<ddi:DDIInstance xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="ddi:instance:3_3 http://ddialliance.org/Specification/DDI-Lifecycle/3.3/XMLSchema/instance.xsd" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:ddi="ddi:instance:3_3" xmlns:r="ddi:reusable:3_3" xmlns:s="ddi:studyunit:3_3" xmlns:d="ddi:datacollection:3_3" xmlns:a="ddi:archive:3_3" xmlns:c="ddi:conceptualcomponent:3_3" xmlns:cm="ddi:comparative:3_3" xmlns:g="ddi:group:3_3" xmlns:l="ddi:logicalproduct:3_3" xmlns:p="ddi:physicaldataproduct:3_3" xmlns:pi="ddi:physicalinstance:3_3" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xhtml="http://www.w3.org/1999/xhtml" xmlns:xml="http://www.w3.org/XML/1998/namespace" isMaintainable="true" scopeOfUniqueness="Agency">
  <r:URN>urn:ddi:se.researchdata:2023-166:1</r:URN>
  <r:Agency>SND</r:Agency>
  <r:ID>2023-166</r:ID>
  <r:Version>1</r:Version>
  <g:ResourcePackage>
    <r:URN>urn:ddi:se.researchdata:2023-166.ResourcePackage:2.0</r:URN>
    <r:OtherMaterialScheme>
      <r:URN>urn:ddi:se.researchdata:2023-166.OtherMaterialScheme:2.0</r:URN>
    </r:OtherMaterialScheme>
    <a:OrganizationScheme>
      <r:URN>urn:ddi:se.researchdata:2023-166.OrganizationScheme-0:2.0</r:URN>
      <a:Individual>
        <r:URN>urn:ddi:se.researchdata:2023-166.Individual-0:2.0</r:URN>
        <r:UserAttributePair>
          <r:AttributeKey>affiliation</r:AttributeKey>
          <r:AttributeValue>Institute of Biomedicine, University of Gothenburg</r:AttributeValue>
        </r:UserAttributePair>
        <a:IndividualIdentification>
          <a:IndividualName>
            <a:FirstGiven>Mattias</a:FirstGiven>
            <a:LastFamily>Erhardsson</a:LastFamily>
            <a:FullName>
              <r:String>Mattias Erhardsson</r:String>
            </a:FullName>
          </a:IndividualName>
          <a:ResearcherID>
            <a:TypeOfID>ORCID</a:TypeOfID>
            <a:ResearcherIdentification>0000-0002-5631-2033</a:ResearcherIdentification>
          </a:ResearcherID>
        </a:IndividualIdentification>
      </a:Individual>
      <a:Individual>
        <r:URN>urn:ddi:se.researchdata:2023-166.Individual-0:2.0</r:URN>
        <r:UserAttributePair>
          <r:AttributeKey>affiliation</r:AttributeKey>
          <r:AttributeValue>Institute of Biomedicine, University of Gothenburg</r:AttributeValue>
        </r:UserAttributePair>
        <a:IndividualIdentification>
          <a:IndividualName>
            <a:FirstGiven>Sara</a:FirstGiven>
            <a:LastFamily>Lindén</a:LastFamily>
            <a:FullName>
              <r:String>Sara Lindén</r:String>
            </a:FullName>
          </a:IndividualName>
          <a:ResearcherID>
            <a:TypeOfID>ORCID</a:TypeOfID>
            <a:ResearcherIdentification>0000-0002-7751-9586</a:ResearcherIdentification>
          </a:ResearcherID>
        </a:IndividualIdentification>
      </a:Individual>
      <a:Individual>
        <r:URN>urn:ddi:se.researchdata:2023-166.Individual-0:2.0</r:URN>
        <r:UserAttributePair>
          <r:AttributeKey>affiliation</r:AttributeKey>
          <r:AttributeValue>Institute for Biomedicine, University of Gothenburg</r:AttributeValue>
        </r:UserAttributePair>
        <a:IndividualIdentification>
          <a:IndividualName>
            <a:FirstGiven>Sinan</a:FirstGiven>
            <a:LastFamily>Sharba</a:LastFamily>
            <a:FullName>
              <r:String>Sinan Sharba</r:String>
            </a:FullName>
          </a:IndividualName>
          <a:ResearcherID>
            <a:TypeOfID>ORCID</a:TypeOfID>
            <a:ResearcherIdentification>0000-0003-0531-2137</a:ResearcherIdentification>
          </a:ResearcherID>
        </a:IndividualIdentification>
      </a:Individual>
      <a:Individual>
        <r:URN>urn:ddi:se.researchdata:2023-166.Individual-0:2.0</r:URN>
        <r:UserAttributePair>
          <r:AttributeKey>affiliation</r:AttributeKey>
          <r:AttributeValue>Institute of Biomedicine, University of Gothenburg</r:AttributeValue>
        </r:UserAttributePair>
        <a:IndividualIdentification>
          <a:IndividualName>
            <a:FirstGiven>Licínia</a:FirstGiven>
            <a:LastFamily>Santos</a:LastFamily>
            <a:FullName>
              <r:String>Licínia Santos</r:String>
            </a:FullName>
          </a:IndividualName>
          <a:ResearcherID>
            <a:TypeOfID>ORCID</a:TypeOfID>
            <a:ResearcherIdentification>0000-0003-0056-4490</a:ResearcherIdentification>
          </a:ResearcherID>
        </a:IndividualIdentification>
      </a:Individual>
    </a:OrganizationScheme>
  </g:ResourcePackage>
  <s:StudyUnit>
    <r:URN>urn:ddi:se.researchdata:2023-166.StudyUnit:2.0</r:URN>
    <r:UserID typeOfUserID="datasetIdentifier">2023-166</r:UserID>
    <r:Citation>
      <r:Title>
        <r:String xml:lang="sv">RNA-sekvensering av slemproducerande celler som med hjälp av laserbaserad mikrodissektion hämtats från musmagsäckar som är infekterade med Helicobacter pylori-stammen Sydney Strain 1</r:String>
        <r:String xml:lang="en">RNA sequencing of surface mucus producing cells captured with Laser Microdissection and Pressure Catapulting in mouse stomachs infected with Helicobacter pylori Sydney Strain 1</r:String>
      </r:Title>
      <r:Creator>
        <r:CreatorReference>
          <r:URN>urn:ddi:se.researchdata:2023-166.Individual-0:2.0</r:URN>
          <r:TypeOfObject>Individual</r:TypeOfObject>
        </r:CreatorReference>
      </r:Creator>
      <r:Publisher>
        <r:PublisherName>
          <r:String xml:lang="sv">Göteborgs universitet</r:String>
          <r:String xml:lang="en">University of Gothenburg</r:String>
        </r:PublisherName>
      </r:Publisher>
      <r:Publisher>
        <r:PublisherName>
          <r:String xml:lang="sv">Göteborgs universitet</r:String>
          <r:String xml:lang="en">University of Gothenburg</r:String>
        </r:PublisherName>
      </r:Publisher>
      <r:PublicationDate>
        <r:SimpleDate>2026-02-23</r:SimpleDate>
      </r:PublicationDate>
      <r:InternationalIdentifier>
        <r:IdentifierContent>10.5878/ejy9-2895</r:IdentifierContent>
        <r:ManagingAgency controlledVocabularyAgencyName="DOI">DOI</r:ManagingAgency>
      </r:InternationalIdentifier>
    </r:Citation>
    <r:Abstract>
      <r:Content xml:lang="sv">Denna RNA-sekvenserings (RNAseq)-data kommer från slemproducerande epitelceller i magsäcken från C57/BL6-möss.

