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accession-icon SRP081249
ADAR1 controls apoptosis of stressed cells by inhibiting Staufen-mediated mRNA decay
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Both p150 and p110 isoforms of ADAR1 convert adenosine to inosine in double-stranded RNA (dsRNA). The p150 isoform suppresses the dsRNA sensing mechanism that activates the interferon induction mediated by the MDA5-MAVS signaling. In contrast, the biological function of the p110 isoform localized in the nucleus remains largely unknown. Here we show that stress-activated phosphorylation of ADAR1p110 by MKK6/p38 MAP kinases promotes its binding to Exportin-5 and nuclear export to the cytoplasm. Once translocated to the cytoplasmic, ADAR1p110 suppresses apoptosis of stressed cells by protecting many anti-apoptotic gene transcripts that contain 3'UTR dsRNA structures such as those consisting of inverted Alu repeats. ADAR1p110 competitively inhibits binding of Staufen1 to the 3'UTR dsRNAs and antagonizes the Staufen1-mediated mRNA decay mechanism. Our studies revealed a new stress response mechanism regulated by MAP kinases, in which ADAR1p110 translocates to the cytoplasm and regulates a class of mRNAs required for survival of stressed cells. Overall design: Examination of transcription changes due to ADAR1 and double ADAR1/STAU1 knockdown using RNA-seq

Publication Title

ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE145367
GeneChip Expression Array
  • organism-icon Rattus norvegicus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Gene expression analysis to compare control cells and sorted cells

Publication Title

Identification of two major autoantigens negatively regulating endothelial activation in Takayasu arteritis.

Sample Metadata Fields

Specimen part

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accession-icon DRP003299
Gene expression of granulosa cells and oocytes in sus scrofa
  • organism-icon Sus scrofa
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Gene expression was examined in granulosa cells and oocytes in various stage of follicle and in vitro grown oocytes and granulosa cells complexes in sus scrofa.

Publication Title

Gene expression patterns in granulosa cells and oocytes at various stages of follicle development as well as in in vitro grown oocyte-and-granulosa cell complexes.

Sample Metadata Fields

Specimen part

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accession-icon GSE55285
Expression data from undifferentiated human ES cell line, khES3, grown using complete, methionine, leucine or lysine deprived media and ES cell derived endoderm
  • organism-icon Homo sapiens
  • sample-icon 7 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

Methionine metabolism regulates maintenance and differentiation of human pluripotent stem cells.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE55283
Expression data from undifferentiated human ES cell line, khES3, grown using complete or methionine deprived media and ES cell derived endoderm
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

In undifferentiated human ES cells, 5hr Met deprivation (delta Met) led to decreased proliferation, and prolonged 24hr Met deprivation resulted in G0-G1 phase cell cycle arrest, which then led to apoptosis.

Publication Title

Methionine metabolism regulates maintenance and differentiation of human pluripotent stem cells.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE55284
Expression data from undifferentiated human ES cell line, khES3 grown using complete, leucine or lysine deprived media
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

In undifferentiated human ES cells, 48hr Leucine deprivation (delta Leu) or Lysine deprivation (delta Lys) led to apoptosis.

Publication Title

Methionine metabolism regulates maintenance and differentiation of human pluripotent stem cells.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE50687
Expression data from testes of the mouse X-chromosome substitution strains
  • organism-icon Mus musculus
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

To investigate the evolutionary divergence of transcriptional regulation between the mouse subspecies, we performed transcriptome analysis by microarray on testes from the X-chromosome substitution strain, which carries different subspecies-derived X chromosome on the host subspecies genome. Transcription profiling showed that large-scale aberrations in gene expression were occurred on the introgressed X chromosome. This improper expression was restored by introducing chromosome 1 from the same donor strain as the X chromosome, suggesting that the genetic incompatibility between trans-acting regulatory gene(s) on chromosome 1 and X-linked downstream genes might be a cause of the misregulation.

Publication Title

Evolutionarily diverged regulation of X-chromosomal genes as a primal event in mouse reproductive isolation.

Sample Metadata Fields

Specimen part

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accession-icon GSE19679
The influence of Snail expression on mRNA transcription levels in II-18 cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HumanWG-6 v3.0 expression beadchip

Description

Snail is a transcriptional repressor, which induces epithelial-mesenchymal transition. However, overall functions of Snail remain to be elucidated. This microarray was performed to investigate the influence of Snail expression on mRNA transcription levels in a lung adenocarcinoma cell line, II-18.

Publication Title

Epithelial-mesenchymal transition abolishes the susceptibility of polarized epithelial cell lines to measles virus.

Sample Metadata Fields

Cell line

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accession-icon SRP188416
Transcriptome analysis of cultured human alveolar epithelial type 2 cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIon Torrent S5

Description

We investigated whether in vitro expansion of human alveolar epithelial type II cells is possible. We found that human endogenous human alveolar epithelial type II cells can be cultured and passaged. The culture system enabled retroviral gene transduction into human alveolar epithelial type II cells. We performed RNA sequencing of human alveolar epithelial type II cells transduced with mutant surfactant protein C or control vector. Overall design: Cultured human alveolar epithelial type II cells were transfected with retroviral vector containing mutant surfactant protein C or control retroviral vector. The retroviral vector contained LNGFR as a marker. After gene transduction, transduced cells were purified by magnetic-activated cell sorting. The transcriptome of the cells was generated by 5'Tag-seq using Ion Genestudio S5 Sequencer.

Publication Title

In vitro expansion of endogenous human alveolar epithelial type II cells in fibroblast-free spheroid culture.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE98424
Expression data from Hm mutant
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Mouse Hammer toe (Hm) shows syndactyly. To reveal the molecular mechanisms of Hm phenotype, we performed microarray analysis to search differencially expressed genes in Hm limb.

Publication Title

Enhancer adoption caused by genomic insertion elicits interdigital <i>Shh</i> expression and syndactyly in mouse.

Sample Metadata Fields

Specimen part

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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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