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accession-icon GSE20247
C-peptide and/or transforming growth factor beta 1 effect on human proximal tubular cell line
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconIllumina HumanWG-6 v3.0 expression beadchip

Description

Microarray analysis reveals up-regulation of retinoic acid and hepatocyte growth factor related signaling pathways by pro-insulin C-peptide in kidney proximal tubular cells: Antagonism of the pro-fibrotic effects of TGF-b1

Publication Title

Proinsulin C-peptide antagonizes the profibrotic effects of TGF-beta1 via up-regulation of retinoic acid and HGF-related signaling pathways.

Sample Metadata Fields

Cell line

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accession-icon SRP071332
Expression profiling of IL-13 stimulated PBMCs with and without an IL-13R antagonist
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

This experiment aims to identify the biological pathways and diseases associated with the cytokine Interleukin 13 (IL-13) using gene expression measured in peripheral blood mononuclear cells (PBMCs). Overall design: The experiment comprised of samples obtained from 3 healthy donors. The expression profiles of in vitro IL-13 stimulation were generated using RNA-seq technology for 3 PBMC samples at 24 hours. The transcriptional profiles of PBMCs without IL-13 stimulation were also generated to be used as controls. An IL-13R-alpha antagonist (Redpath et al. Biochemical Journal, 2013) was introduced into IL-13 stimulated PBMCs and the gene expression levels after 24h were profiled to examine the neutralization of IL-13 signaling by the antagonist.

Publication Title

Combining multiple tools outperforms individual methods in gene set enrichment analyses.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE87090
Genome-wide analysis of gene expression by IFN-beta in U6A cells expressing WT or T387A STAT2
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

We used an Illumina Gene Expression Array to understand in more detail how T387 phosphorylation affects ISG induction. mRNA preparations from U6A cells expressing wild-type or T387A STAT2, treated with IFN- for 0, 4, 8, or 24 h, were analyzed.

Publication Title

Negative regulation of type I IFN signaling by phosphorylation of STAT2 on T387.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE12079
Molecular profiling of CD3- CD4+ T-cells from patients with the lymphocytic variant of hypereosinophilic syndrome
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The clonal CD3- CD4+ Th2 cell population characterizing some hypereosinophilic syndrome patients stably endures for years provoking a chronic inflammatory skin disease, with a subgroup of patients ultimately progressing to T-cell lymphoma. The aim of this study is the identification of the molecular changes (1) associated with the persistence of the pre-malignant clone (2) associated with the activation of co-stimulatory receptors and (3) associated with the emergence of malignant T-cell subclones.

Publication Title

Molecular profiling of CD3-CD4+ T cells from patients with the lymphocytic variant of hypereosinophilic syndrome reveals targeting of growth control pathways.

Sample Metadata Fields

Specimen part, Disease, Disease stage, Time

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accession-icon SRP151594
RNA-seq in wild type and dCAP-D3 mutant tissues
  • organism-icon Drosophila melanogaster
  • sample-icon 11 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

The goal of this experiment was to identify transcripts that are differentially expressed in dCAP-D3 mutant tissues. Overall design: RNA was isolated from wing discs and salivary glands of wild type (w1118) or dCap-D3 homozygous mutant (dCap-D3c07081/c07081) larvae. Directional (wing disc) or nondirectional (salivary gland) cDNA libraries (50 bp, paired end) were made at the University of Chicago Genomics Core and sequenced on an Illumina HiSeq2500, according to standard protocols.

Publication Title

Comparing and Contrasting the Effects of <i>Drosophila</i> Condensin II Subunit dCAP-D3 Overexpression and Depletion <i>in Vivo</i>.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE15805
Duke-UNC-Texas-EBI ENCODE expression project
  • organism-icon Homo sapiens
  • sample-icon 154 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [GENCODE v10 (huex10st)

Description

These samples are being analyzed by the Duke-UNC-Texas-EBI ENCODE consortium. Expression from these cell types will compared to three whole genome open chromatin methodologies: DNaseI hypersensitivity (DNase-seq), Formaldehyde-Assisted Isolation of Regulatory elements (FAIRE-seq), and Chromatin Immunoprecipitation (ChIP-seq) .

Publication Title

Heritable individual-specific and allele-specific chromatin signatures in humans.

