DOI: 10.5061/dryad.89s4n70
title: Data from: Separating golgi proteins from cis to trans reveals underlying properties of cisternal localization

description: The order of enzymatic activity across Golgi cisternae is essential for
 complex molecule biosynthesis. However, an inability to separate Golgi
 cisternae has meant the cisternal distribution of most resident proteins,
 and their underlying localization mechanisms, are unknown. Here, we
 exploit differences in surface charge of intact cisternae to perform
 separation of early to late Golgi sub-compartments. We determine protein
 and glycan abundance profiles across the Golgi; over 390 resident proteins
 are identified, including 136 new additions, with over 180 cisternal
 assignments. These assignments provide a means to better understand the
 functional roles of Golgi proteins and how they operate sequentially.
 Protein and glycan distributions are validated in vivo, using high
 resolution microscopy. Results reveal distinct functional
 compartmentalization among resident Golgi proteins. Analysis of
 transmembrane proteins shows several sequence-based characteristics
 relating to pI, hydrophobicity, Ser abundance and Phe bilayer asymmetry
 that change across the Golgi. Overall our results suggest that a continuum
 of TM features, rather than discrete rules, guide proteins to earlier or
 later locations within the Golgi stack.
description: Supplemental Dataset
 1Supplemental Dataset 1:
 Resident organelle proteomes from LOPIT experiments (Fig. 2, S1) after
 SVM-based classification. Proteins are identified by their AGI accession
 code for the TAIR database. Proteins annotated with an 'x'
 formed the training datasets used for SVM classification and those
 annotated as '-' were newly classified as organelle residents.
 Classification thresholds and SVM parameters were as described in
 Experimental Procedures.Table
 S1.xlsxSupplemental Dataset
 2Supplemental Dataset 2.
 Additional information for monoclonal antibodies, polysaccharide epitopes
 and protein targets featured in Fig. 3. Antibody names in column A refer
 to antibodies featured in Fig. 3a, b, and c. For each antibody the
 original publication reference (column B), epitope strucutre (column C)
 and polysaccaride containing that epitope (column D) is given. Group
 members (Fig. 3c) are detailed in column F. For peptide markers assayed in
 Fig. 3e, localization and relevant localization references are supplied in
 columns H-J.Table
 S2.xlsxSupplemental Dataset
 3Supplemental Dataset 3.
 Protein lists for sub-Golgi proteomes. Proteins (column A) are annotated
 with sub-Golgi classification (column B) , MapMan functional
 classifications (column D) and gene descriptions (column E). 'x'
 (column C) denotes which proteins formed the SVM training set shown in
 Fig. 4c that was used in the final classification in Fig. 4d. Proteins
 were annotated with functional categorization and gene descriptions using
 the MapMan tool (http://mapman.gabipd.org/mapman). Peptide spectral
 matches, averaged from replicates, give an overview of protein abundance
 columns G - J). Further quantitative information is available at the
 ProteomeXchange Consortium via the PRIDE partner repository (PXD004596,
 PXD009978).Table
 S3.xlsxSupplemental_Dataset_4_part1of3Image regions analyzed in Figure 5CSupplemental_Dataset_S4_part1.zipSupplemental_Dataset_S4_part2of3Image regions analyzed in Figure 5CSupplemental_Dataset_S4_part2.zipSupplemental_Dataset_S4_part3of3Image regions analyzed in Figure 5CSupplemental_Dataset_S4_part3.zip