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of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"2_test","denotations":[{"id":"23472114-2744487-87899174","span":{"begin":1398,"end":1400},"obj":"2744487"},{"id":"T12110","span":{"begin":1398,"end":1400},"obj":"2744487"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

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of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"bionlp-st-ge-2016-test-proteins","denotations":[{"id":"T4782","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T4781","span":{"begin":16,"end":38},"obj":"Protein"},{"id":"T4800","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T4799","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T4798","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T4797","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T4796","span":{"begin":1159,"end":1178},"obj":"Protein"},{"id":"T4795","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T4794","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T4793","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T4792","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T4791","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T4790","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T4789","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T4788","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T4787","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T4786","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T4785","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T4784","span":{"begin":511,"end":539},"obj":"Protein"},{"id":"T4783","span":{"begin":418,"end":426},"obj":"Protein"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"bionlp-st-ge-2016-uniprot","denotations":[{"id":"T5247","span":{"begin":1266,"end":1270},"obj":"http://www.uniprot.org/uniprot/P17947"},{"id":"T5246","span":{"begin":1159,"end":1169},"obj":"http://www.uniprot.org/uniprot/P08659"},{"id":"T5245","span":{"begin":520,"end":530},"obj":"http://www.uniprot.org/uniprot/P08659"},{"id":"T5244","span":{"begin":2153,"end":2161},"obj":"http://www.uniprot.org/uniprot/P05120"},{"id":"T5243","span":{"begin":1218,"end":1226},"obj":"http://www.uniprot.org/uniprot/P05120"},{"id":"T5242","span":{"begin":986,"end":994},"obj":"http://www.uniprot.org/uniprot/P05120"},{"id":"T5241","span":{"begin":511,"end":519},"obj":"http://www.uniprot.org/uniprot/P05120"},{"id":"T5240","span":{"begin":418,"end":426},"obj":"http://www.uniprot.org/uniprot/P05120"},{"id":"T5239","span":{"begin":200,"end":208},"obj":"http://www.uniprot.org/uniprot/P05120"},{"id":"T5238","span":{"begin":16,"end":24},"obj":"http://www.uniprot.org/uniprot/P05120"}],"namespaces":[{"prefix":"_base","uri":"http://www.uniprot.org/uniprot/"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"sentences","denotations":[{"id":"T4752","span":{"begin":2172,"end":2230},"obj":"Sentence"},{"id":"T4751","span":{"begin":1965,"end":2171},"obj":"Sentence"},{"id":"T4750","span":{"begin":1825,"end":1964},"obj":"Sentence"},{"id":"T4749","span":{"begin":1684,"end":1824},"obj":"Sentence"},{"id":"T4748","span":{"begin":1403,"end":1683},"obj":"Sentence"},{"id":"T4747","span":{"begin":1159,"end":1402},"obj":"Sentence"},{"id":"T4746","span":{"begin":1108,"end":1158},"obj":"Sentence"},{"id":"T4745","span":{"begin":918,"end":1107},"obj":"Sentence"},{"id":"T4744","span":{"begin":493,"end":917},"obj":"Sentence"},{"id":"T4743","span":{"begin":343,"end":492},"obj":"Sentence"},{"id":"T4742","span":{"begin":48,"end":342},"obj":"Sentence"},{"id":"T4741","span":{"begin":0,"end":47},"obj":"Sentence"},{"id":"T57","span":{"begin":0,"end":47},"obj":"Sentence"},{"id":"T58","span":{"begin":48,"end":342},"obj":"Sentence"},{"id":"T59","span":{"begin":343,"end":492},"obj":"Sentence"},{"id":"T60","span":{"begin":493,"end":917},"obj":"Sentence"},{"id":"T61","span":{"begin":918,"end":1107},"obj":"Sentence"},{"id":"T62","span":{"begin":1108,"end":1158},"obj":"Sentence"},{"id":"T63","span":{"begin":1159,"end":1402},"obj":"Sentence"},{"id":"T64","span":{"begin":1403,"end":1683},"obj":"Sentence"},{"id":"T65","span":{"begin":1684,"end":1824},"obj":"Sentence"},{"id":"T66","span":{"begin":1825,"end":1964},"obj":"Sentence"},{"id":"T67","span":{"begin":1965,"end":2171},"obj":"Sentence"},{"id":"T68","span":{"begin":2172,"end":2230},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"simple1","denotations":[{"id":"T4820","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T4