5 möss var icke-infekterade kontroller, 5 var infekterade med Helicobacter Pylori-stammen SS1 14 dagar före skörd, och ytterligare 5 var också infekterade med Helicobacter Pylori-stammen SS1 14 dagar före skörd, samt dessutom behandlades dessa sista 5 med oralt R-alfa-Metylhistamin 13, 10 och 7 dagar före skörd. Totalt 15 möss skördades.

Ytliga slemproducerande epitelceller samlades in från mössen med laseravskiljning och tryckkatapult (LMPC) med en PALM MicroBeam (Carl Zeiss, Oberkochen, Tyskland) vid CCI (Center för Cellulär Avbildning, Sahlgrenska Akademin, Göteborg, Sverige).

Library prep utfördes med kitet SMARTer Total Stranded RNA-seq, Pico input mammalian - V3 (Takara Bio, Kusatsu, Japan). Library prep för provet från en mus i den infekterade/icke-behandlade gruppen misslyckades.

De återstående 14 proverna sekvenserades med NovaSeq 6000 (Illumina, San Diego, USA) vid NGI (National Genomics Infrastructure, Solna, Sverige).

Fastq-filerna bearbetades med nf-core/rnaseq-analyspipelinen, som kördes av NGI vid UPPMAX (Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala, Sverige).

