PMC:7321036 / 7017-7878 JSONTXT

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T150","span":{"begin":4,"end":8},"obj":"CL_6"},{"id":"T151","span":{"begin":37,"end":47},"obj":"SP_7"},{"id":"T152","span":{"begin":72,"end":77},"obj":"NCBITaxon:10239"},{"id":"T153","span":{"begin":173,"end":177},"obj":"CL_6"},{"id":"T154","span":{"begin":386,"end":391},"obj":"GO:0019835"},{"id":"T155","span":{"begin":837,"end":842},"obj":"SP_6;NCBITaxon:9606"},{"id":"T156","span":{"begin":851,"end":860},"obj":"SO:0000855"}],"text":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T39940","span":{"begin":12,"end":17},"obj":"Body_part"},{"id":"T68158","span":{"begin":86,"end":91},"obj":"Body_part"},{"id":"T52662","span":{"begin":181,"end":186},"obj":"Body_part"},{"id":"T6256","span":{"begin":361,"end":365},"obj":"Body_part"},{"id":"T95345","span":{"begin":375,"end":380},"obj":"Body_part"},{"id":"T75308","span":{"begin":397,"end":405},"obj":"Body_part"},{"id":"T16865","span":{"begin":521,"end":528},"obj":"Body_part"},{"id":"T73440","span":{"begin":785,"end":792},"obj":"Body_part"},{"id":"T71250","span":{"begin":843,"end":850},"obj":"Body_part"}],"attributes":[{"id":"A14844","pred":"fma_id","subj":"T39940","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A99461","pred":"fma_id","subj":"T68158","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A60112","pred":"fma_id","subj":"T52662","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A87542","pred":"fma_id","subj":"T6256","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A59030","pred":"fma_id","subj":"T95345","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A28782","pred":"fma_id","subj":"T75308","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A90019","pred":"fma_id","subj":"T16865","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A75548","pred":"fma_id","subj":"T73440","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A89460","pred":"fma_id","subj":"T71250","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T62","span":{"begin":37,"end":45},"obj":"Disease"},{"id":"T63","span":{"begin":284,"end":293},"obj":"Disease"},{"id":"T64","span":{"begin":544,"end":553},"obj":"Disease"},{"id":"T65","span":{"begin":702,"end":705},"obj":"Disease"}],"attributes":[{"id":"A62","pred":"mondo_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A63","pred":"mondo_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A64","pred":"mondo_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A65","pred":"mondo_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/MONDO_0022963"}],"text":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T71578","span":{"begin":1,"end":2},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T69924","span":{"begin":4,"end":17},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T67115","span":{"begin":86,"end":91},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3201","span":{"begin":140,"end":144},"obj":"http://purl.obolibrary.org/obo/CLO_0001382"},{"id":"T66033","span":{"begin":162,"end":163},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T14454","span":{"begin":173,"end":186},"obj":"http://purl.obolibrary.org/obo/CLO_0051719"},{"id":"T7941","span":{"begin":361,"end":365},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T78869","span":{"begin":375,"end":380},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T14567","span":{"begin":425,"end":433},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T22339","span":{"begin":495,"end":497},"obj":"http://purl.obolibrary.org/obo/CLO_0007874"},{"id":"T38966","span":{"begin":616,"end":624},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T47323","span":{"begin":689,"end":698},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T20014","span":{"begin":700,"end":701},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1296","span":{"begin":732,"end":734},"obj":"http://purl.obolibrary.org/obo/CLO_0007874"},{"id":"T57282","span":{"begin":837,"end":850},"obj":"http://purl.obolibrary.org/obo/PR_000029067"}],"text":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T29","span":{"begin":397,"end":405},"obj":"Chemical"},{"id":"T30","span":{"begin":425,"end":433},"obj":"Chemical"},{"id":"T31","span":{"begin":495,"end":497},"obj":"Chemical"},{"id":"T32","span":{"begin":521,"end":528},"obj":"Chemical"},{"id":"T33","span":{"begin":616,"end":624},"obj":"Chemical"},{"id":"T34","span":{"begin":732,"end":734},"obj":"Chemical"},{"id":"T35","span":{"begin":785,"end":792},"obj":"Chemical"},{"id":"T36","span":{"begin":843,"end":850},"obj":"Chemical"}],"attributes":[{"id":"A29","pred":"chebi_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A30","pred":"chebi_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A31","pred":"chebi_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/CHEBI_73613"},{"id":"A32","pred":"chebi_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A33","pred":"chebi_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A34","pred":"chebi_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/CHEBI_73613"},{"id":"A35","pred":"chebi_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A36","pred":"chebi_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T60087","span":{"begin":78,"end":84},"obj":"http://purl.obolibrary.org/obo/GO_0098739"},{"id":"T26491","span":{"begin":78,"end":84},"obj":"http://purl.obolibrary.org/obo/GO_0098657"},{"id":"T13196","span":{"begin":673,"end":688},"obj":"http://purl.obolibrary.org/obo/GO_0016310"},{"id":"T28719","span":{"begin":689,"end":698},"obj":"http://purl.obolibrary.org/obo/GO_0023052"},{"id":"T63425","span":{"begin":759,"end":774},"obj":"http://purl.obolibrary.org/obo/GO_0016310"}],"text":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}

