PMC:7640975 / 17407-19151
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7640975","sourcedb":"PMC","sourceid":"7640975","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7640975","text":"To verify the DEPs identified by iTRAQ at the transcriptional level, the mRNA of two representative DEPs, the downregulated ANAPC7 and the upregulated IFIT1, were detected by qPCR. Total cellular RNA of both PDCoV- and mock-infected IPEC-J2 cells was extracted using the TaKaRa MiniBEST universal RNA extraction kit (Dalian, China). The first strand cDNA was synthesized using 2 μg of cellular RNA and with a RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific) following the manufacturer’s instructions. The qPCR assays were conducted using a TaKaRa SYBR Premix Ex Taq kit on an ABI 7500 real-time PCR machine along with β-actin as a housekeeping gene. The primers used for the qPCR assay were designed based on the NCBI reference sequences for ANAPC7, IFIT1 and β-actin genes under GenBank accession numbers NM_016238, HQ679904 and NM_001101, respectively. The information for the designed primers was as following: ANAPC7 (Forward: 5′-CTTTGCTGAGGAACGCACTG-3′, Reverse: 5′-TCCATGTCGTCCACATCCTC-3′); IFIT1 (Forward: 5′-GAAGATTTAACCCAACAAGAACATA-3′, Reverse: 5′-CTTTCGATACGTAAGGTAATACAGC-3′); β-actin (Forward: 5′-TCCCTGGAGAAGAGCTACGA-3′, Reverse: 5′-AGCACTGTGTTGGCGTACAG-3′). The qPCR assays were carried out in a 20-μL reaction volume comprised 10 μL of TaKaRa SYBR Premix Ex Taq, 0.4 μL of each forward and reverse primer (10 μM), 7.2 μL of nuclease-free water, and 2 μL of template. The qPCR amplifications were carried out using a thermal profile with an initial step at 95 °C for 2 min, followed by 40 cycles of 95 °C for 10 s, 60 °C for 10 s (for ANAPC7 and β-actin) or 55 °C for 10 s (for IFIT1) and 72 °C for 40 s. Fold-change values were calculated in term of the 2–ΔΔCt method and normalized to the β-actin reference gene.33","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T114","span":{"begin":73,"end":77},"obj":"Body_part"},{"id":"T115","span":{"begin":196,"end":199},"obj":"Body_part"},{"id":"T116","span":{"begin":241,"end":246},"obj":"Body_part"},{"id":"T117","span":{"begin":297,"end":300},"obj":"Body_part"},{"id":"T118","span":{"begin":394,"end":397},"obj":"Body_part"},{"id":"T119","span":{"begin":633,"end":638},"obj":"Body_part"},{"id":"T120","span":{"begin":657,"end":661},"obj":"Body_part"},{"id":"T121","span":{"begin":775,"end":780},"obj":"Body_part"},{"id":"T122","span":{"begin":1104,"end":1109},"obj":"Body_part"},{"id":"T123","span":{"begin":1576,"end":1581},"obj":"Body_part"},{"id":"T124","span":{"begin":1721,"end":1726},"obj":"Body_part"},{"id":"T125","span":{"begin":1737,"end":1741},"obj":"Body_part"}],"attributes":[{"id":"A114","pred":"fma_id","subj":"T114","obj":"http://purl.org/sig/ont/fma/fma67122"},{"id":"A115","pred":"fma_id","subj":"T115","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A116","pred":"fma_id","subj":"T116","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A117","pred":"fma_id","subj":"T117","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A118","pred":"fma_id","subj":"T118","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma67843"},{"id":"A120","pred":"fma_id","subj":"T120","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A121","pred":"fma_id","subj":"T121","obj":"http://purl.org/sig/ont/fma/fma67843"},{"id":"A122","pred":"fma_id","subj":"T122","obj":"http://purl.org/sig/ont/fma/fma67843"},{"id":"A123","pred":"fma_id","subj":"T123","obj":"http://purl.org/sig/ont/fma/fma67843"},{"id":"A124","pred":"fma_id","subj":"T124","obj":"http://purl.org/sig/ont/fma/fma67843"},{"id":"A125","pred":"fma_id","subj":"T125","obj":"http://purl.org/sig/ont/fma/fma74402"},{"subj":"T114","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T115","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T116","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T117","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T118","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T119","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