Filerna är packade enligt NGIs standard för distribution, förutom mappstrukturerna 00-Reports/  och 01-RNA-Results/ vilka har blivit packade som zip-filer för att underlätta nedladdning.</r:Content>
      <r:Content xml:lang="en">This RNA sequencing (RNAseq) data comes from mouse strain C57/BL6 gastric surface mucus cells, also known as foveolar cells.

5 mice were non-infected controls, 5 were infected with Helicobacter Pylori strain SS1 14 days prior to harvest, and another 5 were also infected with Helicobacter Pylori strain SS1 14 days prior to harvest, and furthermore these last 5 were also treated with R-alpha-Methylhistamine through oral gavage at 13, 10, and 7 days prior to harvest. 15 mice total.

Surface mucous-producing epithelial cells were collected from the mice using laser microdissection and pressure catapulting  (LMPC) with a PALM MicroBeam (Carl Zeiss, Oberkochen, Germany) at CCI (Centre for Cellular Imaging, Sahlgrenska Academy, Gothenburg, Sweden).

Libraries were prepared with SMARTer Total Stranded RNA-seq, Pico input mammalian - V3 (Takara Bio, Kusatsu, Japan). The sample from one mouse in the infected/non-treated group failed library prep.

The remaining 14 samples were sequenced with NovaSeq 6000 (Illumina, San Diego, USA at NGI (National Genomics Infrastructure, Solna, Sweden).

The fastq-files were processed with the nf-core/rnaseq analysis pipeline, which was was run by NGI at UPPMAX (Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala, Sweden).

