Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiles of liver from 7dpf zebrafish larvae from control, sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing

ABSTRACT: We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene (sec31anju221) exhibited hepatic steatosis accompanied with activation of unfolded protein response (UPR). As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation, critical effectors of the UPR (xbp1, atf4a/4b, atf6, srebf1 and srebf2) were separately knock-outed on sec31anju221 background. In order to access the changes on transcriptome landscape, livers were dissected from the 7 dpf zebrafish larvae and low input RNA-seq was applied.

ORGANISM(S): Danio rerio

PROVIDER: GSE248098 | GEO | 2024/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Obesity Disrupts the Pituitary-Hepatic UPR Communication Leading to NAFLD Progression (pituitary scRNA seq)

Project description:Obesity alters circulating levels of pituitary hormones that govern hepatic immune-metabolic homeostasis, and dysregulation of which leads to NAFLD. Here, using diet induced obese and IRE1PKO mice, we uncovered an blunted unfolded protein response (UPR) but elevated inflammatory signatures in pituitary glands of obese mice. Mechanistically, we demonstrated that the pituitary IRE1alpha-XBP1 UPR branch is essential for protecting against pituitary endocrine defects and NAFLD progression in obesity.

2024-04-30 | GSE263189 | GEO

Obesity Disrupts the Pituitary-Hepatic UPR Communication Leading to NAFLD Progression (pituitary bulk RNA seq)

Project description:Obesity alters circulating levels of pituitary hormones that govern hepatic immune-metabolic homeostasis, and dysregulation of which leads to NAFLD. Here, using diet induced obese mouse, we uncovered an blunted unfolded protein response (UPR) but elevated inflammatory signatures in pituitary glands of obese mice. Mechanistically, we demonstrated that the pituitary IRE1alpha-XBP1 UPR branch is essential for protecting against pituitary endocrine defects and NAFLD progression in obesity.

2024-04-30 | GSE263188 | GEO

Obesity Disrupts the Pituitary-Hepatic UPR Communication Leading to NAFLD Progression (liver bulk RNA seq)

Project description:Obesity alters circulating levels of pituitary hormones that govern hepatic immune-metabolic homeostasis, and dysregulation of which leads to NAFLD. Here, using diet induced obese mouse and IRE1PKO mice, we uncovered an blunted unfolded protein response (UPR) but elevated inflammatory signatures in pituitary glands of obese mice. Mechanistically, we demonstrated that the pituitary IRE1alpha-XBP1 UPR branch is essential for protecting against pituitary endocrine defects and NAFLD progression in obesity.

2024-04-30 | GSE263187 | GEO

mRNA-seq of Arabidopsis mutants of UPR modulators responding to UPR inducers

Project description:The NGS-associated mRNA-seq analysis was conducted to survey transcriptome changes responding to three UPR inducers (tunicamycin, DTT, & Azetidine-2-cytosine) by four double mutant of three UPR-associated transcription factors (bZIP17, bZIP28, & bZIP60) and two activators (S1P & S2P).

2018-03-07 | GSE100371 | GEO

Angiogenesis induced by aminoacyl-tRNA synthetase deficiency is dependent on AAR but not UPR pathways

Project description:The amino acid response (AAR) and the unfolded protein response (UPR) pathways are closely interconnected and both implicated in regulation of stress-induced angiogenesis. Two kinases, Gcn2 and Perk, transduce signals from AAR and UPR, respectively, and phosphorylate the common target, eIF2alpha, the key regulator of protein translation. However, this interconnection makes it difficult to specify different contributions of AAR and UPR to angiogenesis. In this study, we generated a zebrafish angiogenic model harboring a loss-of-function mutation in the threonyl-tRNA synthetase (tars) gene. While previous studies approximately implicated both AAR and UPR into the angiogenic phenotypes, our gene expression profiling of the tars-/- and sibling embryos, as well as those with knockdown of either Gcn2 or Perk in both genotypes, reveal that only AAR is activated by the tars-deficiency. Phenotypic validations using genetic and pharmacological interference with AAR and UPR confirm that AAR, but not UPR, is required for the tars-deficiency-induced angiogenesis. Thus, this study demonstrates that the closely interconnected AAR and UPR can be independently activated and differentially regulate angiogenesis, which reflects the specificity and efficiency of multiple stress response pathways that are evolved integrally to benefit the organism by ensuring sensing and responding precisely to different types of stress.

