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accession-icon GSE33459
Gene expression in Citrus sinensis (L.) Osbeck following infection with the bacterial pathogen Candidatus Liberibacter asiaticus causing Huanglongbing in Florida
  • organism-icon Citrus sinensis
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Citrus Genome Array (citrus)

Description

Huanglongbing (HLB) (=citrus greening) is a destructive disease of citrus which is caused by a fastidious, phloem-inhabiting bacterium of the genus Candidatus Liberibacter. Large-scale analysis of gene expression changes in Valencia orange leaves were studied during the course of 19 weeks after inoculation with Ca. L. asiaticus using the Affymetrix GeneChip citrus genome array to provide new insights into the molecular basis of citrus response to this pathogen. Of the more than 33,000 probe sets on the microarray 21,067 were expressed in the leaves, of which 279 and 515 were differentially expressed (FDR 0.05) five to nine and 13-17 weeks after inoculation, respectively. Results from semi-quantitative RT-PCR analysis performed on 14 selected genes were highly correlated with those observed with the microarray. Gene expression changes involved a variety of different processes including cell defense, transport, cellular organization, photosynthesis, and carbohydrate metabolism. Notable was the pathogen-induced accumulation of transcripts for a phloem-specific lectin PP2-like protein. Transcriptional changes and their relation to disease symptom development are discussed. This is the first study of transcriptional profiling in citrus in response to liberibacter infection using microarray technology.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-33459

Sample Metadata Fields

Specimen part

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accession-icon SRP115379
Zea mays Mo17 Meiocyte RNAseq
  • organism-icon Zea mays
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We used isolated zygotene meiocytes, corresponding anthers and 2-week-old seedlings from the Zea mays inbred line Mo17 for RNA extraction and library construction for sequencing with Illumina technology to gain insight on gene expression during a key step in meiosis when recombination initiates.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE85573
Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-85573

Sample Metadata Fields

Sex, Age, Treatment, Race

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accession-icon GSE66175
Imporatance of substantial weight loss for altering gene expression during intensive cardiovascular lifestyle modification
  • organism-icon Homo sapiens
  • sample-icon 479 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

The objective of this study was to examine relationships between weight loss through changes in lifestyle and peripheral blood gene expression profiles. Substantial weight loss (-15.2+3.8%) in lifestyle participants was associated with improvement in selected cardiovascular risk factors and significant changes in peripheral blood gene expression from pre- to post-intervention: 132 unique genes showed significant expression changes related to immune function and inflammatory responses involving endothelial activation.

Publication Title

Importance of substantial weight loss for altering gene expression during cardiovascular lifestyle modification.

Alternate Accession IDs

E-GEOD-66175

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE78958
Effect of obesity on molecular characteristics of invasive breast tumors: gene expression analysis of 405 tumors by BMI
  • organism-icon Homo sapiens
  • sample-icon 424 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

Background: Obesity is a risk factor for breast cancer in postmenopausal women and is associated with decreased survival and less favorable clinical characteristics such as greater tumor burden, higher grade, and poor prognosis, regardless of menopausal status. Despite the negative impact of obesity on clinical outcome, molecular mechanisms through which excess adiposity influences breast cancer etiology are not well-defined.

Publication Title

Effect of obesity on molecular characteristics of invasive breast tumors: gene expression analysis in a large cohort of female patients.

Alternate Accession IDs

E-GEOD-78958

Sample Metadata Fields

Disease stage

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accession-icon GSE46097
Expression data of Participants of Ornish intervention and Control group
  • organism-icon Homo sapiens
  • sample-icon 377 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

Intensive lifestyle modification is believed to mediate cardiovascular disease (CVD) risk through traditional pathways that affect endothelial function and progression of atherosclerosis; however, the extent, persistence, and clinical significance of molecular change during lifestyle modification are not well known. Our study reveals that gene expression signatures are significantly modulated by rigorous lifestyle behaviors and track with CVD risk profiles over time.

Publication Title

Intensive cardiovascular risk reduction induces sustainable changes in expression of genes and pathways important to vascular function.

Alternate Accession IDs

E-GEOD-46097

Sample Metadata Fields

Sex, Age

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accession-icon GSE48931
Master regulators of FGFR2 signalling and breast cancer risk
  • organism-icon Homo sapiens
  • sample-icon 260 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Master regulators of FGFR2 signalling and breast cancer risk.

Alternate Accession IDs

E-GEOD-48931

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE40752
Transcriptional analysis of whole blood, primary fibroblasts, and PBMCs upon TNF-alpha or IL-1beta stimulation from HOIL-1-deficient patients
  • organism-icon Homo sapiens
  • sample-icon 68 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip, Illumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency.

Alternate Accession IDs

E-GEOD-40752

Sample Metadata Fields

Specimen part, Disease, Disease stage, Subject, Time

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accession-icon GSE48927
Over-expression of FGFR2b from a tetracycline-inducible expression vector
  • organism-icon Homo sapiens
  • sample-icon 125 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

Genome-wide association studies for breast cancer have identified over 80 different risk regions in the genome, with the FGFR2 locus consistently identified as the most strongly associated locus. However, we know little about the mechanisms by which the FGFR2 locus mediates risk or the pathways in which multiple risk loci may combine to cause disease. Here we use a systems biology approach to elucidate the regulatory networks operating in breast cancer and examine the role of FGFR2 in mediating risk. Using model systems we identify FGFR2-regulated genes and, combining variant set enrichment and eQTL analysis, show that these are preferentially linked to breast cancer risk loci. Our results support the concept that cancer-risk associated genes cluster in pathways

Publication Title

Master regulators of FGFR2 signalling and breast cancer risk.

Alternate Accession IDs

E-GEOD-48927

Sample Metadata Fields

Cell line

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accession-icon GSE30053
Dynamics of two oscillation phenotypes in S. cerevisiae reveal a network of genome-wide transcriptional and cell cycle oscillators.
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 80 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators.

Alternate Accession IDs

E-GEOD-30053

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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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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