PMC:7252096 / 89745-90460 JSONTXT

Annnotations TAB JSON ListView MergeView

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7252096","sourcedb":"PMC","sourceid":"7252096","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7252096","text":"Human Ileum\nSingle-cell suspensions were collected from biopsies as described (Smillie et al., 2019). Briefly, biopsies were rinsed in cold PBS, the epithelial layer was separated from the underlying lamina propria by end over end rotation for 15 min. The lamina propria and epithelial fractions were digested separately, using Liberase TM (Roche) and DNase I (Roche) for the lamina propria, and TrypLE (ThermoFisher) for the epithelial fraction. Following digestion, cells were pelleted by centrifugation, subjected to ACK lysis for 3 min, and filtered through a 40 μm strainer. Following centrifugation, the cells were counted and prepared as a single cell suspension for scRNA-seq using 10X 3′ v2 (10X Genomics).","divisions":[{"label":"title","span":{"begin":0,"end":11}}],"tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1015","span":{"begin":6,"end":11},"obj":"Body_part"},{"id":"T1016","span":{"begin":19,"end":23},"obj":"Body_part"},{"id":"T1017","span":{"begin":200,"end":214},"obj":"Body_part"},{"id":"T1018","span":{"begin":256,"end":270},"obj":"Body_part"},{"id":"T1019","span":{"begin":376,"end":390},"obj":"Body_part"},{"id":"T1020","span":{"begin":468,"end":473},"obj":"Body_part"},{"id":"T1021","span":{"begin":610,"end":615},"obj":"Body_part"},{"id":"T1022","span":{"begin":654,"end":658},"obj":"Body_part"},{"id":"T1023","span":{"begin":697,"end":699},"obj":"Body_part"}],"attributes":[{"id":"A1015","pred":"fma_id","subj":"T1015","obj":"http://purl.org/sig/ont/fma/fma7208"},{"id":"A1016","pred":"fma_id","subj":"T1016","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A1017","pred":"fma_id","subj":"T1017","obj":"http://purl.org/sig/ont/fma/fma62517"},{"id":"A1018","pred":"fma_id","subj":"T1018","obj":"http://purl.org/sig/ont/fma/fma62517"},{"id":"A1019","pred":"fma_id","subj":"T1019","obj":"http://purl.org/sig/ont/fma/fma62517"},{"id":"A1020","pred":"fma_id","subj":"T1020","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A1021","pred":"fma_id","subj":"T1021","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A1022","pred":"fma_id","subj":"T1022","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A1023","pred":"fma_id","subj":"T1023","obj":"http://purl.org/sig/ont/fma/fma13443"},{"id":"A1024","pred":"fma_id","subj":"T1023","obj":"http://purl.org/sig/ont/fma/fma68615"},{"subj":"T1015","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1016","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1017","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1018","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1019","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1020","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1021","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1022","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T1023","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T208","span":{"begin":6,"end":11},"obj":"Body_part"},{"id":"T209","span":{"begin":200,"end":214},"obj":"Body_part"},{"id":"T210","span":{"begin":200,"end":206},"obj":"Body_part"},{"id":"T211","span":{"begin":256,"end":270},"obj":"Body_part"},{"id":"T212","span":{"begin":256,"end":262},"obj":"Body_part"},{"id":"T213","span":{"begin":376,"end":390},"obj":"Body_part"},{"id":"T214","span":{"begin":376,"end":382},"obj":"Body_part"}],"attributes":[{"id":"A208","pred":"uberon_id","subj":"T208","obj":"http://purl.obolibrary.org/obo/UBERON_0002116"},{"id":"A209","pred":"uberon_id","subj":"T209","obj":"http://purl.obolibrary.org/obo/UBERON_0000030"},{"id":"A210","pred":"uberon_id","subj":"T210","obj":"http://purl.obolibrary.org/obo/UBERON_0000957"},{"id":"A211","pred":"uberon_id","subj":"T211","obj":"http://purl.obolibrary.org/obo/UBERON_0000030"},{"id":"A212","pred":"uberon_id","subj":"T212","obj":"http://purl.obolibrary.org/obo/UBERON_0000957"},{"id":"A213","pred":"uberon_id","subj":"T213","obj":"http://purl.obolibrary.org/obo/UBERON_0000030"},{"id":"A214","pred":"uberon_id","subj":"T214","obj":"http://purl.obolibrary.org/obo/UBERON_0000957"},{"subj":"T208","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T209","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T210","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T211","