819","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T4818","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T4817","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T4816","span":{"begin":1159,"end":1178},"obj":"Protein"},{"id":"T4815","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T4814","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T4813","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T4812","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T4811","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T4810","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T4809","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T4808","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T4807","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T4806","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T4805","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T4804","span":{"begin":511,"end":539},"obj":"Protein"},{"id":"T4803","span":{"begin":418,"end":426},"obj":"Protein"},{"id":"T4802","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T4801","span":{"begin":16,"end":38},"obj":"Protein"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"BioNLP16_DUT","denotations":[{"id":"T5237","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T5236","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T5235","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T5234","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T5233","span":{"begin":1159,"end":1178},"obj":"Protein"},{"id":"T5232","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T5231","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T5230","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T5229","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T5228","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T5227","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T5226","span":{"begin":511,"end":539},"obj":"Protein"},{"id":"T5225","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T5224","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T5223","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T5222","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T5221","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T5220","span":{"begin":418,"end":426},"obj":"Protein"},{"id":"T5219","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T5218","span":{"begin":16,"end":38},"obj":"Protein"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"BioNLP16_Messiy","denotations":[{"id":"T5308","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T5307","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T5306","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T5305","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T5304","span":{"begin":1159,"end":1178},"obj":"Protein"},{"id":"T5303","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T5302","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T5301","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T5300","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T5299","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T5298","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T5297","span":{"begin":511,"end":539},"obj":"Protein"},{"id":"T5296","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T5295","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T5294","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T5293","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T5292","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T5291","span":{"begin":418,"end":426},"obj":"Protein"},{"id":"T5290","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T5289","span":{"begin":16,"end":38},"obj":"Protein"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

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{"project":"bionlp-st-ge-2016-test-ihmc","denotations":[{"id":"T5482","span":{"begin":842,"end":865},"obj":"Protein"},{"id":"T5481","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T5480","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T5479","span":{"begin":511,"end":550},"obj":"Protein"},{"id":"T5478","span":{"begin":576,"end":579},"obj":"Protein"},{"id":"T5477","span":{"begin":975,"end":1011},"obj":"Entity"},{"id":"T5476","span":{"begin":460,"end":464},"obj":"Protein"},{"id":"T5475","span":{"begin":1503,"end":1507},"obj":"Protein"},{"id":"T5474","span":{"begin":1639,"end":1643},"obj":"Protein"},{"id":"T5473","span":{"begin":2045,"end