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pmc-enju-pas

bionlp-st-ge-2016-spacy-parsed

GO-MF

{"project":"GO-MF","denotations":[{"id":"T26429","span":{"begin":402,"end":409},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T26430","span":{"begin":591,"end":598},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T26431","span":{"begin":1158,"end":1166},"obj":"http://purl.obolibrary.org/obo/GO_0003823"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

GO-CC

{"project":"GO-CC","denotations":[{"id":"T26432","span":{"begin":75,"end":80},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T26433","span":{"begin":1213,"end":1217},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T26434","span":{"begin":1158,"end":1166},"obj":"http://purl.obolibrary.org/obo/GO_0019815"},{"id":"T26435","span":{"begin":1158,"end":1166},"obj":"http://purl.obolibrary.org/obo/GO_0042571"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

sentences

{"project":"sentences","denotations":[{"id":"T25839","span":{"begin":0,"end":29},"obj":"Sentence"},{"id":"T25840","span":{"begin":30,"end":141},"obj":"Sentence"},{"id":"T25841","span":{"begin":142,"end":191},"obj":"Sentence"},{"id":"T25842","span":{"begin":192,"end":329},"obj":"Sentence"},{"id":"T25843","span":{"begin":330,"end":499},"obj":"Sentence"},{"id":"T25844","span":{"begin":500,"end":664},"obj":"Sentence"},{"id":"T25845","span":{"begin":665,"end":894},"obj":"Sentence"},{"id":"T25846","span":{"begin":895,"end":1101},"obj":"Sentence"},{"id":"T25847","span":{"begin":1102,"end":1392},"obj":"Sentence"},{"id":"T25848","span":{"begin":1393,"end":1451},"obj":"Sentence"},{"id":"T25849","span":{"begin":1452,"end":1536},"obj":"Sentence"},{"id":"T362","span":{"begin":0,"end":29},"obj":"Sentence"},{"id":"T363","span":{"begin":30,"end":141},"obj":"Sentence"},{"id":"T364","span":{"begin":142,"end":191},"obj":"Sentence"},{"id":"T365","span":{"begin":192,"end":329},"obj":"Sentence"},{"id":"T366","span":{"begin":330,"end":499},"obj":"Sentence"},{"id":"T367","span":{"begin":500,"end":664},"obj":"Sentence"},{"id":"T368","span":{"begin":665,"end":797},"obj":"Sentence"},{"id":"T369","span":{"begin":798,"end":894},"obj":"Sentence"},{"id":"T370","span":{"begin":895,"end":1101},"obj":"Sentence"},{"id":"T371","span":{"begin":1102,"end":1294},"obj":"Sentence"},{"id":"T372","span":{"begin":1295,"end":1392},"obj":"Sentence"},{"id":"T373","span":{"begin":1393,"end":1451},"obj":"Sentence"},{"id":"T374","span":{"begin":1452,"end":1536},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

events-check-again

{"project":"events-check-again","denotations":[{"id":"T26459","span":{"begin":67,"end":80},"obj":"Protein"},{"id":"T26460","span":{"begin":86,"end":97},"obj":"Gene_expression"},{"id":"T26461","span":{"begin":86,"end":97},"obj":"Gene_expression"},{"id":"T26462","span":{"begin":103,"end":108},"obj":"Protein"},{"id":"T26463","span":{"begin":112,"end":117},"obj":"Protein"},{"id":"T26464","span":{"begin":343,"end":348},"obj":"Protein"},{"id":"T26465","span":{"begin":985,"end":990},"obj":"Protein"},{"id":"T26466","span":{"begin":1041,"end":1046},"obj":"Protein"}],"relations":[{"id":"R20709","pred":"themeOf","subj":"T26462","obj":"T26460"},{"id":"R20710","pred":"themeOf","subj":"T26463","obj":"T26461"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

bionlp-st-ge-2016-reference-tees

{"project":"bionlp-st-ge-2016-reference-tees","denotations":[{"id":"T26444","span":{"begin":103,"end":108},"obj":"Protein"},{"id":"T26445","span":{"begin":112,"end":117},"obj":"Protein"},{"id":"T26446","span":{"begin":86,"end":97},"obj":"Gene_expression"},{"id":"T26447","span":{"begin":86,"end":97},"obj":"Gene_expression"},{"id":"T26448","span":{"begin":343,"end":348},"obj":"Protein"},{"id":"T26449","span":{"begin":1180,"end":1183},"obj":"Protein"},{"id":"T26450","span":{"begin":1184,"end":1187},"obj":"Protein"}],"relations":[{"id":"R20705","pred":"themeOf","subj":"T26444","obj":"T26446"},{"id":"R20706","pred":"themeOf","subj":"T26445","obj":"T26447"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

