PMC:7402624 / 64080-65577 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T520","span":{"begin":0,"end":8},"obj":"Body_part"},{"id":"T521","span":{"begin":160,"end":168},"obj":"Body_part"},{"id":"T522","span":{"begin":460,"end":469},"obj":"Body_part"},{"id":"T523","span":{"begin":753,"end":761},"obj":"Body_part"},{"id":"T524","span":{"begin":1342,"end":1351},"obj":"Body_part"}],"attributes":[{"id":"A520","pred":"fma_id","subj":"T520","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A521","pred":"fma_id","subj":"T521","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A522","pred":"fma_id","subj":"T522","obj":"http://purl.org/sig/ont/fma/fma241981"},{"id":"A523","pred":"fma_id","subj":"T523","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A524","pred":"fma_id","subj":"T524","obj":"http://purl.org/sig/ont/fma/fma241981"}],"text":"Antibody panels and staining\nApproximately 1-5×106 freshly isolated PBMCs were used per patient per stain. See table S7 for buffer information and table S8 for antibody panel information. PBMCs were stained with live/dead mix (100 μl, 10 min, RT), washed with FACS buffer, and spun down (1500 rpm, 5 min, RT). PBMCs were incubated with 100 μl of Fc block (RT, 10 min) before a second wash (FACS buffer, 1500 rpm, 5 min, RT). Pellet was resuspended in 25 μl of chemokine receptor staining mix, and incubated at 37°C for 20 min. Following incubation, 25 μl of surface receptor staining mix was directly added and the PBMCs were incubated at RT for a further 45 min. PBMCs were washed (FACS buffer, 1500 rpm, 5 min, RT) and stained with 50 μl of secondary antibody mix for 20 min at RT, then washed again (FACS buffer, 1500 rpm, 5 min, RT). Samples were fixed and permeabilized by incubating in 100 μl of Fix/Perm buffer (RT, 30 min) and washed in Perm Buffer (1800 rpm, 5 min, RT). PBMCs were stained with 50μl of intracellular mix overnight at 4°C. The following morning, samples were washed (Perm Buffer, 1800 rpm, 5 min, RT) and further fixed in 50 μl of 4% PFA. Prior to acquisition, samples were diluted to 1% PFA and 10,000 counting beads added per sample (BD, Cat#335925). Live/dead mix was prepared in PBS. For the surface receptor and chemokine staining mix, antibodies were diluted in FACS buffer with 50% BD Brilliant Buffer (BD, Cat#566349). Intracellular mix was diluted in Perm Buffer."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1986","span":{"begin":88,"end":95},"obj":"Species"},{"id":"1987","span":{"begin":260,"end":271},"obj":"Chemical"},{"id":"1988","span":{"begin":1159,"end":1162},"obj":"Chemical"},{"id":"1989","span":{"begin":1213,"end":1216},"obj":"Chemical"},{"id":"1990","span":{"begin":1308,"end":1311},"obj":"Chemical"},{"id":"1991","span":{"begin":1414,"end":1433},"obj":"Chemical"}],"attributes":[{"id":"A1986","pred":"tao:has_database_id","subj":"1986","obj":"Tax:9606"},{"id":"A1990","pred":"tao:has_database_id","subj":"1990","obj":"MESH:D007854"}],"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":"Antibody panels and staining\nApproximately 1-5×106 freshly isolated PBMCs were used per patient per stain. See table S7 for buffer information and table S8 for antibody panel information. PBMCs were stained with live/dead mix (100 μl, 10 min, RT), washed with FACS buffer, and spun down (1500 rpm, 5 min, RT). PBMCs were incubated with 100 μl of Fc block (RT, 10 min) before a second wash (FACS buffer, 1500 rpm, 5 min, RT). Pellet was resuspended in 25 μl of chemokine receptor staining mix, and incubated at 37°C for 20 min. Following incubation, 25 μl of surface receptor staining mix was directly added and the PBMCs were incubated at RT for a further 45 min. PBMCs were washed (FACS buffer, 1500 rpm, 5 min, RT) and stained with 50 μl of secondary antibody mix for 20 min at RT, then washed again (FACS buffer, 