<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <ProteomeXchangeDataset id="PXD003281" formatVersion="1.3.0" xsi:noNamespaceSchemaLocation="proteomeXchange-1.3.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <CvList> <Cv fullName="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" id="MS"/> <Cv fullName="PRIDE" uri="https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo" id="PRIDE"/> <Cv fullName="PSI-MOD" uri="https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo" id="MOD"/> <Cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/> </CvList> <ChangeLog> <ChangeLogEntry date="2019-02-12">Updated publication reference for PubMed record(s): 29043977.</ChangeLogEntry> </ChangeLog> <DatasetSummary announceDate="2017-10-18" hostingRepository="PRIDE" title="A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis"> <Description>Epidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation. The transition between the two cell states,termed commitment, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension to induce differentiation. Cell detachment induces several protein phosphatases, five of which - DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA – promote differentiation by negatively regulating ERK MAPK and positively regulating AP1 transcription factors. Conversely, DUSP10 expression antagonises commitment. The phosphatases form a dynamic network of transient positive and negative interactions that change over time, with DUSP6 predominating at commitment. Boolean network modelling identifies a mandatory switch between two stable states (stem and differentiated) via an unstable (committed) state. Phosphatase expression is also spatially regulated in vivo and in vitro. We conclude that an auto-regulatory phosphatase network maintains epidermal homeostasis by controlling the onset and duration of commitment.</Description> <ReviewLevel> <cvParam cvRef="PRIDE" accession="PRIDE:0000414" name="Peer-reviewed dataset"/> </ReviewLevel> <RepositorySupport> <cvParam cvRef="PRIDE" accession="PRIDE:0000417" name="Unsupported dataset by repository"/> </RepositorySupport> </DatasetSummary> <DatasetIdentifierList> <DatasetIdentifier> <cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD003281"/> </DatasetIdentifier> </DatasetIdentifierList> <DatasetOriginList> <DatasetOrigin> <cvParam cvRef="PRIDE" accession="PRIDE:0000402" name="Original data"/> </DatasetOrigin> </DatasetOriginList> <SpeciesList> <Species> <cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Homo sapiens (Human)"/> <cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="9606"/> </Species> </SpeciesList> <InstrumentList> <Instrument id="Instrument_1"> <cvParam cvRef="MS" accession="MS:1001911" name="Q Exactive"/> </Instrument> </InstrumentList> <ModificationList> <cvParam cvRef="MOD" accession="MOD:01160" name="deaminated residue"/> <cvParam cvRef="MOD" accession="MOD:00394" name="acetylated residue"/> <cvParam cvRef="MOD" accession="MOD:00425" name="monohydroxylated residue"/> <cvParam cvRef="MOD" accession="MOD:00397" name="iodoacetamide derivatized residue"/> </ModificationList> <ContactList> <Contact id="project_submitter"> <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Vackar Afzal"/> <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="v.z.afzal@dundee.ac.uk"/> <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="School of Life Sciences"/> <cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/> </Contact> <Contact id="project_lab_head"> <cvParam cvRef="MS" accession="MS:1002332" name="lab head"/> <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Angus Lamond"/> <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="ailamond@dundee.ac.uk"/> <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Principle Investigator"/> </Contact> </ContactList> <PublicationList> <Publication id="PMID29043977"> <cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="29043977"/> <cvParam cvRef="PRIDE" accession="PRIDE:0000400" name="Reference" value="Mishra A, Oulès B, Pisco AO, Ly T, Liakath-Ali K, Walko G, Viswanathan P, Tihy M, Nijjher J, Dunn SJ, Lamond AI, Watt FM. A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis. Elife. 2017 6"/> </Publication> </PublicationList> <KeywordList> <cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="Human, Keratinocytes, U2OS, PKC, Timecourse"/> <cvParam cvRef="MS" accession="MS:1001926" name="curator keyword" value="Biological"/> </KeywordList> <FullDatasetLinkList> <FullDatasetLink> <cvParam cvRef="PRIDE" accession="PRIDE:0000411" name="Dataset FTP location" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/10/PXD003281"/> </FullDatasetLink> <FullDatasetLink> <cvParam cvRef="MS" accession="MS:1001930" name="PRIDE project URI" value="http://www.ebi.ac.uk/pride/archive/projects/PXD003281"/> </FullDatasetLink> </FullDatasetLinkList> <DatasetFileList> <DatasetFile id="FILE_0" name="1101L1AIL00.raw"> <cvParam cvRef="PRIDE" accession="PRIDE:0000404" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/10/PXD003281/1101L1AIL00.raw"/> </DatasetFile> <DatasetFile id="FILE_1" name="1101L1AIL01.raw"> <cvParam 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