<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:2023-122-1:1</r:URN>
  <r:Agency>SND</r:Agency>
  <r:ID>2023-122-1</r:ID>
  <r:Version>1</r:Version>
  <g:ResourcePackage>
    <r:URN>urn:ddi:se.researchdata:2023-122-1.ResourcePackage:2.0</r:URN>
    <r:OtherMaterialScheme>
      <r:URN>urn:ddi:se.researchdata:2023-122-1.OtherMaterialScheme:2.0</r:URN>
    </r:OtherMaterialScheme>
    <a:OrganizationScheme>
      <r:URN>urn:ddi:se.researchdata:2023-122-1.OrganizationScheme-0:2.0</r:URN>
      <a:Individual>
        <r:URN>urn:ddi:se.researchdata:2023-122-1.Individual-0:2.0</r:URN>
        <r:UserAttributePair>
          <r:AttributeKey>affiliation</r:AttributeKey>
          <r:AttributeValue>Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM), Karolinska Institutet</r:AttributeValue>
        </r:UserAttributePair>
        <a:IndividualIdentification>
          <a:IndividualName>
            <a:FirstGiven>Pedro Luis</a:FirstGiven>
            <a:LastFamily>Moura</a:LastFamily>
            <a:FullName>
              <r:String>Pedro Luis Moura</r:String>
            </a:FullName>
          </a:IndividualName>
          <a:ResearcherID>
            <a:TypeOfID>ORCID</a:TypeOfID>
            <a:ResearcherIdentification>0000-0002-0493-5394</a:ResearcherIdentification>
          </a:ResearcherID>
        </a:IndividualIdentification>
      </a:Individual>
      <a:Individual>
        <r:URN>urn:ddi:se.researchdata:2023-122-1.Individual-0:2.0</r:URN>
        <r:UserAttributePair>
          <r:AttributeKey>affiliation</r:AttributeKey>
          <r:AttributeValue>Department of Medicine, Huddinge / Center for Hematology and Regenerative Medicine (HERM), Karolinska Institutet</r:AttributeValue>
        </r:UserAttributePair>
        <a:IndividualIdentification>
          <a:IndividualName>
            <a:FirstGiven>Eva</a:FirstGiven>
            <a:LastFamily>Hellström-Lindberg</a:LastFamily>
            <a:FullName>
              <r:String>Eva Hellström-Lindberg</r:String>
            </a:FullName>
          </a:IndividualName>
          <a:ResearcherID>
            <a:TypeOfID>ORCID</a:TypeOfID>
            <a:ResearcherIdentification>0000-0002-7839-3743</a:ResearcherIdentification>
          </a:ResearcherID>
        </a:IndividualIdentification>
      </a:Individual>
    </a:OrganizationScheme>
  </g:ResourcePackage>
  <s:StudyUnit>
    <r:URN>urn:ddi:se.researchdata:2023-122-1.StudyUnit:2.0</r:URN>
    <r:UserID typeOfUserID="datasetIdentifier">2023-122-1</r:UserID>
    <r:Citation>
      <r:Title>
        <r:String xml:lang="sv">Smart-seq3 och Smart-seq3xpress singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter</r:String>
        <r:String xml:lang="en">Smart-seq3 and Smart-seq3xpress single-cell RNA sequencing of bone marrow cells from MDS-RS patients</r:String>
      </r:Title>
      <r:Creator>
        <r:CreatorReference>
          <r:URN>urn:ddi:se.researchdata:2023-122-1.Individual-0:2.0</r:URN>
          <r:TypeOfObject>Individual</r:TypeOfObject>
        </r:CreatorReference>
      </r:Creator>
      <r:Publisher>
        <r:PublisherName>
          <r:String xml:lang="sv">Karolinska Institutet</r:String>
          <r:String xml:lang="en">Karolinska Institutet</r:String>
        </r:PublisherName>
      </r:Publisher>
      <r:Publisher>
        <r:PublisherName>
          <r:String xml:lang="sv">Karolinska Institutet</r:String>
          <r:String xml:lang="en">Karolinska Institutet</r:String>
        </r:PublisherName>
      </r:Publisher>
      <r:PublicationDate>
        <r:SimpleDate>2023-10-19</r:SimpleDate>
      </r:PublicationDate>
      <r:InternationalIdentifier>
        <r:IdentifierContent>10.48723/0f0c-p816</r:IdentifierContent>
        <r:ManagingAgency controlledVocabularyAgencyName="DOI">DOI</r:ManagingAgency>
      </r:InternationalIdentifier>
    </r:Citation>
    <r:Abstract>
      <r:Content xml:lang="sv">Syftet med denna datainsamling var att bedöma flera parametrar om hur benmärgen hos MDS-RS-patienter skiljer sig från den hos friska donatorer. Denna datauppsättning består av Smart-seq3 och Smart-seq3xpress singel-cell RNA sekvensering av benmärgsceller från MDS-RS patienter. Se den engelska beskrivningen för mer information.

Datasetet består av 2 mappar:
- SS3_FACS_PB-BM_RS	
- SS3xpress_FACS_HSC_MPP_MEP_EB

Mappen SS3_FACS_PB-BM_RS innehåller 1 rds-fil, 3 txt-filer och 1 komprimerad mapp (tar.gz) med fastq-filer.
Mappen SS3xpress_FACS_HSC_MPP_MEP_EB innehåller 1 rds fil, 7 txt-filer och 2 GNU-zippade fastq-filer.