":2055},"obj":"Protein"},{"id":"T5472","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T5471","span":{"begin":1638,"end":1653},"obj":"Protein"},{"id":"T5470","span":{"begin":1854,"end":1857},"obj":"Protein"},{"id":"T5469","span":{"begin":1214,"end":1250},"obj":"Entity"},{"id":"T5468","span":{"begin":174,"end":177},"obj":"Protein"},{"id":"T5467","span":{"begin":304,"end":319},"obj":"Protein"},{"id":"T5466","span":{"begin":552,"end":553},"obj":"Entity"},{"id":"T5465","span":{"begin":1825,"end":1865},"obj":"Entity"},{"id":"T5464","span":{"begin":347,"end":353},"obj":"Protein"},{"id":"T5463","span":{"begin":565,"end":569},"obj":"Protein"},{"id":"T5462","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T5461","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T5460","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T5459","span":{"begin":1467,"end":1470},"obj":"Protein"},{"id":"T5458","span":{"begin":1672,"end":1676},"obj":"Protein"},{"id":"T5457","span":{"begin":1757,"end":1772},"obj":"Protein"},{"id":"T5456","span":{"begin":459,"end":491},"obj":"Entity"},{"id":"T5455","span":{"begin":600,"end":601},"obj":"Entity"},{"id":"T5454","span":{"begin":1593,"end":1597},"obj":"Protein"},{"id":"T5453","span":{"begin":1282,"end":1287},"obj":"Protein"},{"id":"T5452","span":{"begin":1758,"end":1762},"obj":"Protein"},{"id":"T5451","span":{"begin":332,"end":336},"obj":"Protein"},{"id":"T5450","span":{"begin":84,"end":108},"obj":"Entity"},{"id":"T5449","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T5448","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T5447","span":{"begin":2129,"end":2170},"obj":"Entity"},{"id":"T5446","span":{"begin":611,"end":616},"obj":"Protein"},{"id":"T5445","span":{"begin":414,"end":455},"obj":"Entity"},{"id":"T5444","span":{"begin":482,"end":486},"obj":"Protein"},{"id":"T5443","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T5442","span":{"begin":1671,"end":1682},"obj":"Protein"},{"id":"T5441","span":{"begin":1403,"end":1450},"obj":"Entity"},{"id":"T5440","span":{"begin":1137,"end":1141},"obj":"Protein"},{"id":"T5439","span":{"begin":414,"end":455},"obj":"Entity"},{"id":"T5438","span":{"begin":1339,"end":1354},"obj":"Protein"},{"id":"T5437","span":{"begin":1081,"end":1106},"obj":"Protein"},{"id":"T5436","span":{"begin":1655,"end":1666},"obj":"Protein"},{"id":"T5435","span":{"begin":481,"end":491},"obj":"Entity"},{"id":"T5434","span":{"begin":564,"end":565},"obj":"Entity"},{"id":"T5433","span":{"begin":436,"end":442},"obj":"Protein"},{"id":"T5432","span":{"begin":1656,"end":1660},"obj":"Protein"},{"id":"T5431","span":{"begin":137,"end":142},"obj":"Protein"},{"id":"T5430","span":{"begin":903,"end":905},"obj":"Entity"},{"id":"T5429","span":{"begin":1778,"end":1793},"obj":"Protein"},{"id":"T5428","span":{"begin":1742,"end":1752},"obj":"Protein"},{"id":"T5427","span":{"begin":52,"end":55},"obj":"Protein"},{"id":"T5426","span":{"begin":1684,"end":1715},"obj":"Entity"},{"id":"T5425","span":{"begin":664,"end":669},"obj":"Protein"},{"id":"T5424","span":{"begin":418,"end":426},"obj":"Protein"},{"id":"T5423","span":{"begin":1159,"end":1169},"obj":"Protein"},{"id":"T5422","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T5421","span":{"begin":1137,"end":1157},"obj":"Protein"},{"id":"T5420","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T5419","span":{"begin":1779,"end":1783},"obj":"Protein"},{"id":"T5418","span":{"begin":1977,"end":1980},"obj":"Protein"},{"id":"T5417","span":{"begin":922,"end":925},"obj":"Protein"},{"id":"T5416","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T5415","span":{"begin":1266,"end":1270},"obj":"Protein"},{"id":"T5414","span":{"begin":712,"end":726},"obj":"Protein"},{"id":"T5413","span":{"begin":601,"end":605},"obj":"Protein"},{"id":"T5412","span":{"begin":1290,"end":1294},"obj":"Protein"},{"id":"T5411","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T5410","span":{"begin":1321,"end":1334},"obj":"Protein"},{"id":"T5409","span":{"begin":13,"end":47},"obj":"Protein"},{"id":"T5408","span":{"begin":1704,"end":1707},"obj":"Protein"},{"id":"T5407","span":{"begin":196,"end":232},"obj":"Entity"},{"id":"T5406","span":{"begin":2088,"end":2092},"obj":"Protein"},{"id":"T5405","span":{"begin":331,"end":341},"obj":"Entity"},{"id":"T5404","span":{"begin":2060,"end":2065},"obj":"Pro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of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"bionlp-st-ge-2016-test-tees","denotations":[{"id":"T5348","span":{"begin":2153,"end":2170},"