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efo_slice.owl
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efo_slice.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
xml:base="http://www.w3.org/2002/07/owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:efo="http://www.ebi.ac.uk/efo/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<Ontology/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<rdfs:label>definition</rdfs:label>
</AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
<rdfs:label>term editor</rdfs:label>
</AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/creator -->
<AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator">
<oboInOwl:hasDbXref>http://purl.org/dc/elements/1.1/creator</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>dc-creator</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>dc-creator</oboInOwl:shorthand>
<rdfs:label>creator</rdfs:label>
</AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/date -->
<AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/date"/>
<!-- http://purl.org/dc/terms/date -->
<AnnotationProperty rdf:about="http://purl.org/dc/terms/date"/>
<!-- http://www.ebi.ac.uk/efo/definition_citation -->
<AnnotationProperty rdf:about="http://www.ebi.ac.uk/efo/definition_citation"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym">
<rdfs:label>has_broad_synonym</rdfs:label>
</AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
<rdfs:label>database_cross_reference</rdfs:label>
</AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
<obo:IAO_0000115>An alternative label for a given entity such as a commonly used abbreviation or synonym. </obo:IAO_0000115>
<rdfs:label>has_exact_synonym</rdfs:label>
</AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym">
<rdfs:label>has_narrow_synonym</rdfs:label>
</AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace">
<rdfs:label>has_obo_namespace</rdfs:label>
</AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym">
<rdfs:label>has_related_synonym</rdfs:label>
</AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#id -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset">
<rdfs:label>in_subset</rdfs:label>
</AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#is_metadata_tag -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_metadata_tag"/>
<!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
<AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
<rdfs:label>shorthand</rdfs:label>
</AnnotationProperty>
<!-- http://www.w3.org/2000/01/rdf-schema#comment -->
<AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
<!-- http://www.w3.org/2000/01/rdf-schema#label -->
<AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<!-- http://www.w3.org/2000/01/rdf-schema#seeAlso -->
<AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#seeAlso">
<oboInOwl:hasDbXref>http://www.w3.org/2000/01/rdf-schema#seeAlso</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>seeAlso</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>seeAlso</oboInOwl:shorthand>
<rdfs:label>see also</rdfs:label>
</AnnotationProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.ebi.ac.uk/efo/EFO_0008679 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008679">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Cell expression by linear amplification and sequencing (CEL-Seq).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:22939981</oboInOwl:hasDbXref>
<rdfs:label>CEL-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008720 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008720">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Massively parallel sNuc-Seq with droplet technology.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:28846088</oboInOwl:hasDbXref>
<rdfs:label>DroNc-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008722 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008722">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Analyze mRNA transcripts from individual cells in droplets (Drop-seq).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:26000488</oboInOwl:hasDbXref>
<rdfs:label>Drop-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008780 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008780">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Indexing droplets (inDrop).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:26000487</oboInOwl:hasDbXref>
<rdfs:label>inDrop</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008796 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008796">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Massively parallel RNA single-cell sequencing framework.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:24531970</oboInOwl:hasDbXref>
<rdfs:label>MARS-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008877 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008877">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Whole-transcript amplification for single-cells (Quartz-Seq).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:23594475</oboInOwl:hasDbXref>
<rdfs:label>Quartz-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008904 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008904">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010891"/>
<obo:IAO_0000115>A single cell ATAC-seq method for mapping single cell genomes for transposase-accessible chromatin. Single nuclei are isolated using a microfluidics platform such as Fluidigm C1.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:26083756</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>single cell ATAC-seq (Microfluidics)</oboInOwl:hasExactSynonym>
<rdfs:label>scATAC-seq (Microfluidics)</rdfs:label>
</Class>
<Axiom>
<annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_0008904"/>
<annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<annotatedTarget>A single cell ATAC-seq method for mapping single cell genomes for transposase-accessible chromatin. Single nuclei are isolated using a microfluidics platform such as Fluidigm C1.</annotatedTarget>
