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accession-icon GSE52571
The long non-coding RNA Paupar regulates the expression of both local and distal genes
  • organism-icon Mus musculus
  • sample-icon 12 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

The long non-coding RNA Paupar regulates the expression of both local and distal genes.

Sample Metadata Fields

Specimen part, Cell line

View Samples
accession-icon GSE52568
The long non-coding RNA Paupar regulates the expression of both local and distal genes [Pax6 KD]
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a vertebrate-conserved and central nervous system-expressed lncRNA transcribed from a locus upstream of the gene encoding the Pax6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neuronal differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with Pax6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. Our findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes.

Publication Title

The long non-coding RNA Paupar regulates the expression of both local and distal genes.

Sample Metadata Fields

Specimen part, Cell line

View Samples
accession-icon GSE52569
The long non-coding RNA Paupar regulates the expression of both local and distal genes [Paupar KD]
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a vertebrate-conserved and central nervous system-expressed lncRNA transcribed from a locus upstream of the gene encoding the Pax6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neuronal differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with Pax6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. Our findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes.

Publication Title

The long non-coding RNA Paupar regulates the expression of both local and distal genes.

Sample Metadata Fields

Specimen part, Cell line

View Samples
accession-icon GSE45229
Unique pharmacological actions of atypical neuroleptic quetiapine: possible role in cell cycle/fate control
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Quetiapine is an atypical neuroleptic with a pharmacological profile distinct from classic neuroleptics. It is currently approved for treating patients with schizophrenia, major depression and bipolar I disorder. However, its cellular effects remain elusive.

Publication Title

Unique pharmacological actions of atypical neuroleptic quetiapine: possible role in cell cycle/fate control.

Sample Metadata Fields

Sex, Treatment

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accession-icon GSE21336
GBM_SC_retinoic acid_gene_expression
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

This study compared the gene expression change of glioblastoma stem-like cells before and after retinoic acid treatment

Publication Title

Regulation of glioblastoma stem cells by retinoic acid: role for Notch pathway inhibition.

Sample Metadata Fields

Specimen part, Cell line, Treatment

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accession-icon GSE63739
Expression data from bone marrow neutrophils with or without LPS stimulation in wild type and miR-125a deficient mice
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Neutrophil activation plays a critical role in the inflammatory response to gram-negative bacterial infections. Lipopolysaccharide (LPS) from gram-negative bacterial has been shown to be a major mediator of neutrophil activation to produce pro-inflammatory cytokines, chemokines and ROS which are important to tissue damage in LPS induced septic shock.

Publication Title

No associated publication

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE52392
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas
  • organism-icon Homo sapiens
  • sample-icon 94 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas.

Sample Metadata Fields

Sex, Age

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accession-icon GSE52847
Gene signature predictive of response to chemotherapy in mCRC
  • organism-icon Homo sapiens
  • sample-icon 37 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

No associated publication

Sample Metadata Fields

Specimen part, Disease, Disease stage

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accession-icon SRP065758
Homo sapiens raw sequence reads
  • organism-icon Homo sapiens
  • sample-icon 119 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Aim to identify the potential relationship between DNA methylation and gene expression.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE52390
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas [gene expression]
  • organism-icon Homo sapiens
  • sample-icon 94 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip

Description

We used the Infinium HumanHT-12 platform to profile gene expression in 79 primary, untreated high-grade soft tissue sarcomas, representing eight relevant subtypes, two non-neoplastic fat samples and 13 representative sarcoma cell lines.

Publication Title

Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas.

Sample Metadata Fields

Sex

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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