1500 rpm, 5 min, RT). Samples were fixed and permeabilized by incubating in 100 μl of Fix/Perm buffer (RT, 30 min) and washed in Perm Buffer (1800 rpm, 5 min, RT). PBMCs were stained with 50μl of intracellular mix overnight at 4°C. The following morning, samples were washed (Perm Buffer, 1800 rpm, 5 min, RT) and further fixed in 50 μl of 4% PFA. Prior to acquisition, samples were diluted to 1% PFA and 10,000 counting beads added per sample (BD, Cat#335925). Live/dead mix was prepared in PBS. For the surface receptor and chemokine staining mix, antibodies were diluted in FACS buffer with 50% BD Brilliant Buffer (BD, Cat#566349). Intracellular mix was diluted in Perm Buffer."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T421","span":{"begin":260,"end":264},"obj":"Disease"},{"id":"T422","span":{"begin":390,"end":394},"obj":"Disease"},{"id":"T423","span":{"begin":683,"end":687},"obj":"Disease"},{"id":"T424","span":{"begin":803,"end":807},"obj":"Disease"},{"id":"T425","span":{"begin":1261,"end":1263},"obj":"Disease"},{"id":"T426","span":{"begin":1393,"end":1397},"obj":"Disease"},{"id":"T427","span":{"begin":1414,"end":1416},"obj":"Disease"},{"id":"T428","span":{"begin":1435,"end":1437},"obj":"Disease"}],"attributes":[{"id":"A421","pred":"mondo_id","subj":"T421","obj":"http://purl.obolibrary.org/obo/MONDO_0018262"},{"id":"A422","pred":"mondo_id","subj":"T422","obj":"http://purl.obolibrary.org/obo/MONDO_0018262"},{"id":"A423","pred":"mondo_id","subj":"T423","obj":"http://purl.obolibrary.org/obo/MONDO_0018262"},{"id":"A424","pred":"mondo_id","subj":"T424","obj":"http://purl.obolibrary.org/obo/MONDO_0018262"},{"id":"A425","pred":"mondo_id","subj":"T425","obj":"http://purl.obolibrary.org/obo/MONDO_0007191"},{"id":"A426","pred":"mondo_id","subj":"T426","obj":"http://purl.obolibrary.org/obo/MONDO_0018262"},{"id":"A427","pred":"mondo_id","subj":"T427","obj":"http://purl.obolibrary.org/obo/MONDO_0007191"},{"id":"A428","pred":"mondo_id","subj":"T428","obj":"http://purl.obolibrary.org/obo/MONDO_0007191"}],"text":"Antibody panels and staining\nApproximately 1-5×106 freshly isolated PBMCs were used per patient per stain. See table S7 for buffer information and table S8 for antibody panel information. PBMCs were stained with live/dead mix (100 μl, 10 min, RT), washed with FACS buffer, and spun down (1500 rpm, 5 min, RT). PBMCs were incubated with 100 μl of Fc block (RT, 10 min) before a second wash (FACS buffer, 1500 rpm, 5 min, RT). Pellet was resuspended in 25 μl of chemokine receptor staining mix, and incubated at 37°C for 20 min. Following incubation, 25 μl of surface receptor staining mix was directly added and the PBMCs were incubated at RT for a further 45 min. PBMCs were washed (FACS buffer, 1500 rpm, 5 min, RT) and stained with 50 μl of secondary antibody mix for 20 min at RT, then washed again (FACS buffer, 1500 rpm, 5 min, RT). Samples were fixed and permeabilized by incubating in 100 μl of Fix/Perm buffer (RT, 30 min) and washed in Perm Buffer (1800 rpm, 5 min, RT). PBMCs were stained with 50μl of intracellular mix overnight at 4°C. The following morning, samples were washed (Perm Buffer, 1800 rpm, 5 min, RT) and further fixed in 50 μl of 4% PFA. Prior to acquisition, samples were diluted to 1% PFA and 10,000 counting beads added per sample (BD, Cat#335925). Live/dead mix was prepared in PBS. For the surface receptor and chemokine staining mix, antibodies were diluted in FACS buffer with 50% BD Brilliant Buffer (BD, Cat#566349). Intracellular mix was diluted in Perm Buffer."