bionlp-st-ge-2016-reference

{"project":"bionlp-st-ge-2016-reference","denotations":[{"id":"T25831","span":{"begin":67,"end":80},"obj":"Protein"},{"id":"T25832","span":{"begin":86,"end":97},"obj":"Gene_expression"},{"id":"T25833","span":{"begin":86,"end":97},"obj":"Gene_expression"},{"id":"T25834","span":{"begin":103,"end":108},"obj":"Protein"},{"id":"T25835","span":{"begin":112,"end":117},"obj":"Protein"},{"id":"T25836","span":{"begin":343,"end":348},"obj":"Protein"},{"id":"T25837","span":{"begin":985,"end":990},"obj":"Protein"},{"id":"T25838","span":{"begin":1041,"end":1046},"obj":"Protein"}],"relations":[{"id":"R20132","pred":"themeOf","subj":"T25834","obj":"T25832"},{"id":"R20133","pred":"themeOf","subj":"T25835","obj":"T25833"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

bionlp-st-ge-2016-uniprot

{"project":"bionlp-st-ge-2016-uniprot","denotations":[{"id":"T26122","span":{"begin":103,"end":108},"obj":"Q01196"},{"id":"T26123","span":{"begin":112,"end":117},"obj":"Q13761"},{"id":"T26124","span":{"begin":343,"end":348},"obj":"Q9BZS1"},{"id":"T26125","span":{"begin":397,"end":401},"obj":"Q01196"},{"id":"T26126","span":{"begin":397,"end":401},"obj":"Q13950"},{"id":"T26127","span":{"begin":397,"end":401},"obj":"Q13761"},{"id":"T26128","span":{"begin":985,"end":990},"obj":"Q01196"},{"id":"T26129","span":{"begin":1041,"end":1046},"obj":"Q13761"}],"namespaces":[{"prefix":"_base","uri":"http://www.uniprot.org/uniprot/"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

test2

{"project":"test2","denotations":[{"id":"T25824","span":{"begin":67,"end":80},"obj":"Protein"},{"id":"T25825","span":{"begin":86,"end":97},"obj":"Gene_expression"},{"id":"T25826","span":{"begin":103,"end":108},"obj":"Protein"},{"id":"T25827","span":{"begin":112,"end":117},"obj":"Protein"},{"id":"T25828","span":{"begin":343,"end":348},"obj":"Protein"},{"id":"T25829","span":{"begin":985,"end":990},"obj":"Protein"},{"id":"T25830","span":{"begin":1041,"end":1046},"obj":"Protein"}],"relations":[{"id":"R20129","pred":"themeOf","subj":"T25824","obj":"T25825"},{"id":"R20130","pred":"themeOf","subj":"T25826","obj":"T25825"},{"id":"R20131","pred":"themeOf","subj":"T25827","obj":"T25825"}],"text":"Promoter enzyme immuno assay.\nAs performed in the pull-down assay, HEK293T cells were transfected with RUNX1 or RUNX3 and subsequently lysed. Insoluble material was removed by centrifugation. 384-well plates, precoated with streptavidin (Thermo Fisher Scientific) were washed 3 times with washing buffer (PBS and 0.05% Tween 20). Biotinylated FOXP3 promoter/oligonucleotides probes containing the RUNX binding sites were added (1 pmol per well; 50 fmol/µl) and incubated for 1 h at room temperature. Either a combination of all three oligonucleotides containing the mutated or the wild-type binding sites was used or single oligonucleotides were used in the assay. After 3 washing steps with washing buffer, the nuclear extract was added (concentration \u003e 0.2 µg/µl) and incubated overnight at 4°C. The lysates were incubated with 10 µg of poly-deoxyinosinic-deoxycytidylic acid (Sigma-Aldrich). The plate was washed with HKMG buffer and incubated with a 1:1000 dilution of rabbit anti-RUNX1 (ab11903, Abcam) or 1:200 dilution of rabbit anti-RUNX3 (H-50, Santa Cruz Biotechnology, Inc.) at 4°C for 2 h. After three washing steps with HKMG buffer, a secondary antibody (anti–rabbit IgG-HRP, 1:3,000 in HKMG buffer, Cell Signaling Technology) was added, and the plate was incubated for 1 h at 4°C. The wells were washed 4 times with HKMG buffer before adding the substrate reagent (R\u0026D Systems). The colorimetric reaction was stopped by adding 2 M H2SO4. Absorbance at 450 nm was measured using a microplate reader (Berthold Technologies)."}

PMC:2806624 / 53017-54553 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:2806624 / 53017-54553 JSON TXT