obj":"Protein"},{"id":"T5347","span":{"begin":2060,"end":2065},"obj":"Protein"},{"id":"T5346","span":{"begin":2049,"end":2055},"obj":"Protein"},{"id":"T5345","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T5344","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T5343","span":{"begin":1965,"end":1989},"obj":"Protein"},{"id":"T5342","span":{"begin":1671,"end":1682},"obj":"Protein"},{"id":"T5341","span":{"begin":1655,"end":1666},"obj":"Protein"},{"id":"T5340","span":{"begin":1638,"end":1653},"obj":"Protein"},{"id":"T5339","span":{"begin":1624,"end":1636},"obj":"Protein"},{"id":"T5338","span":{"begin":1607,"end":1619},"obj":"Protein"},{"id":"T5337","span":{"begin":1592,"end":1605},"obj":"Protein"},{"id":"T5336","span":{"begin":1579,"end":1590},"obj":"Protein"},{"id":"T5335","span":{"begin":1563,"end":1574},"obj":"Protein"},{"id":"T5334","span":{"begin":1467,"end":1470},"obj":"Protein"},{"id":"T5333","span":{"begin":1282,"end":1287},"obj":"Protein"},{"id":"T5332","span":{"begin":1272,"end":1277},"obj":"Protein"},{"id":"T5331","span":{"begin":1266,"end":1270},"obj":"Protein"},{"id":"T5330","span":{"begin":1159,"end":1189},"obj":"Protein"},{"id":"T5329","span":{"begin":1090,"end":1097},"obj":"Gene_expression"},{"id":"T5328","span":{"begin":1076,"end":1080},"obj":"Protein"},{"id":"T5327","span":{"begin":1032,"end":1043},"obj":"Protein"},{"id":"T5326","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T5325","span":{"begin":861,"end":864},"obj":"Protein"},{"id":"T5324","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T5323","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T5322","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T5321","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T5320","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T5319","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T5318","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T5317","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T5316","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T5315","span":{"begin":504,"end":539},"obj":"Protein"},{"id":"T5314","span":{"begin":473,"end":480},"obj":"Gene_expression"},{"id":"T5313","span":{"begin":347,"end":353},"obj":"Protein"},{"id":"T5312","span":{"begin":299,"end":303},"obj":"Protein"},{"id":"T5311","span":{"begin":255,"end":266},"obj":"Protein"},{"id":"T5310","span":{"begin":86,"end":91},"obj":"Protein"},{"id":"T5309","span":{"begin":16,"end":38},"obj":"Protein"}],"relations":[{"id":"R3837","pred":"themeOf","subj":"T5313","obj":"T5314"},{"id":"R3838","pred":"themeOf","subj":"T5328","obj":"T5329"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"testone","denotations":[{"id":"T4698","span":{"begin":1090,"end":1097},"obj":"Gene_expression"},{"id":"T4697","span":{"begin":473,"end":480},"obj":"Gene_expression"},{"id":"T4696","span":{"begin":323,"end":330},"obj":"Gene_expression"},{"id":"T4695","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T4694","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T4693","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T4692","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T4691","span":{"begin":1159,"end":1178},"obj":"Protein"},{"id":"T4690","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T4689","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T4688","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T4687","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T4686","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T4685","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T4684","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T4683","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T4682","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T4681","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T4680","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T4679","span":{"begin":511,"end":539},"obj":"Protein"},{"id":"T4678","span":{"begin":418,"end":426},"obj":"Protein"},{"id":"T4677","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T4676","span":{"begin":16,"end":38},"obj":"Protein"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}

