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Ribo-seq analysis in HEK293A cells with or without IRE1a knockdown

ABSTRACT: Ribo-seq analysis in HEK293A cells with or without IRE1a knockdown

PROVIDER: PRJNA822351 | ENA |

REPOSITORIES: ENA

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Ribo-seq analysis in HEK293A cells with or without IRE1a knockdown

Project description:We conducted RNA-seq and Ribo-seq for the same samples. IRE1a was knockde down by siRNA. There are two replicates for each group.

2023-12-31 | GSE199948 | GEO

Effect of IRE1a and XBP1 knockdown on gene expression in primary mouse keratinocytes expressing an HRas oncogene

Project description:IRE1a is a critical modulator of the unfolded protein response. Its RNAse activity generates the mature transcript for the XBP1 transcription factor and also degrades other ER associated mRNAs in a process termed Regulated IRE1a Dependent mRNA Decay or RIDD. To determine if IRE1a is critical in the response to oncogenic Ras we used ShRNA to knockdown Ire1a or Xbp1 in primary mouse epidermal keratinocytes transduced with a v-HRAS retrovirus.

2017-06-01 | GSE70899 | GEO

Ribo-seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation

Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation to determine effects on translation.

2021-09-30 | E-MTAB-9094 | biostudies-arrayexpress

Expression data from IRE1a or XBP1 deficient mouse liver

Project description:IRE1a and XBP1 are key regulators of the unfolded protein response (UPR). XBP1 ablation causes profound hypolipidemia in mice, and triggers feedback activation of its upstream enzyme IRE1a, instigating regulated IRE1-dependent decay (RIDD), an mRNA degradation mechanism dependent on IRE1a's endoribonuclease activity. Comprehensive microarray analysis of XBP1 and/or IRE1a deficient liver identified genes involved in lipogenesis and lipoprotein metabolism as RIDD substrates, which might contribute to the suppression of plasma lipid levels by activated IRE1a. To identify RIDD substrate mRNAs and direct XBP1 targets in the liver, we performed a comprehensive comparative microarray analysis of three groups of RNA samples: WT and XBP1 deficient mice, WT and IRE1a deficient mice untreated or injected with tunicamycin, and XBP1 deficient mice injected with luciferase or IRE1a siRNA.

2012-10-17 | E-GEOD-40515 | biostudies-arrayexpress

Expression data from primary hepatocytes knocking down or overexpressing IRE1a

Project description:The ER-resident protein kinase/endoribonuclease IRE1 is activated through trans-autophosphorylation in response to protein folding overload in the ER lumen and maintains ER homeostasis by triggering a key branch of the unfolded protein response. Here we show that mammalian IRE1a in liver cells is also phosphorylated by a kinase other than itself in response to metabolic stimuli. Glucagon stimulated protein kinase PKA, which in turn phosphorylated IRE1a at Ser724, a highly conserved site within the kinase activation domain. Blocking Ser724 phosphorylation impaired the ability of IRE1a to augment the upregulation by glucagon signaling of the expression of gluconeogenic genes. Moreover, hepatic IRE1a was highly phosphorylated at Ser724 by PKA in mice with obesity, and silencing hepatic IRE1a markedly reduced hyperglycemia and glucose intolerance. Hence, these results suggest that IRE1a integrates signals from both the ER lumen and the cytoplasm in the liver and is coupled to the glucagon signaling in the regulation of glucose metabolism. We used DNA microarray to analyze the transcriptomic change upon IRE1a overexpression or IRE1a depletion in primary hepatocytes, to study the changes related to IRE1a Primary hepatocytes were infected with the desired adenoviruses (Ad-EGFP, Ad-WT, Ad-S724A, Ad-shCON, Ad-shIRE1a#2) or treated with glucagon. Total cellular RNA was isolated with TRIzol (Invitrogen) and subjected to analysis by Affymetrix Mouse Genome 430 2.0 Arrays. Three experiments were independently conducted.

2011-08-30 | E-GEOD-31638 | biostudies-arrayexpress

Expression data from primary hepatocytes knocking down or overexpressing IRE1a

2011-08-31 | GSE31638 | GEO

Expression data from IRE1a or XBP1 deficient mouse liver

2012-10-17 | GSE40515 | GEO

Effect of the IRE1a-XBP1 pathway inhibition during T helper 2 differentiation

Project description:The purpose of the study was to examine the role of the IRE1a-XBP1 pathway during Th2 lymphocyte activation and differentiation. In vitro Th2 cells were treated with 4μ8c, a drug that specifically inhibits IRE1a endonuclease activity, and transcriptomes were compared.

2018-07-20 | E-MTAB-6894 | biostudies-arrayexpress

Transcriptomic analysis of glioblastoma cells bearing different IRE1a mutants

Project description:Transcriptomic analysis of glioblastoma cells bearing different IRE1a mutants

| PRJNA421725 | ENA

Transcriptome analysis of ire1 mutants after treatment with or without tunicamycin in the presence of actinomycin D

Project description:Arabidopsis seedlings of wildtype or ire1a ire1b double mutant were treated with or without tunicamycine in the presence of actinomycin D (ActD).

2013-03-19 | GSE39690 | GEO

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