<oboInOwl:hasDbXref>http://orcid.org/0000-0001-7505-5418</oboInOwl:hasDbXref>
</Axiom>
<!-- http://www.ebi.ac.uk/efo/EFO_0008905 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008905">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Single-cell bisulfite sequencing (scBS-seq).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:25042786</oboInOwl:hasDbXref>
<rdfs:label>scBS-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008906 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008906">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Droplet-based single-cell ChIP-seq (Drop-ChIP).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:26458175</oboInOwl:hasDbXref>
<rdfs:label>scChIP-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008919 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008919">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:28192419</oboInOwl:hasDbXref>
<rdfs:label>Seq-Well</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008925 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008925">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010891"/>
<obo:IAO_0000115>A single cell ATAC-seq method for multiplex profiling of chromatin accessibility by combinatorial cellular indexing. Single nuclei are identified by the unique combination of n5 barcodes and indices rather than by isolation.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:25953818</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>sci-ATAC-seq</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>single cell ATAC-seq (cell index)</oboInOwl:hasExactSynonym>
<rdfs:label>scATAC-seq (cell index)</rdfs:label>
</Class>
<Axiom>
<annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_0008925"/>
<annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<annotatedTarget>A single cell ATAC-seq method for multiplex profiling of chromatin accessibility by combinatorial cellular indexing. Single nuclei are identified by the unique combination of n5 barcodes and indices rather than by isolation.</annotatedTarget>
<oboInOwl:hasDbXref>http://orcid.org/0000-0001-7505-5418</oboInOwl:hasDbXref>
</Axiom>
<!-- http://www.ebi.ac.uk/efo/EFO_0008930 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008930">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010184"/>
<obo:IAO_0000115>Switch mechanism at the 5’ end of RNA templates (Smart).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:22820318</oboInOwl:hasDbXref>
<rdfs:label>Smart-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008931 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008931">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010184"/>
<obo:IAO_0000115>Switch mechanism at the 5’ end of RNA templates (Smart). According to the authors, Smart-seq2 transcriptome libraries have improved detection, coverage, bias and accuracy compared to Smart-seq libraries, and are generated with off-the-shelf reagents at lower cost.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:24056875</oboInOwl:hasDbXref>
<rdfs:label>Smart-seq2</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008953 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008953">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Single-cell tagged reverse transcription (STRT).</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:21543516</oboInOwl:hasDbXref>
<rdfs:label>STRT-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0008995 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0008995">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>10x is a "synthetic long-read" technology and works by capturing a barcoded oligo-coated gel-bead and 0.3x genome copies into a single emulsion droplet, processing the equivalent of 1 million pipetting steps. Successive versions of the 10x chemistry use different barcode locations to improve the sequencing yield and quality of 10x experiments.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasBroadSynonym>10X</oboInOwl:hasBroadSynonym>
<oboInOwl:hasBroadSynonym>10x</oboInOwl:hasBroadSynonym>
<oboInOwl:hasExactSynonym>10x Genomics</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>10x single cell library construction</oboInOwl:hasExactSynonym>
<oboInOwl:hasRelatedSynonym>10X sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x sequencing</oboInOwl:hasRelatedSynonym>
<rdfs:label>10x technology</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009294 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009294">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>CITE-seq is a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:28759029</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>cellular indexing of transcriptomes and epitopes by sequencing</oboInOwl:hasExactSynonym>
<rdfs:label>CITE-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009899 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009899">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030003"/>
<obo:IAO_0000115>10X 3' v2 is the second version of the 10x sequencing technology that sequences from the 3' end of nucleic acid molecules. In the 3' assay, the polyd(T) sequence is part of the gel bead oligo (which also contains the 10x Barcode, UMI, and partial Illumina Read 1 sequence), with the template switch oligo (TSO) supplied in the RT Primer.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasExactSynonym>10X 3' v2</oboInOwl:hasExactSynonym>
<oboInOwl:hasRelatedSynonym>10X 3' v2 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10X v2</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10X v2 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10XV2</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x 3' v2 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x v2</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x v2 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x_v2</oboInOwl:hasRelatedSynonym>
