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Egg proteome in vtg1 and vtg3 knocked-out zebrafish females

ABSTRACT: CRISPR/Cas9 knock-out of the vtg1 and vtg3 genes was performed in zebrafish separately. This project involves proteomics screening for validation of the absence of targeted proteins in vtg1 and vtg3 and their variants in knocked out female zebrafish in eggs and investigating possible changes within the corresponding proteomes as a results of the absence of these specific vitellogenins and their variants.

INSTRUMENT(S): LTQ Orbitrap

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

TISSUE(S): Egg

SUBMITTER: E Com

LAB HEAD: Charles Pineau

PROVIDER: PXD021302 | Pride | 2021-09-09

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	280_03_1E1.RAW	Raw
	280_03_1E1.temp.mgf	Mgf
	280_03_1E2.RAW	Raw
	280_03_1E2.temp.mgf	Mgf
	280_03_1E3.RAW	Raw

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Publications

Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs.

Yilmaz Ozlem O Patinote Amelie A Com Emmanuelle E Pineau Charles C Bobe Julien J

BMC genomics 20210428 1

<h4>Background</h4>We previously reported the results of CRISPR/Cas9 knock-out (KO) of type-I and type-III vitellogenins (Vtgs) in zebrafish, which provided the first experimental evidence on essentiality and disparate functioning of Vtgs at different stages during early development. However, the specific contributions of different types of Vtg to major cellular processes remained to be investigated. The present study employed liquid chromatography and tandem mass spectrometry (LC-MS/MS) to meet ...[more]

PMID: 33910518

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Egg and liver proteome in vtg2 knocked-out zebrafish females

Project description:CRISPR/Cas9 knock-out of the vtg1 and vtg3 genes was performed in zebrafish separately. This project involves proteomics screening for validation of the absence of targeted proteins in vtg1 and vtg3 and their variants in knocked out female zebrafish in eggs and investigating possible changes within the corresponding proteomes as a results of the absence of these specific vitellogenins and their variants.

2023-10-09 | PXD042791 | Pride

Comparative proteomics analysis of Brassica napus in response to drought stress

Project description:Drought is one of the most severe stresses leading to retardation of plant growth and development and loss of crop yield. Here we examined the proteome changes of an important oil seed crop canola Brassica napus under drought stress over a 14 day period. Using iTRAQ LC-MS/MS, we identified 2,244 proteins expressed during drought stress. Among them, 412 proteins showed significant changes in abundance under stress, and 67, 243, 287, and 79 proteins were differentially expressed in 3rd, 7th, 10th, and 14th day of drought stress, respectively. Functional analysis of the 412 proteins indicated that the number of proteins associated with “Metabolism”, “Protein synthesis”, and “Signaling” decreased, while those related to “Photosynthesis” and “Stress and defense” increased in response to drought stress. In particular, the proteome profiles at the 7th and 10th day were similar to each other, although there were much more post-translational modifications (PTM) at the 10th day of drought. Interestingly, 286 of 2,244 proteins exhibited PTMs in response to drought stress, 82 of which were differentially changed in drought-stressed plants, and 60 were observed at the 10th day. Furthermore, comparison of protein expression changes with those of gene transcription showed that there was positive correlation in B. napus, although there were different patterns between transcripts and proteins at each time point. As drought stress prolongs, most of the protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to the protein diversity and functions.

2016-07-06 | PXD001409 | Pride

Zebrafish 27hpf embryos: hdac1 mutant (hi1618) vs sibling

Project description:Transcriptional profiling of hdac1 mutant zebrafish in comparison to their sibling embryos. Embryos resulting from a cross between heterozygous hdac1 mutant zebrafish (hi1618/+) where cultured together then mutants separated from the siblings one the basis of phenotype and RNA extracted from the two groups at 27hpf was compared in a two-colour hybridisation. Two-condition experiment, hdac1 mutants vs. sibling. Biological replicates: 2 (separate mating) Technical replicates: 4 (2 of which are dye-swap)

2011-01-21 | E-GEOD-26707 | biostudies-arrayexpress

Zebrafish hdac1 mutant and morphant embryos

Project description:This SuperSeries is composed of the following subset Series: GSE26707: Zebrafish 27hpf embryos: hdac1 mutant (hi1618) vs sibling GSE26708: Zebrafish embryos: hdac1 Morphants vs Standard control morphants GSE26709: Zebrafish embryos: hdac1 Morphants vs Standard control morphants at 12, 18 and 27 hpf Refer to individual Series

2011-01-21 | E-GEOD-26710 | biostudies-arrayexpress

Comparative proteomics of defense response to AAL toxin

Project description:A comparative proteomics analysis on AAL toxin treated jai1 mutant and its wild type revealed that JA pathway promoted AAL toxin induced PCD by regulating the relevant PCD components and/or through other hormone pathways in a SlCOI1 dependent manner.</br></br>Additional contact: <a href="mailto:xixizhangmin@123.com" target="_top">Min Zhang</a>, Zhejiang University.

2016-06-27 | PXD002864 | Pride

Zebrafish embryos: hdac1 Morphants vs Standard control morphants

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2011-01-21 | E-GEOD-26708 | biostudies-arrayexpress

Changes in gene expression in implantation and inter-implantation sites by absence of Cbs

Project description:This SuperSeries is composed of the following subset Series: GSE22187: Changes in gene expression in implantation sites by absence of Cbs GSE22189: Changes in gene expression in inter-implantation sites by absence of Cbs Refer to individual Series

2012-05-30 | E-GEOD-22310 | biostudies-arrayexpress

Zebrafish embryos: hdac1 Morphants vs Standard control morphants at 12, 18 and 27 hpf

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2011-01-21 | E-GEOD-26709 | biostudies-arrayexpress

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

Project description:Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. This analysis identified thousands of novel splicing events, including hundreds of developmentally regulated AS events. To make these data easily accessible and informative, we constructed the C. elegans Splice Browser, a web resource in which researchers can mine AS events of interest and retrieve information about their relative levels and regulation across development. The data presented in this study, along with the Splice Browser, provides the most comprehensive set of annotated splice variants in C. elegans to date, and is therefore expected to faciliate focused, high resolution in vivo functional assays of AS function. Alternative splicing events were identified from alignments of C. elegans mRNA/EST sequences (UniGene Build #26) to C. elegans genomic sequence (NCBI timestamp: Sept. 25, 2006), essentially as previously described (Pan et al. 2005; Pan et al. 2004). In total, 499 cassette type AS events were identified. For each AS event, 3 exon probes and 3 exon junction probes were designed to profile the AS event on the microarray, essentially as previously described (Pan et al. 2004). This submission represents the expression microarray component of the study.

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