PXD033001-3

PXD033001 is an original dataset announced via ProteomeXchange.

Title	Genetic dissection of the pluripotent proteome through multi-omics data integration
Description	Genetic background is a major driver of the phenotypic variability observed across pluripotent stem cells (PSCs), and studies addressing it have relied on transcript abundance as the primary molecular readout of cell state. However, little is known about how proteins, the functional units in the cell, vary across genetically diverse PSCs and how this relates to variation in other measures of gene output. Here we present the first comprehensive genetic study characterizing the pluripotent proteome using 190 unique mouse embryonic stem cell lines derived from highly heterogeneous Diversity Outbred mice. Moreover, we integrated the proteome with chromatin accessibility and transcript abundance in 163 cell lines with matching genotypes using multi-omics factor analysis to distinguish shared and unique drivers of variability across molecular layers. Our findings highlight the power of multi-omics data integration in revealing the distal impacts of genetic variation. We show that limitations in mapping of individual molecular traits may be overcome by utilizing data integration to consolidate the influence of genetic signals shared across molecular traits and increase detection power.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:45:38.604.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tian Zhang
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-06 07:10:48	ID requested
1	2023-05-10 14:52:22	announced
2	2023-11-14 08:48:02	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:45:43	announced	2024-10-22: Updated project metadata.

Aydin S, Pham DT, Zhang T, Keele GR, Skelly DA, Paulo JA, Pankratz M, Choi T, Gygi SP, Reinholdt LG, Baker CL, Churchill GA, Munger SC, Genetic dissection of the pluripotent proteome through multi-omics data integration. Cell Genom, 3(4):100283(2023) [pubmed]

10.1016/j.xgen.2023.100283;

submitter keyword: Diversity Outbred Mice, Chromatin Accessibility, Multi-Omics Factor Analysis, eQTL, Transcriptomics,Embryonic Stem Cells, Ground State Metastability, Proteomics, pQTL, Pluripotency

Steven Gygi
contact affiliation	Cell Biology Department, Harvard Medical School
contact email	steven_gygi@hms.harvard.edu
lab head
Tian Zhang
contact affiliation	Harvard Medical School
contact email	tian_zhang@hms.harvard.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/2023/05/PXD033001

PRIDE project URI

• PRIDE
  1. PXD033001
     1. Label: PRIDE project
     2. Name: Genetic dissection of the pluripotent proteome through multi-omics data integration