<rdfs:label>10x 3' v2</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009900 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009900">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030004"/>
<obo:IAO_0000115>10X 5' v2 is the second version of the 10x sequencing technology that sequences from the 5' end of nucleic acid molecules. In the 5' assay, the polyd(T) is supplied in the RT Primer, and the template switch oligo (TSO) is part of the gel bead oligo.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasExactSynonym>10X 5' v2</oboInOwl:hasExactSynonym>
<oboInOwl:hasRelatedSynonym>10X 5' v2 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x 5' v2 sequencing</oboInOwl:hasRelatedSynonym>
<rdfs:label>10x 5' v2</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009901 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009901">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030003"/>
<obo:IAO_0000115>10x 3' v1 is the first version of the 10X sequencing technology that sequences from the 3' end of nucleic acid molecules. Differs from 5' v1 in the captured end from the polyadenylated transcript.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasExactSynonym>10X 3' v1</oboInOwl:hasExactSynonym>
<oboInOwl:hasRelatedSynonym>10X 3' v1 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10X v1</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10XV1</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x 3' v1 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x v1</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x v1 sequencing</oboInOwl:hasRelatedSynonym>
<rdfs:label>10x 3' v1</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009919 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009919">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Split-pool ligation-based transcriptome sequencing (SPLiT-seq) is a single-cell RNA-seq method that labels the cellular origin of RNA through combinatorial barcoding.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:29545511</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>split-pool ligation-based transcriptome sequencing</oboInOwl:hasExactSynonym>
<rdfs:label>SPLiT-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009920 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009920">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>A method for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:29545511</oboInOwl:hasDbXref>
<rdfs:label>Slide-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009922 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009922">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030003"/>
<obo:IAO_0000115>10X 3' v3 is the third version of the 10x sequencing technology that sequences from the 3' end of nucleic acid molecules.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasExactSynonym>10X 3' v3</oboInOwl:hasExactSynonym>
<oboInOwl:hasRelatedSynonym>10X v3</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10X v3 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10XV3</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x 3' v3 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x v3</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x v3 sequencing</oboInOwl:hasRelatedSynonym>
<rdfs:label>10x 3' v3</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0009979 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0009979">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>A single cell Hi-C assay.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<rdfs:label>single cell Hi-C</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010004 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010004">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>SCRB-Seq is a cost-efficient, multiplexed, single-cell mRNA sequencing technique.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasExactSynonym>Single cell RNA barcoding and sequencing</oboInOwl:hasExactSynonym>
<rdfs:label>SCRB-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010010 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010010">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>A modified version of CEL-Seq with higher sensitivity.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:27121950</oboInOwl:hasDbXref>
<rdfs:label>CEL-seq2</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010022 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010022">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010184"/>
<obo:IAO_0000115>Method that accurately quantifies transcript abundance even with small amounts of total RNA and effectively characterizes small samples extracted by laser-capture microdissection (LCM) from FFPE tissue. Modified 3Seq method - omitted poly (A) enrichment and replaced dsDNA ligation with template-switching cDNA synthesis</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<oboInOwl:hasExactSynonym>Smart-3seq</oboInOwl:hasExactSynonym>
<rdfs:label>Smart-3SEQ</rdfs:label>
</Class>
<Axiom>
<annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010022"/>
<annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<annotatedTarget>Smart-3seq</annotatedTarget>
<efo:definition_citation>PMID:31519740</efo:definition_citation>
</Axiom>
<!-- http://www.ebi.ac.uk/efo/EFO_0010058 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010058">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Dissociation of a sample into individual cells using the Fluidigm C1 platform. Cells are captured on the C1 system (Fluidigm) and processed using the SMARTer chemistry (Clontech) according to the Fluidigm protocol.</obo:IAO_0000115>
<obo:IAO_0000117>Dani Welter</obo:IAO_0000117>
<rdfs:label>Fluidigm C1-based library preparation</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010183 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010183">
<obo:IAO_0000115>A library preparation process that starts from a single cell.</obo:IAO_0000115>
<dc:creator>Olamidipupo Ajigboye</dc:creator>
