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accession-icon GSE54285
Analysis of impact of Toxoplasma effector MAF1 during Type II infection in WT MEFs and during Type I infection in WT and MAVS KO MEFs
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The goals of the microarray experiment were to determine the role of MAF1, the Toxoplasma gondii mediator of host mitochondrial association, on host cell gene expression by comparing infection of WT cells with Type II and Type II:MAF1 parasites. We also explored the role of MAF1 on host cell gene expression by comparing profiles of WT and MAVS KO MEFs infected with Type I and Type Imaf1KO parasites.

Publication Title

Toxoplasma effector MAF1 mediates recruitment of host mitochondria and impacts the host response.

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE69408
Expression data from human HSPCs
  • organism-icon Homo sapiens
  • sample-icon 39 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.1 ST Array (hugene11st)

Description

Aging within the human hematopoietic system associates with increased incidence of anemia and myeloid neoplasms, decreased bone marrow (BM) cellularity and reduced adaptive immune responses. Similar phenotypes have been observed in mice and shown, at least in part, to involve hematopoietic stem cells (HSCs). However, evidence supporting such an association within human hematopoiesis is still sparse and prompted us to detail characteristics of human hematopoietic stem and progenitor cells throughout ontogeny.

Publication Title

Human and Murine Hematopoietic Stem Cell Aging Is Associated with Functional Impairments and Intrinsic Megakaryocytic/Erythroid Bias.

Sample Metadata Fields

Specimen part

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accession-icon SRP053363
Analysis of wildtype and Xbp1-deficient hematopoietic progenitor cell transcriptomes
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Purpose: The goals of this study are to assess the transcriptional networks governed by the transcription factor XBP1 in lineage-uncommitted myeloid progenitors and in eosinophil-committed myeloid progenitors. Methods: mRNA profiles of FACS-purified granulocyte-macrophage progenitors (GMPs) from XBP1 flox/flox or XBP1 flox/flox Vav1-Cre mice were generated by sequencing, in biological triplicates, using an Illumina HiSeq2000 sequencer. The Illumina HiSeq2000 sequencer was also used to obtain mRNA profiles of FACS-purified GMPs transduced with the transcription factor GATA2, resorted 36 hours post-transduction, and cultured for 48 hours, again in biological triplicates per genotype. Sequence data from Illumina''s HiSeq2000 sequencer were demuxed to generate FASTQ files for each sample using Illumina''s CASAVA pipeline (version 1.8.2). The reads that passed illumina''s quality/purity filter were aligned to the mouse genome (Illumina iGenomes mm9 build) using STAR aligner (version 2.3.0) with default parameters. The resulting SAM alignment files were then converted to the BAM file format, sorted and indexed using SAMtools (version 0.1.14).  Mapped reads were counted with the python module HTSeq, and differential expression analyzed with the Bioconductor package DESeq. Results and conclusions: By monitoring XBP1-dependent transcriptional changes at different stages of eosinophil development, we demonstrated that classical XBP1-dependent networks such as glycosylation, chaperone production, and ERAD were downregulated in GMPs prior to eosinophil commitment, though there were no major defects in differentiation or survival. However, mRNA profiling clearly demonstrated that XBP1 deficiency causes a state of cellular stress upon eosinophil commitment. The eosinophil transcriptome was largely intact, and most dysregulated genes were associated with ER stress. However key granule protein genes required for eosinophil development such as Prg2 and Epx were selectively downregulated only after eosinophil commitment, but not in pre-committed myeloid progenitors, and this correlated with Ingenuity Pathway Analysis predictions that GATA1 function was impaired. This study documents the interplay between cellular stress and the ability to maintain key facets of cellular differentiation. Overall design: Analyses of XBP1-dependent transcriptional networks at two stages of eosinophil development.

Publication Title

The transcription factor XBP1 is selectively required for eosinophil differentiation.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE69675
Functional investigation of miRNAs by characterization of SH-SY5Y cells overexpressing wild type or mutant miRNA genes
  • organism-icon Homo sapiens
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Genome wide mRNA and miRNA profiling was performed in SH-SY5Y cells stably overexpressing wild type or mutant MIR204 or MIR618. Mutants came from a large scale genetic screening of brain expressed miRNA genes in patients with schizophrenia or idiopathic generalized epilepsy and in control individuals. Based on enrichment of the variants with the schizophrenic or epileptic phenotype and based on impact prediction, two variants, one near MIR204 (rs7861254) and one in MIR618 (rs2682818) were selected for functional validation. Genome wide profiling of mRNA (micro-array) and mature miRNAs (small RNA sequencing, submitted to SRA) was performed in the created stable cells to assess the effect of the variants and to investigate the function of these miRNA genes.

Publication Title

Schizophrenia-Associated MIR204 Regulates Noncoding RNAs and Affects Neurotransmitter and Ion Channel Gene Sets.

Sample Metadata Fields

Cell line

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accession-icon GSE21728
Global analysis of the impact of environmental perturbation on cis-regulation of gene expression
  • organism-icon Homo sapiens
  • sample-icon 237 Downloadable Samples
  • Technology Badge IconIllumina humanRef-8 v2.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Global analysis of the impact of environmental perturbation on cis-regulation of gene expression.

