PXD012307

PXD012307 is an original dataset announced via ProteomeXchange.

Title	An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
Description	Aging promotes lung function decline and susceptibility to chronic lung diseases, which are the third leading cause of death worldwide. We used single cell transcriptomics and mass spectrometry to quantify changes in cellular activity states of 30 cell types and the tissue proteome from lungs of young and old mice. Aging led to increased transcriptional noise, indicating deregulated epigenetic control. We observed highly distinct effects of aging on cell type level, uncovering increased cholesterol biosynthesis in type-2 pneumocytes and lipofibroblasts as a novel hallmark of lung aging. Proteomic profiling revealed extracellular matrix remodeling in old mice, including increased collagen IV and XVI and decreased Fraser syndrome complex proteins and Collagen XIV. Computational integration of the aging proteome and single cell transcriptomes predicted the cellular source of regulated proteins and created a first unbiased reference of the aging lung. The lung aging atlas can be accessed via an interactive user-friendly webtool at: https://theislab.github.io/LungAgingAtlas
HostingRepository	PRIDE
AnnounceDate	2019-01-21
AnnouncementXML	Submission_2019-04-03_04:33:24.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christoph Mayr
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-11 05:22:15	ID requested
1	2019-01-21 03:14:04	announced
⏵ 2	2019-04-03 04:33:25	announced	Updated publication reference for PubMed record(s): 30814501.

Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, Tsitsiridis G, Ansari M, Graf E, Strom TM, Nagendran M, Desai T, Eickelberg O, Mann M, Theis FJ, Schiller HB, An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat Commun, 10(1):963(2019) [pubmed]

curator keyword: Biological

submitter keyword: lung, aging, total proteome, QDSP, chronic lung disease, single cell transcriptomics, extracellular matrix, lipid metabolism, lung cell atlas

Herbert B Schiller
contact affiliation	Helmholtz Zentrum München, Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
contact email	herbert.schiller@helmholtz-muenchen.de
lab head
Christoph Mayr
contact affiliation	CPC/ILBD HemholtzZentrum München
contact email	Christoph.Mayr@helmholtz-muenchen.de
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/2019/01/PXD012307

PRIDE project URI

• PRIDE
  1. PXD012307
     1. Label: PRIDE project
     2. Name: An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics