PMC:7417788 / 72390-73294 JSONTXT

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T1506","span":{"begin":674,"end":678},"obj":"PR:000001006"}],"text":"Mass cytometry processing and quality control\nCyTOF data were acquired with a CyTOF2 system using a SuperSampler fluidics system (Victorian Airships) at an event rate of \u003c 400 events per second and normalized with Helios normalizer software (Fluidigm version 6.7.1016). Acquisitions from different days (three independent acquisitions were performed) were normalized using five-element beads (Fluidigm). Barcoded samples were deconvoluted and cross-sample doublets were filtered using cytobank application. CyTOF data was pre-processed with Cytobank (https://mtsinai.cytobank.org; Cytobank, 7.0) to sequentially remove calibration beads, dead cells, debris and barcodes for CD45+ PBMCs based on event length, DNA (191Ir and 193Ir) and live cell (195Pt) channels and then export the FCS files. We analyzed 200,000 PBMCs in cohort-1 and 160,000 PBMC in cohort-2, with an average of 20,000 cells per sample."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T537","span":{"begin":643,"end":648},"obj":"Body_part"},{"id":"T538","span":{"begin":709,"end":712},"obj":"Body_part"},{"id":"T539","span":{"begin":740,"end":744},"obj":"Body_part"},{"id":"T540","span":{"begin":887,"end":892},"obj":"Body_part"}],"attributes":[{"id":"A537","pred":"fma_id","subj":"T537","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A538","pred":"fma_id","subj":"T538","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A539","pred":"fma_id","subj":"T539","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A540","pred":"fma_id","subj":"T540","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Mass cytometry processing and quality control\nCyTOF data were acquired with a CyTOF2 system using a SuperSampler fluidics system (Victorian Airships) at an event rate of \u003c 400 events per second and normalized with Helios normalizer software (Fluidigm version 6.7.1016). Acquisitions from different days (three independent acquisitions were performed) were normalized using five-element beads (Fluidigm). Barcoded samples were deconvoluted and cross-sample doublets were filtered using cytobank application. CyTOF data was pre-processed with Cytobank (https://mtsinai.cytobank.org; Cytobank, 7.0) to sequentially remove calibration beads, dead cells, debris and barcodes for CD45+ PBMCs based on event length, DNA (191Ir and 193Ir) and live cell (195Pt) channels and then export the FCS files. We analyzed 200,000 PBMCs in cohort-1 and 160,000 PBMC in cohort-2, with an average of 20,000 cells per sample."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1181","span":{"begin":76,"end":77},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1182","span":{"begin":98,"end":99},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1183","span":{"begin":643,"end":648},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1184","span":{"begin":740,"end":744},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1185","span":{"begin":887,"end":892},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Mass cytometry processing and quality control\nCyTOF data were acquired with a CyTOF2 system using a SuperSampler fluidics system (Victorian Airships) at an event rate of \u003c 400 events per second and normalized with Helios normalizer software (Fluidigm version 6.7.1016). Acquisitions from different days (three independent acquisitions were performed) were normalized using five-element beads (Fluidigm). Barcoded samples were deconvoluted and cross-sample doublets were filtered using cytobank application. CyTOF data was pre-processed with Cytobank (https://mtsinai.cytobank.org; Cytobank, 7.0) to sequentially remove calibration beads, dead cells, debris and barcodes for CD45+ PBMCs based on event length, DNA (191Ir and 193Ir) and live cell (195Pt) channels and then export the FCS files. We analyzed 200,000 PBMCs in cohort-1 and 160,000 PBMC in cohort-2, with an average of 20,000 cells per sample."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T53634","span":{"begin":494,"end":505},"obj":"Chemical"},{"id":"T52481","span":{"begin":709,"end":712},"obj":"Chemical"}],"attributes":[{"id":"A67093","pred":"chebi_id","subj":"T53634","obj":"http://purl.obolibrary.org/obo/CHEBI_33232"},{"id":"A16224","pred":"chebi_id","subj":"T52481","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"}],"text":"Mass cytometry processing and quality control\nCyTOF data were acquired with a CyTOF2 system using a SuperSampler fluidics system (Victorian Airships) at an event rate of \u003c 400 events per second and normalized with Helios normalizer software (Fluidigm version 6.7.1016). Acquisitions from different days (three independent acquisitions were performed) were normalized using five-element beads (Fluidigm). Barcoded samples were deconvoluted and cross-sample doublets were filtered using cytobank application. CyTOF data was pre-processed with Cytobank (https://mtsinai.cytobank.org; Cytobank, 7.0) to sequentially remove calibration beads, dead cells, debris and barcodes for CD45+ PBMCs based on event length, DNA (191Ir and 193Ir) and live cell (195Pt) channels and then export the FCS files. We analyzed 200,000 PBMCs in cohort-1 and 160,000 PBMC in cohort-2, with an average of 20,000 cells per sample."}

{"project":"LitCovid-sentences","denotations":[{"id":"T405","span":{"begin":0,"end":45},"obj":"Sentence"},{"id":"T406","span":{"begin":46,"end":269},"obj":"Sentence"},{"id":"T407","span":{"begin":270,"end":403},"obj":"Sentence"},{"id":"T408","span":{"begin":404,"end":506},"obj":"Sentence"},{"id":"T409","span":{"begin":507,"end":792},"obj":"Sentence"},{"id":"T410","span":{"begin":793,"end":904},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Mass cytometry processing and quality control\nCyTOF data were acquired with a CyTOF2 system using a SuperSampler fluidics system (Victorian Airships) at an event rate of \u003c 400 events per second and normalized with Helios normalizer software (Fluidigm version 6.7.1016). Acquisitions from different days (three independent acquisitions were performed) were normalized using five-element beads (Fluidigm). Barcoded samples were deconvoluted and cross-sample doublets were filtered using cytobank application. CyTOF data was pre-processed with Cytobank (https://mtsinai.cytobank.org; Cytobank, 7.0) to sequentially remove calibration beads, dead cells, debris and barcodes for CD45+ PBMCs based on event length, DNA (191Ir and 193Ir) and live cell (195Pt) channels and then export the FCS files. We analyzed 200,000 PBMCs in cohort-1 and 160,000 PBMC in cohort-2, with an average of 20,000 cells per sample."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1496","span":{"begin":674,"end":678},"obj":"Gene"},{"id":"1497","span":{"begin":214,"end":220},"obj":"Gene"}],"attributes":[{"id":"A1496","pred":"tao:has_database_id","subj":"1496","obj":"Gene:5788"},{"id":"A1497","pred":"tao:has_database_id","subj":"1497","obj":"Gene:22807"}],"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":"Mass cytometry processing and quality control\nCyTOF data were acquired with a CyTOF2 system using a SuperSampler fluidics system (Victorian Airships) at an event rate of \u003c 400 events per second and normalized with Helios normalizer software (Fluidigm version 6.7.1016). Acquisitions from different days (three independent acquisitions were performed) were normalized using five-element beads (Fluidigm). Barcoded samples were deconvoluted and cross-sample doublets were filtered using cytobank application. CyTOF data was pre-processed with Cytobank (https://mtsinai.cytobank.org; Cytobank, 7.0) to sequentially remove calibration beads, dead cells, debris and barcodes for CD45+ PBMCs based on event length, DNA (191Ir and 193Ir) and live cell (195Pt) channels and then export the FCS files. We analyzed 200,000 PBMCs in cohort-1 and 160,000 PBMC in cohort-2, with an average of 20,000 cells per sample."}