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T953","span":{"begin":346,"end":348},"obj":"http://purl.obolibrary.org/obo/CLO_0052676"},{"id":"T954","span":{"begin":375,"end":376},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T955","span":{"begin":646,"end":647},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T956","span":{"begin":656,"end":658},"obj":"http://purl.obolibrary.org/obo/CLO_0053799"},{"id":"T957","span":{"begin":1043,"end":1046},"obj":"http://purl.obolibrary.org/obo/CLO_0001387"}],"text":"Antibody panels and staining\nApproximately 1-5×106 freshly isolated PBMCs were used per patient per stain. See table S7 for buffer information and table S8 for antibody panel information. PBMCs were stained with live/dead mix (100 μl, 10 min, RT), washed with FACS buffer, and spun down (1500 rpm, 5 min, RT). PBMCs were incubated with 100 μl of Fc block (RT, 10 min) before a second wash (FACS buffer, 1500 rpm, 5 min, RT). Pellet was resuspended in 25 μl of chemokine receptor staining mix, and incubated at 37°C for 20 min. Following incubation, 25 μl of surface receptor staining mix was directly added and the PBMCs were incubated at RT for a further 45 min. PBMCs were washed (FACS buffer, 1500 rpm, 5 min, RT) and stained with 50 μl of secondary antibody mix for 20 min at RT, then washed again (FACS buffer, 1500 rpm, 5 min, RT). Samples were fixed and permeabilized by incubating in 100 μl of Fix/Perm buffer (RT, 30 min) and washed in Perm Buffer (1800 rpm, 5 min, RT). PBMCs were stained with 50μl of intracellular mix overnight at 4°C. The following morning, samples were washed (Perm Buffer, 1800 rpm, 5 min, RT) and further fixed in 50 μl of 4% PFA. Prior to acquisition, samples were diluted to 1% PFA and 10,000 counting beads added per sample (BD, Cat#335925). Live/dead mix was prepared in PBS. For the surface receptor and chemokine staining mix, antibodies were diluted in FACS buffer with 50% BD Brilliant Buffer (BD, Cat#566349). Intracellular mix was diluted in Perm Buffer."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T83633","span":{"begin":124,"end":130},"obj":"Chemical"},{"id":"T45213","span":{"begin":153,"end":155},"obj":"Chemical"},{"id":"T6104","span":{"begin":265,"end":271},"obj":"Chemical"},{"id":"T38115","span":{"begin":395,"end":401},"obj":"Chemical"},{"id":"T13410","span":{"begin":688,"end":694},"obj":"Chemical"},{"id":"T22243","span":{"begin":808,"end":814},"obj":"Chemical"},{"id":"T74159","span":{"begin":911,"end":917},"obj":"Chemical"},{"id":"T86249","span":{"begin":1159,"end":1162},"obj":"Chemical"},{"id":"T30642","span":{"begin":1213,"end":1216},"obj":"Chemical"},{"id":"T40902","span":{"begin":1398,"end":1404},"obj":"Chemical"}],"attributes":[{"id":"A70653","pred":"chebi_id","subj":"T83633","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A87218","pred":"chebi_id","subj":"T45213","obj":"http://purl.obolibrary.org/obo/CHEBI_29385"},{"id":"A48005","pred":"chebi_id","subj":"T6104","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A14730","pred":"chebi_id","subj":"T38115","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A80678","pred":"chebi_id","subj":"T13410","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A58972","pred":"chebi_id","subj":"T22243","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A78767","pred":"chebi_id","subj":"T74159","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A51827","pred":"chebi_id","subj":"T86249","obj":"http://purl.obolibrary.org/obo/CHEBI_53371"},{"id":"A15021","pred":"chebi_id","subj":"T86249","obj":"http://purl.obolibrary.org/obo/CHEBI_60594"},{"id":"A5657","pred":"chebi_id","subj":"T30642","obj":"http://purl.obolibrary.org/obo/CHEBI_53371"},{"id":"A39647","pred":"chebi_id","subj":"T30642","obj":"http://purl.obolibrary.org/obo/CHEBI_60594"},{"id":"A21827","pred":"chebi_id","subj":"T40902","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"}],"text":"Antibody panels and staining\nApproximately 1-5×106 freshly isolated PBMCs were used per patient per stain. See table S7 for buffer information and table S8 for antibody panel information. PBMCs