2021-11-03 | GSE130193 | GEO

SARS-COV2-UPR

Project description:Enhanced SARS-CoV-2 entry via UPR-dependent AMPK-related kinase NUAK2

| PRJEB51271 | ENA

Genome-wide CRISPR screen for ER stress-UPR pathway

Project description:Perturbation of tissue homeostasis accompanies a diversity of inflammatory pathologies and imposes metabolic constraints at the cellular level that elicit ER stress, protein misfolding, and cell death. In response to ER stress, cells initiate the unfolded protein response (UPR), which determines divergent cell fate decisions, either promoting recovery of ER proteostasis and cell survival or triggering programmed cell death. However, the mechanisms by which the UPR transitions from the adaptive to terminal state are not fully understood. To discover novel UPR pathway regulators that influence the outcome of cellular ER stress responses, we performed genome-scale genetic perturbations. Our genome-wide screens revealed that distinct sets of genes regulate UPR activity and maintenance of ER homeostasis. This expansive dataset provides a rich resource that can be leveraged to elucidate signaling crosstalk during ER stress and discover novel UPR regulators.

2021-02-17 | GSE146841 | GEO

Expression data from human cancer cells treated with UPR modulators under ER stress conditions

Project description:The unfolded protein response (UPR) is a cellular defense mechanism against glucose deprivation, a cell condition that occurs in solid tumors. A key feature of the UPR is the activation of the transcription program that allows the cell to cope with endoplasmic reticulum (ER) stress. We used micoarrays to show that the UPR transcription program is disrupted by the antitumor macrocyclic compound versipelostatin (VST) and antidiabetic biguanides metformin, buformin and phenformin, depending on cellular glucose availability. Keywords: stress response, drug response

2009-05-20 | GSE13548 | GEO

Genomic profiling of neoplasms developed in SEC31A-JAK2 expressing mice

Project description:The genetics of classical Hodgkin lymphoma (cHL) is poorly understood. The finding of a JAK2-involving t(4;9)(q21;p24) in one case of cHL prompted us to characterize this translocation on a molecular level and to determine the prevalence of JAK2 rearrangements in cHL. We showed that the t(4;9)(q21;p24) leads to a novel SEC31A-JAK2 fusion. Screening of 131 cHL cases identified one additional case with SEC31A-JAK2 and two additional cases with rearrangements involving JAK2. We demonstrated that SEC31A-JAK2 is oncogenic in vitro and acts as a constitutively activated tyrosine kinase that is sensitive to JAK inhibitors. In vivo, SEC31A-JAK2 was found to induce a T-lymphoblastic lymphoma or myeloid hyperplasia in a murine bone marrow transplant model. Altogether, we identified SEC31A-JAK2 as a first aberration characteristic for cHL and provide evidence that JAK2 rearrangements occur in a minority of cHL cases. Given the proven oncogenic potential of this novel fusion, our studies provide new insights into the pathogenesis of cHL and indicate that in at least some cases, constitutive activation of the JAK-STAT pathway is caused by JAK2 rearrangements. The finding that SEC31A-JAK2 responds to JAK inhibitors indicates that patients with cHL and JAK2 rearrangements may benefit from targeted therapies. Genomic profiling of primary and secondary transplanted mice expressing SEC31A-JAK2 with myeloid hyperplasia and T-lymphoblastic lymphoma Individual sample against a normal control

2010-07-08 | E-GEOD-22404 | biostudies-arrayexpress

A network-based approach reveals the dysregulated transcriptional regulation in non-alcohol fatty liver disease

Project description:Non-alcohol-related fatty liver disease (NAFLD) is a leading cause of chronic liver disease worldwide. We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD. Based on network analysis, we identified a highly conserved disease-associated gene module across three different NAFLD cohorts and highlighted the predominant role of key transcriptional regulators associated with lipid and cholesterol metabolism. In addition, we revealed the detailed metabolic differences between heterogenous NAFLD patients through integrative systems analysis of transcriptomic data and liver-specific genome-scale metabolic model. Furthermore, we identified transcription factors (TFs), including SREBF2, HNF4A, SREBF1, YY1 and KLF13, showing regulation of hepatic expression of genes in the NAFLD-associated modules and validated the TFs using data generated from a mouse NAFLD model. In conclusion, our integrative analysis facilitated our understanding of the regulatory mechanism of these perturbed TFs and associated biological processes.

2021-10-27 | GSE184019 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data