The files follow the standard NGI distribution packaging, except for the folder structures 00-Reports/ and 01-RNA-Results/ which have been packaged as zip files for easier downloading.</r:Content>
    </r:Abstract>
    <r:Coverage>
      <r:TopicalCoverage>
        <r:URN>urn:ddi:se.researchdata:2023-166.TopicalCoverage:2.0</r:URN>
        <r:Subject xml:lang="en" controlledVocabularyID="Health.MedicationAndTreatment" controlledVocabularyName="CESSDA Topic Classification">Medication and treatment</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="Health.MedicationAndTreatment" controlledVocabularyName="CESSDA Topic Classification">Medicinering och behandlingar</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="Health.SpecificDiseasesDisordersAndMedicalConditions" controlledVocabularyName="CESSDA Topic Classification">Specific diseases, disorders and medical conditions</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="Health.SpecificDiseasesDisordersAndMedicalConditions" controlledVocabularyName="CESSDA Topic Classification">Specifika sjukdomar, störningar och medicinska tillstånd</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="10203" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Bioinformatics (Computational Biology)</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10203" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Bioinformatik (beräkningsbiologi)</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="10604" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Cell Biology</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10604" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Cellbiologi</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="10605" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Immunology</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10605" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Immunologi</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="10606" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Microbiology</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10606" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Mikrobiologi</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="10610" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Bioinformatics and Computational Biology</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10610" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Bioinformatik och beräkningsbiologi</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="Health.SignsAndSymptomsPathologicalConditions" controlledVocabularyName="CESSDA Topic Classification">Signs and symptoms; pathological conditions</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="Health.SignsAndSymptomsPathologicalConditions" controlledVocabularyName="CESSDA Topic Classification">Tecken och symtom; patologiska tillstånd</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="Health.PublicHealth" controlledVocabularyName="CESSDA Topic Classification">Public health</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="Health.PublicHealth" controlledVocabularyName="CESSDA Topic Classification">Folkhälsa</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="10616" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Molecular Biology</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10616" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Molekylärbiologi</r:Subject>
        <r:Keyword xml:lang="en" controlledVocabularyID="D004847" controlledVocabularyName="MeSH">Epithelial Cells</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D004847" controlledVocabularyName="MeSH">Epitelceller</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D005752" controlledVocabularyName="MeSH">Gastric Mucins</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D005752" controlledVocabularyName="MeSH">Magmuciner</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D005753" controlledVocabularyName="MeSH">Gastric Mucosa</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D005753" controlledVocabularyName="MeSH">Magslemhinna</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D008761" controlledVocabularyName="MeSH">Methylhistamines</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D008761" controlledVocabularyName="MeSH">Metylhistaminer</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D008810" controlledVocabularyName="MeSH">Mice, Inbred C57BL</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D008810" controlledVocabularyName="MeSH">Möss, inavlade C57BL</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D009077" controlledVocabularyName="MeSH">Mucins</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D009077" controlledVocabularyName="MeSH">Muciner</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D009093" controlledVocabularyName="MeSH">Mucus</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D009093" controlledVocabularyName="MeSH">Slem</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D015870" controlledVocabularyName="MeSH">Gene Expression</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D015870" controlledVocabularyName="MeSH">Genuttryck</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D016480" controlledVocabularyName="MeSH">Helicobacter pylori</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D016480" controlledVocabularyName="MeSH">Helicobacter pylori</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D016481" controlledVocabularyName="MeSH">Helicobacter Infections</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D016481" controlledVocabularyName="MeSH">Helicobacterinfektioner</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D017423" controlledVocabularyName="MeSH">Sequence Analysis, RNA</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D017423" controlledVocabularyName="MeSH">RNA-sekvensanalys</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D020869" controlledVocabularyName="MeSH">Gene Expression Profiling</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D020869" controlledVocabularyName="MeSH">Genuttrycksprofilering</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="D061346" controlledVocabularyName="MeSH">Laser Capture Microdissection</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D061346" controlledVocabularyName="MeSH">Lasermikrodissektion</r:Keyword>
        <r:Keyword xml:lang="en" controlledVocabularyID="B980" controlledVocabularyName="ICD-10">Helicobacter pylori [H.pylori] as the cause of diseases classified to other chapters</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="B980" controlledVocabularyName="ICD-10">Helicobacter pylori [H.pylori] som orsak till sjukdomar som klassificeras på annan plats</r:Keyword>
      </r:TopicalCoverage>
      <r:SpatialCoverage>
        <r:URN>urn:ddi:se.researchdata:2023-166.SpatialCoverage:2.0</r:URN>
        <r:Description>
          <r:Content xml:lang="en">The animal experiment was conducted at Experimental Biomedicine (EBM) in Gothenburg,</r:Content>
        </r:Description>
        <r:CountryCode>SE</r:CountryCode>
      </r:SpatialCoverage>
    </r:Coverage>
    <r:AnalysisUnit controlledVocabularyID="AnalysisUnit" controlledVocabularyAgencyName="DDI Alliance">snd.a01</r:AnalysisUnit>
    <r:AnalysisUnitsCovered>
      <r:String xml:lang="en">Cells</r:String>
      <r:String xml:lang="sv">Celler</r:String>
    </r:AnalysisUnitsCovered>
    <d:DataCollection>
      <r:URN>urn:ddi:se.researchdata:2023-166.DataCollection:2.0</r:URN>
      <d:CollectionEvent>
        <r:URN>urn:ddi:se.researchdata:2023-166.CollectionEvent:2.0</r:URN>
        <d:DataCollectorOrganizationReference>
          <r:URN>urn:ddi:se.researchdata:2023-166.Organization-0:2.0</r:URN>
          <d:ID />
          <d:Version />
          <d:TypeOfObject>Organization</d:TypeOfObject>
        </d:DataCollectorOrganizationReference>
        <d:DataCollectionDate>
          <r:StartDate>2022-03-26</r:StartDate>
          <r:EndDate>2022-08-10</r:EndDate>
        </d:DataCollectionDate>
        <d:ModeOfCollection>
          <r:URN>urn:ddi:se.researchdata:2023-166.CollectionEvent-0-ModeOfCollectionType:2.0</r:URN>
          <d:TypeOfModeOfCollection>Physical measurements and tests</d:TypeOfModeOfCollection>
          <r:Description>
            <r:Content xml:lang="en">Physical measurements and tests</r:Content>
            <r:Content xml:lang="sv">Fysiska mätningar och tester</r:Content>
          </r:Description>
        </d:ModeOfCollection>
      </d:CollectionEvent>
    </d:DataCollection>
    <a:Archive>
      <r:URN>urn:ddi:se.researchdata:2023-166.Archive:2.0</r:URN>
      <a:ArchiveSpecific>
        <a:Item>
          <a:Access>
            <r:URN>urn:ddi:se.researchdata:2023-166.Archive-ArchiveSpecificType-AccessType:2.0</r:URN>
            <a:TypeOfAccess controlledVocabularyName="info:eu-repo-Access-Terms vocabulary">openAccess</a:TypeOfAccess>
          </a:Access>
          <a:DataFileQuantity>63</a:DataFileQuantity>
        </a:Item>
      </a:ArchiveSpecific>
    </a:Archive>
  </s:StudyUnit>
</ddi:DDIInstance>