T120","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T121","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T122","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T123","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T124","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T125","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T232","span":{"begin":241,"end":246},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T233","span":{"begin":407,"end":408},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T234","span":{"begin":551,"end":552},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T235","span":{"begin":642,"end":643},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T236","span":{"begin":657,"end":661},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T237","span":{"begin":781,"end":786},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T238","span":{"begin":1222,"end":1226},"obj":"http://purl.obolibrary.org/obo/CLO_0001564"},{"id":"T239","span":{"begin":1222,"end":1226},"obj":"http://purl.obolibrary.org/obo/CLO_0050194"},{"id":"T240","span":{"begin":1443,"end":1444},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T241","span":{"begin":1737,"end":1741},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"attributes":[{"subj":"T232","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T233","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T234","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T235","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T236","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T237","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T238","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T239","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T240","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T241","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T133","span":{"begin":1367,"end":1372},"obj":"Chemical"}],"attributes":[{"id":"A133","pred":"chebi_id","subj":"T133","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"subj":"T133","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T32","span":{"begin":46,"end":61},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T33","span":{"begin":437,"end":446},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"attributes":[{"subj":"T32","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T33","pred":"source","obj":"LitCovid-PD-GO-BP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T92","span":{"begin":0,"end":180},"obj":"Sentence"},{"id":"T93","span":{"begin":181,"end":332},"obj":"Sentence"},{"id":"T94","span":{"begin":333,"end":513},"obj":"Sentence"},{"id":"T95","span":{"begin":514,"end":662},"obj":"Sentence"},{"id":"T96","span":{"begin":663,"end":867},"obj":"Sentence"},{"id":"T97","span":{"begin":868,"end":943},"obj":"Sentence"},{"id":"T98","span":{"begin":944,"end":980},"obj":"Sentence"},{"id":"T99","span":{"begin":981,"end":1025},"obj":"Sentence"},{"id":"T100","span":{"begin":1026,"end":1067},"obj":"Sentence"},{"id":"T101","span":{"begin":1068,"end":1119},"obj":"Sentence"},{"id":"T102","span":{"begin":1120,"end":1156},"obj":"Sentence"},{"id":"T103","span":{"begin":1157,"end":1185},"obj":"Sentence"},{"id":"T104","span":{"begin":1186,"end":1395},"obj":"Sentence"},{"id":"T105","span":{"begin":1396,"end":1632},"obj":"Sentence"},{"id":"T106","span":{"begin":1633,"end":1744},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T92","pred":"source","obj":"LitCovid-sentences"},{"subj":"T93","pred":"source","obj":"LitCovid-sentences"},{"subj":"T94","pred":"source","obj":"LitCovid-sentences"},{"subj":"T95","pred":"source","obj":"LitCovid-sentences"},{"subj":"T96","pred":"source","obj":"LitCovid-sentences"},{"subj":"T97","pred":"source","obj":"LitCovid-sentences"},{"subj":"T98","pred":"source","obj":"LitCovid-sentences"},{"subj":"T99","pred":"source","obj":"LitCovid-sentences"},{"subj":"T100","pred":"source","obj":"LitCovid-sentences"},{"subj":"T101","pred":"source","obj":"LitCovid-sentences"},{"subj":"T102","pred":"source","obj":"LitCovid-sentences"},{"subj":"T103","pred":