PXD003562

PXD003562 is an original dataset announced via ProteomeXchange.

Title	Global analysis of protein degradation rates in wildtype, Atg5-/- and Atg7-/- primary human fibroblasts
Description	In this project, we employed a dynamic mass spectrometry-based proteomic approach to obtain global maps of basal autophagic flux in human primary fibroblasts (HCA2-hTert). The data provide a comparison of protein degradation rates between wildtype and autophagy deficient (Atg5-/- and Atg7-/-) cells. The media utilized for isotopic labeling was Eagle’s Minimum Essential Medium (ATCC) supplemented with 15% dialyzed fetal bovine serum (Thermo Scientific), 100U/mL penicillin, 100U/mL streptomycin. Prior to labeling, cells were gradually adapted to unlabeled media over the course of multiple passages. Cells were then plated at a density of 500,000 cells per 10 cm plate. 8 days after plating, the confluent quiescent cultures were switched to MEM labeling media for SILAC (Thermo Scientific) supplemented with L-Arginine:HCl (13C6, 99%) and L-Lysine:2HCl (13C6, 99%)(Cambridge Isotope Laboratories) at concentrations of 0.1264 g/L and 0.087 g/L and 15% dialyzed fetal bovine serum (Thermo scientific). Cells were collected after 0d, 2d, 4d, 6d of labeling, washed with PBS and cell pellets were frozen prior to further analysis. In order to assess the precision of our measurements, biological replicate experiments were conducted for WT+vector and Atg5-/- experiments and cells were collected after 4d for analysis
HostingRepository	PRIDE
AnnounceDate	2016-06-14
AnnouncementXML	Submission_2016-06-14_00:08:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tian Zhang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-03 01:31:02	ID requested
⏵ 1	2016-06-14 00:08:24	announced

Zhang T, Shen S, Qu J, Ghaemmaghami S, Global Analysis of Cellular Protein Flux Quantifies the Selectivity of Basal Autophagy. Cell Rep, 14(10):2426-39(2016) [pubmed]

curator keyword: Biological

submitter keyword: autophagy, Atg5, Atg7, human primary fibroblasts, protein degradation rates

Sina Ghaemmaghami
contact affiliation	Department of Biology, University of Rochester, NY, USA
contact email	sghaemma@UR.Rochester.edu
lab head
Tian Zhang
contact affiliation	UNIVERSITY OF ROCHESTER
contact email	tzhang24@ur.rochester.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/2016/06/PXD003562

PRIDE project URI

• PRIDE
  1. PXD003562
     1. Label: PRIDE project
     2. Name: Global analysis of protein degradation rates in wildtype, Atg5-/- and Atg7-/- primary human fibroblasts