{"project":"LitCovid-PubTator","denotations":[{"id":"147","span":{"begin":37,"end":47},"obj":"Species"},{"id":"148","span":{"begin":837,"end":842},"obj":"Species"},{"id":"149","span":{"begin":616,"end":624},"obj":"Chemical"},{"id":"150","span":{"begin":23,"end":31},"obj":"Disease"},{"id":"151","span":{"begin":202,"end":210},"obj":"Disease"},{"id":"152","span":{"begin":284,"end":293},"obj":"Disease"},{"id":"153","span":{"begin":544,"end":553},"obj":"Disease"},{"id":"154","span":{"begin":9,"end":11},"obj":"CellLine"},{"id":"155","span":{"begin":178,"end":180},"obj":"CellLine"}],"attributes":[{"id":"A147","pred":"tao:has_database_id","subj":"147","obj":"Tax:2697049"},{"id":"A148","pred":"tao:has_database_id","subj":"148","obj":"Tax:9606"},{"id":"A149","pred":"tao:has_database_id","subj":"149","obj":"MESH:D010455"},{"id":"A150","pred":"tao:has_database_id","subj":"150","obj":"MESH:D007239"},{"id":"A151","pred":"tao:has_database_id","subj":"151","obj":"MESH:D007239"},{"id":"A152","pred":"tao:has_database_id","subj":"152","obj":"MESH:D007239"},{"id":"A153","pred":"tao:has_database_id","subj":"153","obj":"MESH:D007239"},{"id":"A154","pred":"tao:has_database_id","subj":"154","obj":"CVCL:4582"},{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"CVCL:4582"}],"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":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}

{"project":"LitCovid-sentences","denotations":[{"id":"T44","span":{"begin":0,"end":58},"obj":"Sentence"},{"id":"T45","span":{"begin":59,"end":158},"obj":"Sentence"},{"id":"T46","span":{"begin":159,"end":294},"obj":"Sentence"},{"id":"T47","span":{"begin":295,"end":350},"obj":"Sentence"},{"id":"T48","span":{"begin":351,"end":434},"obj":"Sentence"},{"id":"T49","span":{"begin":435,"end":699},"obj":"Sentence"},{"id":"T50","span":{"begin":700,"end":748},"obj":"Sentence"},{"id":"T51","span":{"begin":749,"end":861},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"(A) Vero E6 cells were infected with SARS-CoV-2 (MOI 1.0). After 1 h of viral uptake, cells were harvested (0 h) or, subsequently, after 2, 4, 8, 12, or 24 h. As a control, Vero E6 cells were also mock infected for 1 h and harvested immediately thereafter (0 h) or after 24 h of mock infection. All conditions were performed in biological triplicate. Following cell harvest, cells were lysed, and proteins were digested into peptides. Aliquots of all samples were analyzed by mass spectrometry (MS) to measure changes in protein abundance upon infection, whereas the remaining sample was enriched for phosphorylated peptides and subsequently analyzed to measure changes in phosphorylation signaling. A DIA approach was used for all MS acquisitions. Last, all phosphorylation sites and protein identifiers were mapped to their respective human protein orthologs."}