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PMC:3342329 / 32522-33684 JSONTXT

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pmc-enju-pas

Id Subject Object Predicate Lexical cue
T15916 1156-1161 NN denotes -70°C
T15915 1153-1155 IN denotes at
T15914 1143-1152 NN denotes overnight
T15913 1138-1142 VB denotes film
T15912 1135-1137 TO denotes to
T15911 1127-1134 VB denotes exposed
T15910 1123-1126 CC denotes and
T15909 1118-1122 NN denotes 80°C
T15908 1115-1117 IN denotes at
T15907 1113-1114 NN denotes h
T15906 1111-1112 CD denotes 1
T15905 1107-1110 IN denotes for
T15904 1101-1106 VB denotes dried
T15903 1097-1100 VB denotes was
T15902 1093-1096 NN denotes gel
T15901 1089-1092 DT denotes The
T15900 1084-1087 NN denotes gel
T15899 1080-1083 DT denotes the
T15898 1075-1079 IN denotes down
T15897 1071-1074 NN denotes way
T15896 1067-1070 DT denotes the
T15895 1064-1066 IN denotes of
T15894 1052-1063 NN denotes four-fifths
T15893 1048-1051 VB denotes was
T15892 1044-1047 NN denotes dye
T15891 1040-1043 DT denotes the
T15890 1034-1039 IN denotes until
T15889 1018-1033 NN denotes electrophoresis
T15888 1015-1017 TO denotes to
T15887 1005-1014 VB denotes subjected
T15886 1001-1004 VB denotes was
T15885 997-1000 NN denotes gel
T15884 993-996 DT denotes The
T15883 988-991 NN denotes gel
T15882 971-987 JJ denotes non-denaturating
T15881 969-970 NN denotes %
T15880 968-969 CD denotes 6
T15879 966-967 DT denotes a
T15878 961-965 IN denotes onto
T15877 954-960 VB denotes loaded
T15876 950-953 CC denotes and
T15875 941-949 NN denotes reaction
T15874 936-940 DT denotes each
T15873 933-935 TO denotes to
T15872 927-932 VB denotes added
T15871 923-926 VB denotes was
T15870 916-922 NN denotes buffer
T15869 908-915 NN denotes loading
T15868 904-907 NN denotes gel
T15867 901-903 IN denotes of
T15866 898-900 NN denotes ml
T15865 896-897 CD denotes 1
T15864 894-895 -COMMA- denotes ,
T15863 882-894 RB denotes Subsequently
T15862 869-880 NN denotes temperature
T15861 864-868 NN denotes room
T15860 861-863 IN denotes at
T15859 851-860 VB denotes incubated
T15858 847-850 CC denotes and
T15857 837-846 VB denotes assembled
T15856 832-836 VB denotes were
T15855 822-831 NN denotes reactions
T15854 816-821 NN denotes shift
T15853 812-815 NN denotes gel
T15852 808-811 DT denotes The
T15851 802-807 NNP denotes 37°C.
T15850 799-801 IN denotes at
T15849 795-798 NN denotes min
T15848 792-794 CD denotes 10
T15847 788-791 IN denotes for
T15846 783-787 NN denotes -ATP
T15845 782-783 -RRB- denotes ]
T15844 779-782 NN denotes P32
T15843 778-779 -LRB- denotes [
T15842 774-777 CC denotes and
T15841 767-773 NN denotes kinase
T15840 752-766 NN denotes polynucleotide
T15839 749-751 NN denotes T4
T15838 743-748 VB denotes using
T15837 731-742 VB denotes end-labeled
T15836 726-730 VB denotes were
T15835 709-725 NN denotes oligonucleotides
T15834 699-708 NNP denotes Consensus
T15833 693-697 NN denotes tube
T15832 683-692 NNP denotes Eppendorf
T15831 675-682 JJ denotes chilled
T15830 673-674 DT denotes a
T15829 670-672 IN denotes in
T15828 660-669 VB denotes collected
T15827 655-659 VB denotes were
T15826 643-654 NN denotes supernatant
T15825 634-642 NN denotes extracts
T15824 626-633 JJ denotes nuclear
T15823 616-625 VB denotes resulting
T15822 612-615 DT denotes the
T15821 608-611 CC denotes and
T15820 606-607 -COMMA- denotes ,
T15819 603-606 NN denotes min
T15818 600-602 CD denotes 15
T15817 596-599 IN denotes for
T15816 592-595 NN denotes rpm
T15815 586-591 CD denotes 15000
T15814 583-585 IN denotes at
T15813 571-582 VB denotes centrifuged
T15812 567-570 VB denotes was
T15811 560-566 NN denotes pellet
T15810 548-559 JJ denotes resuspended
T15809 544-547 DT denotes The
T15808 539-542 NN denotes min
T15807 536-538 CD denotes 20
T15806 532-535 IN denotes for
T15805 528-531 NN denotes ice