{"project":"test3","denotations":[{"id":"T4740","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T4739","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T4738","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T4737","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T4736","span":{"begin":1159,"end":1178},"obj":"Protein"},{"id":"T4735","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T4734","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T4733","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T4732","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T4731","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T4730","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T4729","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T4728","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T4727","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T4726","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T4725","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T4724","span":{"begin":511,"end":539},"obj":"Protein"},{"id":"T4723","span":{"begin":473,"end":480},"obj":"Gene_expression"},{"id":"T4722","span":{"begin":418,"end":426},"obj":"Protein"},{"id":"T4721","span":{"begin":323,"end":330},"obj":"Gene_expression"},{"id":"T4720","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T4719","span":{"begin":16,"end":38},"obj":"Protein"},{"id":"T4718","span":{"begin":2153,"end":2161},"obj":"Protein"},{"id":"T4717","span":{"begin":2020,"end":2025},"obj":"Protein"},{"id":"T4716","span":{"begin":2009,"end":2015},"obj":"Protein"},{"id":"T4715","span":{"begin":1218,"end":1226},"obj":"Protein"},{"id":"T4714","span":{"begin":1159,"end":1178},"obj":"Protein"},{"id":"T4713","span":{"begin":986,"end":994},"obj":"Protein"},{"id":"T4712","span":{"begin":903,"end":916},"obj":"Protein"},{"id":"T4711","span":{"begin":842,"end":859},"obj":"Protein"},{"id":"T4710","span":{"begin":770,"end":775},"obj":"Protein"},{"id":"T4709","span":{"begin":758,"end":765},"obj":"Protein"},{"id":"T4708","span":{"begin":751,"end":756},"obj":"Protein"},{"id":"T4707","span":{"begin":742,"end":749},"obj":"Protein"},{"id":"T4706","span":{"begin":734,"end":740},"obj":"Protein"},{"id":"T4705","span":{"begin":727,"end":732},"obj":"Protein"},{"id":"T4704","span":{"begin":720,"end":725},"obj":"Protein"},{"id":"T4703","span":{"begin":680,"end":686},"obj":"Protein"},{"id":"T4702","span":{"begin":511,"end":539},"obj":"Protein"},{"id":"T4701","span":{"begin":418,"end":426},"obj":"Protein"},{"id":"T4700","span":{"begin":200,"end":208},"obj":"Protein"},{"id":"T4699","span":{"begin":16,"end":38},"obj":"Protein"}],"text":"Construction of SerpinB2 Reporter Gene Plasmids\nThe PCR primers DW5’LUC, containing a Kpn I restriction site, and DW3’LUC, containing an Xho I restriction site, were used to PCR amplify and clone the SerpinB2 promoter (−3261 to +92) from pDB9406 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic (Promega) to produce pGLmP-3261. The EcoR I insert of pDB9402-42 was sub-cloned immediately upstream of the SerpinB2 promoter EcoR I site (−3261) of pGLmP-3261 to produce pGLmP-4480. Additional murine SerpinB2 luciferase reporter constructs (pGLmP-2751, pGLmP-2614, pGLmP-1686, pGLmP-1341, pGLmP-694, pGLmP-539 and pGLmP-189) were generated by digesting pGLmP-3261 with EcoR I and a second restriction enzyme (Sfi I, Apa I, BstX I, Bsu36 I, Pac I, Hae III and Apo I respectively), blunt ending the resultant 5′ or 3′ overhangs with T4 DNA polymerase (NEB) and re-ligating the vector ends with T4 DNA ligase. The PCR primers BSPCR2 and DW3’LUC were used to subclone the murine SerpinB2 promoter regions −87 to +92 into the Kpn I/Xho I polylinker restriction sites of pGL3 Basic to produce pGLmP-87. The control empty vector was pGL3 Basic (Promega).\nLuciferase reporter constructs containing mutations in the SerpinB2 promoter LPS-responsive regions E box, PU.1, Oct-1 and C/EBP (pGLmP-539mEbox, pGLmP-539mPU.1, pGLmP-539mOct and pGLmP-539mC/EBP respectively) were generated as described [36]. The mutant oligonucleotide PCR primer sequences are provided in Fig. S1, and were used as follows: pGLmP-539mEbox: mPAI2mEboxa and mPAI2mEboxb; pGLmP-539mPU.1: mPAI2mPU.1a and mPAI2mPU.1b; pGLmP-539mOct: mPAI2mOct-2a and mPAI2mOct-2b; pGLmP-539mC/EBP: mPAI2mCEBPa and mPAI2mCEBPb. The oligonucleotide PCR primers used to generate mutants, pGLmP-539mCRE, pGLmP-539mAP-1a, and pGLmP-539mAP-1b were reported previously [37]. The flanking oligonucleotide PCR primers were RVprimer3 (Promega) and GLprimer2 (Promega). pGLmP-539 was used as the template in each case. Recombinant PCR products were digested with EcoR I and Xho I and cloned between the EcoR I and Xho I restriction sites of pGLmP-539 in place of the −539/+92 region of the wild-type murine SerpinB2 promoter. Sequence verified constructs were used in the experiments."}