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@prefix sub: <https://w3id.org/np/RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU/> .
@prefix schema: <http://schema.org/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix edam: <http://edamontology.org/> .
@prefix pav: <http://purl.org/pav/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix orcid: <https://orcid.org/> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix bibo: <http://purl.org/ontology/bibo/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .

sub:Head {
  this: np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo;
    a np:Nanopublication .
}

sub:assertion {
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    schema:name "Bioinformatic Analysis Pipeline"@en;
    schema:qualityControl "30-read cut-off for untreated samples; exclusion of cross-mapped sequences; parameter dependency <0.3"@en;
    schema:tool "Origin 2021b (v9.8.5.212)"@en, "READemption (v0.4.3)"@en, "cutadapt (v2.8)"@en,
      "segemehl (v0.2.0-418)"@en;
    schema:workExample "Adapter trimming; read alignment to GRCh38.p13; kinetics model fitting"@en;
    a schema:Thing .
  
  <http://purl.org/coloc-seq/protocol> edam:has_function edam:operation_3207, edam:operation_3801;
    schema:name "CoLoC-seq Experimental Protocol"@en;
    schema:step <http://purl.org/coloc-seq/step-isolation>, <http://purl.org/coloc-seq/step-library-prep>,
      <http://purl.org/coloc-seq/step-rnase-treatment>, <http://purl.org/coloc-seq/step-sequencing>;
    a schema:Thing .
  
  <http://purl.org/coloc-seq/step-isolation> schema:description "Differential centrifugation of crude mitochondria"@en;
    schema:name "Organelle Isolation"@en;
    schema:workExample "14,000 g for 20 min at 4°C to pellet mitochondria"@en;
    a schema:Thing;
    rdfs:comment "Optional isopycnic centrifugation in sucrose gradient for enhanced purity"@en .
  
  <http://purl.org/coloc-seq/step-library-prep> schema:description "Selective sequencing of intact (non-RNase-cleaved) transcripts"@en;
    schema:name "Custom Library Preparation"@en;
    schema:substep "3'-adapter ligation to hydroxyl ends"@en, "5'-adapter ligation to phosphorylated ends"@en,
      "Cap removal (RNA 5'-pyrophosphohydrolase)"@en, "First-strand cDNA synthesis (M-MLV reverse transcriptase)"@en,
      "PCR amplification (15 cycles, high-fidelity polymerase)"@en, "Size selection: 10-220 nt on agarose gel"@en;
    a schema:Thing;
    rdfs:comment "Excludes RNase-cleaved transcripts (5'-OH and 3'-PO4 incompatible with ligation)"@en .
  
  <http://purl.org/coloc-seq/step-rnase-treatment> schema:duration "10 minutes at 25°C"@en;
    schema:name "RNase A Gradient Treatment"@en;
    schema:numberOfSamples "9-10 samples per gradient"@en;
    schema:range "0 - 3 μg/ml RNase A"@en;
    a schema:Thing;
    rdfs:comment "Parallel Mock CoLoC-seq with detergent-permeabilized membranes as control"@en .
  
  <http://purl.org/coloc-seq/step-sequencing> schema:name "High-Throughput Sequencing"@en;
    schema:platform "Illumina NextSeq 500"@en;
    schema:readLength "75 nt"@en;
    schema:readType "single-end"@en;
    a schema:Thing .
  
  this: edam:has_function edam:operation_3207, edam:operation_3801;
    npx:relatesTo <https://w3id.org/np/RAMVUimnATifJYJw0VP2zAesw4OK_Gw30p9NgcEU4oVW8>;
    schema:about <https://doi.org/10.1093/nar/gkac1205>;
    schema:text "The CoLoC-seq experimental protocol integrates organellar isolation, RNase gradient treatment, custom library preparation with selective sequencing of intact transcripts, and kinetics model-based bioinformatic analysis."@en;
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}

sub:provenance {
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    schema:datePublished "2023"^^xsd:gYear;
    schema:isPartOf sub:__1;
    schema:name "CoLoC-seq probes the global topology of organelle transcriptomes"@en;
    a schema:ScholarlyArticle .
  
  sub:__1 schema:name "Nucleic Acids Research"@en;
    a schema:Periodical .
  
  sub:assertion prov:wasAttributedTo orcid:0000-0001-8763-6703, orcid:0000-0002-1481-2996,
      orcid:0000-0002-9142-7979;
    prov:wasDerivedFrom <https://doi.org/10.1093/nar/gkac1205>, <https://w3id.org/np/RAMVUimnATifJYJw0VP2zAesw4OK_Gw30p9NgcEU4oVW8> .
}

sub:pubinfo {
  orcid:0009-0005-7752-8203 foaf:name "Tiado Kollender" .
  
  this: dct:created "2026-01-11T00:00:00Z"^^xsd:dateTime;
    dct:license <https://creativecommons.org/publicdomain/zero/1.0/>;
    npx:wasCreatedFromPubinfoTemplate <https://w3id.org/np/RA0J4vUn_dekg-U1kK3AOEt02p9mT2WO03uGxLDec1jLw>,
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    pav:createdBy orcid:0009-0005-7752-8203;
    a npx:ExampleNanopub;
    rdfs:comment "AIDA-based assertion about the CoLoC-seq experimental protocol"@en;
    rdfs:label "Nanopublication: CoLoC-seq experimental protocol and methods"@en;
    prov:wasAttributedTo orcid:0009-0005-7752-8203 .
  
  sub:sig npx:hasAlgorithm "RSA";
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    npx:hasSignatureTarget this: .
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