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accession-icon GSE37209
Expression data from Paneth cells isolated from mice on calorie restricted or ad libitum diet
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Paneth cells recide in the intestinal crypt bottom and are part of the innate immunity and of the intestinal stem cell niche.

Publication Title

mTORC1 in the Paneth cell niche couples intestinal stem-cell function to calorie intake.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE64766
Selective Loss of RB in Resistant EGFR Mutant Lung Adenocarcinomas that Transform to SCLC
  • organism-icon Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer.

Sample Metadata Fields

Sex, Specimen part, Disease, Subject

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accession-icon GSE64322
Selective Loss of RB in Resistant EGFR Mutant Lung Adenocarcinomas that Transform to SCLC [gene expression]
  • organism-icon Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The study was designed to identify the molecular changes that occur in EGFR mutant NSCLCs that become resistant to TKI by transforming to SCLC.

Publication Title

RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer.

Sample Metadata Fields

Subject

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accession-icon GSE51498
Regulation of HSF1-mediated transcriptional programs by PGC-1alpha
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

We examined global gene expression patterns in response to PGC-1 expression in cells derived from liver or muscle.

Publication Title

Direct link between metabolic regulation and the heat-shock response through the transcriptional regulator PGC-1α.

Sample Metadata Fields

Specimen part

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accession-icon GSE81171
Inhibition of adhesion molecule gene expression and cell adhesion by the metabolic regulator PGC-1alpha
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Cell adhesion plays an important role in determining cell shape and function in a variety of physiological and pathophysiological conditions. While links between metabolism and cell adhesion were previously suggested, the exact context and molecular details of such a cross-talk remain incompletely understood.

Publication Title

Inhibition of Adhesion Molecule Gene Expression and Cell Adhesion by the Metabolic Regulator PGC-1α.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE87100
Control of secreted protein gene expression and the mammalian secretome by the metabolic regulator PGC-1a
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Secreted proteins serve pivotal roles in the development of multicellular organisms, acting as structural matrix, extracellular enzymes and signal molecules. In this study we demonstrate, unexpectedly, that PGC-1, a critical transcriptional co-activator of metabolic gene expression, functions to down-regulate expression of diverse genes encoding secreted molecules and extracellular matrix (ECM) components to modulate the secretome. We show that both endogenous and exogenous PGC-1 down-regulate expression of numerous genes encoding secreted molecules. Mechanistically, results obtained using mRNA stability measurements as well as intronic RNA expression analysis are consistent with a transcriptional effect of PGC-1 on expression of genes encoding secreted proteins. Interestingly, PGC-1 requires the central heat shock response regulator HSF1 to affect some of its targets, and both factors co-reside on several target genes encoding secreted molecules in cells. Finally, using a mass spectrometric analysis of secreted proteins, we demonstrate that PGC-1 modulates the secretome of mouse embryonic fibroblasts (MEFs).

Publication Title

Control of Secreted Protein Gene Expression and the Mammalian Secretome by the Metabolic Regulator PGC-1α.

Sample Metadata Fields

Specimen part

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accession-icon E-MEXP-2291
Transcription profiling of bovine nucleus pulposus, carticular cartilage and annulus fibrosus cells to further determine expression in normal and degenerate human intervertebral disc
  • organism-icon Bos taurus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Bovine Genome Array (bovine)

Description

The aim of this transcription profiling study was to identify novel genes that could be used to distinguish bovine Nucleus pulposus (NP) cells from articular cartilage (AC) and annulus fibrosus (AF) cells and to further determine their expression in normal and degenerate human intervertebral disc (IVD). This study has identified a number of novel genes that characterise the bovine and human NP and IVD cell phenotypes and allows for discrimination between AC, AF and NP cells.<br></br><br></br>

Publication Title

Transcriptional profiling of bovine intervertebral disc cells: implications for identification of normal and degenerate human intervertebral disc cell phenotypes.

Sample Metadata Fields

Specimen part

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accession-icon SRP076716
Three different in vivo models of synovial sarcoma (xenograft: Fuji; PDX: CTG-0331 and CTG-0771) treated with or without the indicated dose of the EZH2 inhibitor, tazemetostat
  • organism-icon Homo sapiens
  • sample-icon 54 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The catalytic activities of covalent and ATP-dependent chromatin remodeling are central to regulating the conformational state of chromatin and the resultant transcriptional output. The enzymes that catalyze these activities are often contained within multiprotein complexes in nature. Two such multiprotein complexes, the polycomb repressive complex 2 (PRC2) methyltransferase and the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler have been reported to act in opposition to each other during development and homeostasis. An imbalance in their activities induced by mutations/deletions in complex members (e.g. SMARCB1) has been suggested to be a pathogenic mechanism in certain human cancers. Here we show that preclinical models of synovial sarcoma - a cancer characterized by functional SMARCB1 loss via its displacement from the SWI/SNF complex through the pathognomonic SS18-SSX fusion protein - display sensitivity to pharmacologic inhibition of EZH2, the catalytic subunit of PRC2. Treatment with tazemetostat, a clinical-stage, selective and orally bioavailable small-molecule inhibitor of EZH2 enzymatic activity reverses a subset of synovial sarcoma gene expression and results in concentration-dependent cell growth inhibition and cell death specifically in SS18-SSX fusion-positive cells in vitro. Treatment of mice bearing either a cell line or two patient-derived xenograft models of synovial sarcoma leads to dose-dependent tumor growth inhibition with correlative inhibition of trimethylation levels of the EZH2-specific substrate, lysine 27 on histone H3. These data demonstrate a dependency of SS18-SSX-positive, SMARCB1-deficient synovial sarcomas on EZH2 enzymatic activity and suggests the potential utility of EZH2-targeted drugs in these genetically defined cancers. Overall design: Three different in vivo models of synovial sarcoma (xenograft: Fuji; PDX: CTG-0331 and CTG-0771) treated with or without the indicated dose of the EZH2 inhibitor, tazemetostat

Publication Title

Preclinical Evidence of Anti-Tumor Activity Induced by EZH2 Inhibition in Human Models of Synovial Sarcoma.

Sample Metadata Fields

Subject

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accession-icon GSE34551
NPTX1 is a Critical Regulator of Neural Induction in Human Pluripotent Stem Cells
  • organism-icon Homo sapiens
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

NPTX1 is a key inducer of neural lineages from the human ESC.

Publication Title

NPTX1 regulates neural lineage specification from human pluripotent stem cells.

Sample Metadata Fields

Cell line, Time

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accession-icon SRP115458
PDGFRa+gp38+ mesenchymal cells in the peripheral tissues support terminal differentiation of ILC2 originated from fetal liver progenitor cells.
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Group 2 innate lymphoid cells (ILC2) are tissue-resident innate lymphocytes that are derived from common lymphoid progenitor (CLP). While specific progenitors and transcription factors essential for ILC2 differentiation have been well studied, external factors that regulate the commitment from CLP to ILC lineage, site that promote ILC2 terminal differentiation, and stromal cells that provide optimal microenvironment for ILC2 specific development are not fully understood. we demonstrated that the three key external factors such as concentration of IL-7 and the strength and duration of Notch signaling conditionally determined the fate of CLP toward T cell, B cell, or ILC lineages, which seems to be an important process from CLP to CHILP differentiation in the fetal liver. Furthermore, we identified ILC progenitors lacking the developmental potential to become T or B cells, and KLRG1- immature ILC2 that require STAT5 for functional maturation in the mesentery. We also identified PDGFRa+gp38+ mesenchymal cells in the mesentery that support ILC2 differentiation from ILC progenitors but not from CLP. Finally, single-cell RNA-sequencing (scRNA-seq) analysis of mesenteric cells demonstrated that PDGFRa+gp38+ cells are heterogeneous populations. Collectively, our result suggested that early differentiation of ILC2 occurs in the primary lymphoid organ with regulation of environmental factors, and final differentiation occurs in the peripheral tissues once after CHILP migrate into the periphery. Overall design: Duplicate samples (mouse 1 and mouse 2) were processed for single cell-based RNA sequencing with Illumina HiSeq 2500 with 50 paired-end reads, using barcorded RNA library.

Publication Title

Peripheral PDGFRα<sup>+</sup>gp38<sup>+</sup> mesenchymal cells support the differentiation of fetal liver-derived ILC2.

Sample Metadata Fields

Sex, Cell line, Subject

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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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