T15804 525-527 IN denotes on
T15803 515-524 VB denotes incubated
T15802 511-514 CC denotes and
T15801 509-510 -COMMA- denotes ,
T15800 508-509 -RRB- denotes )
T15799 500-508 NN denotes glycerol
T15798 498-499 NN denotes %
T15797 496-498 CD denotes 20
T15795 487-491 NN denotes NaCl
T15794 484-486 NN denotes mM
T15793 480-483 CD denotes 420
T15792 475-479 IN denotes with
T15791 462-474 VB denotes supplemented
T15790 460-461 NN denotes A
T15789 451-459 NN denotes solution
T15788 450-451 -LRB- denotes (
T15787 448-449 NN denotes C
T15786 439-447 NN denotes solution
T15785 436-438 IN denotes in
T15784 424-435 VB denotes resuspended
T15783 419-423 VB denotes were
T15782 412-418 NN denotes nuclei
T15781 403-411 VB denotes pelleted
T15780 399-402 DT denotes The
T15779 394-397 NN denotes min
T15778 391-393 CD denotes 15
T15777 387-390 IN denotes for
T15776 383-386 NN denotes rpm
T15775 377-382 CD denotes 15000
T15774 374-376 IN denotes at
T15773 362-373 VB denotes centrifuged
T15772 357-361 RB denotes then
T15771 353-356 CC denotes and
T15770 351-352 -COMMA- denotes ,
T15769 348-351 NN denotes min
T15768 345-347 CD denotes 10
T15767 341-344 IN denotes for
T15766 337-340 NN denotes ice
T15765 334-336 IN denotes on
T15764 324-333 VB denotes incubated
T15763 322-323 -COMMA- denotes ,
T15762 312-322 RB denotes vigorously
T15761 303-311 VB denotes vortexed
T15760 301-302 -COMMA- denotes ,
T15759 300-301 -RRB- denotes )
T15758 272-300 NN denotes phenylmethylsulfonylfluoride
T15757 269-271 NN denotes mM
T15756 265-268 CD denotes 0.2
T15755 263-264 -COMMA- denotes ,
T15754 249-263 NN denotes dithiothreitol
T15753 246-248 NN denotes mM
T15752 242-245 CD denotes 0.5
T15751 240-241 -COMMA- denotes ,
T15750 237-240 NN denotes KCl
T15749 234-236 NN denotes mM
T15748 231-233 CD denotes 10
T15747 229-230 -COMMA- denotes ,
T15746 224-229 NN denotes MgCl2
T15745 221-223 NN denotes mM
T15744 217-220 CD denotes 1.5
T15743 215-216 -COMMA- denotes ,
T15742 214-215 -RRB- denotes ]
T15741 211-214 CD denotes 7.9
T15740 208-210 NN denotes pH
T15739 207-208 -LRB- denotes [
T15738 201-206 NN denotes HEPES
T15737 198-200 NN denotes mM
T15736 195-197 CD denotes 10
T15735 194-195 -LRB- denotes (
T15734 192-193 NN denotes A
T15733 183-191 NN denotes solution
T15732 180-182 IN denotes of
T15731 177-179 NN denotes µl
T15730 173-176 CD denotes 200
T15729 170-172 IN denotes in
T15728 158-169 VB denotes homogenized
T15727 150-157 RB denotes briefly
T15726 145-149 VB denotes were
T15725 137-144 NN denotes tissues
T15724 131-136 NN denotes tumor
T15723 127-130 DT denotes The
T15722 124-125 -RRB- denotes )
T15721 122-124 NNP denotes WI
T15720 120-121 -COMMA- denotes ,
T15719 113-120 NNP denotes Madison
T15718 111-112 -COMMA- denotes ,
T15717 104-111 NNP denotes Promega
T15716 103-104 -LRB- denotes (
T15715 87-102 NN denotes recommendations
T15714 72-86 NN denotes manufacturer’s
T15713 68-71 DT denotes the
T15712 65-67 TO denotes to
T15711 55-64 VB denotes according
T15710 45-54 VB denotes performed
T15709 41-44 VB denotes was
T15708 39-40 -RRB- denotes )
T15707 35-39 NN denotes EMSA
T15706 34-35 -LRB- denotes (
T15705 28-33 NN denotes assay
T15704 22-27 NN denotes shift
T15703 6-21 NN denotes electromobility
T15702 2-5 NN denotes gel
T15701 0-1 DT denotes A
T15796 492-495 CC denotes and
R11128 T15705 T15701 arg1Of assay,A
R11129 T15705 T15702 arg1Of assay,gel
R11130 T15705 T15703 arg1Of assay,electromobility
R11131 T15705 T15704 arg1Of assay,shift
R11132 T15705 T15706 arg1Of assay,(
R11133 T15705 T15709 arg1Of assay,was
R11134 T15705 T15710 arg2Of assay,performed
R11135 T15707 T15706 arg2Of EMSA,(
R11136 T15708 T15706 arg3Of ),(
R11137 T15710 T15709 arg2Of performed,was
R11138 T15710 T15711 arg1Of performed,according
R11139 T15710 T15716 arg1Of performed,(
R11140 T15712 T15711 arg2Of to,according