were stained with live/dead mix (100 μl, 10 min, RT), washed with FACS buffer, and spun down (1500 rpm, 5 min, RT). PBMCs were incubated with 100 μl of Fc block (RT, 10 min) before a second wash (FACS buffer, 1500 rpm, 5 min, RT). Pellet was resuspended in 25 μl of chemokine receptor staining mix, and incubated at 37°C for 20 min. Following incubation, 25 μl of surface receptor staining mix was directly added and the PBMCs were incubated at RT for a further 45 min. PBMCs were washed (FACS buffer, 1500 rpm, 5 min, RT) and stained with 50 μl of secondary antibody mix for 20 min at RT, then washed again (FACS buffer, 1500 rpm, 5 min, RT). Samples were fixed and permeabilized by incubating in 100 μl of Fix/Perm buffer (RT, 30 min) and washed in Perm Buffer (1800 rpm, 5 min, RT). PBMCs were stained with 50μl of intracellular mix overnight at 4°C. The following morning, samples were washed (Perm Buffer, 1800 rpm, 5 min, RT) and further fixed in 50 μl of 4% PFA. Prior to acquisition, samples were diluted to 1% PFA and 10,000 counting beads added per sample (BD, Cat#335925). Live/dead mix was prepared in PBS. For the surface receptor and chemokine staining mix, antibodies were diluted in FACS buffer with 50% BD Brilliant Buffer (BD, Cat#566349). Intracellular mix was diluted in Perm Buffer."}

{"project":"LitCovid-sentences","denotations":[{"id":"T379","span":{"begin":0,"end":28},"obj":"Sentence"},{"id":"T380","span":{"begin":29,"end":106},"obj":"Sentence"},{"id":"T381","span":{"begin":107,"end":187},"obj":"Sentence"},{"id":"T382","span":{"begin":188,"end":309},"obj":"Sentence"},{"id":"T383","span":{"begin":310,"end":424},"obj":"Sentence"},{"id":"T384","span":{"begin":425,"end":526},"obj":"Sentence"},{"id":"T385","span":{"begin":527,"end":663},"obj":"Sentence"},{"id":"T386","span":{"begin":664,"end":837},"obj":"Sentence"},{"id":"T387","span":{"begin":838,"end":979},"obj":"Sentence"},{"id":"T388","span":{"begin":980,"end":1047},"obj":"Sentence"},{"id":"T389","span":{"begin":1048,"end":1163},"obj":"Sentence"},{"id":"T390","span":{"begin":1164,"end":1277},"obj":"Sentence"},{"id":"T391","span":{"begin":1278,"end":1312},"obj":"Sentence"},{"id":"T392","span":{"begin":1313,"end":1451},"obj":"Sentence"},{"id":"T393","span":{"begin":1452,"end":1497},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Antibody panels and staining\nApproximately 1-5×106 freshly isolated PBMCs were used per patient per stain. See table S7 for buffer information and table S8 for antibody panel information. PBMCs were stained with live/dead mix (100 μl, 10 min, RT), washed with FACS buffer, and spun down (1500 rpm, 5 min, RT). PBMCs were incubated with 100 μl of Fc block (RT, 10 min) before a second wash (FACS buffer, 1500 rpm, 5 min, RT). Pellet was resuspended in 25 μl of chemokine receptor staining mix, and incubated at 37°C for 20 min. Following incubation, 25 μl of surface receptor staining mix was directly added and the PBMCs were incubated at RT for a further 45 min. PBMCs were washed (FACS buffer, 1500 rpm, 5 min, RT) and stained with 50 μl of secondary antibody mix for 20 min at RT, then washed again (FACS buffer, 1500 rpm, 5 min, RT). Samples were fixed and permeabilized by incubating in 100 μl of Fix/Perm buffer (RT, 30 min) and washed in Perm Buffer (1800 rpm, 5 min, RT). PBMCs were stained with 50μl of intracellular mix overnight at 4°C. The following morning, samples were washed (Perm Buffer, 1800 rpm, 5 min, RT) and further fixed in 50 μl of 4% PFA. Prior to acquisition, samples were diluted to 1% PFA and 10,000 counting beads added per sample (BD, Cat#335925). Live/dead mix was prepared in PBS. For the surface receptor and chemokine staining mix, antibodies were diluted in FACS buffer with 50% BD Brilliant Buffer (BD, Cat#566349). Intracellular mix was diluted in Perm Buffer."}