Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The proteomics effects of HSP60 chaperone deficiency in zebrafish larvae

ABSTRACT: To understand the effects of Hsp60 deficiency in developing vertebrates, we generated CRISPR/Cas9-mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the proteome changes in zebrafish larvae at 5 days post fertilization (DPF). Wildtype control and hspd1-/- larvae at 5dpf, were analyzed by TMT and nanoLC-MS/MS based proteomcis. For this purpose, we studied five pools from each genotype, and each pool consisted of five larvae.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Embryo

SUBMITTER: Johan Palmfeldt

LAB HEAD: Johan Palmfeldt

PROVIDER: PXD048920 | Pride | 2024-09-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

HSP60 chaperone deficiency disrupts the mitochondrial matrix proteome and dysregulates cholesterol synthesis.

Cömert Cagla C Kjær-Sørensen Kasper K Hansen Jakob J Carlsen Jasper J Just Jesper J Meaney Brandon F BF Østergaard Elsebet E Luo Yonglun Y Oxvig Claus C Schmidt-Laursen Lisbeth L Palmfeldt Johan J Fernandez-Guerra Paula P Bross Peter P

Molecular metabolism 20240814

<h4>Objective</h4>Mitochondrial proteostasis is critical for cellular function. The molecular chaperone HSP60 is essential for cell function and dysregulation of HSP60 expression has been implicated in cancer and diabetes. The few reported patients carrying HSP60 gene variants show neurodevelopmental delay and brain hypomyelination. Hsp60 interacts with more than 260 mitochondrial proteins but the mitochondrial proteins and functions affected by HSP60 deficiency are poorly characterized.<h4>Meth ...[more]

PMID: 39147275

Similar Datasets

Transcription profiling of zebrafish response to Mycobacterium marinum infection

Project description:Mycobacteria infect macrophages that aggregate with additional macrophages and lymphocytes to form granulomas. We have used a functional genomics approach to identify immune response genes expressed during granuloma formation in Mycobacterium marinum-infected transparent zebrafish larvae where individual infection steps can be viewed in real time. We assessed RNA expression profiles from zebrafish larvae that were either infected with Mycobacterium marinum, mock-infected, or uninfected. Zebrafish infections were performed at 1 day post-fertilization (dpf), and samples were derived from pools of 6dpf zebrafish larvae. Experiment Overall Design: Total RNA was purified from pooled intact zebrafish larvae (31-82 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols. Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (30ug/replicate) were fragmented using standard methods. Hybridization and scanning were performed using standard Affymetrix protocol. Raw expression values were normalized (Invariant set method) and modeled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).

2008-06-16 | E-GEOD-8327 | biostudies-arrayexpress

Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish

Project description:ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase (FASN). Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tg(fabp10:nls-mCherry) control larvae, 2 batches of ethanol-treated Tg(fabp10:nls-mCherry) larvae, and 1 batch of Tg(fabp10:nAtf6-cherry; cmlc2:GFP). Each batch was purified for preparation of high-throughput sequencing libraries.

2014-05-01 | E-GEOD-56498 | biostudies-arrayexpress

RNA-seq experiment of sv2a-/-, sv2a+/- and sv2a+/+ zebrafish larvae

Project description:Transcriptome analysis of the heads of 6 dpf sv2a-/-, sv2a+/- and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a-/- zebrafish larvae.

2022-04-21 | E-MTAB-11505 | biostudies-arrayexpress

RNA-seq of depdc5-/-, tsc2-/-, depdc5-/- x tsc2-/- and wildtype zebrafish larvae

Project description:Transcriptome analysis of the heads of 5 dpf epdc5-/-, tsc2-/-, depdc5-/- x tsc2-/- and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a-/- zebrafish larvae.