R11141 T15715 T15712 arg2Of recommendations,to
R11142 T15715 T15713 arg1Of recommendations,the
R11143 T15715 T15714 arg1Of recommendations,manufacturer’s
R11144 T15717 T15718 arg1Of Promega,","
R11145 T15718 T15716 arg2Of ",",(
R11146 T15718 T15720 arg1Of ",",","
R11147 T15719 T15718 arg2Of Madison,","
R11148 T15721 T15720 arg2Of WI,","
R11149 T15722 T15716 arg3Of ),(
R11150 T15725 T15723 arg1Of tissues,The
R11151 T15725 T15724 arg1Of tissues,tumor
R11152 T15725 T15726 arg1Of tissues,were
R11153 T15725 T15728 arg2Of tissues,homogenized
R11154 T15725 T15761 arg1Of tissues,vortexed
R11155 T15725 T15764 arg1Of tissues,incubated
R11156 T15725 T15773 arg1Of tissues,centrifuged
R11157 T15728 T15726 arg2Of homogenized,were
R11158 T15728 T15727 arg1Of homogenized,briefly
R11159 T15728 T15729 arg1Of homogenized,in
R11160 T15728 T15760 arg1Of homogenized,","
R11161 T15731 T15729 arg2Of µl,in
R11162 T15731 T15730 arg1Of µl,200
R11163 T15731 T15732 arg1Of µl,of
R11164 T15731 T15735 arg1Of µl,(
R11165 T15734 T15732 arg2Of A,of
R11166 T15734 T15733 arg1Of A,solution
R11167 T15736 T15737 arg1Of 10,mM
R11168 T15738 T15736 arg1Of HEPES,10
R11169 T15738 T15739 arg1Of HEPES,[
R11170 T15738 T15743 arg1Of HEPES,","
R11171 T15740 T15739 arg2Of pH,[
R11172 T15740 T15741 arg1Of pH,7.9
R11173 T15742 T15739 arg3Of ],[
R11174 T15743 T15747 arg1Of ",",","
R11175 T15744 T15745 arg1Of 1.5,mM
R11176 T15746 T15743 arg2Of MgCl2,","
R11177 T15746 T15744 arg1Of MgCl2,1.5
R11178 T15747 T15751 arg1Of ",",","
R11179 T15748 T15749 arg1Of 10,mM
R11180 T15750 T15747 arg2Of KCl,","
R11181 T15750 T15748 arg1Of KCl,10
R11182 T15751 T15735 arg2Of ",",(
R11183 T15751 T15755 arg1Of ",",","
R11184 T15752 T15753 arg1Of 0.5,mM
R11185 T15754 T15751 arg2Of dithiothreitol,","
R11186 T15754 T15752 arg1Of dithiothreitol,0.5
R11187 T15756 T15757 arg1Of 0.2,mM
R11188 T15758 T15755 arg2Of phenylmethylsulfonylfluoride,","
R11189 T15758 T15756 arg1Of phenylmethylsulfonylfluoride,0.2
R11190 T15759 T15735 arg3Of ),(
R11191 T15760 T15763 arg1Of ",",","
R11192 T15761 T15760 arg2Of vortexed,","
R11193 T15761 T15762 arg1Of vortexed,vigorously
R11194 T15763 T15771 arg1Of ",",and
R11195 T15764 T15763 arg2Of incubated,","
R11196 T15764 T15765 arg1Of incubated,on
R11197 T15764 T15767 arg1Of incubated,for
R11198 T15766 T15765 arg2Of ice,on
R11199 T15769 T15767 arg2Of min,for
R11200 T15769 T15768 arg1Of min,10
R11201 T15771 T15770 arg1Of and,","
R11202 T15773 T15771 arg2Of centrifuged,and
R11203 T15773 T15772 arg1Of centrifuged,then
R11204 T15773 T15774 arg1Of centrifuged,at
R11205 T15773 T15777 arg1Of centrifuged,for
R11206 T15776 T15774 arg2Of rpm,at
R11207 T15776 T15775 arg1Of rpm,15000
R11208 T15779 T15777 arg2Of min,for
R11209 T15779 T15778 arg1Of min,15
R11210 T15782 T15780 arg1Of nuclei,The
R11211 T15782 T15781 arg2Of nuclei,pelleted
R11212 T15782 T15783 arg1Of nuclei,were
R11213 T15782 T15784 arg2Of nuclei,resuspended
R11214 T15782 T15803 arg2Of nuclei,incubated
R11215 T15784 T15785 arg1Of resuspended,in
R11216 T15784 T15802 arg1Of resuspended,and
R11217 T15787 T15785 arg2Of C,in
R11218 T15787 T15786 arg1Of C,solution
R11219 T15787 T15788 arg1Of C,(
R11220 T15790 T15788 arg2Of A,(
R11221 T15790 T15789 arg1Of A,solution
R11222 T15790 T15791 arg2Of A,supplemented
R11223 T15791 T15792 arg1Of supplemented,with
R11224 T15793 T15794 arg1Of 420,mM
R11225 T15795 T15793 arg1Of NaCl,420
R11226 T15795 T15796 arg1Of NaCl,and
R11227 T15796 T15792 arg2Of and,with
R11228 T15797 T15798 arg1Of 20,%
R11229 T15799 T15796 arg2Of glycerol,and
R11230 T15799 T15797 arg1Of glycerol,20
R11231 T15800 T15788 arg3Of ),(
R11232 T15802 T15783 arg2Of and,were
R11233 T15802 T15801 arg1Of and,","
R11234 T15803 T15802 arg2Of incubated,and
R11235 T15803 T15804 arg1Of incubated,on
R11236 T15803 T15806 arg1Of incubated,for
