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accession-icon GSE28976
Expression data from human breast cancer cell lines after demethylation treatment
  • organism-icon Homo sapiens
  • sample-icon 39 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Integrated epigenetics of human breast cancer: synoptic investigation of targeted genes, microRNAs and proteins upon demethylation treatment.

Sample Metadata Fields

Treatment

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accession-icon GSE28968
MRNA expression data from human breast cancer cell lines after demethylation treatment.
  • organism-icon Homo sapiens
  • sample-icon 39 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The contribution of aberrant DNA methylation and the downstream effects in tumorogenesis through silencing of tumor suppressor genes (TSGs) and microRNAs has been investigated. Since these epigenetic alterations can be reversed, we investigated the effects of the epigenetic therapy in breast cancer cell lines.

Publication Title

Integrated epigenetics of human breast cancer: synoptic investigation of targeted genes, microRNAs and proteins upon demethylation treatment.

Sample Metadata Fields

Treatment

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accession-icon SRP185924
RNA-seq using the Cel-Seq2 method, of wild type and 35-polyglutamine (polyQ35) expressing C. elegans worms treated with RNAi toward anc-1, or left untreated (EV) gene expression profiles.
  • organism-icon Caenorhabditis elegans
  • sample-icon 14 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Purpose: We observed protein homeostasis modulations when anc-1 is knocked-down. We wanted to measure changes in gene expression profiles following this manipulation. Methods: We treated wild type (strain N2) or polyQ35-YFP (strain AM140) nematodes, which express toxic aggregative proteins that challenge their protein homeostasis, with anc-1 RNAi until day six of adulthood, and compared their gene expression levels to those of untreated worms. Results: The knockdown of anc-1 leads to modified expression levels of hundreds of genes. There is an enrichment of transcription factors and protein homeostasis modulators, such as E3 ubiquitin ligases. Conclusions: anc-1 regulates protection from toxic aggregative proteins, at least partially, by regulating the expression of genes that encode protein homeostasis factors. Overall design: Wild type strain, three repeats; polyQ35-YFP strain, four repeats. Each repeat has two conditions: untreated (EV), and RNAi toward anc-1.

Publication Title

Gene expression modulation by the linker of nucleoskeleton and cytoskeleton complex contributes to proteostasis.

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE16798
Genes regulated after knock-down of Pirin in U937 cells
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Pirin (PIR) is a putative transcriptional regulator whose expression is silenced in cells bearing the AML1/ETO and PML/RAR leukemogenic fusion proteins and is significantly repressed in a large proportion of acute myeloid leukemias. PIR expression increases during in vitro myeloid differentiation of primary hematopoietic precursor cells, and ablation of PIR in the U937 myelomonocytic cell line or in murine primary hematopoietic precursor cells results in impairment of terminal myeloid differentiation.

Publication Title

Pirin downregulation is a feature of AML and leads to impairment of terminal myeloid differentiation.

Sample Metadata Fields

Cell line

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accession-icon SRP065825
Heterogenous ribonucleoprotein C suppresses cleavage and polyadenylation at poly(A) sites located in poly(U)-rich regions
  • organism-icon Homo sapiens
  • sample-icon 7 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Human transcripts can typically be processed at multiple polyadenylation sites to yield mRNA isoforms with distinct 3 ends. A multitude of factors contributes to the choice of individual polyadenylation sites in different cell types and tissues. In this study we have found that the heterogenous ribonucleoprotein C (hnRNP C), an RNA binding protein that was previously linked to splicing and polyadenylation at Alu repeat elements, is a general regulator of pre-mRNA cleavage and polyadenylation. By sequencing mRNA 3 ends from cells expressing normal and reduced levels of hnRNP C we found that transcripts that contain poly(U) tracts around their poly(A) sites respond in a manner indicative of hnRNP C repressing cleavage and polyadenylation. The 3 UTR isoforms whose abundance is modulated by hnRNP C contain U-rich elements and can thereby interact with A/U-rich element binding proteins that have been shown to alter transcript stability, sub-cellular localization and even the localization of the translated proteins.

Publication Title

A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE35640
Identification of a predictive gene signature to recMAGE A3 antigen-specific cancer immunotherapy in metastatic melanoma and non-small-cell lung cancer
  • organism-icon Homo sapiens
  • sample-icon 64 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Purpose: To evaluate the presence of a gene expression signature present before treatment as predictive of response to treatment with MAGEA3

Publication Title

Predictive gene signature in MAGE-A3 antigen-specific cancer immunotherapy.

Sample Metadata Fields

Specimen part

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accession-icon GSE63336
Enterohemorrhagic Escherichia coli (EHEC) deletions of glmY and glmZ
  • organism-icon Escherichia coli
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix E. coli Genome 2.0 Array (ecoli2)

Description

Transcriptional analysis of the effects of the deletion of the sRNAs glmY and glmZ in EHEC

Publication Title

Global analysis of posttranscriptional regulation by GlmY and GlmZ in enterohemorrhagic Escherichia coli O157:H7.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE77112
Regulation of Fetal Liver Growth in a Model of Diet Restriction in the Pregnant Rat
  • organism-icon Rattus norvegicus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 1.0 ST Array (ragene10st)

Description

The present study was designed to test the hypothesis that limited growth of the fetal liver in the model of maternal fasting is independent of well-characterized signaling mechanisms that are known to regulate somatic growth in adult animals.

Publication Title

Regulation of fetal liver growth in a model of diet restriction in the pregnant rat.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE16765
Transcriptomic and phenotypic variation for salt stress response in Arabidopsis
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to salinity for two widely used Arabidopsis thaliana ecotypes, Wassilewskija (Ws) and Columbia (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences.

Publication Title

Global gene expression analysis of transgenic, mannitol-producing, and salt-tolerant Arabidopsis thaliana indicates widespread changes in abiotic and biotic stress-related genes.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE18217
Global gene expression analysis of transgenic, mannitol-producing, and salt-tolerant Arabidopsis thaliana indicates widespread changes in abiotic and biotic stress-related genes
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Mannitol is a putative osmoprotectant contributing to salt tolerance in several species. Arabidopsis plants transformed with the mannose-6-phosphate reductase (M6PR) gene from celery were dramatically more salt tolerant (at 100mM NaCl) as exhibited by reduced salt injury, less inhibition of vegetative growth, and increased seed production relative to the wild type (WT). When treated with 200mM NaCl, transformants produced no seeds, but did bolt, and exhibited less chlorosis/necrosis and greater survival and dry weights than the WT. Without salt there were no M6PR effects on growth or phenotype, but expression levels of 2272 genes were altered. Many fewer differences (1039) were observed between M6PR and WT plants in the presence of salt, suggesting that M6PR pre-conditioned the plants to stress. Previous work suggested that mannitol is an osmoprotectant, but mannitol levels are invariably quite low, perhaps inadequate for osmoprotectant effects. In this study, transcriptome analysis reveals that the M6PR transgene activated the downstream abscisic acid (ABA) pathway by up-regulation of ABA receptor genes (PYL4, PYL5, and PYL6) and down-regulation of protein phosphatase 2C genes (ABI1 and ABI2). In the M6PR transgenic lines there were also increases in transcripts related to redox and cell wall-strengthening pathways. These data indicate that mannitol-enhanced stress tolerance is due at least in part to increased expression of a variety of stress-inducible genes.

Publication Title

Global gene expression analysis of transgenic, mannitol-producing, and salt-tolerant Arabidopsis thaliana indicates widespread changes in abiotic and biotic stress-related genes.

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)

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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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