PXD014512

PXD014512 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS of mouse hepatocytes sorted by lobule layers
Description	Hepatocytes of the mammalian liver are organized in liver lobules and operate in a spatially-dependent manner. Cells in different positions along the lobule’s porto-cenrtal axis, defined by the directionality of blood flow, express different genes and perform different liver tasks. Gradients of the transcriptome along liver lobule axis has been recently established, yet not for the hepatocyte proteome. We used two surface markers whose levels are inversely zonated – CD73 with a decreasing gradient from pericentral to periportal hepatocytes and E-cadherin with increasing gradient from portal to central hepatocytes. By staining for both surface markers, we efficiently isolated bulk populations of hepatocytes from distinct lobule layers by Fluorescence Activated Cell Sorting (FACS). Over all, we sorted 100,000 hepatocytes from each of eight spatially distinct populations, from five different mice. Cells were washed, digested by trypsin and subjected to LC-MS/MS. More cells from same populations from the same mice were also collected for mRNA sequencing and microRNA microarray profiling, to achieve a multi-omic view on spatially sorted hepatocytes, for better understanding of the transcriptomic and post-transcriptomic levels of regulation of liver zonation.
HostingRepository	PRIDE
AnnounceDate	2019-09-25
AnnouncementXML	Submission_2019-09-25_01:58:26.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shani Ben-Moshe
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-08 02:36:25	ID requested
1	2019-08-06 03:21:13	announced
⏵ 2	2019-09-25 01:58:27	announced	2019-09-25: Updated publication reference for PubMed record(s): 31535084.

Ben-Moshe S, Shapira Y, Moor AE, Manco R, Veg T, Bahar Halpern K, Itzkovitz S, Spatial sorting enables comprehensive characterization of liver zonation. Nat Metab, 1(9):899-911(2019) [pubmed]

submitter keyword: liver zonation, LC-MS/MS, mouse, hepatocytes

Shalev Itzkovitz
contact affiliation	Department of Molecular Cell Biology Weizmann Institute of Science Israel
contact email	shalev.itzkovitz@weizmann.ac.il
lab head
Shani Ben-Moshe
contact affiliation	Weizmann Institute of Science
contact email	shani.benmoshe@weizmann.ac.il
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/2019/08/PXD014512

PRIDE project URI

• PRIDE
  1. PXD014512
     1. Label: PRIDE project
     2. Name: LC-MS/MS of mouse hepatocytes sorted by lobule layers