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accession-icon GSE83423
Expression data from human intestinal enteroids altered for Tgfbeta signaling
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We treated intestinal enteroids continuously for 6 days with or without TgfbR1/2 inhibitor (LY2109761) or Tgfb1 ligand

Publication Title

Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation.

Sample Metadata Fields

Specimen part

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accession-icon GSE58296
Expression data from intestinal organoids altered for Tgfbeta signaling
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We treated intestinal organoids continuously for 5 days with or without TgfbR1/2 inhibitor (LY2109761) or Tgfb1 ligand

Publication Title

Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon SRP023259
Transcriptome Sequencing (RNA-seq) of Ara-C Resistant Murine AML Cell Lines Identifies Mechanisms of Resistance
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

An RNA-seq study of altered gene expression and mutations in Ara-C resistant acute myeloid leukemia murine cell lines. The analysis of the RNA-seq data led to the identification of a large deletion within the Dck coding sequence of the B117H cell line, which produced an alternatively processed form of Dck mRNA. The RNA-seq analysis also identified the presence of an insertion mutation in Dck in the B140H cell line. The RNA-seq analysis also identified a number of significant expression changes which did not appear in a previous microarray analysis (GSE18322), as well as identified other mutations which may be contributing to Ara-C resistance. Overall design: Two highly Ara-C resistant cell lines, B117H and B140H were derived from Ara-C sensitive parental cell lines, B117P and B140P. Variations in gene expression as well identification of acquired mutations between these Ara-C resistant/sensitive sets were studied using various RNA-seq analysis tools.

Publication Title

Using RNA-seq and targeted nucleases to identify mechanisms of drug resistance in acute myeloid leukemia.

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE26155
Advanced Study of Aortic Pathology (ASAP)
  • organism-icon Homo sapiens
  • sample-icon 96 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

BACKGROUND: The vast majority of thoracic aortic aneurysms (TAAs) are observed either together with a bicuspid aortic valve (BAV), a common congenital disorder, or in idiopathic cases such as patients with a normal tricuspid aortic valve (TAV). The main objective of our study was to identify shared and unique gene expression properties underlying the aortic dilation of BAV and TAV patients.

Publication Title

Unraveling divergent gene expression profiles in bicuspid and tricuspid aortic valve patients with thoracic aortic dilatation: the ASAP study.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE40231
The Stockholm Atherosclerosis Gene Expression (STAGE) study: Global Gene Expression data from coronary and carotid artery disease patients
  • organism-icon Homo sapiens
  • sample-icon 275 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Tissue samples have been isolated during corornary artery by-pass grafting (CABG)surgery from the atheroscelrotic arterial wall (AAW, aortic root puncture for proxmal ligation of by-pass vessel), non-atherosclertoci arterial wall (NAAW, distal part of mammary artery used a graft for LAD), liver, skeletal muscle (Recturs m), pericardial mediastinal visceral fat) in CAD patients. Carotid lesions samples from 25 validation patients.

Publication Title

Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

Sample Metadata Fields

Specimen part

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accession-icon SRP067067
Injury-dependent hydrogen peroxide oxidation of IKK-alpha regulates keratinocyte migration through induction of EGF
  • organism-icon Danio rerio
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

Hydrogen peroxide is known to promote skin keratinocyte migration, although the mechanism of action is unclear. In an attempt to identify signaling pathways regulated by hydrogen peroxide in the skin, 3 day post fertilized (dpf) zebrafish larvae (nacre strain) were treated with 3mM hydrogen peroxide for 2 hours and subjected to RNA-seq analyses. Pools of about 1000 embryos for each of three biological replicates were derived from 5 independent mating pairs and raised to larval stages until 3 dpf. All larvae were subsequently homogenized in Trizol and total RNA was extracted using a chloroform extraction protocol treated with DNAse. Messenger RNA (mRNA) was subsequently purified from total RNA using biotin-tagged poly dT oligonucleotides and streptavidin-coated magnetic beads, followed by quality control using an Agilent Technologies 2100 Bioanalyzer (values >7 were used for sequencing). The poly(A)-tailed mRNA samples were fragmented and double-stranded cDNA generated by random priming for deep sequencing studies. Overall design: 6 samples total were analyzed. 3 untreated, and 3 hydrogen peroxide treated (3mM, 2hr)

Publication Title

Comparative transcriptomic profiling of hydrogen peroxide signaling networks in zebrafish and human keratinocytes: Implications toward conservation, migration and wound healing.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE18327
Lubiprostone effects on small intestinal gene expression in wild type and Cftr-null mice
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Background: Cystic fibrosis (CF) is caused by mutations in the CFTR gene that impair function of this cAMP-regulated Cl- channel. In the small intestine, loss of CFTR function creates a dehydrated, acidic luminal environment which is believed to cause an accumulation of mucus, a phenotype characteristic of CF. CF mice have an innate immune response and impaired intestinal transit as well. We investigated whether lubiprostone, which activates the CLC2 Cl- channel, would improve the CF intestinal phenotype.

