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accession-icon GSE21547
Angio-modulation in endothelial cells: an unexpected role of desmoglein-2 in regulating actin dynamics and its relevance to angiogenesis deregulation in systemic sclerosis
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Gene expression study of DSG2 silenced human microvascular endothelial cells

Publication Title

Desmoglein-2-integrin Beta-8 interaction regulates actin assembly in endothelial cells: deregulation in systemic sclerosis.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE2531
JEG3 vs BeWo
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

In this experiment we compared total RNA from two commonly used choriocarcinoma cell lines, JEG3 and BeWo, to identify differentially expressed transcripts.

Publication Title

Microarray analysis of BeWo and JEG3 trophoblast cell lines: identification of differentially expressed transcripts.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE41509
Yap role in intestine
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Restriction of intestinal stem cell expansion and the regenerative response by YAP.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE41507
RSpondin1 treatment of control and Yap cKO mice
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

RSpondin1 adenovirus was administered to mice and intestine was isolated for expression analysis 1 week later.

Publication Title

Restriction of intestinal stem cell expansion and the regenerative response by YAP.

Sample Metadata Fields

Specimen part, Treatment

View Samples
accession-icon GSE6908
Transcript Profiling of the Aerobic and Anoxic Rice Coleoptile
  • organism-icon Oryza sativa
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Rice (Oryza sativa L.) seeds can germinate in complete absence of oxygen. Under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. In this series, we compare the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions.

Publication Title

Transcript profiling of the anoxic rice coleoptile.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE65906
Aspartoacylase-dependent transcriptome changes in immortalized brown adipocytes
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Here we investigated the effect of stable knock-down of the NAA-catabolizing enzyme, Aspartoacylase (Aspa), on global gene expression in a brown adipocyte cell line.

Publication Title

N-acetylaspartate catabolism determines cytosolic acetyl-CoA levels and histone acetylation in brown adipocytes.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE81440
Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

To investigate the role of NKX3.1 in prostate differentiation, we employed transcriptome analysis of mouse seminal vesicle (from 15-month-old Nkx3.1+/+ mice); mouse prostate (from 4-month-old Nkx3.1+/+ and Nkx3.1-/- mice); human prostate cells (RWPE1 cells engineered with empty vector (altered pTRIPZ), NKX3.1 wild type over-expression, and NKX3.1 (T164A) mutant over-expression); and tissue recombinants (generated from combining engineered mouse epithelial cells (seminal vesicle epithelial cells or prostate epithelial cells from 2-month-old mice) and rat UGS mesenchymal cells). Mouse tissue or human cells were snap frozen for subsequent molecular analysis.

Publication Title

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.

Sample Metadata Fields

Age, Specimen part, Cell line

View Samples
accession-icon SRP075116
Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Mouse_Recomb_RNA-Seq)
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Analysis of transcriptome of tissue recombinants (mouse seminal vesicle epithelial [SVE] cells or prostate epithelial [PE] cells, and rat urogenital sinus [UGS] mesenchymal cells) grown under the kidney capsule in athymic nude mice for 3 months. Overall design: Total RNA obtained from tissue recombinants generated from combining engineered mouse epithelial cells (SVE or PE from 2-month-old C57Bl/6J mice) and rat UGS mesenchymal cells. Tissue recombinants were harvested and processed for RNA isolation and transcriptome analysis using the RNeasy kit (Qiagen).

Publication Title

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.

Sample Metadata Fields

Age, Specimen part, Subject

View Samples
accession-icon SRP075117
Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Human_RWPE1_RNA-Seq)
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Analysis of transcriptome of human RWPE1 cells over-expressing wild type NKX3.1 and mutant NKX3.1 (T164A). Overall design: Total RNA obtained from RWPE1 cells engineered with empty vector (altered pTRIPZ), NKX3.1 wild type over-expression, and NKX3.1 (T164A) mutant over-expression. Engineered RWPE1 cells were harvested and processed for RNA isolation and transcriptome analysis using the MagMAX RNA isolation kit (Ambion).

Publication Title

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.

Sample Metadata Fields

Cell line, Subject

View Samples
accession-icon SRP075114
Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Mouse_4M-Prostate_RNA-Seq)
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Analysis of transcriptome of prostate tissue from 4-month-old Nkx3.1 +/+ and Nkx3.1 -/- mice. Overall design: Total RNA obtained from prostate tissues from 4-month-old Nkx3.1 +/+ and Nkx3.1 -/- mice. Prostate tissues were harvested and processed for RNA isolation and transcriptome analysis using the MagMAX RNA isolation kit (Ambion).

Publication Title

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.

Sample Metadata Fields

Age, Specimen part, Subject

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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