2022-09-12 | E-MTAB-11776 | biostudies-arrayexpress

Next Generation Sequencing (NGS) of zebrafish larvae transcriptome by 2,2',4,4'-tetrabromodiphenyl ether (BDE47) treatment

Project description:Purpose: We report the application of NGS for profiling the impacts of BDE47 exposure on the transcriptome of zebrafish larvae. Methods: mRNA profiles of 6-day-old BDE47-treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control, 2235 transcripts were affected after 500 μg/l exposure, in which 1338 were up-regulated and 897 were down-regulated, and 552 transcripts were affected after 5 μg/l exposure, in which 155 were up-regulated and 397 were down-regulated. High concentration of BDE47 exposure resulted in more up-regulated genes. Conclusions: This study provides a framework for the application of high-throughput RNA sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval transcriptome. Examination of zebrafish larvae transcriptomes with vehicle and 2 different concentrations of BDE47 treatments.

2014-12-16 | E-GEOD-59968 | biostudies-arrayexpress

Transcription profiling time series of zebrafish hearts treated with dioxin (TCDD)

Project description:For analysis of gene expression changes in the zebrafish larvae heart in response to TCDD exposure, three replicate samples of heart tissue were collected at 73, 74, 76 and 84 hours post fertilization from larvae exposed to 1 ng/ml TCDD or vehicle from 72 - 73 hours post fertilization. For analysis of gene expression changes in the extracardiac tissue in response to TCDD exposure, three replicate samples of zebrafish larvae bodies with the heart tissue removed were collected at 73, 74, 76 and 84 hours post fertilization from larvae exposed to 1 ng/ml TCDD or vehicle from 72 - 73 hours post fertilization.

2006-06-29 | E-MEXP-758 | biostudies-arrayexpress

Zebrafish larvae response to AgNPs and AgNO3

Project description:Transcriptional profiling of zebrafish larvae comparing control with AgNO3 or AgNPs exposed zebrafish larvae. Three-condition experiment, Control vs. AgNO3 and Control vs. AgNPs exposed zebrafish. Biological replicates: 6 control replicates, 6 AgNO3 replicates and 6 AgNPs replicates.

2015-09-01 | E-GEOD-61186 | biostudies-arrayexpress

Differentially expressed genes after inhibition of methylation

Project description:Expression microarray of livers from 4 dpf control zebrafish larvae, larvae treated with azacytidine, and ahcy mutant larvae Comparison of expression from livers obtained from ahcy+/+ treated with vehicle, ahcy+/+ treated with azacytidine, and ahcy-/- treated with vehicle. We treated larvae starting at 2 dpf with 1 mM azacytidine or vehicle control. Livers were removed at 4 dpf, RNA isolated, and double amplified.

2013-07-11 | E-GEOD-48804 | biostudies-arrayexpress

Zebrafish response to microbiota

Project description:Vertebrates are colonized at birth by complex microbial communities (microbiota) that influence diverse aspects of host biology. We have used a functional genomics approach to identify zebrafish genes that are differentially expressed in response to the microbiota. We assessed RNA expression profiles from zebrafish larvae at 6 days post-fertilization (dpf) that were either raised continuously in the absence of any microorganism (germ-free or GF), or raised GF through 3dpf then colonized with a normal zebrafish microbiota (conventionalized or CONVD). Total RNA was purified from pooled intact zebrafish larvae (28-80 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols. Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (20ug/replicate) were fragmented using standard methods. Hybridization and scanning were performed using standard Affymetrix protocol. Raw expression values were normalized (Invariant set method) and modeled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).

2009-12-31 | E-GEOD-16857 | biostudies-arrayexpress

Transcriptomic characterization of temperature stress responses in larval zebrafish

Project description:96 hpf zebrafish larvae were exposed to cold (16 C) or heat (34 C) stress for 2 and 48h. Time-matched controls were maintained at 28 C. The transcriptional responses elicited by temperature stress in larval zebrafish were investigated by microarray.

2012-02-15 | E-MTAB-983 | biostudies-arrayexpress

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