PXD010216

PXD010216 is an original dataset announced via ProteomeXchange.

Title	Tissue-based mapping of the fathead minnow (Pimephales promelas) transcriptome and proteome
Description	Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we surveyed the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads. We also performed RNA sequencing and proteomics analysis on the telencephalon, hypothalamus, liver, and gut of male fish. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.
HostingRepository	PRIDE
AnnounceDate	2018-10-15
AnnouncementXML	Submission_2018-11-23_06:49:51.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ley Smith
SpeciesList	scientific name: Pimephales promelas; NCBI TaxID: 90988;
ModificationList	iTRAQ8plex-116 reporter+balance reagent acylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-25 05:34:56	ID requested
1	2018-10-15 14:36:34	announced
⏵ 2	2018-11-23 06:49:52	announced	Updated publication reference for PubMed record(s): 30459712.

Lavelle C, Smith LC, Bisesi JH, Yu F, Silva-Sanchez C, Moraga-Amador D, Buerger AN, Garcia-Reyero N, Sabo-Attwood T, Denslow ND, ) Transcriptome and Proteome. Front Endocrinol (Lausanne), 9():611(2018) [pubmed]

curator keyword: Biological

submitter keyword: Fathead minnows, transcriptome, proteome, tissue-specific, endocrine system

Tara Sabo-Attwood
contact affiliation	Chair, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida
contact email	sabo@phhp.ufl.edu
lab head
Ley Smith
contact affiliation	University of Florida
contact email	leycodysmith@gmail.com
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/2018/10/PXD010216

PRIDE project URI

• PRIDE
  1. PXD010216
     1. Label: PRIDE project
     2. Name: Tissue-based mapping of the fathead minnow (Pimephales promelas) transcriptome and proteome