PXD054066

PXD054066 is an original dataset announced via ProteomeXchange.

Title	Deep single-cell proteomics quantifies low-abundant embryonic transcription factors and lineage markers during induced pluripotent stem cell differentiation
Description	Single-cell proteomics (SCP) promises to revolutionize biomedicine by providing an unparalleled view of the proteome in individual cells. Here, we present a high-sensitivity SCP workflow identifying >5000 proteins in individual HeLa cells. It also facilitated direct detection of post-translational modifications (PTMs) in single-cells, negating the need for specific PTM-enrichment. Our study demonstrates the feasibility of processing up to 80 label-free SCP samples per day. An optimized tissue dissociation buffer enabled effective single cell disaggregation of drug-treated cancer cell spheroids, refining overall SCP analysis. Analyzing non-directed induced pluripotent stem cell (iPSC) differentiation, we consistently quantified stem cell markers OCT4 and SOX2 in hiPSCs and lineage markers like GATA4 (mesoderm), HAND1 (endoderm) and MAP2 (ectoderm) in different embryoid body cells. Our workflow sets a new benchmark in SCP for sensitivity and throughput, with broad applications in basic biology and biomedicine for identification of cell type-specific markers and therapeutic targets.
HostingRepository	PRIDE
AnnounceDate	2024-08-17
AnnouncementXML	Submission_2024-08-17_05:18:46.704.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pierre Sabatier
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-19 08:10:17	ID requested
⏵ 1	2024-08-17 05:18:47	announced

Dataset with its publication pending

submitter keyword: Single-cell proteomics

Jesper V. Olsen
contact affiliation	Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
contact email	jesper.olsen@cpr.ku.dk
lab head
Pierre Sabatier
contact affiliation	Department of Surgical Sciences, Uppsala University. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen.
contact email	pierre63.sabatier@gmail.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/2024/08/PXD054066

PRIDE project URI

• PRIDE
  1. PXD054066
     1. Label: PRIDE project
     2. Name: Deep single-cell proteomics quantifies low-abundant embryonic transcription factors and lineage markers during induced pluripotent stem cell differentiation