Sample Metadata Fields

Sex, Specimen part, Time

View Samples
accession-icon GSE21725
Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: DEX, 24hr
  • organism-icon Homo sapiens
  • sample-icon 44 Downloadable Samples
  • Technology Badge IconIllumina humanRef-8 v2.0 expression beadchip

Description

Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent to which environmental perturbation influences such traits has not been studied to date. We carried out large-scale induction experiments using primary human bone cells derived from 113 unrelated donors of Swedish origin harvested under 18 different conditions (seven treatments, two vehicles, each assessed at two time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t=2h), dexamethasone (DEX) (t=24h), and PGE2 (t=24h). Using these treatments, we performed expression profiling for 18,144 RefSeq transcripts applying biological replicates of the complete study cohort (ntotal=782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs. We found that 93% of cis-eQTLs at 1% FDR were replicated in at least one additional treatment and in fact, on average only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment, though treatment-specific cis-regulatory effects were 2-6-fold more abundant among up-or downregulated genes. We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 and 250kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interaction between cellular environment and cis-variants are relatively rare (~1.5%), but that detection of such specific interactions can be achieved by combination of functional genomic tools.

Publication Title

Global analysis of the impact of environmental perturbation on cis-regulation of gene expression.

Sample Metadata Fields

Sex, Specimen part, Time

View Samples
accession-icon GSE21410
Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: BMP2, 2hr
  • organism-icon Homo sapiens
  • sample-icon 35 Downloadable Samples
  • Technology Badge IconIllumina humanRef-8 v2.0 expression beadchip

Description

Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent to which environmental perturbation influences such traits has not been studied to date. We carried out large-scale induction experiments using primary human bone cells derived from 113 unrelated donors of Swedish origin harvested under 18 different conditions (seven treatments, two vehicles, each assessed at two time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t=2h), dexamethasone (DEX) (t=24h), and PGE2 (t=24h). Using these treatments, we performed expression profiling for 18,144 RefSeq transcripts applying biological replicates of the complete study cohort (ntotal=782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs. We found that 93% of cis-eQTLs at 1% FDR were replicated in at least one additional treatment and in fact, on average only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment, though treatment-specific cis-regulatory effects were 2-6-fold more abundant among up-or downregulated genes. We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 and 250kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interaction between cellular environment and cis-variants are relatively rare (~1.5%), but that detection of such specific interactions can be achieved by combination of functional genomic tools.

Publication Title

Global analysis of the impact of environmental perturbation on cis-regulation of gene expression.

Sample Metadata Fields

Sex, Specimen part, Time

View Samples
accession-icon GSE21726
Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: PGE2, 24hr
  • organism-icon Homo sapiens
  • sample-icon 155 Downloadable Samples
  • Technology Badge IconIllumina humanRef-8 v2.0 expression beadchip

Description

Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent to which environmental perturbation influences such traits has not been studied to date. We carried out large-scale induction experiments using primary human bone cells derived from 113 unrelated donors of Swedish origin harvested under 18 different conditions (seven treatments, two vehicles, each assessed at two time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t=2h), dexamethasone (DEX) (t=24h), and PGE2 (t=24h). Using these treatments, we performed expression profiling for 18,144 RefSeq transcripts applying biological replicates of the complete study cohort (ntotal=782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs. We found that 93% of cis-eQTLs at 1% FDR were replicated in at least one additional treatment and in fact, on average only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment, though treatment-specific cis-regulatory effects were 2-6-fold more abundant among up-or downregulated genes. We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 and 250kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interaction between cellular environment and cis-variants are relatively rare (~1.5%), but that detection of such specific interactions can be achieved by combination of functional genomic tools.

Publication Title

Global analysis of the impact of environmental perturbation on cis-regulation of gene expression.

Sample Metadata Fields

Sex, Specimen part, Time

View Samples
accession-icon GSE40278
A multiply redundant genetic switch locks in the transcriptional signature of T regulatory cells
  • organism-icon Mus musculus
  • sample-icon 60 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells.

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon GSE21727
Global analysis of the impact of environmental perturbation on cis-regulation of gene expression: control and variety of treatments, 2hr and 24hr
  • organism-icon Homo sapiens
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconIllumina humanRef-8 v2.0 expression beadchip

Description

Genetic variants altering cis-regulation of normal gene expression (cis-eQTLs) have been extensively mapped in human cells and tissues, but the extent to which environmental perturbation influences such traits has not been studied to date. We carried out large-scale induction experiments using primary human bone cells derived from 113 unrelated donors of Swedish origin harvested under 18 different conditions (seven treatments, two vehicles, each assessed at two time points). The treatments with the largest impact on the transcriptome, verified on two independent expression arrays, included BMP-2 (t=2h), dexamethasone (DEX) (t=24h), and PGE2 (t=24h). Using these treatments, we performed expression profiling for 18,144 RefSeq transcripts applying biological replicates of the complete study cohort (ntotal=782) and combined it with genome-wide SNP-genotyping data in order to map treatment-specific cis-eQTLs. We found that 93% of cis-eQTLs at 1% FDR were replicated in at least one additional treatment and in fact, on average only 1.4% of the cis-eQTLs were considered as treatment-specific at high confidence. The relative invariability of cis-regulation following perturbation was reiterated independently by genome-wide allelic expression tests where only a small proportion of variance could be attributed to treatment, though treatment-specific cis-regulatory effects were 2-6-fold more abundant among up-or downregulated genes. We further followed-up and validated the DEX-specific cis-regulation of the MYO6 and TNC loci and found top cis-regulatory variants located 180 and 250kb upstream of the transcription start sites, respectively. Our results suggest that, as opposed to tissue-specificity of cis-eQTLs, the interaction between cellular environment and cis-variants are relatively rare (~1.5%), but that detection of such specific interactions can be achieved by combination of functional genomic tools.

Publication Title

Global analysis of the impact of environmental perturbation on cis-regulation of gene expression.

Sample Metadata Fields

Sex, Specimen part, Time

View Samples

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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