PMC:7417788 / 70100-70843 JSONTXT

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T1488","span":{"begin":169,"end":177},"obj":"CHEBI:28073;CHEBI:28073"},{"id":"T1489","span":{"begin":256,"end":257},"obj":"CL:0000236"},{"id":"T1490","span":{"begin":258,"end":264},"obj":"CL:0000236"},{"id":"T1491","span":{"begin":357,"end":361},"obj":"PR:000003906"},{"id":"T1492","span":{"begin":398,"end":402},"obj":"SO:0000704"},{"id":"T1493","span":{"begin":638,"end":639},"obj":"CL:0000084"},{"id":"T1494","span":{"begin":641,"end":648},"obj":"CL:0000236"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T506","span":{"begin":185,"end":189},"obj":"Body_part"},{"id":"T507","span":{"begin":260,"end":264},"obj":"Body_part"},{"id":"T508","span":{"begin":398,"end":402},"obj":"Body_part"},{"id":"T509","span":{"begin":643,"end":648},"obj":"Body_part"}],"attributes":[{"id":"A506","pred":"fma_id","subj":"T506","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A507","pred":"fma_id","subj":"T507","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A508","pred":"fma_id","subj":"T508","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A509","pred":"fma_id","subj":"T509","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T140","span":{"begin":689,"end":692},"obj":"Disease"}],"attributes":[{"id":"A140","pred":"mondo_id","subj":"T140","obj":"http://purl.obolibrary.org/obo/MONDO_0018859"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1153","span":{"begin":167,"end":168},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1154","span":{"begin":185,"end":189},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1155","span":{"begin":258,"end":264},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T1156","span":{"begin":398,"end":402},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T1157","span":{"begin":548,"end":549},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1158","span":{"begin":641,"end":648},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T1159","span":{"begin":685,"end":686},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T151","span":{"begin":169,"end":177},"obj":"Chemical"}],"attributes":[{"id":"A18748","pred":"chebi_id","subj":"T151","obj":"http://purl.obolibrary.org/obo/CHEBI_28073"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T393","span":{"begin":0,"end":44},"obj":"Sentence"},{"id":"T394","span":{"begin":45,"end":225},"obj":"Sentence"},{"id":"T395","span":{"begin":226,"end":403},"obj":"Sentence"},{"id":"T396","span":{"begin":404,"end":515},"obj":"Sentence"},{"id":"T397","span":{"begin":516,"end":624},"obj":"Sentence"},{"id":"T398","span":{"begin":625,"end":743},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}

{"project":"2_test","denotations":[{"id":"32780218-29891535-132718731","span":{"begin":737,"end":741},"obj":"29891535"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1470","span":{"begin":27,"end":30},"obj":"Gene"},{"id":"1471","span":{"begin":35,"end":38},"obj":"Gene"},{"id":"1483","span":{"begin":98,"end":101},"obj":"Gene"},{"id":"1484","span":{"begin":102,"end":105},"obj":"Gene"},{"id":"1485","span":{"begin":230,"end":233},"obj":"Gene"},{"id":"1486","span":{"begin":234,"end":237},"obj":"Gene"},{"id":"1487","span":{"begin":390,"end":393},"obj":"Gene"},{"id":"1488","span":{"begin":394,"end":397},"obj":"Gene"},{"id":"1489","span":{"begin":585,"end":588},"obj":"Gene"},{"id":"1490","span":{"begin":589,"end":592},"obj":"Gene"},{"id":"1491","span":{"begin":663,"end":666},"obj":"Gene"},{"id":"1492","span":{"begin":667,"end":670},"obj":"Gene"},{"id":"1493","span":{"begin":207,"end":210},"obj":"Gene"}],"attributes":[{"id":"A1470","pred":"tao:has_database_id","subj":"1470","obj":"Gene:6962"},{"id":"A1471","pred":"tao:has_database_id","subj":"1471","obj":"Gene:613"},{"id":"A1483","pred":"tao:has_database_id","subj":"1483","obj":"Gene:6962"},{"id":"A1484","pred":"tao:has_database_id","subj":"1484","obj":"Gene:613"},{"id":"A1485","pred":"tao:has_database_id","subj":"1485","obj":"Gene:6962"},{"id":"A1486","pred":"tao:has_database_id","subj":"1486","obj":"Gene:613"},{"id":"A1487","pred":"tao:has_database_id","subj":"1487","obj":"Gene:6962"},{"id":"A1488","pred":"tao:has_database_id","subj":"1488","obj":"Gene:613"},{"id":"A1489","pred":"tao:has_database_id","subj":"1489","obj":"Gene:6962"},{"id":"A1490","pred":"tao:has_database_id","subj":"1490","obj":"Gene:613"},{"id":"A1491","pred":"tao:has_database_id","subj":"1491","obj":"Gene:6962"},{"id":"A1492","pred":"tao:has_database_id","subj":"1492","obj":"Gene:613"},{"id":"A1493","pred":"tao:has_database_id","subj":"1493","obj":"Gene:3815"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Sequencing and analysis of TCR and BCR V(D)J\nPCR amplification was done to enrich the full-length TCR/BCR V(D)J segments for the amplified cDNA from 5′ libraries with a Chromium Single-Cell V(D)J Enrichment kit (10 Genomics). The TCR/BCR sequences of each T/B cell were clustered using the CellRanger vdj pipeline (version 3.1.0, allowing identification of CDR3 sequence and the rearranged TCR/BCR gene. Analysis was performed using Loupe V(D)J Browser version 2.0.1 (https://support.10xgenomics.com, 10x Genomics). In summary, barcode information a containing clonotype frequency and TCR/BCR diversity metric were obtained. We projected T /B cells with dominant TCR/BCR clonotypes on a t-SNE plot using barcode information (Wen et al., 2020)."}