PXD001301

PXD001301 is an original dataset announced via ProteomeXchange.

Title	CRISPR-Cas9-based knockout of the prion protein and its effect on the proteome
Description	The molecular function of the cellular prion protein (PrPC) and the mechanism by which it may contribute to neurotoxicity in prion diseases and Alzheimer’s disease (AD) are only partially understood. Mouse neuroblastoma Neuro2a cells and, more recently, C2C12 myocytes and myotubes have emerged as popular models for investigating the cellular biology of PrP. Mouse epithelial NMuMG cells might become attractive models for studying the possible involvement of PrP in a morphogenetic program underlying epithelial-to-mesenchymal transitions. Here we describe the generation of PrP knockout clones from these cell lines using CRISPR-Cas9 knockout technology. More specifically, knockout clones were generated with two separate gRNAs targeting recognition sites on opposite strands within the first hundred nucleotides of the Prnp coding sequence. Several PrP knockout clones were isolated and genomic insertions and deletions near the CRISPR-target sites were characterized. Subsequently, deep quantitative global proteome analyses that recorded the relative abundance of > 3000 proteins were undertaken to begin to characterize the molecular consequences of PrP deficiency. The levels of ~120 proteins were shown to reproducibly correlate with the presence or absence of PrP, with most of these proteins as belonging to extracellular components, cell junctions or the cytoskeleton.
HostingRepository	PRIDE
AnnounceDate	2014-11-19
AnnouncementXML	Submission_2015-04-01_05:53:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gerold Schmitt-Ulms
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-pyridylethyl-L-cysteine; monohydroxylated residue; carbamoylated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2014-09-10 01:33:17	ID requested
1	2014-11-19 00:41:59	announced
⏵ 2	2015-04-01 05:53:11	announced	Updated publication reference for PubMed record(s): 25490046.

Mehrabian M, Brethour D, MacIsaac S, Kim JK, Gunawardana CG, Wang H, Schmitt-Ulms G, CRISPR-Cas9-based knockout of the prion protein and its effect on the proteome. PLoS One, 9(12):e114594(2014) [pubmed]

curator keyword: Biological

submitter keyword: prion, CRISPR-Cas9, knockout, kockdown

Gerold Schmitt-Ulms
contact affiliation	University of Toronto
contact email	g.schmittulms@utoronto.ca
lab head
Gerold Schmitt-Ulms
contact affiliation	University of Toronto
contact email	g.schmittulms@utoronto.ca
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/2014/11/PXD001301

PRIDE project URI

• PRIDE
  1. PXD001301
     1. Label: PRIDE project
     2. Name: CRISPR-Cas9-based knockout of the prion protein and its effect on the proteome