https://w3id.org/np/RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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@prefix sub: <https://w3id.org/np/RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU/> .
@prefix schema: <http://schema.org/> .
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@prefix npx: <http://purl.org/nanopub/x/> .
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@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
<http://purl.org/coloc-seq/data-analysis> a schema:Thing;
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 .
<http://purl.org/coloc-seq/protocol> a schema:Thing;
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> .
<http://purl.org/coloc-seq/step-isolation> a schema:Thing;
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;
rdfs:comment "Optional isopycnic centrifugation in sucrose gradient for enhanced purity"@en .
<http://purl.org/coloc-seq/step-library-prep> a schema:Thing;
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;
rdfs:comment "Excludes RNase-cleaved transcripts (5'-OH and 3'-PO4 incompatible with ligation)"@en .
<http://purl.org/coloc-seq/step-rnase-treatment> a schema:Thing;
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;
rdfs:comment "Parallel Mock CoLoC-seq with detergent-permeabilized membranes as control"@en .
<http://purl.org/coloc-seq/step-sequencing> a schema:Thing;
schema:name "High-Throughput Sequencing"@en;
schema:platform "Illumina NextSeq 500"@en;
schema:readLength "75 nt"@en;
schema:readType "single-end"@en .
this: a <https://w3id.org/np/RALlmEPut18Vg-rl5s7_ZhVAnEy61gPXfDxQIFOXpqqbU/o/ntemplate/AIDA-Sentence>;
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 .
}
sub:provenance {
<https://doi.org/10.1093/nar/gkac1205> a schema:ScholarlyArticle;
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 .
sub:__1 a schema:Periodical;
schema:name "Nucleic Acids Research"@en .
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> .
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sub:pubinfo {
orcid:0009-0005-7752-8203 foaf:name "Tiado Kollender" .
this: a npx:ExampleNanopub;
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;
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 .
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