<oboInOwl:hasExactSynonym>single cell library preparation</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>single-cell library construction</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>single-cell library preparation</oboInOwl:hasExactSynonym>
<rdfs:label>single cell library construction</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010184 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010184">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>Library construction method using the SMART (Switching Mechanism at the 5' end of the RNA Template) or SMARTer technology, producing full-length cDNA libraries.</obo:IAO_0000115>
<dc:creator>Olamidipupo Ajigboye</dc:creator>
<rdfs:label>Smart-like</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010550 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010550">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>The sci-RNA-seq uses the combinatorial indexing to identify single cells without single cell isolation. Two-level indexing (RT barcode + PCR barcodes (i5 + i7)) or three-level indexing (RT barcode + PCR barcodes (i5 + i7) + Tn5 barcodes) can be used. Three-level indexing is a bit more difficult since you need to assemble many indexed Tn5 transposomes.</obo:IAO_0000115>
<obo:IAO_0000117>Zoe May Pendlington</obo:IAO_0000117>
<oboInOwl:hasDbXref>PMID:28818938</oboInOwl:hasDbXref>
<rdfs:label xml:lang="en">sci-RNA-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010713 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010713">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0008995"/>
<obo:IAO_0000115>This method creates libraries that can capture gene expression, V(D)J sequences and feature barcodes from the same cells depending on the type of enrichment used.</obo:IAO_0000115>
<obo:IAO_0000117>Zoe May Pendlington</obo:IAO_0000117>
<oboInOwl:hasExactSynonym xml:lang="en">10X Immune profiling</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>10X V(D)J</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>10X VDJ</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>Chromium Single Cell V(D)J</oboInOwl:hasExactSynonym>
<rdfs:label>10x immune profiling</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010714 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010714">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010713"/>
<obo:IAO_0000115>This method enriches 10X 5' gene expression libraries with alpha and beta chain T cell receptor (TCR) sequences using PCR primers.</obo:IAO_0000115>
<obo:IAO_0000117>Zoe May Pendlington</obo:IAO_0000117>
<oboInOwl:hasExactSynonym xml:lang="en">10X TCR enrichment</oboInOwl:hasExactSynonym>
<rdfs:label>10x TCR enrichment</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010715 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010715">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010713"/>
<obo:IAO_0000115>This method enriches 10X 5' gene expression libraries with heavy and light chain Immunoglobulin (Ig) sequences from B cells using PCR primers.</obo:IAO_0000115>
<obo:IAO_0000117>Zoe May Pendlington</obo:IAO_0000117>
<oboInOwl:hasExactSynonym>10X BCR enrichment</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym xml:lang="en">10X Ig enrichment</oboInOwl:hasExactSynonym>
<rdfs:label>10x Ig enrichment</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010891 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010891">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>A method for detecting the accessible chromatin in individual cells by transposase-accessible chromatin sequencing assay.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
<oboInOwl:hasDbXref>http://orcid.org/0000-0002-8674-0039</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>https://en.wikipedia.org/w/index.php?title=ATAC-seq&oldid=984332600#Single-cell_ATAC-seq</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>ATAC-seq (single cell)</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>single cell ATAC-seq</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>single cell ATAC-sequencing</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>single cell assay for transposase-accessible chromatin using sequencing</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>single-cell ATAC-seq</oboInOwl:hasExactSynonym>
<rdfs:label>scATAC-seq</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0010961 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010961">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0008995"/>
<obo:IAO_0000115>A spatial transcriptomics method developed by 10x Genomics that measures either the whole transcriptome or a defined set of transcripts in intact tissue sections and maps where gene activity is occurring.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
<oboInOwl:hasExactSynonym>10X Visium</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>Visium</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>Visium Spatial Gene Expression</rdfs:label>
</Class>
<Axiom>
<annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010961"/>
<annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<annotatedTarget>A spatial transcriptomics method developed by 10x Genomics that measures either the whole transcriptome or a defined set of transcripts in intact tissue sections and maps where gene activity is occurring.</annotatedTarget>
<oboInOwl:hasDbXref>http://orcid.org/0000-0001-7505-5418</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>https://pages.10xgenomics.com/rs/446-PBO-704/images/10x_LIT059_ProductSheet_VisiumSpatialGeneExpression_Letter_digital.pdf</oboInOwl:hasDbXref>
</Axiom>
<!-- http://www.ebi.ac.uk/efo/EFO_0010964 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0010964">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010183"/>
<obo:IAO_0000115>A single-cell RNA sequencing library construction method that generates barcoded libraries and is plate-based. An example would be a plate-based method that is not Smart-seq2 or a modified, barcoded version of Smart-seq2.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
