Fields

Cell line

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accession-icon GSE62572
Global gene expression profiling human and Chimpanzee induced pluripotent stem (iPS) cell
  • organism-icon Pan troglodytes, Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Gene expression study of human and Chimpanzee iPS cell.

Publication Title

New type of Sendai virus vector provides transgene-free iPS cells derived from chimpanzee blood.

Alternate Accession IDs

E-GEOD-62572

Sample Metadata Fields

Specimen part

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accession-icon GSE11542
Expression data from rat mixed tissues samples
  • organism-icon Rattus norvegicus
  • sample-icon 40 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

To evaluate gene expression changes in mixed tissue samples used as process controls in male Sprague Dawley rats over time.

Publication Title

Assessment of repeated microarray experiments using mixed tissue RNA reference samples.

Alternate Accession IDs

E-GEOD-11542

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP072570
RNA-seq analysis of in vivo- and in vitro-produced mouse oocytes
  • organism-icon Mus musculus
  • sample-icon 23 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The female germline undergoes a unique line of differentiation processes that endows totipotency to the egg. During these processes, biologically significant events such as meiosis and oocyte growth are controlled in an orderly manner, with any disorder causing infertility and developmental arrest of the next generation. Reconstitution in vitro of the entire process of oogenesis from pluripotent stem cells is a key achievement in stem cell biology and regenerative medicine, but a robust and reproducible culture system has not been established. Here, we report successful reconstitution in vitro throughout the entire process of oogenesis from pluripotent stem cells, yielding in vitro-produced eggs that gave rise to healthy pups. Moreover, the pluripotent stem lines were re-derived from the in vitro-generated eggs, thereby reconstituting one generation on a dish. This culture system will provide a unique platform for elucidating the molecular mechanisms underlying totipotency and could open an avenue to producing vast numbers of eggs in vitro. Overall design: The transcriptomes of ES cells (ESCs), primordial germ cell-like cells at day 6 of differentiation (PGCLCs_d6), PGCLCs aggregated with gonadal somatic cells (PGCLCs_agg3), in vitro-produced primary oocytes in secondary follicles (vitro_2nd_fol_oocyte) and MII oocytes (vitro MII oocytes) are determined by RNA-seq analysis. For comparison, the transcriptomes of E12.5 PGCs (vivo_E12.5_PGCs), P8 primary oocytes (vivo_2nd_fol._oocyte) and MII oocytes (vivo_MII_oocyte) in vivo are also determined. Biologically triplicated (rep1-3) or duplicated (rep1-2) samples are sequnced simultaneously.

Publication Title

Mechanical stress accompanied with nuclear rotation is involved in the dormant state of mouse oocytes.

Alternate Accession IDs

GSE79729

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE18913
siRNA-mediated Egr-3 knockdown in VEGF-treated HUVEC
  • organism-icon Homo sapiens
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Analysis of umbilical vein endothelial cells (HUVEC) treated with Egr-3 siRNA under the VEGF treatment for 0,1, and 4 h. Egr-3, a member of early growth response family, is immediately and dramatically induced by VEGF in HUVEC, which regulates expression of many genes related to endothelial activation.

Publication Title

Vascular endothelial growth factor activation of endothelial cells is mediated by early growth response-3.

Alternate Accession IDs

E-GEOD-18913

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE26206
Expression data in whole Arabidopsis seedlings after treatment with Rhizoctonia solani AG8 and AG2-1
  • organism-icon Arabidopsis thaliana
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Rhizoctonia solani is an economically important soil-borne necrotrophic fungal pathogen, with a broad host range and for which little effective resistance exists in crop plants. Arabidopsis is resistant to the R. solani AG8 isolate but susceptible to R. solani AG2-1. Affymetrix microarray analysis was performed to determine genes that are affected in common and specifically by AG8 and AG2-1.

Publication Title

Genetic and genomic analysis of Rhizoctonia solani interactions with Arabidopsis; evidence of resistance mediated through NADPH oxidases.

Alternate Accession IDs

E-GEOD-26206

Sample Metadata Fields

Age, Specimen part, Treatment

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accession-icon GSE55687
Expression data of mouse embyonic fibroblasts established from Phgdh KO embryos (KO-MEFs) cultured with or without L-Ser
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

L-Ser deficiency leads to growth arrest, tissue malformation and embryonic lethality in mice. However, the molecular mechanism by which L-Ser deficiency impairs basic cellular function remains largely unexplored.

Publication Title

Microarray data on altered transcriptional program of Phgdh-deficient mouse embryonic fibroblasts caused by ʟ-serine depletion.

Alternate Accession IDs

E-GEOD-55687

Sample Metadata Fields

Specimen part

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accession-icon GSE29355
Transcriptional profile of an eca39 mutant fission yeast
  • organism-icon Schizosaccharomyces pombe
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

An branched-chain amino acids auxotroph eca39 mutant fission yeast exhibits an unusual adaptive growth phenotype on solid minimal media containing Ile, Leu and Val when other strains are growing nearby.

Publication Title

The SAGA histone acetyltransferase complex regulates leucine uptake through the Agp3 permease in fission yeast.

Alternate Accession IDs

E-GEOD-29355

Sample Metadata Fields

No sample metadata fields

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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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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