Publication Title

Lubiprostone ameliorates the cystic fibrosis mouse intestinal phenotype.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE22443
Expression data for nave IL-2 and IL-12 primed Pmel-1 CD8+ T-cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

The expansion, trafficking and functional effectiveness of adoptively transferred CD8+ T-cells play a critical role in mediating effective anti-tumor immunity. However, the mechanisms which program the highly proliferative and functional state of CD8+ T-cells are not completely understood. We hypothesized that IL-12, a cytokine commonly induced by TLR activation, could enhance T-cell priming by altering responsiveness to antigen and cytokines. Priming of tumor specific CD8+ T-cells in the presence of IL-12 induced the acquisition of a 'polyfunctional' effector response and increased the generation of memory cells. Moreover, IL-12 priming also promoted high levels of the IL-2 receptor alpha-chain (CD25) and robust IL-2 mediated activation of STAT5. This sensitivity to IL-2 translated into enhanced in vivo proliferation of adoptively transferred CD8+ T-cells. Furthermore, real-time, in vivo imaging of T-cell trafficking confirmed the ability of IL-12 priming to drive in vivo proliferation. IL-12 priming enhanced the anti-tumor function of adoptively transferred cells by reducing established subcutaneous tumor burden, and significantly increasing survival in an established intracranial tumor model. Finally, IL-12 priming of human PBMCs generates tumor specific T-cells phenotypically and functionally similar to IL-12 primed Pmel-1 T-cells. These results highlight IL-12 as an important mediator of CD8+ T-cell effector function and anti-tumor immunity.

Publication Title

Enhanced sensitivity to IL-2 signaling regulates the clinical responsiveness of IL-12-primed CD8(+) T cells in a melanoma model.

Sample Metadata Fields

Sex, Specimen part, Treatment

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accession-icon E-MEXP-1743
Transcription profiling by array of Arabidopsis EXORDIUM mutants
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Wild-type and exo mutant (SALK_098602) were grown in parallel in three independent experiments in a greenhouse. 3 x 2 profiles were established.

Publication Title

The extracellular EXO protein mediates cell expansion in Arabidopsis leaves.

Sample Metadata Fields

Age, Specimen part, Time

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accession-icon GSE62821
EIF4E AND EIF4GI HAVE DISTINCT AND DIFFERENTIAL IMPRINTS ON MULTIPLE MYELOMA'S PROTEOME AND SIGNALING
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Accumulating data indicate translation plays a role in cancer biology, particularly its rate limiting stage of initiation. Despite this evolving recognition, the function and importance of specific translation initiation factors is unresolved. The eukaryotic translation initiation complex eIF4F consists of eIF4E and eIF4G at a 1:1 ratio. Although it is expected that they display interdependent functions, several publications suggest independent mechanisms. This study is the first to directly assess the relative contribution of eIF4F components to the expressed cellular proteome, transcription factors, microRNAs, and phenotype in a malignancy known for extensive protein synthesis- multiple myeloma (MM). Previously, we have shown that eIF4E/eIF4GI attenuation (siRNA/ Avastin) deleteriously affected MM cells' fate and reduced levels of eIF4E/eIF4GI established targets. Here, we demonstrated that eIF4E/eIF4GI indeed have individual influences on cell proteome. We used an objective, high throughput assay of mRNA microarrays to examine the significance of eIF4E/eIF4GI silencing to several cellular facets such as transcription factors, microRNAs and phenotype. We showed different imprints for eIF4E and eIF4GI in all assayed aspects. These results promote our understanding of the relative contribution and importance of eIF4E and eIF4GI to the malignant phenotype and shed light on their function in eIF4F translation initiation complex.

Publication Title

eIF4E and eIF4GI have distinct and differential imprints on multiple myeloma's proteome and signaling.

Sample Metadata Fields

Specimen part, Cell line, Treatment

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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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