Nanopublications

@prefix this: <https://w3id.org/np/RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU> .
@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 {
  <http://purl.org/coloc-seq/data-analysis> edam:has_function edam:operation_3680 ;
    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 ;
    a <https://w3id.org/np/RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU/o/ntemplate/AIDA-Sentence> .
}

sub:provenance {
  <https://doi.org/10.1093/nar/gkac1205> bibo:doi "10.1093/nar/gkac1205" ;
    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> , <https://w3id.org/np/RAukAcWHRDlkqxk7H2XNSegc1WnHI569INvNr-xdptDGI> ;
    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" ;
    npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAoSR/rqhnkTPQO8u4l2JQAemJo5cN83rT54nA5NXHUqaeu26bEjT/rsX1PCVBhhJ3cV2uu4wjI0NfcVaKPKmODSf6p579tdOykOnjbWLbxxPMe5DC5eV1ThMHsFsNU/6vCYIfS00E7wre7fnFYz7FAG7v1MZEyWeSXsHgk9jHoqQQDPqup5PHReKp1dd6J0Nht/OfSYnUancKAgIFyPhkTlThsLK5xSNyNEgiTR7pwkP5pGq2AnD6bPw4G3kiPnIpIGZNsaeIOvhn64gwbrtoJVdoun/namw6FQ7StEC5km/0evaBZc4qIextwO/s32Wru77ukblJ0Xi/YzbC0iLuIQIDAQAB" ;
    npx:hasSignature "k+sBTpymBYvAamFSBWMyYKb6xDwo/DvfM1FaHaPytPifKIOcRUDGCk8Fhb8JSRsueOdFCMxcClMCXLUwwKGg+hVfpHGeDKIjrRh2tr4xjsokKJCP5dSg9Tskt/f77++BgRqh02g1B39shCGxXyUHAHIaTwK6aAtjPbJvhVStCm5EGS1LvMKXsrNFLWGHSFBnDeindeFh9GqwbRmd1U1YliQbU+T/ZynxptsZLs64elGrm7Dh4Nfez86L0KE1s+VHM4iUNI0M/5b/441Ir4mr1z4tb8ctiXSLyDkWpD3vQGko4Bdzdq0z6iUZld4i4i3jR5G8j4IYhxISZ+tQGGH2Bg==" ;
    npx:hasSignatureTarget this: .
}