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accession-icon GSE46216
Role of glucocorticoids and an RNA binding protein (RBP) in early erythroid progenitors
  • organism-icon Mus musculus
  • sample-icon 4 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

ZFP36L2 is required for self-renewal of early burst-forming unit erythroid progenitors.

Sample Metadata Fields

Specimen part

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accession-icon GSE46108
Identification of transcripts bound by an RNA binding protein (RBP) in early erythroid progenitor using RNA-binding protein immunoprecipitation-microarray (RIP-Chip) experiment
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Early erythroid progenitors were isolated from mouse E14.5 fetal liver. After cell lysing, control IgG or RBP specific antibody were incubated with cell lysis. Immunoprecipitation followed by microarray experiments were carried out to identify transcripts that are immunoprecipitated by either control IgG or RBP specific antibody.

Publication Title

ZFP36L2 is required for self-renewal of early burst-forming unit erythroid progenitors.

Sample Metadata Fields

Specimen part

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accession-icon GSE24202
Expression data from genetically modified HMLE human mammary epithelial cells
  • organism-icon Homo sapiens
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix HT Human Genome U133A Array (hthgu133a)

Description

Microarrays were used to determine relative global gene expression changes upon introduction of EMT-inducing or control vectors.

Publication Title

Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes.

Sample Metadata Fields

Specimen part

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accession-icon GSE17215
Expression data from paclitaxel and salinomycin-treated HMLER breast cancer cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix HT Human Genome U133A Array (hthgu133a)

Description

Screens for agents that specifically kill epithelial cancer stem cells (CSCs) have not been possible due to the rarity of these cells within tumor cell populations and their relative instability in culture. We describe here an approach to screening for agents with epithelial CSC-specific toxicity. We implemented this method in a chemical screen and discovered compounds showing selective toxicity for breast CSCs. One compound, salinomycin, reduces the proportion of CSCs by >100-fold relative to paclitaxel, a commonly used breast cancer chemotherapeutic drug. Treatment of mice with salinomycin inhibits mammary tumor growth in vivo and induces increased epithelial differentiation of tumor cells. In addition, global gene expression analyses show that salinomycin treatment results in the loss of expression of breast CSC genes previously identified by analyses of breast tissues isolated directly from patients. This study demonstrates the ability to identify agents with specific toxicity for epithelial CSCs

Publication Title

Identification of selective inhibitors of cancer stem cells by high-throughput screening.

Sample Metadata Fields

Specimen part

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accession-icon GSE61073
mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues.

Sample Metadata Fields

Sex, Age, Specimen part, Cell line, Treatment, Time

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accession-icon GSE38912
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix HT Human Genome U133A Array (hthgu133a)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers.

Sample Metadata Fields

Specimen part, Cell line, Treatment

View Samples
accession-icon GSE29181
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T-cell acute lymphoblastic leukemia
  • organism-icon Homo sapiens
  • sample-icon 11 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia.

Sample Metadata Fields

Disease, Cell line

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accession-icon GSE45853
Tight coordination of protein translation and heat shock factor 1 activation supports the anabolic malignant state
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000, Affymetrix HT Human Genome U133A Array (hthgu133a)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state.

Sample Metadata Fields

Specimen part, Cell line, Treatment

View Samples
accession-icon GSE29179
Identification of differentially expressed genes upon shRNA knockdown of TAL1 and its regulatory partners in T-ALL cells (Jurkat)
  • organism-icon Homo sapiens
  • sample-icon 11 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. We find that TAL1 forms an interconnected auto-regulatory loop with its partners, which contributes to the sustained upregulation of its direct target genes. Importantly, we also find the MYB oncogenic transcription factor is directly activated by the TAL1 complex and positively regulates many of the same target genes, thus forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program.

Publication Title

Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia.

Sample Metadata Fields

Cell line

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accession-icon GSE38232
HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers [gene expression]
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix HT Human Genome U133A Array (hthgu133a)

Description

Heat-Shock Factor 1 (HSF1), master regulator of the heat-shock response, facilitates malignant transformation, cancer cell survival and proliferation in model systems. The common assumption is that these effects are mediated through regulation of heat-shock protein (HSP) expression. However, the transcriptional network that HSF1 coordinates directly in malignancy and its relationship to the heat-shock response have never been defined. By comparing cells with high and low malignant potential alongside their non-transformed counterparts, we identify an HSF1-regulated transcriptional program specific to highly malignant cells and distinct from heat shock. Cancer-specific genes in this program support oncogenic processes: cell-cycle regulation, signaling, metabolism, adhesion and translation. HSP genes are integral to this program, however, even these genes are uniquely regulated in malignancy. This HSF1 cancer program is active in breast, colon and lung tumors isolated directly from human patients and is strongly associated with metastasis and death. Thus, HSF1 rewires the transcriptome in tumorigenesis, with prognostic and therapeutic implications.

Publication Title

HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers.

Sample Metadata Fields

Cell line, Treatment

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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