PXD034370

PXD034370 is an original dataset announced via ProteomeXchange.

Title	Microscopy-based functional single cell proteomic profiling of cells with abnormal DNA damage response dynamics
Description	Tumor heterogeneity is an important source of cancer therapy resistance. Single cell proteomics has the potential to decipher protein content leading to heterogeneous cellular phenotypes. Single-Cell ProtEomics by Mass Spectrometry (SCoPE-MS) is a recently developed, promising, unbiased proteomic profiling techniques, which allows profiling several tens of single cells for >1000 proteins per cell. However, a method to link single cell proteomes with cellular behaviors is needed to advance this type of profiling technique. Here, we developed a microscopy-based functional single cell proteomic profiling technology, called FUNpro, to link the proteome of individual cells with phenotypes of interest, even if the phenotypes are dynamic or the cells of interest are sparse. FUNpro enables one i) to screen thousands of cells with subcellular resolution and monitor (intra)cellular dynamics using a custom-built microscope, ii) to real-time analyze (intra)cellular dynamics of individual cells using an integrated cell tracking algorithm, iii) to promptly isolate the cells displaying phenotypes of interest, and iv) to single cell proteomically profile the isolated cells. We applied FUNpro to proteomically profile a newly identified small subpopulation of U2OS osteosarcoma cells displaying an abnormal, prolonged DNA damage response (DDR) after ionizing radiation (IR). With this, we identified the PDS5A protein contributing to the abnormal DDR dynamics and helping the cells survive after IR.
HostingRepository	PRIDE
AnnounceDate	2022-07-07
AnnouncementXML	Submission_2022-07-07_06:24:04.749.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pin-Rui Su
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-06 06:38:31	ID requested
⏵ 1	2022-07-07 06:24:05	announced

Dataset with its publication pending

submitter keyword: single-cell proteomics

Miao-Ping Chien
contact affiliation	Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands. Erasmus MC Cancer Institute, The Netherlands. Oncode Institute, Utrecht, The Netherlands.
contact email	m.p.chien@erasmusmc.nl
lab head
Pin-Rui Su
contact affiliation	Erasmus MC
contact email	p.su@erasmusmc.nl
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/2022/07/PXD034370

PRIDE project URI

• PRIDE
  1. PXD034370
     1. Label: PRIDE project
     2. Name: Microscopy-based functional single cell proteomic profiling of cells with abnormal DNA damage response dynamics