PXD018985

PXD018985 is an original dataset announced via ProteomeXchange.

Title	Enhancing the cardiac pig transcriptome by long-read sequencing and in-depth proteomics
Description	Clinically translatable large animal models have become indispensable for cardiovascular research, clinically relevant proof of concept studies and for novel diagnostic and therapeutic interventions. In particular, the pig as emerged as an essential cardiovascular disease model, because its heart, circulatory system, and blood supply are anatomically and functionally similar to that of humans. Unfortunately, molecular and omics-based studies in the pig are hampered by the incompleteness of the genome and the lack of diversity of the corresponding transcriptome annotation. Here, we employed Nanopore long-read sequencing and in-depth proteomics on top of Illumina RNA-seq to enhance the pig cardiac transcriptome annotation. We assembled 15,926 transcripts, stratified into coding and non-coding, and validated our results by complementary mass spectrometry. A manual review of several gene loci, which are associated with cardiac function, corroborated the utility of our enhanced annotation. All our data are available for download and is also provided as tracks for integration in genome browsers. We deem this resource as highly valuable for molecular research in an increasingly relevant large animal model.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:14:23.912.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Torsten Mueller
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-04 18:23:12	ID requested
1	2020-10-29 06:45:10	announced
⏵ 2	2024-10-22 05:14:24	announced	2024-10-22: Updated project metadata.

M, ü, ller T, Boileau E, Talyan S, Kehr D, Varadi K, Busch M, Most P, Krijgsveld J, Dieterich C, Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics. J Mol Cell Cardiol, 150():23-31(2021) [pubmed]

10.1016/j.yjmcc.2020.10.005;

submitter keyword: Pig, TMT, Annotation, Proteomics, Transcriptomics, Cardiac,Nanopore, LCMS

Christoph Dieterich
contact affiliation	University Hospital Heidelberg
contact email	christoph.dieterich@uni-heidelberg.de
lab head
Torsten Mueller
contact affiliation	DKFZ
contact email	torsten.mueller84@googlemail.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/2020/10/PXD018985

PRIDE project URI

• PRIDE
  1. PXD018985
     1. Label: PRIDE project
     2. Name: Enhancing the cardiac pig transcriptome by long-read sequencing and in-depth proteomics