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accession-icon GSE5680
Expression data for an eQTL experiment in rat eye
  • organism-icon Rattus norvegicus
  • sample-icon 120 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

We used expression quantitative trait locus mapping in the laboratory rat (Rattus norvegicus) to gain a broad perspective of gene regulation in the mammalian eye and to identify genetic variation relevant to human eye disease. Of >31,000 gene probes represented on an Affymetrix expression microarray, 18,976 exhibited sufficient signal for reliable analysis and at least 2-fold variation in expression among 120 F2 rats generated from an SR/JrHsd x SHRSP intercross. Genome-wide linkage analysis with 399 genetic markers revealed significant linkage with at least one marker for 1,300 probes (alpha = 0.001; estimated empirical false discovery rate = 2%). Both contiguous and noncontiguous loci were found to be important in regulating mammalian eye gene expression. We investigated one locus of each type in greater detail and identified putative transcription-altering variations in both cases. We found an inserted cREL binding sequence in the 5' flanking sequence of the Abca4 gene associated with an increased expression level of that gene, and we found a mutation of the gene encoding thyroid hormone receptor beta 2 associated with a decreased expression level of the gene encoding short-wave sensitive opsin (Opn1sw). In addition to these positional studies, we performed a pairwise analysis of gene expression to identify genes that are regulated in a coordinated manner and used this approach to validate two previously undescribed genes involved in the human disease Bardet-Biedl syndrome. These data and analytic approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease.

Publication Title

Regulation of gene expression in the mammalian eye and its relevance to eye disease.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE137634
Lymphocyte DNA methylation mediates genetic risk at shared immune mediated disease loci
  • organism-icon Homo sapiens
  • sample-icon 209 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci.

Sample Metadata Fields

Sex, Age, Specimen part, Subject

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accession-icon GSE142049
Transcriptional data of inflamatory arthritis B cells
  • organism-icon Homo sapiens
  • sample-icon 109 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

With a focus on rheumatoid arthritis (RA), we sought new insight into genetic mechanisms of adaptive immune dysregulation to help prioritise molecular pathways for targeting in this and related immune pathologies. Whole genome methylation and transcriptional data from isolated CD4+ T cells and B cells of >100 genotyped and phenotyped inflammatory arthritis patients, all of whom were naïve to immunomodulatory treatments, were obtained. Analysis integrated these comprehensive data with GWAS findings across IMDs and other publically available resources.

Publication Title

Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci.

Sample Metadata Fields

Sex, Age, Specimen part, Subject

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accession-icon GSE141934
Transcriptional data of inflamatory arthritis T cells.
  • organism-icon Homo sapiens
  • sample-icon 100 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

With a focus on rheumatoid arthritis (RA), we sought new insight into genetic mechanisms of adaptive immune dysregulation to help prioritise molecular pathways for targeting in this and related immune pathologies. Whole genome methylation and transcriptional data from isolated CD4+ T cells and B cells of >100 genotyped and phenotyped inflammatory arthritis patients, all of whom were naïve to immunomodulatory treatments, were obtained. Analysis integrated these comprehensive data with GWAS findings across IMDs and other publically available resources.

Publication Title

Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci.

Sample Metadata Fields

Sex, Age, Specimen part, Subject

View Samples
accession-icon GSE100648
Early arthritis B cell gene expression profiling
  • organism-icon Homo sapiens
  • sample-icon 242 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

242 patients recruited from an early arthritis clinic donated RNA and DNA from freshly isolated and purified peripheral blood CD19+ B cells. Global gene expression measurement was carried out using Illumina BeadChip HT12v4 microarrays. Objectives included the identification of B cell transcripts differentially expressed between disease phenotypes, where all patients were naive to immunomodulatory therapy. In addition an eQTL analysis was carried out with reference to known genotype data for this cohort of patients

Publication Title

CD4+ and B Lymphocyte Expression Quantitative Traits at Rheumatoid Arthritis Risk Loci in Patients With Untreated Early Arthritis: Implications for Causal Gene Identification.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE6787
Expression data from wildtype and Rb-/- fetal liver at e12.5
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

Rb null embryos exhibit defective fetal liver erythropoiesis. We used microarrays to compare Wt and Rb null fetal livers and to analyse gene expression differences which accompany and may underlie Rb null fetal liver degeneration, erythroid failure, and erythropoietic island dissolution.

Publication Title

Hypoxic stress underlies defects in erythroblast islands in the Rb-null mouse.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE57178
Gene Expression Profiles in Chronic Idiopathic Urticaria
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Lesions of chronic idiopathic urticaria (CIU) showed significant up-regulation of 506 genes and reduced expression of 51 genes.

Publication Title

Gene expression profiles in chronic idiopathic (spontaneous) urticaria.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE55200
Gene expression data from human subcutaneous adipose tissue
  • organism-icon Homo sapiens
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.1 ST Array (hugene21st)

Description

Obesity is a heterogeneous conditions comprising obese individuals with metabolic disorders (termed metabolically unhealthy obese; MUO) and obese individuals who are metabolically healthy (termed metabolically healthy obese; MHO).

Publication Title

Serum and adipose tissue amino acid homeostasis in the metabolically healthy obese.

Sample Metadata Fields

Specimen part, Disease, Disease stage

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accession-icon SRP072996
RNA-seq of Lmnb1-/- and Lmnb1+/- olfactory lineages
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Lamins, the major components of the nuclear lamina, have diverse functions in many cellular processes. Despite broad expression, lamins have been implicated in cell type-specific roles in development, aging and disease by regulating gene expression. Yet, due to the lack of in depth lineage-specific functional studies, it remains unclear whether or how lamins regulate cell type-specific functions. Using targeted knockout of lamin B1 in the olfactory sensory neuron lineage, we show that lamin B1 is not required for early stages of olfactory sensory neuron differentiation but is needed for formation of mature neurons that properly respond to odor stimulation. Lamin B1 mutant cells exhibited decreased expression of genes involved in mature neuron function, increased expression of genes atypical of the olfactory lineage and clustered nuclear pore distribution. These results demonstrate that the universally expressed lamin B1 regulates cell type-specific gene expression and terminal differentiation. Overall design: Transcriptome profiles were generated from sorted regenerated olfactory epithelium cells lacking Lamin B1 (Lmnb1) and control (heterozygous cells). Each sample is collected from one mouse. Data are from two experimental groups (G1,G2), each containing a control and a mutant sample. Different groups differ in treatment, parents, age and sex. Within a group, treatment, sample preparation, sequencing, animal sex, age, and parents are the same.

Publication Title

Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation.

Sample Metadata Fields

Specimen part, Treatment, Subject

View Samples
accession-icon GSE7486
Gene expression analysis in absence epilepsy using a monozygotic twin design
  • organism-icon Homo sapiens
  • sample-icon 28 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Objective:

Publication Title

Gene expression analysis in absence epilepsy using a monozygotic twin design.

Sample Metadata Fields

Sex

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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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