PXD001285

PXD001285 is an original dataset announced via ProteomeXchange.

Title	Apteronotus leptorhynchus central nervous system proteome
Description	The brown ghost knifefish (Apteronotus leptorhynchus) is a weakly electric teleost fish of particular interest as a model organism for a variety of research areas in neuroscience, including neurophysiology, neuroethology, and neurobiology. This versatile model system has been more recently used in the study of central nervous system development and regeneration during adulthood, as well as in the study of vertebrate aging and senescence. Despite substantial scientific interest in this species, no genomic resources are currently available. After evaluating several trimming and transcript reconstruction strategies, de novo assembly using Trinity uncovered at least 11,847 unique components (“genes”) containing full or near-full length protein sequences based on alignment to a reference set of known Actinopterygii protein sequences, with as many as 42,459 components containing at least a partial protein-coding sequence, providing broad coverage of the proteome. Shotgun proteomics confirmed translation of open reading frames from over 2,000 transcripts, including alternative splice variants. Assignment of tandem mass spectra obtained was shown to be greatly improved with the assembly compared with using databases of sequences from closely related organisms.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_00:17:44.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001285
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Joseph Salisbury
SpeciesList	scientific name: Apteronotus leptorhynchus; NCBI TaxID: 36674;
ModificationList	Deamidated; Oxidation; Carbamidomethyl
Instrument	maXis

Revision	Datetime	Status	ChangeLog Entry
0	2014-09-04 02:23:14	ID requested
1	2015-07-16 02:36:39	announced
2	2017-06-20 05:42:50	announced	Updated project metadata.
⏵ 3	2017-10-24 00:17:45	announced	Updated project metadata.

Salisbury JP, S, î, rbulescu RF, Moran BM, Auclair JR, Zupanc GK, Agar JN, The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation. BMC Genomics, 16(1):166(2015) [pubmed]

curator keyword: Biological

submitter keyword: brain, spinal cord, apteronotus leptorhynchus

Jeffrey N. Agar
contact affiliation	Northeastern University
contact email	j.agar@neu.edu
lab head
Joseph Salisbury
contact affiliation	Northeastern University
contact email	j.salisbury@neu.edu
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/2015/07/PXD001285

PRIDE project URI

• PRIDE
  1. PXD001285
     1. Label: PRIDE project
     2. Name: Apteronotus leptorhynchus central nervous system proteome