PXD000145

PXD000145 is an original dataset announced via ProteomeXchange.

Title	Zebrafish embryo gene and protein expression comparison
Description	Sensitivity and throughput of transcriptomics and proteomomics technologies have advanced tremendously in recent years. With the use of deep sequencing of RNA samples (RNAseq) and mass spectrometry technology for protein identification and quantitation, it is now feasible to compare gene and protein expression on a massive scale and on any organism for which genomic data is available. Although these technologies are currently applied to many research questions in various model systems ranging from cell cultures to the entire organism level, there are few comparative studies of these technologies in the same system, let alone on the same samples. Here we present a comparison between gene and protein expression in zebrafish embryos, which is an upcoming model in disease studies. We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis, showing as expected a high degree of correlation of expression of a common set of 15,927 genes. Gene expression was also found to correlate with the abundance of 1,017 quantified proteins, with several categories of genes as exceptions. These exceptions include ribosomal proteins, histones and vitellogenins, for which biological and technical explanations are discussed. By comparing state of the art transcriptomic and proteomic technologies on samples derived from the same group of organisms we have for the first time benchmarked the differences in these technologies with regard to sensitivity and bias towards detection of particular gene categories. Our datasets submitted to public repositories are a good starting point for researchers interested in disease progression in zebrafish at a stage of development highly suited for high throughput screening technologies. The transcriptomics data is deposited in NCBI GEO. Proteomics informatics: Spectra were identified by Mascot and validated by PeptideProphet  and ProteinProphet in the Trans-Proteomic Pipeline (TPP). The main search parameters are: full tryptic specificity, precursor mass searched within -0.5 to +2.5 Da, product ions within [-0.5,0.5] Da and allowing for one missed cleavage. Carbamidomethylation was assumed as the only and fixed PTM.
HostingRepository	PRIDE
AnnounceDate	2016-06-09
AnnouncementXML	Submission_2016-06-09_06:31:39.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000145
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Magnus Palmblad
SpeciesList	scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955;
ModificationList	iodoacetamide derivatized residue
Instrument	Bruker Daltonics HCT Series; instrument model: IonTrap HCT ultra

Revision	Datetime	Status	ChangeLog Entry
0	2013-02-12 14:04:04	ID requested
⏵ 1	2016-06-09 06:31:40	announced

Palmblad M, Henkel CV, Dirks RP, Meijer AH, Deelder AM, Spaink HP, Parallel deep transcriptome and proteome analysis of zebrafish larvae. BMC Res Notes, 6():428(2013) [pubmed]

submitter keyword: zebrafish, embryos

Magnus Palmblad
contact affiliation	Leiden University Medical Center
contact email	n.m.palmblad@lumc.nl
lab head
Magnus Palmblad
contact affiliation	Deparment of Parasitology
contact email	n.m.palmblad@lumc.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD000145

PRIDE project URI

• PRIDE
  1. PXD000145
     1. Label: PRIDE project
     2. Name: Zebrafish embryo gene and protein expression comparison