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T212","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T213","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T214","pred":"source","obj":"LitCovid-PD-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T1491","span":{"begin":0,"end":5},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T1492","span":{"begin":6,"end":11},"obj":"http://purl.obolibrary.org/obo/UBERON_0002116"},{"id":"T1493","span":{"begin":19,"end":23},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1494","span":{"begin":149,"end":159},"obj":"http://purl.obolibrary.org/obo/CL_0000066"},{"id":"T1495","span":{"begin":275,"end":285},"obj":"http://purl.obolibrary.org/obo/CL_0000066"},{"id":"T1496","span":{"begin":426,"end":436},"obj":"http://purl.obolibrary.org/obo/CL_0000066"},{"id":"T1497","span":{"begin":468,"end":473},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1498","span":{"begin":562,"end":563},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1499","span":{"begin":610,"end":615},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T1500","span":{"begin":645,"end":646},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T1501","span":{"begin":654,"end":658},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"attributes":[{"subj":"T1491","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1492","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1493","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1494","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1495","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1496","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1497","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1498","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1499","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1500","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T1501","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T15583","span":{"begin":337,"end":339},"obj":"Chemical"}],"attributes":[{"id":"A87704","pred":"chebi_id","subj":"T15583","obj":"http://purl.obolibrary.org/obo/CHEBI_55460"},{"id":"A89741","pred":"chebi_id","subj":"T15583","obj":"http://purl.obolibrary.org/obo/CHEBI_74861"},{"subj":"T15583","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T60","span":{"begin":352,"end":359},"obj":"http://purl.obolibrary.org/obo/GO_0004530"},{"id":"T61","span":{"begin":457,"end":466},"obj":"http://purl.obolibrary.org/obo/GO_0007586"},{"id":"T62","span":{"begin":524,"end":529},"obj":"http://purl.obolibrary.org/obo/GO_0019835"}],"attributes":[{"subj":"T60","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T61","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T62","pred":"source","obj":"LitCovid-PD-GO-BP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T638","span":{"begin":0,"end":11},"obj":"Sentence"},{"id":"T639","span":{"begin":12,"end":101},"obj":"Sentence"},{"id":"T640","span":{"begin":102,"end":251},"obj":"Sentence"},{"id":"T641","span":{"begin":252,"end":446},"obj":"Sentence"},{"id":"T642","span":{"begin":447,"end":579},"obj":"Sentence"},{"id":"T643","span":{"begin":580,"end":715},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T638","pred":"source","obj":"LitCovid-sentences"},{"subj":"T639","pred":"source","obj":"LitCovid-sentences"},{"subj":"T640","pred":"source","obj":"LitCovid-sentences"},{"subj":"T641","pred":"source","obj":"LitCovid-sentences"},{"subj":"T642","pred":"source","obj":"LitCovid-sentences"},{"subj":"T643","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"2475","span":{"begin":0,"end":5},"obj":"Species"},{"id":"2478","span":{"begin":520,"end":523},"obj":"Gene"},{"id":"2479","span":{"begin":135,"end":143},"obj":"Disease"}],"attributes":[{"id":"A2475","pred":"tao:has_database_id","subj":"2475","obj":"Tax:9606"},{"id":"A2478","pred":"tao:has_database_id","subj":"2478","obj":"Gene:10188"},{"id":"A2479","pred":"tao:has_database_id","subj":"2479","obj":"MESH:D011535"},{"subj":"2475","pred":"source","obj":"LitCovid-PubTator"},{"subj":"2478","pred":"source","obj":"LitCovid-PubTator"},{"subj":"2479","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#ec939f","default":true},{"id":"LitCovid-PD-UBERON","color":"#93b9ec"},{"id":"LitCovid-PD-CLO","color":"#d3ec93"},{"id":"LitCovid-PD-CHEBI","color":"#eb93ec"},{"id":"LitCovid-PD-GO-BP","color":"#93ecd1"},{"id":"LitCovid-sentences","color":"#ecb793"},{"id":"LitCovid-PubTator","color":"#9d93ec"}]}]}}