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accession-icon GSE13901
Treatment of human monocyte-derived dendritic cells with Saccaromyces cerevisiae in exponential growth phase
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

In vitro experiment of stimulation of monocyte-derived dendritic cells with Saccaromyces cerevisiae in exponential growth phase. This experiment was performed to verify the comparability of microarray

Publication Title

Using pathway signatures as means of identifying similarities among microarray experiments.

Alternate Accession IDs

E-GEOD-13901

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon E-MEXP-445
Transcription profiling by array of human primary monocytes grown in hypoxia
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Experiment with 6 hybridizations, using 30 samples of species [Homo sapiens], using 6 arrays of array design [Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]], producing 6 raw data files and 6 transformed and/or normalized data files.

Publication Title

Hypoxia modifies the transcriptome of primary human monocytes: modulation of novel immune-related genes and identification of CC-chemokine ligand 20 as a new hypoxia-inducible gene.

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Disease

View Samples
accession-icon GSE47122
Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro
  • organism-icon Homo sapiens
  • sample-icon 60 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

To investigate the time-dependent and coordinated sequence of inflammation-related events, and the dynamic features of macrophage polarisation/activation, we build and validated an in vitro model based on primary human monocytes

Publication Title

Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro.

Alternate Accession IDs

E-GEOD-47122

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE16122
A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma
  • organism-icon Homo sapiens
  • sample-icon 158 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a), Affymetrix Human Mapping 50K Xba240 SNP Array (mapping50kxba240)

Description

A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide dosage effect on gene and microRNA expression

Publication Title

A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide gene dosage effect.

Alternate Accession IDs

E-GEOD-16122

Sample Metadata Fields

Specimen part, Disease

View Samples
accession-icon GSE13591
Integrated genomics approach to detect allelic imbalances in multiple myeloma
  • organism-icon Homo sapiens
  • sample-icon 158 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Multiple myeloma (MM) is characterized by marked genomic instability. Beyond structural rearrangements, a relevant role in its biology is represented by allelic imbalances leading to significant variations in ploidy status. To better elucidate the genomic complexity of MM, we analyzed a panel of 45 patients using combined FISH and microarray approaches. Using a self-developed procedure to infer exact local copy numbers for each sample, we identified a significant fraction of patients showing marked aneuploidy. A conventional clustering analysis showed that aneuploidy, chromosome 1 alterations, hyperdiploidy and recursive deletions at 1p and chromosomes 13, 14 and 22 were the main aberrations driving samples grouping. Then, we integrated mapping information with gene and microRNAs expression profiles: a multiclass analysis of the identified clusters showed a marked gene-dosage effect, particularly concerning 1q transcripts, also confirmed by correlating gene expression levels and local copy number alterations. A wide dosage effect affected also microRNAs, indicating that structural abnormalities in MM closely reflect in their expression imbalances. Finally, we identified several loci in which genes and microRNAs expression correlated with loss-of-heterozygosity occurrence. Our results provide insights into the composite network linking genome structure and gene/microRNA transcriptional features in MM.

Publication Title

A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide gene dosage effect.

Alternate Accession IDs

E-GEOD-13591

Sample Metadata Fields

Specimen part, Disease

View Samples
accession-icon SRP122528
Obesity Weight Loss Study
  • organism-icon Homo sapiens
  • sample-icon 32 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

RNA Sequencing of human adipose tissue before and after diet-induced weight loss Overall design: Prospective cohort study https://academic.oup.com/jes/article/1/6/625/3754346/Effects-of-Rapid-Weight-Loss-on-Systemic-and?searchresult=1

Publication Title

Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women.

Alternate Accession IDs

GSE106289

Sample Metadata Fields

Sex, Specimen part, Subject, Time

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accession-icon GSE47032
Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell Renal Cell Carcinoma
  • organism-icon Homo sapiens
  • sample-icon 40 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

In this study we performed a genome wide analysis of the entire complement of mRNAs in clear cell renal cell carcinomas (ccRCC) by means of the Affymetrix Exon Array platform. The analyses were performed both at gene and exon level.

Publication Title

Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell renal cell carcinoma.

Alternate Accession IDs

E-GEOD-47032

Sample Metadata Fields

Sex, Age, Specimen part, Subject

View Samples
accession-icon E-MEXP-232
Platform comparison and transcription profiling of MDA-MB-231 human metastatic breast cancer cells, cultured for 48 h in the absence (control) or presence (treated) of 32 ?M resveratrol to evaluate Amersham CodeLink UniSet Human 10K I BioArray and Affymetrix GeneChip HG-U133A)
  • organism-icon Homo sapiens
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconUNKNOWN

Description

Evaluation of two commercial microarray platforms (Amersham CodeLink UniSet Human 10K I BioArray and Affymetrix GeneChip HG-U133A). Both platforms have been tested on gene expression profiling of MDA-MB-231 human metastatic breast cancer cells, cultured for 48 h in the absence (control) or presence (treated) of 32 µM resveratrol.

Publication Title

Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment.

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage, Cell line, Compound

View Samples
accession-icon GSE6357
Activation of human CD8+ T cells in renal cell carcinoma
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

BACKGROUND: Mammalian microRNAs (miR) regulate the expression of genes relevant for the development of adaptive and innate immunity against cancer. Since T cell dysfunction has previously been reported in patients with renal cell carcinoma (RCC; clear cell type), we aimed to analyse these immune cells for genetic and protein differences when compared to normal donor T cells freshly after isolation and 35 days after in vitro stimulation (IVS) with HLA-matched RCC tumor cells.

Publication Title

miR-29b and miR-198 overexpression in CD8+ T cells of renal cell carcinoma patients down-modulates JAK3 and MCL-1 leading to immune dysfunction.

Alternate Accession IDs

E-GEOD-6357

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Subject, Time

View Samples
accession-icon GSE49970
Expression Data from 12 week old APCmin/+ and littermate matched Wildtype B6 mouse Terminal Ileum (TI)
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

APCmin/+ mice develop spontaneous gastrointestinal polyposis due to a dominantly inhereited germline loss-of-function mutation in the tumor suppressor adenomatous polyposis coli (APC). Changes in intestinal immune activity have been documented to occur prior to the development of fulminate polyposis. Such changes are thought to contribute to disease development.

Publication Title

Oral interleukin-10 alleviates polyposis via neutralization of pathogenic T-regulatory cells.

Alternate Accession IDs

E-GEOD-49970

Sample Metadata Fields

Age, Specimen part

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)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

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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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