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Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"GO-BP","denotations":[{"id":"T2690","span":{"begin":135,"end":150},"obj":"http://purl.obolibrary.org/obo/GO_0010467"},{"id":"T2691","span":{"begin":741,"end":756},"obj":"http://purl.obolibrary.org/obo/GO_0010467"},{"id":"T2692","span":{"begin":165,"end":185},"obj":"http://purl.obolibrary.org/obo/GO_0030154"},{"id":"T2693","span":{"begin":215,"end":218},"obj":"http://purl.obolibrary.org/obo/GO_0006283"},{"id":"T2694","span":{"begin":431,"end":434},"obj":"http://purl.obolibrary.org/obo/GO_0006283"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"GO-MF","denotations":[{"id":"T3138","span":{"begin":408,"end":412},"obj":"http://purl.obolibrary.org/obo/GO_0005134"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"GO-CC","denotations":[{"id":"T3144","span":{"begin":585,"end":590},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3145","span":{"begin":973,"end":978},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3146","span":{"begin":1145,"end":1150},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3147","span":{"begin":215,"end":218},"obj":"http://purl.obolibrary.org/obo/GO_0042101"},{"id":"T3148","span":{"begin":431,"end":434},"obj":"http://purl.obolibrary.org/obo/GO_0042101"},{"id":"T3149","span":{"begin":799,"end":802},"obj":"http://purl.obolibrary.org/obo/GO_0005680"},{"id":"T3139","span":{"begin":2,"end":6},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3140","span":{"begin":79,"end":83},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3141","span":{"begin":165,"end":169},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3142","span":{"begin":200,"end":205},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3143","span":{"begin":522,"end":527},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"sentences","denotations":[{"id":"T2695","span":{"begin":0,"end":61},"obj":"Sentence"},{"id":"T2696","span":{"begin":62,"end":186},"obj":"Sentence"},{"id":"T2697","span":{"begin":187,"end":422},"obj":"Sentence"},{"id":"T2698","span":{"begin":423,"end":703},"obj":"Sentence"},{"id":"T2699","span":{"begin":704,"end":925},"obj":"Sentence"},{"id":"T2700","span":{"begin":926,"end":1027},"obj":"Sentence"},{"id":"T2701","span":{"begin":1028,"end":1176},"obj":"Sentence"},{"id":"T27","span":{"begin":0,"end":61},"obj":"Sentence"},{"id":"T28","span":{"begin":62,"end":186},"obj":"Sentence"},{"id":"T29","span":{"begin":187,"end":422},"obj":"Sentence"},{"id":"T30","span":{"begin":423,"end":703},"obj":"Sentence"},{"id":"T31","span":{"begin":704,"end":925},"obj":"Sentence"},{"id":"T32","span":{"begin":926,"end":1027},"obj":"Sentence"},{"id":"T33","span":{"begin":1028,"end":1176},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"events-check-again","denotations":[{"id":"T3205","span":{"begin":158,"end":161},"obj":"Protein"},{"id":"T3206","span":{"begin":193,"end":196},"obj":"Protein"},{"id":"T3207","span":{"begin":268,"end":271},"obj":"Protein"},{"id":"T3208","span":{"begin":281,"end":285},"obj":"Protein"},{"id":"T3209","span":{"begin":408,"end":412},"obj":"Protein"},{"id":"T3210","span":{"begin":414,"end":420},"obj":"Protein"},{"id":"T3211","span":{"begin":515,"end":518},"obj":"Protein"},{"id":"T3212","span":{"begin":815,"end":818},"obj":"Protein"},{"id":"T3213","span":{"begin":824,"end":828},"obj":"Protein"},{"id":"T3214","span":{"begin":966,"end":969},"obj":"Protein"},{"id":"T3215","span":{"begin":1138,"end":1141},"obj":"Protein"}],"relations":[{"id":"R2489","pred":"equivalentTo","subj":"T3210","obj":"T3209"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"bionlp-st-ge-2016-reference-tees","denotations":[{"id":"T3216","span":{"begin":158,"end":162},"obj":"Protein"},{"id":"T3217","span":{"begin":193,"end":197},"obj":"Protein"},{"id":"T3218","span":{"begin":211,"end":214},"obj":"Protein"},{"id":"T3219","span":{"begin":263,"end":271},"obj":"Protein"},{"id":"T3220","span":{"begin":276,"end":285},"obj":"Protein"},{"id":"T3221","span":{"begin":326,"end":338},"obj":"Protein"},{"id":"T3222","span":{"begin":390,"end":412},"obj":"Protein"},{"id":"T3223","span":{"begin":414,"end":420},"obj":"Protein"},{"id":"T3224","span":{"begin":515,"end":519},"obj":"Protein"},{"id":"T3225","span":{"begin":815,"end":818},"obj":"Protein