Proteomics

Dataset Information

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LC-MS/MS of mouse hepatocytes sorted by lobule layers


ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Hepatocyte, Liver

SUBMITTER: Shani Ben-Moshe  

LAB HEAD: Shalev Itzkovitz

PROVIDER: PXD014512 | Pride | 2019-08-06

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
55910_2ev_proteinGroups_perseus.xlsx Xlsx
Seq55910_HFX.raw Raw
Seq55911_HFX_B.raw Raw
Seq55912_HFX.raw Raw
Seq55913_HFX.raw Raw
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Publications

Spatial sorting enables comprehensive characterization of liver zonation.

Ben-Moshe Shani S   Shapira Yonatan Y   Moor Andreas E AE   Manco Rita R   Veg Tamar T   Bahar Halpern Keren K   Itzkovitz Shalev S  

Nature metabolism 20190916 9


The mammalian liver is composed of repeating hexagonal units termed lobules. Spatially resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule, yet technical limitations impeded reconstructing similar global spatial maps of other hepatocyte features. Here, we show how zonated surface markers can be used to sort hepatocytes from defined lobule zones with high spatial resolution. We apply transcriptomics, miRNA array measurem  ...[more]

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