R11237 T15805 T15804 arg2Of ice,on
R11238 T15808 T15806 arg2Of min,for
R11239 T15808 T15807 arg1Of min,20
R11240 T15811 T15809 arg1Of pellet,The
R11241 T15811 T15810 arg1Of pellet,resuspended
R11242 T15811 T15812 arg1Of pellet,was
R11243 T15811 T15813 arg2Of pellet,centrifuged
R11244 T15813 T15812 arg2Of centrifuged,was
R11245 T15813 T15814 arg1Of centrifuged,at
R11246 T15813 T15817 arg1Of centrifuged,for
R11247 T15813 T15821 arg1Of centrifuged,and
R11248 T15816 T15814 arg2Of rpm,at
R11249 T15816 T15815 arg1Of rpm,15000
R11250 T15819 T15817 arg2Of min,for
R11251 T15819 T15818 arg1Of min,15
R11252 T15821 T15820 arg1Of and,","
R11253 T15826 T15822 arg1Of supernatant,the
R11254 T15826 T15823 arg1Of supernatant,resulting
R11255 T15826 T15824 arg1Of supernatant,nuclear
R11256 T15826 T15825 arg1Of supernatant,extracts
R11257 T15826 T15827 arg1Of supernatant,were
R11258 T15826 T15828 arg2Of supernatant,collected
R11259 T15828 T15821 arg2Of collected,and
R11260 T15828 T15827 arg2Of collected,were
R11261 T15828 T15829 arg1Of collected,in
R11262 T15833 T15829 arg2Of tube,in
R11263 T15833 T15830 arg1Of tube,a
R11264 T15833 T15831 arg1Of tube,chilled
R11265 T15833 T15832 arg1Of tube,Eppendorf
R11266 T15835 T15834 arg1Of oligonucleotides,Consensus
R11267 T15835 T15836 arg1Of oligonucleotides,were
R11268 T15835 T15837 arg2Of oligonucleotides,end-labeled
R11269 T15835 T15859 arg2Of oligonucleotides,incubated
R11270 T15837 T15858 arg1Of end-labeled,and
R11271 T15838 T15837 arg3Of using,end-labeled
R11272 T15838 T15847 arg1Of using,for
R11273 T15841 T15839 arg1Of kinase,T4
R11274 T15841 T15840 arg1Of kinase,polynucleotide
R11275 T15841 T15842 arg1Of kinase,and
R11276 T15842 T15838 arg2Of and,using
R11277 T15844 T15843 arg2Of P32,[
R11278 T15845 T15843 arg3Of ],[
R11279 T15846 T15842 arg2Of -ATP,and
R11280 T15846 T15843 arg1Of -ATP,[
R11281 T15849 T15847 arg2Of min,for
R11282 T15849 T15848 arg1Of min,10
R11283 T15849 T15850 arg1Of min,at
R11284 T15851 T15850 arg2Of 37°C.,at
R11285 T15851 T15856 modOf 37°C.,were
R11286 T15855 T15852 arg1Of reactions,The
R11287 T15855 T15853 arg1Of reactions,gel
R11288 T15855 T15854 arg1Of reactions,shift
R11289 T15855 T15856 arg1Of reactions,were
R11290 T15855 T15857 arg2Of reactions,assembled
R11291 T15857 T15856 arg2Of assembled,were
R11292 T15858 T15836 arg2Of and,were
R11293 T15859 T15858 arg2Of incubated,and
R11294 T15859 T15860 arg1Of incubated,at
R11295 T15862 T15860 arg2Of temperature,at
R11296 T15862 T15861 arg1Of temperature,room
R11297 T15866 T15865 arg1Of ml,1
R11298 T15866 T15867 arg1Of ml,of
R11299 T15866 T15871 arg1Of ml,was
R11300 T15866 T15872 arg2Of ml,added
R11301 T15866 T15877 arg2Of ml,loaded
R11302 T15870 T15867 arg2Of buffer,of
R11303 T15870 T15868 arg1Of buffer,gel
R11304 T15870 T15869 arg1Of buffer,loading
R11305 T15872 T15873 arg1Of added,to
R11306 T15872 T15876 arg1Of added,and
R11307 T15875 T15873 arg2Of reaction,to
R11308 T15875 T15874 arg1Of reaction,each
R11309 T15876 T15863 arg1Of and,Subsequently
R11310 T15876 T15864 arg1Of and,","
R11311 T15876 T15871 arg2Of and,was
R11312 T15877 T15876 arg2Of loaded,and
R11313 T15877 T15878 arg1Of loaded,onto
R11314 T15880 T15881 arg1Of 6,%
R11315 T15883 T15878 arg2Of gel,onto
R11316 T15883 T15879 arg1Of gel,a
R11317 T15883 T15880 arg1Of gel,6
R11318 T15883 T15882 arg1Of gel,non-denaturating
R11319 T15885 T15884 arg1Of gel,The
R11320 T15885 T15886 arg1Of gel,was
R11321 T15885 T15887 arg2Of gel,subjected
R11322 T15887 T15890 arg1Of subjected,until
R11323 T15887 T15886 arg2Of subjected,was
R11324 T15887 T15888 arg1Of subjected,to
R11325 T15889 T15888 arg2Of electrophoresis,to
R11326 T15892 T15891 arg1Of dye,the
R11327 T15892 T15893 arg1Of dye,was
R11328 T15893 T15890 arg2Of was,until
R11329 T15894 T15893 arg2Of four-fifths,was
R11330 T15894 T15895 arg1Of four-fifths,of