"},{"id":"T3226","span":{"begin":824,"end":828},"obj":"Protein"},{"id":"T3227","span":{"begin":966,"end":970},"obj":"Protein"},{"id":"T3228","span":{"begin":1138,"end":1142},"obj":"Protein"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"bionlp-st-ge-2016-reference","denotations":[{"id":"T2679","span":{"begin":158,"end":161},"obj":"Protein"},{"id":"T2680","span":{"begin":193,"end":196},"obj":"Protein"},{"id":"T2681","span":{"begin":268,"end":271},"obj":"Protein"},{"id":"T2682","span":{"begin":281,"end":285},"obj":"Protein"},{"id":"T2683","span":{"begin":408,"end":412},"obj":"Protein"},{"id":"T2684","span":{"begin":414,"end":420},"obj":"Protein"},{"id":"T2685","span":{"begin":515,"end":518},"obj":"Protein"},{"id":"T2686","span":{"begin":815,"end":818},"obj":"Protein"},{"id":"T2687","span":{"begin":824,"end":828},"obj":"Protein"},{"id":"T2688","span":{"begin":966,"end":969},"obj":"Protein"},{"id":"T2689","span":{"begin":1138,"end":1141},"obj":"Protein"}],"relations":[{"id":"R2074","pred":"equivalentTo","subj":"T2684","obj":"T2683"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"bionlp-st-ge-2016-uniprot","denotations":[{"id":"T3110","span":{"begin":158,"end":161},"obj":"P01732"},{"id":"T3111","span":{"begin":158,"end":161},"obj":"P10966"},{"id":"T3112","span":{"begin":193,"end":196},"obj":"P01732"},{"id":"T3113","span":{"begin":193,"end":196},"obj":"P10966"},{"id":"T3114","span":{"begin":268,"end":271},"obj":"P04234"},{"id":"T3115","span":{"begin":268,"end":271},"obj":"P20963"},{"id":"T3116","span":{"begin":268,"end":271},"obj":"P09693"},{"id":"T3117","span":{"begin":268,"end":271},"obj":"P07766"},{"id":"T3118","span":{"begin":281,"end":285},"obj":"P10747"},{"id":"T3119","span":{"begin":408,"end":412},"obj":"P60568"},{"id":"T3120","span":{"begin":515,"end":518},"obj":"P01732"},{"id":"T3121","span":{"begin":515,"end":518},"obj":"P10966"},{"id":"T3122","span":{"begin":815,"end":818},"obj":"P20963"},{"id":"T3123","span":{"begin":815,"end":818},"obj":"P04234"},{"id":"T3124","span":{"begin":815,"end":818},"obj":"P09693"},{"id":"T3125","span":{"begin":815,"end":818},"obj":"P07766"},{"id":"T3126","span":{"begin":824,"end":828},"obj":"P10747"},{"id":"T3127","span":{"begin":966,"end":969},"obj":"P10966"},{"id":"T3128","span":{"begin":966,"end":969},"obj":"P01732"},{"id":"T3129","span":{"begin":1138,"end":1141},"obj":"P01732"},{"id":"T3130","span":{"begin":1138,"end":1141},"obj":"P10966"}],"namespaces":[{"prefix":"_base","uri":"http://www.uniprot.org/uniprot/"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}

{"project":"test2","denotations":[{"id":"T2668","span":{"begin":158,"end":161},"obj":"Protein"},{"id":"T2669","span":{"begin":193,"end":196},"obj":"Protein"},{"id":"T2670","span":{"begin":268,"end":271},"obj":"Protein"},{"id":"T2671","span":{"begin":281,"end":285},"obj":"Protein"},{"id":"T2672","span":{"begin":408,"end":412},"obj":"Protein"},{"id":"T2673","span":{"begin":414,"end":420},"obj":"Protein"},{"id":"T2674","span":{"begin":515,"end":518},"obj":"Protein"},{"id":"T2675","span":{"begin":815,"end":818},"obj":"Protein"},{"id":"T2676","span":{"begin":824,"end":828},"obj":"Protein"},{"id":"T2677","span":{"begin":966,"end":969},"obj":"Protein"},{"id":"T2678","span":{"begin":1138,"end":1141},"obj":"Protein"}],"relations":[{"id":"R2073","pred":"equivalentTo","subj":"T2673","obj":"T2672"}],"text":"A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splenic APCs in the presence of Gp33 peptide, and were cultured in media containing 100 U/ml of recombinant human IL-2 (rhIL-2). We used TCR transgenic mice for these experiments because they provide a reliable source of CD8+ T cells that are truly naive; however, we chose not to stimulate cells with antigen in most experiments so as to avoid contamination with proteins and nucleic acids derived from APCs. There were only minor differences in gene expression during differentiation induced by antigen/APC versus anti-CD3/anti-CD28, and the major conclusions presented in this report are the same for both activating conditions.\nUnder our culture conditions, activated CD8+ T cells expanded exponentially and accumulated for \u003e8 d. We limited our analysis to the first 6–8 d after activation, a period that coincides with clonal expansion of CD8+ T cells after activation in vivo."}