"source","obj":"LitCovid-sentences"},{"subj":"T104","pred":"source","obj":"LitCovid-sentences"},{"subj":"T105","pred":"source","obj":"LitCovid-sentences"},{"subj":"T106","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"293","span":{"begin":124,"end":130},"obj":"Gene"},{"id":"294","span":{"begin":151,"end":156},"obj":"Gene"},{"id":"295","span":{"begin":631,"end":638},"obj":"Gene"},{"id":"296","span":{"begin":755,"end":761},"obj":"Gene"},{"id":"297","span":{"begin":763,"end":768},"obj":"Gene"},{"id":"298","span":{"begin":773,"end":780},"obj":"Gene"},{"id":"299","span":{"begin":927,"end":933},"obj":"Gene"},{"id":"300","span":{"begin":1010,"end":1015},"obj":"Gene"},{"id":"301","span":{"begin":1102,"end":1109},"obj":"Gene"},{"id":"302","span":{"begin":1563,"end":1569},"obj":"Gene"},{"id":"303","span":{"begin":1574,"end":1581},"obj":"Gene"},{"id":"304","span":{"begin":1606,"end":1611},"obj":"Gene"},{"id":"305","span":{"begin":447,"end":450},"obj":"Gene"},{"id":"306","span":{"begin":579,"end":582},"obj":"Gene"},{"id":"307","span":{"begin":312,"end":315},"obj":"Gene"},{"id":"308","span":{"begin":1719,"end":1726},"obj":"Gene"},{"id":"309","span":{"begin":1367,"end":1372},"obj":"Chemical"},{"id":"310","span":{"begin":224,"end":232},"obj":"Disease"},{"id":"311","span":{"begin":233,"end":240},"obj":"CellLine"}],"attributes":[{"id":"A293","pred":"tao:has_database_id","subj":"293","obj":"Gene:51434"},{"id":"A294","pred":"tao:has_database_id","subj":"294","obj":"Gene:3434"},{"id":"A295","pred":"tao:has_database_id","subj":"295","obj":"Gene:728378"},{"id":"A296","pred":"tao:has_database_id","subj":"296","obj":"Gene:51434"},{"id":"A297","pred":"tao:has_database_id","subj":"297","obj":"Gene:3434"},{"id":"A298","pred":"tao:has_database_id","subj":"298","obj":"Gene:728378"},{"id":"A299","pred":"tao:has_database_id","subj":"299","obj":"Gene:51434"},{"id":"A300","pred":"tao:has_database_id","subj":"300","obj":"Gene:3434"},{"id":"A301","pred":"tao:has_database_id","subj":"301","obj":"Gene:728378"},{"id":"A302","pred":"tao:has_database_id","subj":"302","obj":"Gene:51434"},{"id":"A303","pred":"tao:has_database_id","subj":"303","obj":"Gene:728378"},{"id":"A304","pred":"tao:has_database_id","subj":"304","obj":"Gene:3434"},{"id":"A305","pred":"tao:has_database_id","subj":"305","obj":"Gene:396810"},{"id":"A306","pred":"tao:has_database_id","subj":"306","obj":"Gene:396810"},{"id":"A307","pred":"tao:has_database_id","subj":"307","obj":"Gene:396810"},{"id":"A308","pred":"tao:has_database_id","subj":"308","obj":"Gene:728378"},{"id":"A309","pred":"tao:has_database_id","subj":"309","obj":"MESH:D014867"},{"id":"A310","pred":"tao:has_database_id","subj":"310","obj":"MESH:D007239"},{"id":"A311","pred":"tao:has_database_id","subj":"311","obj":"CVCL:2246"},{"subj":"293","pred":"source","obj":"LitCovid-PubTator"},{"subj":"294","pred":"source","obj":"LitCovid-PubTator"},{"subj":"295","pred":"source","obj":"LitCovid-PubTator"},{"subj":"296","pred":"source","obj":"LitCovid-PubTator"},{"subj":"297","pred":"source","obj":"LitCovid-PubTator"},{"subj":"298","pred":"source","obj":"LitCovid-PubTator"},{"subj":"299","pred":"source","obj":"LitCovid-PubTator"},{"subj":"300","pred":"source","obj":"LitCovid-PubTator"},{"subj":"301","pred":"source","obj":"LitCovid-PubTator"},{"subj":"302","pred":"source","obj":"LitCovid-PubTator"},{"subj":"303","pred":"source","obj":"LitCovid-PubTator"},{"subj":"304","pred":"source","obj":"LitCovid-PubTator"},{"subj":"305","pred":"source","obj":"LitCovid-PubTator"},{"subj":"306","pred":"source","obj":"LitCovid-PubTator"},{"subj":"307","pred":"source","obj":"LitCovid-PubTator"},{"subj":"308","pred":"source","obj":"LitCovid-PubTator"},{"subj":"309","pred":"source","obj":"LitCovid-PubTator"},{"subj":"310","pred":"source","obj":"LitCovid-PubTator"},{"subj":"311","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":"#93ec99","default":true},{"id":"LitCovid-PD-CLO","color":"#ec93a6"},{"id":"LitCovid-PD-CHEBI","color":"#93c0ec"},{"id":"LitCovid-PD-GO-BP","color":"#daec93"},{"id":"LitCovid-sentences","color":"#e493ec"},{"id":"LitCovid-PubTator","color":"#93ecca"}]}]}}