R11331 T15897 T15895 arg2Of way,of
R11332 T15897 T15896 arg1Of way,the
R11333 T15897 T15898 arg1Of way,down
R11334 T15900 T15898 arg2Of gel,down
R11335 T15900 T15899 arg1Of gel,the
R11336 T15902 T15901 arg1Of gel,The
R11337 T15902 T15903 arg1Of gel,was
R11338 T15902 T15904 arg2Of gel,dried
R11339 T15902 T15911 arg2Of gel,exposed
R11340 T15904 T15905 arg1Of dried,for
R11341 T15904 T15908 arg1Of dried,at
R11342 T15904 T15910 arg1Of dried,and
R11343 T15907 T15905 arg2Of h,for
R11344 T15907 T15906 arg1Of h,1
R11345 T15909 T15908 arg2Of 80°C,at
R11346 T15910 T15903 arg2Of and,was
R11347 T15911 T15910 arg2Of exposed,and
R11348 T15911 T15912 modOf exposed,to
R11349 T15913 T15912 arg1Of film,to
R11350 T15913 T15915 arg1Of film,at
R11351 T15914 T15913 arg2Of overnight,film
R11352 T15916 T15915 arg2Of -70°C,at

UBERON-AE

Id Subject Object Predicate Lexical cue
T15687 693-697 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T15686 137-144 http://purl.obolibrary.org/obo/UBERON_0000479 denotes tissues

sentences

Id Subject Object Predicate Lexical cue
T15696 1089-1162 Sentence denotes The gel was dried for 1 h at 80°C and exposed to film overnight at -70°C.
T15695 993-1088 Sentence denotes The gel was subjected to electrophoresis until the dye was four-fifths of the way down the gel.
T15694 882-992 Sentence denotes Subsequently, 1 ml of gel loading buffer was added to each reaction and loaded onto a 6% non-denaturating gel.
T15693 699-881 Sentence denotes Consensus oligonucleotides were end-labeled using T4 polynucleotide kinase and [P32]-ATP for 10 min at 37°C. The gel shift reactions were assembled and incubated at room temperature.
T15692 544-698 Sentence denotes The resuspended pellet was centrifuged at 15000 rpm for 15 min, and the resulting nuclear extracts supernatant were collected in a chilled Eppendorf tube.
T15691 399-543 Sentence denotes The pelleted nuclei were resuspended in solution C (solution A supplemented with 420 mM NaCl and 20% glycerol), and incubated on ice for 20 min.
T15690 127-398 Sentence denotes The tumor tissues were briefly homogenized in 200 µl of solution A (10 mM HEPES [pH 7.9], 1.5 mM MgCl2, 10 mM KCl, 0.5 mM dithiothreitol, 0.2 mM phenylmethylsulfonylfluoride), vortexed vigorously, incubated on ice for 10 min, and then centrifuged at 15000 rpm for 15 min.
T15689 0-126 Sentence denotes A gel electromobility shift assay (EMSA) was performed according to the manufacturer’s recommendations (Promega, Madison, WI).
T243 0-126 Sentence denotes A gel electromobility shift assay (EMSA) was performed according to the manufacturer’s recommendations (Promega, Madison, WI).
T244 127-398 Sentence denotes The tumor tissues were briefly homogenized in 200 µl of solution A (10 mM HEPES [pH 7.9], 1.5 mM MgCl2, 10 mM KCl, 0.5 mM dithiothreitol, 0.2 mM phenylmethylsulfonylfluoride), vortexed vigorously, incubated on ice for 10 min, and then centrifuged at 15000 rpm for 15 min.
T245 399-543 Sentence denotes The pelleted nuclei were resuspended in solution C (solution A supplemented with 420 mM NaCl and 20% glycerol), and incubated on ice for 20 min.
T246 544-698 Sentence denotes The resuspended pellet was centrifuged at 15000 rpm for 15 min, and the resulting nuclear extracts supernatant were collected in a chilled Eppendorf tube.
T247 699-807 Sentence denotes Consensus oligonucleotides were end-labeled using T4 polynucleotide kinase and [P32]-ATP for 10 min at 37°C.
T248 808-881 Sentence denotes The gel shift reactions were assembled and incubated at room temperature.
T249 882-992 Sentence denotes Subsequently, 1 ml of gel loading buffer was added to each reaction and loaded onto a 6% non-denaturating gel.
T250 993-1088 Sentence denotes The gel was subjected to electrophoresis until the dye was four-fifths of the way down the gel.