Sample Metadata Fields

Specimen part

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accession-icon SRP150419
Haemopedia: Human Haematopoietic Gene Expression
  • organism-icon Homo sapiens
  • sample-icon 84 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Database of gene expression in different haematopoietic cell types at haemosphere.org Overall design: Comparison of gene expression in different haematopoietic cell types

Publication Title

Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE76966
G-CSF receptor targeting in inflammatory arthritis
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

G-CSF is a hemopoietic growth factor that has a role in steady state granulopoiesis, as well as in mature neutrophil activation and function. We developed a neutralizing monoclonal antibody to the murine G-CSF receptor (G-CSFR), which antagonizes binding of murine G-CSF and inhibits G-CSFR signalling. Anti-G-CSFR rapidly halts the progression of established disease in collagen antibody-induced arthritis (CAbIA). Neutrophil accumulation in joints is inhibited, without rendering animals neutropenic, suggesting an effect on homing to inflammatory sites. Neutrophils in the blood and arthritic joints of anti-G-CSFR treated mice show alterations in cell adhesion receptors, while anti-G-CSFR suppresses local production of proinflammatory cytokines and chemokines known to drive tissue damage. Our aim in this study was to use differential gene expression analysis of joint and blood neutrophils to more thoroughly understand the effect of G-CSFR blockade on the inflammatory response following anti-G-CSFR therapy in CAbIA.

Publication Title

Therapeutic Targeting of the G-CSF Receptor Reduces Neutrophil Trafficking and Joint Inflammation in Antibody-Mediated Inflammatory Arthritis.

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage, Treatment

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accession-icon GSE48359
Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo
  • organism-icon Gallus gallus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Genome Array (chicken)

Description

A systematic survey of the transcriptional status of individual segments of the developing chick hindbrain (r1-5) and the adjacent region of the embryonic midbrain (m) during the HH11 stage of chick development

Publication Title

Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo.

Sample Metadata Fields

Specimen part

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accession-icon GSE34141
Phenotypic and Genome-Wide Analysis of an Antibiotic-Resistant Small Colony Variant of Pseudomonas aeruginosa
  • organism-icon Pseudomonas aeruginosa
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Pseudomonas aeruginosa Array (paeg1a)

Description

Background Small colony variants (SCVs) are slow-growing bacteria, which often show increased resistance to antibiotics and cause latent or recurrent infections. It is therefore important to understand the mechanisms at the basis of this phenotypic switch. Methodology/Principal findings One SCV (termed PAO-SCV) was isolated, showing high resistance to gentamicin and to the cephalosporine cefotaxime. PAO-SCV was prone to reversion as evidenced by emergence of large colonies with a frequency of 10-5 on media without antibiotics while it was stably maintained in presence of gentamicin. PAO-SCV showed a delayed growth, defective motility, and strongly reduced levels of the quorum sensing Pseudomonas quinolone signal (PQS). Whole genome expression analysis further suggested a multi-layered antibiotic resistance mechanism, including simultaneous over-expression of two drug efflux pumps (MexAB-OprM, MexXY-OprM), the LPS modification operon arnBCADTEF, and the PhoP-PhoQ two-component system. Conversely, the genes for the synthesis of PQS were strongly down-regulated in PAOSCV. Finally, genomic analysis revealed the presence of mutations in phoP and phoQ genes as well as in the mexZ gene encoding a repressor of the mexXY and mexABoprM genes. Only one mutation occurred only in REV, at nucleotide 1020 of the tufA gene, a paralog of tufB, both encoding the elongation factor Tu, causing a change of the rarely used aspartic acid codon GAU to the more common GAC, possibly causing an increase of tufA mRNA translation. High expression of phoP and phoQ was confirmed for the SCV variant while the revertant showed expression levels reduced to wild-type levels. Conclusions By combining data coming from phenotypic, gene expression and proteome analysis, we could demonstrate that resistance to aminoglycosides in one SCV mutant is multifactorial including overexpression of efflux mechanisms, LPS modification and is accompanied by a drastic down-regulation of the Pseudomonas quinolone signal quorum sensing system.

Publication Title

Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV) of Pseudomonas aeruginosa.

Sample Metadata Fields

No sample metadata fields

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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.
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Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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