Dokumentationsfilen File_list_SS3_SS3xpress.txt innehåller en lista över datasetets alla filer.</r:Content>
      <r:Content xml:lang="en">This dataset consists of Smart-seq3 single-cell RNA sequencing data of purified RS from the bone marrow and peripheral blood of 2 MDS-RS patients; and Smart-seq3xpress single-cell RNA sequencing data of FACS-sorted hematopoietic stem cells (HSC), multipotent progenitors (MPP), megakaryocyte-erythroid progenitors (MEP) and erythroblasts from 1 MDS-RS patient. The objective of this data collection was to assess several parameters on how the bone marrow of MDS-RS patients differs from that of healthy donors.

This dataset includes raw sequencing data in .fastq format, processed count matrices and associated pseudonymized metadata.
 
Processing: In brief, cells were sorted into 384-well plates containing 3uL Vapor-Lock (Qiagen) and 0.3uL lysis buffer consisting of 0.125 µM OligodT30VN (5'-Biotin-ACGAGCATCAGCAGCATACGAT30VN-3'; IDT) adjusted to reverse transcription (RT), 0.5mM dNTPs/each adjusted to RT volume, 0.1% Triton X-100, 5% PEG8000 adjusted to RT volume, 0.4u RNase Inhibitor (Takara Bio, 40 U/µL). After cell sorting plates were briefly centrifuged before storage at -80C. Before RT, plates were denatured at 72 degrees for 10 min followed by addition of 0.1 µL of RT mix; 25 mM Tris-HCL pH 8.4 (Fischer Scientific), 30mM NaCl (Ambion), 1 mM GTP (Thermo Fisher Scientific), 2.5 mM MgCl2 (Ambion), 8 mM DTT (Thermo Fisher Scientific), 0.25 U/µl RNase Inhibitor (Takara Bio), 0.75 µM Template Switching Oligo (TSO) (5′-Biotin-AGAGACAGATTGCGCAATGNNNNNNNNWWrGrGrG-3′; IDT) and 2 U/µl of Maxima H Minus reverse transcriptase (Thermo Fisher Scientific). Plates were quickly centrifuged after dispensing to ensure merge of lysis and RT volumes. RT was incubated at 42 °C for 90 minutes, followed by ten cycles of 50 °C for 2 minutes and 42 °C for 2 minutes. After RT, 0.6 µL PCR mix was dispensed to each well containing the following; 1× SeqAmp PCR buffer (Takara Bio), 0.025 U/µl of SeqAmp polymerase (Takara Bio) and 0.5 µM Smartseq3 forward and reverse primer. Plates were quickly spun down before being incubated as follows: 1 minute at 95 °C for initial denaturation, 14 cycles of 10 seconds at 98 °C, 30 seconds at 65 °C and 2–6 minutes at 68 °C. Final elongation was performed for 10 minutes at 72 °C.

The dataset consists of 2 folders: 
- SS3_FACS_PB-BM_RS	
- SS3xpress_FACS_HSC_MPP_MEP_EB

The folder SS3_FACS_PB-BM_RS contains 1 rds file, 3 txt files, and 1 compressed folder (tar.gz) with fastq files.
The folder SS3xpress_FACS_HSC_MPP_MEP_EB contains 1 rds file, 7 txt files, and 2 GNU zipped fastq files.

The documentation file File_list_SS3_SS3xpress.txt contains a full list of the files in the dataset.</r:Content>
    </r:Abstract>
    <r:Coverage>
      <r:TopicalCoverage>
        <r:URN>urn:ddi:se.researchdata:2023-122-1.TopicalCoverage:2.0</r:URN>
        <r:Subject xml:lang="en" controlledVocabularyID="1" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Natural Sciences</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="1" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Naturvetenskap</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="106" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Biological Sciences</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="106" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Biologi</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="10609" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Genetics and Genomics</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="10609" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Genetik och genomik</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="30202" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Hematology</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="30202" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Hematologi</r:Subject>
        <r:Subject xml:lang="en" controlledVocabularyID="30112" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Basic Cancer Research</r:Subject>
        <r:Subject xml:lang="sv" controlledVocabularyID="30112" controlledVocabularyName="Standard för svensk indelning av forskningsämnen 2025">Basal cancerforskning</r:Subject>
        <r:Keyword xml:lang="en" controlledVocabularyID="D009190" controlledVocabularyName="MeSH">Myelodysplastic Syndromes</r:Keyword>
        <r:Keyword xml:lang="sv" controlledVocabularyID="D009190" controlledVocabularyName="MeSH">Myelodysplastiskt syndrom</r:Keyword>
      </r:TopicalCoverage>
      <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>
    <a:Archive>
      <r:URN>urn:ddi:se.researchdata:2023-122-1.Archive:2.0</r:URN>
      <a:ArchiveSpecific>
        <a:Item>
          <a:Access>
            <r:URN>urn:ddi:se.researchdata:2023-122-1.Archive-ArchiveSpecificType-AccessType:2.0</r:URN>
            <a:TypeOfAccess controlledVocabularyName="info:eu-repo-Access-Terms vocabulary">restrictedAccess</a:TypeOfAccess>
          </a:Access>
          <a:DataFileQuantity>3</a:DataFileQuantity>
        </a:Item>
      </a:ArchiveSpecific>
    </a:Archive>
  </s:StudyUnit>
</ddi:DDIInstance>