T251 1089-1162 Sentence denotes The gel was dried for 1 h at 80°C and exposed to film overnight at -70°C.

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T16182 525-538 Entity denotes on ice for 20
T16181 399-418 Entity denotes The pelleted nuclei
T16180 612-654 Entity denotes the resulting nuclear extracts supernatant
T16179 303-311 Entity denotes vortexed
T16178 993-1000 Entity denotes The gel
T16177 180-191 Entity denotes of solution
T16176 731-773 Protein denotes end-labeled using T4 polynucleotide kinase
T16175 808-831 Entity denotes The gel shift reactions
T16174 195-215 Entity denotes 10 mM HEPES [pH 7.9]
T16173 749-751 Entity denotes T4
T16172 699-725 Entity denotes Consensus oligonucleotides
T16171 1080-1087 Entity denotes the gel
T16170 779-782 Entity denotes P32
T16169 439-509 Entity denotes solution C (solution A supplemented with 420 mM NaCl and 20% glycerol)
T16168 0-27 Entity denotes A gel electromobility shift
T16167 242-301 Entity denotes 0.5 mM dithiothreitol, 0.2 mM phenylmethylsulfonylfluoride)
T16166 1089-1096 Entity denotes The gel
T16165 231-240 Entity denotes 10 mM KCl
T16164 265-300 Entity denotes 0.2 mM phenylmethylsulfonylfluoride
T16163 224-241 Entity denotes MgCl2, 10 mM KCl,
T16162 496-508 Entity denotes 20% glycerol
T16161 904-991 Entity denotes gel loading buffer was added to each reaction and loaded onto a 6% non-denaturating gel
T16160 480-491 Entity denotes 420 mM NaCl
T16159 337-340 Entity denotes ice
T16158 1111-1114 Entity denotes 1 h
T16157 783-798 Entity denotes -ATP for 10 min
T16155 673-697 Protein denotes a chilled Eppendorf tube
T16154 966-991 Entity denotes a 6% non-denaturating gel

bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T16153 1160-1162 NNP denotes C.
T16152 1159-1160 CD denotes °
T16151 1156-1159 CD denotes -70
T16150 1153-1155 IN denotes at
T16149 1143-1152 JJ denotes overnight
T16148 1138-1142 NN denotes film
T16147 1135-1137 TO denotes to
T16146 1127-1134 VBN denotes exposed
T16145 1123-1126 CC denotes and
T16144 1121-1122 NNP denotes C
T16143 1120-1121 CD denotes °
T16142 1118-1120 CD denotes 80
T16141 1115-1117 IN denotes at
T16140 1113-1114 NN denotes h
T16139 1111-1112 CD denotes 1
T16138 1107-1110 IN denotes for
T16137 1101-1106 VBN denotes dried
T16136 1097-1100 VBD denotes was
T16135 1093-1096 NN denotes gel
T16134 1089-1092 DT denotes The
T16133 1087-1088 . denotes .
T16132 1084-1087 NN denotes gel
T16131 1080-1083 DT denotes the
T16130 1075-1079 IN denotes down
T16129 1071-1074 NN denotes way
T16128 1067-1070 DT denotes the
T16127 1064-1066 IN denotes of
T16126 1052-1063 NNS denotes four-fifths
T16125 1048-1051 VBD denotes was
T16124 1044-1047 NN denotes dye
T16123 1040-1043 DT denotes the
T16122 1034-1039 IN denotes until
T16121 1018-1033 NN denotes electrophoresis
T16120 1015-1017 TO denotes to
T16119 1005-1014 VBN denotes subjected
T16118 1001-1004 VBD denotes was
T16117 997-1000 NN denotes gel
T16116 993-996 DT denotes The
T16115 991-992 . denotes .
T16114 988-991 NN denotes gel
T16113 971-987 JJ denotes non-denaturating
T16112 969-970 NN denotes %
T16111 968-969 CD denotes 6
T16110 966-967 DT denotes a
T16109 961-965 IN denotes onto
T16108 954-960 VBN denotes loaded
T16107 950-953 CC denotes and
T16106 941-949 NN denotes reaction
T16105 936-940 DT denotes each
T16104 933-935 TO denotes to
T16103 927-932 VBN denotes added
T16102 923-926 VBD denotes was
T16101 916-922 NN denotes buffer
T16100 908-915 VBG denotes loading
T16099 904-907 NN denotes gel
T16098 901-903 IN denotes of
T16097 898-900 NN denotes ml
T16096 896-897 CD denotes 1
T16095 894-895 , denotes ,
T16094 882-894 RB denotes Subsequently
T16093 880-881 . denotes .
T16092 869-880 NN denotes temperature
T16091 864-868 NN denotes room
T16090 861-863 IN denotes at
T16089 851-860 VBN denotes incubated
T16088 847-850 CC denotes and
T16087 837-846 VBN denotes assembled
T16086 832-836 VBD denotes were
T16085 822-831 NNS denotes reactions
T16084 816-821 NN denotes shift
T16083 812-815 NN denotes gel
T16082 808-811 DT denotes The
T16081 806-807 . denotes .