<oboInOwl:hasExactSynonym>barcoded plate-based single-cell RNA-seq</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>barcoded plate-based single cell RNA-seq</rdfs:label>
</Class>
<Axiom>
<annotatedSource rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010964"/>
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<annotatedTarget>A single-cell RNA sequencing library construction method that generates barcoded libraries and is plate-based. An example would be a plate-based method that is not Smart-seq2 or a modified, barcoded version of Smart-seq2.</annotatedTarget>
<oboInOwl:hasDbXref>http://orcid.org/0000-0002-2443-7325</oboInOwl:hasDbXref>
</Axiom>
<!-- http://www.ebi.ac.uk/efo/EFO_0011025 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0011025">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0030004"/>
<obo:IAO_0000115>10x 5' v1 is the first version of the 10X sequencing technology that sequences from the 5' end of nucleic acid molecules. Differs from 3' v1 in the captured end from the polyadenylated transcript.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
<oboInOwl:hasExactSynonym>10X 5' v1</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>10x 5' v1</oboInOwl:hasExactSynonym>
<oboInOwl:hasRelatedSynonym>10X 5' v3</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x 5' v1 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x 5' v3</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x 5' v3 sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>10x v1 5' sequencing</oboInOwl:hasRelatedSynonym>
<oboInOwl:inSubset rdf:resource="http://www.ebi.ac.uk/efo/added_for_HCA"/>
<rdfs:label>10x 5' v1</rdfs:label>
</Class>
<!-- http://www.ebi.ac.uk/efo/EFO_0022045 -->
<Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0022045">
<rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0010891"/>
<obo:IAO_0000115>A single cell plate-based three-level combinatorial indexing assay that measures chromatin accessibility. The first two rounds of split-pool indexing are achieved by successive ligations to each end of the Tn5 transposase complex, and the third round remains through PCR. The protocol no longer requires cell sorting and has been optimized to maximize recovery of fragments per cell.</obo:IAO_0000115>
<dc:creator>Zoe May Pendlington</dc:creator>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-01-03T10:14:49Z</dc:date>
<rdfs:label xml:lang="en">sci-ATAC-seq3</rdfs:label>
</Class>
<Axiom>
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<annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<annotatedTarget>A single cell plate-based three-level combinatorial indexing assay that measures chromatin accessibility. The first two rounds of split-pool indexing are achieved by successive ligations to each end of the Tn5 transposase complex, and the third round remains through PCR. The protocol no longer requires cell sorting and has been optimized to maximize recovery of fragments per cell.</annotatedTarget>
<efo:definition_citation>PMID:33184180</efo:definition_citation>
<efo:definition_citation>https://orcid.org/0000-0003-4389-9821</efo:definition_citation>
</Axiom>
<!-- http://www.ebi.ac.uk/efo/EFO_0022488 -->
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<obo:IAO_0000115>Smart-seq3 is an advanced single-cell RNA sequencing technology that provides full-length transcriptome coverage. It incorporates a 5' unique molecular identifier (UMI) RNA counting strategy, allowing for the in silico reconstruction of thousands of RNA molecules per cell. This method enhances transcript quantification accuracy and enables the detailed study of allele- and isoform-resolution within single cells. Smart-seq3 is particularly noted for its high sensitivity and ability to reconstruct the full-length transcripts of single cells
Smart-seq3 is a continuation and improvement of the Smart-seq technology, specifically Smart-seq2.</obo:IAO_0000115>
<dc:creator>Zoe May Pendlington</dc:creator>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2023-11-28T13:49:20Z</dc:date>
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<annotatedTarget>Smart-seq3 is an advanced single-cell RNA sequencing technology that provides full-length transcriptome coverage. It incorporates a 5' unique molecular identifier (UMI) RNA counting strategy, allowing for the in silico reconstruction of thousands of RNA molecules per cell. This method enhances transcript quantification accuracy and enables the detailed study of allele- and isoform-resolution within single cells. Smart-seq3 is particularly noted for its high sensitivity and ability to reconstruct the full-length transcripts of single cells
Smart-seq3 is a continuation and improvement of the Smart-seq technology, specifically Smart-seq2.</annotatedTarget>
<efo:definition_citation>PMID:32518404</efo:definition_citation>
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<!-- http://www.ebi.ac.uk/efo/EFO_0022490 -->
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<obo:IAO_0000115>ScaleBio technology that utilizes a plate-based approach with combinatorial indexing to generate single cell libraries.</obo:IAO_0000115>
<dc:creator>Zoe May Pendlington</dc:creator>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2024-01-10T09:12:40Z</dc:date>
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<!-- http://www.ebi.ac.uk/efo/EFO_0022492 -->
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<obo:IAO_0000115>A method to jointly profile chromatin conformation and cytosine DNA methylation from the same cell.</obo:IAO_0000115>
<dc:creator>Zoe May Pendlington</dc:creator>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2024-01-11T09:24:17Z</dc:date>
<oboInOwl:hasExactSynonym>sn-m3C-seq</oboInOwl:hasExactSynonym>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030001 -->
