PXD043926

PXD043926 is an original dataset announced via ProteomeXchange.

Title	Amyloids from WT and mstr C. elegans
Description	200,000 worms were grown to the young adult stage, collected, and washed. Worms were homogenized in lysis buffer (10mM Tris, pH 7.5, 138mM NaCl, 2mM CaCl2, and 0.1% NP-40). After homogenization, 125U/mL Benzonase nuclease was added to homogenates and samples were incubated for 30 mins at room temperature with gentle rocking. Samples were spun at 21,000g for 5 mins, followed by resuspension of the pellet in lysis buffer. Soluble proteins were removed from the pellet with repeated washes in lysis buffer until A280 of the supernatant was equal to A280 of lysis buffer. Resulting pellet was resuspended in ddH2O, spun at 21,000g for 5 mins, and supernatant was transferred to a collection tube. Water resuspensions and recoveries were continued until A280 of H2O supernatants was 0. Recovered water washes were pooled and amyloids salted out by adding NaCl to 200mM final concentration, followed by 1-3 days incubation at 4oC. Precipitated amyloids were recovered by centrifuging at 21,000g for 30 mins, followed by resuspension in 50-100uL ddH2O. Amyloids were digested (trypsin and chymotrypsin) and prepared for mass spectrometry as described in the methods files.
HostingRepository	PRIDE
AnnounceDate	2024-07-09
AnnouncementXML	Submission_2024-07-08_19:00:18.805.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD043926
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew Eroglu
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-19 14:36:15	ID requested
⏵ 1	2024-07-08 19:00:19	announced

10.6019/PXD043926;

submitter keyword: C. elegans,Nematode, worm, amyloids

Brent Derry
contact affiliation	Hospital for Sick Children, Toronto, ON, Canada
contact email	brent.derry@sickkids.ca
lab head
Matthew Eroglu
contact affiliation	University of Toronto
contact email	matt.eroglu@mail.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/2024/07/PXD043926

PRIDE project URI

• PRIDE
  1. PXD043926
     1. Label: PRIDE project
     2. Name: Amyloids from WT and mstr C. elegans