T16080 805-806 NNP denotes C
T16079 804-805 CD denotes °
T16078 802-804 CD denotes 37
T16077 799-801 IN denotes at
T16076 795-798 NN denotes min
T16075 792-794 CD denotes 10
T16012 450-451 -LRB- denotes (
T16011 448-449 NNP denotes C
T16010 439-447 NN denotes solution
T16009 436-438 IN denotes in
T16008 424-435 VBN denotes resuspended
T16007 419-423 VBD denotes were
T16006 412-418 NNS denotes nuclei
T16005 403-411 JJ denotes pelleted
T16004 399-402 DT denotes The
T16003 397-398 . denotes .
T16002 394-397 NN denotes min
T16001 391-393 CD denotes 15
T16000 387-390 IN denotes for
T15999 383-386 NN denotes rpm
T15998 377-382 CD denotes 15000
T15997 374-376 IN denotes at
T15996 362-373 VBD denotes centrifuged
T15995 357-361 RB denotes then
T15994 353-356 CC denotes and
T15993 351-352 , denotes ,
T15992 348-351 NN denotes min
T15991 345-347 CD denotes 10
T15990 341-344 IN denotes for
T15989 337-340 NN denotes ice
T15988 334-336 IN denotes on
T15987 324-333 VBN denotes incubated
T15986 322-323 , denotes ,
T15985 312-322 RB denotes vigorously
T15984 303-311 JJ denotes vortexed
T15983 301-302 , denotes ,
T15982 300-301 -RRB- denotes )
T15981 272-300 NN denotes phenylmethylsulfonylfluoride
T15980 269-271 NNP denotes mM
T15979 265-268 CD denotes 0.2
T15978 263-264 , denotes ,
T15977 249-263 NN denotes dithiothreitol
T15976 246-248 NNP denotes mM
T15975 242-245 CD denotes 0.5
T15974 240-241 , denotes ,
T15973 237-240 NNP denotes KCl
T15972 234-236 NNP denotes mM
T15971 231-233 CD denotes 10
T15970 229-230 , denotes ,
T15969 224-229 NNP denotes MgCl2
T15968 221-223 NNP denotes mM
T15967 217-220 CD denotes 1.5
T15966 215-216 , denotes ,
T15965 214-215 NNP denotes ]
T15964 211-214 CD denotes 7.9
T15963 208-210 NNP denotes pH
T15962 207-208 NNP denotes [
T15961 201-206 NNP denotes HEPES
T15960 198-200 NNP denotes mM
T15959 195-197 CD denotes 10
T15958 194-195 -LRB- denotes (
T15957 192-193 DT denotes A
T15956 183-191 NN denotes solution
T15955 180-182 IN denotes of
T15954 177-179 NN denotes µl
T15953 173-176 CD denotes 200
T15952 170-172 IN denotes in
T15951 158-169 VBN denotes homogenized
T15950 150-157 RB denotes briefly
T15949 145-149 VBD denotes were
T15948 137-144 NNS denotes tissues
T15947 131-136 NN denotes tumor
T15946 127-130 DT denotes The
T15945 125-126 . denotes .
T15944 124-125 -RRB- denotes )
T15943 122-124 NNP denotes WI
T15942 120-121 , denotes ,
T15941 113-120 NNP denotes Madison
T15940 111-112 , denotes ,
T15939 104-111 NNP denotes Promega
T15938 103-104 -LRB- denotes (
T15937 87-102 NNS denotes recommendations
T15936 72-84 NN denotes manufacturer
T15935 68-71 DT denotes the
T15934 65-67 TO denotes to
T15933 55-64 VBG denotes according
T15932 45-54 VBN denotes performed
T15931 41-44 VBD denotes was
T15930 39-40 -RRB- denotes )
T15929 35-39 NNP denotes EMSA
T15928 34-35 -LRB- denotes (
T15927 28-33 NN denotes assay
T15926 22-27 NN denotes shift
T15925 6-21 NN denotes electromobility
T15924 2-5 NN denotes gel
T15923 0-1 NNP denotes A
T16074 788-791 IN denotes for
T16073 784-787 NNP denotes ATP
T16072 783-784 : denotes -
T16071 782-783 NNP denotes ]
T16070 779-782 NNP denotes P32
T16069 778-779 NNP denotes [
T16068 774-777 CC denotes and
T16067 767-773 NN denotes kinase
T16066 752-766 NN denotes polynucleotide
T16065 749-751 CD denotes T4
T16064 743-748 VBG denotes using
T16063 731-742 JJ denotes end-labeled
T16062 726-730 VBD denotes were
T16061 709-725 NNS denotes oligonucleotides
T16060 699-708 NNP denotes Consensus
T16059 697-698 . denotes .