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<obo:IAO_0000115>A combinatorial indexing-based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells, combining sci–ATAC sequencing (sci-ATAC-seq) and sci-RNA-seq into a single protocol.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
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<rdfs:label>sci-CAR</rdfs:label>
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<annotatedTarget>A combinatorial indexing-based coassay that jointly profiles chromatin accessibility and mRNA (CAR) in each of thousands of single cells, combining sci–ATAC sequencing (sci-ATAC-seq) and sci-RNA-seq into a single protocol.</annotatedTarget>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030002 -->
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<obo:IAO_0000115>A platform for high-throughput single-cell RNA-sequencing. An agarose plate with microwells is used to trap 5-10K individual cells. Barcoded magnetic beads are loaded and trapped into each well. Each single bead is conjugated with 107–108 oligonucleotides, which share the same cellular barcode. Each oligonucleotide consists of a primer sequence, a cell barcode, a unique molecular identifier (UMI), and a poly T tail. After incubation of beads and cells in a soft flow of lysis buffer, beads with captured mRNA are retrieved with a magnet. Beads are collected in a tube in which reverse transcription and template switch steps are performed using the Smart-seq2 protocol (Picelli et al., 2013). Amplified cDNA is fragmented by a customized transposase that carries two identical insertion sequences. The 3′ ends of the transcripts are then enriched during library generation using PCR and sequenced using an Illumina Sequencing Platform.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
<oboInOwl:hasExactSynonym>Microwell-Seq</oboInOwl:hasExactSynonym>
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<annotatedTarget>A platform for high-throughput single-cell RNA-sequencing. An agarose plate with microwells is used to trap 5-10K individual cells. Barcoded magnetic beads are loaded and trapped into each well. Each single bead is conjugated with 107–108 oligonucleotides, which share the same cellular barcode. Each oligonucleotide consists of a primer sequence, a cell barcode, a unique molecular identifier (UMI), and a poly T tail. After incubation of beads and cells in a soft flow of lysis buffer, beads with captured mRNA are retrieved with a magnet. Beads are collected in a tube in which reverse transcription and template switch steps are performed using the Smart-seq2 protocol (Picelli et al., 2013). Amplified cDNA is fragmented by a customized transposase that carries two identical insertion sequences. The 3′ ends of the transcripts are then enriched during library generation using PCR and sequenced using an Illumina Sequencing Platform.</annotatedTarget>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030003 -->
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<obo:IAO_0000115>10x 3' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3' end.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
<rdfs:label>10x 3' transcription profiling</rdfs:label>
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<annotatedTarget>10x 3' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3' end.</annotatedTarget>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030004 -->
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<obo:IAO_0000115>10x 5' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5' end.</obo:IAO_0000115>
<dc:creator>paola</dc:creator>
<rdfs:label>10x 5' transcription profiling</rdfs:label>
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<annotatedTarget>10x 5' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5' end.</annotatedTarget>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030007 -->
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<obo:IAO_0000115>A single cell ATAC-seq method for profiling of chromatin accessibility. For library construction, single cells or single nuclei are isolated into droplets using 10x Chromium technnolgy.</obo:IAO_0000115>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030008 -->
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<obo:IAO_0000115>The use of CITE-seq technology with the purpose of quantifying cell surface protein expression in addition to transcriptomic readout in single cells.</obo:IAO_0000115>
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<rdfs:label>CITE-seq (cell surface protein profiling)</rdfs:label>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030009 -->
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<!-- http://www.ebi.ac.uk/efo/EFO_0030010 -->
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<obo:IAO_0000115>10x feature barcode technology is a method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays. This is done by generating additional sequencing libraries within the same droplet containing a single cell. The readout of these libraries are known oligonucleotides that are coupled to cell surface proteins antibodies or sgRNAs.</obo:IAO_0000115>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030011 -->
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<obo:IAO_0000115>The use of 10x Genomics feature barcode technology with the purpose of quantifying cell surface protein expression in addition to transcriptomic readout in single cells.</obo:IAO_0000115>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030012 -->
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<!-- http://www.ebi.ac.uk/efo/EFO_0030013 -->
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<obo:IAO_0000115>The use of 10x Genomics feature barcode technology with the purpose of performing a CRISPR screening.</obo:IAO_0000115>
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<!-- http://www.ebi.ac.uk/efo/EFO_0030019 -->
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<obo:IAO_0000115>Seq-Well with second strand synthesis.</obo:IAO_0000115>
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