T16058 693-697 NN denotes tube
T16057 683-692 NNP denotes Eppendorf
T16056 675-682 VBN denotes chilled
T16055 673-674 DT denotes a
T16054 670-672 IN denotes in
T16053 660-669 VBN denotes collected
T16052 655-659 VBD denotes were
T16051 643-654 JJ denotes supernatant
T16050 634-642 NNS denotes extracts
T16049 626-633 JJ denotes nuclear
T16048 616-625 VBG denotes resulting
T16047 612-615 DT denotes the
T16046 608-611 CC denotes and
T16045 606-607 , denotes ,
T16044 603-606 NN denotes min
T16043 600-602 CD denotes 15
T16042 596-599 IN denotes for
T16041 592-595 NN denotes rpm
T16040 586-591 CD denotes 15000
T16039 583-585 IN denotes at
T16038 571-582 VBN denotes centrifuged
T16037 567-570 VBD denotes was
T16036 560-566 NN denotes pellet
T16035 548-559 JJ denotes resuspended
T16034 544-547 DT denotes The
T16033 542-543 . denotes .
T16032 539-542 NN denotes min
T16031 536-538 CD denotes 20
T16030 532-535 IN denotes for
T16029 528-531 NN denotes ice
T16028 525-527 IN denotes on
T16027 515-524 VBD denotes incubated
T16026 511-514 CC denotes and
T16025 509-510 , denotes ,
T16024 508-509 -RRB- denotes )
T16023 500-508 NN denotes glycerol
T16022 498-499 NN denotes %
T16021 496-498 CD denotes 20
T16020 492-495 CC denotes and
T16019 487-491 NNP denotes NaCl
T16018 484-486 NNP denotes mM
T16017 480-483 CD denotes 420
T16016 475-479 IN denotes with
T16015 462-474 VBN denotes supplemented
T16014 460-461 DT denotes A
T16013 451-459 NN denotes solution
R11357 T15923 T15932 nsubjpass A,performed
R11358 T15924 T15927 nmod gel,assay
R11359 T15925 T15927 compound electromobility,assay
R11360 T15926 T15927 compound shift,assay
R11361 T15927 T15927 ROOT assay,assay
R11362 T15928 T15927 punct (,assay
R11363 T15929 T15927 appos EMSA,assay
R11364 T15930 T15927 punct ),assay
R11365 T15931 T15932 auxpass was,performed
R11366 T15932 T15932 ROOT performed,performed
R11367 T15933 T15932 prep according,performed
R11368 T15934 T15933 prep to,according
R11369 T15935 T15936 det the,manufacturer
R11370 T15936 T15937 poss manufacturer,recommendations
R11371 T15937 T15934 pobj recommendations,to
R11372 T15938 T15932 punct (,performed
R11373 T15939 T15939 ROOT Promega,Promega
R11374 T15940 T15939 punct ",",Promega
R11375 T15941 T15939 conj Madison,Promega
R11376 T15942 T15941 punct ",",Madison
R11377 T15943 T15941 conj WI,Madison
R11378 T15944 T15939 punct ),Promega
R11379 T15945 T15932 punct .,performed
R11380 T15946 T15948 det The,tissues
R11381 T15947 T15948 compound tumor,tissues
R11382 T15948 T15949 nsubj tissues,were
R11383 T15949 T15949 ROOT were,were
R11384 T15950 T15951 advmod briefly,homogenized
R11385 T15951 T15949 acomp homogenized,were
R11386 T15952 T15951 prep in,homogenized
R11387 T15953 T15954 nummod 200,µl
R11388 T15954 T15952 pobj µl,in
R11389 T15955 T15954 prep of,µl
R11390 T15956 T15957 compound solution,A
R11391 T15957 T15987 det A,incubated
R11392 T15958 T15965 punct (,]
R11393 T15959 T15965 nummod 10,]
R11394 T15960 T15963 compound mM,pH
R11395 T15961 T15963 compound HEPES,pH
R11396 T15962 T15963 compound [,pH
R11397 T15963 T15965 nmod pH,]
R11398 T15964 T15965 nummod 7.9,]
R11399 T15965 T15969 nmod ],MgCl2
R11400 T15966 T15969 punct ",",MgCl2
R11401 T15967 T15969 nummod 1.5,MgCl2
R11402 T15968 T15969 compound mM,MgCl2
R11403 T15969 T15987 dep MgCl2,incubated
R11404 T15970 T15969 punct ",",MgCl2
R11405 T15971 T15973 nummod 10,KCl
R11406 T15972 T15973 compound mM,KCl
R11407 T15973 T15969 conj KCl,MgCl2
R11408 T15974 T15973 punct ",",KCl
R11409 T15975 T15977 nummod 0.5,dithiothreitol
R11410 T15976 T15977 compound mM,dithiothreitol
R11411 T15977 T15973 appos dithiothreitol,KCl
R11412 T15978 T15977 punct ",",dithiothreitol
R11413 T15979 T15981 nummod 0.2,phenylmethylsulfonylfluoride
R11414 T15980 T15981 compound mM,phenylmethylsulfonylfluoride
R11415 T15981 T15977 appos phenylmethylsulfonylfluoride,dithiothreitol
R11416 T15982 T15977 punct ),dithiothreitol
R11417 T15983 T15973 punct ",",KCl
R11418 T15984 T15969 conj vortexed,MgCl2
R11419 T15985 T15984 advmod vigorously,vortexed
R11420 T15986 T15984 punct ",",vortexed
R11421 T15987 T15987 ROOT incubated,incubated
R11422 T15988 T15987 prep on,incubated
R11423 T15989 T15988 pobj ice,on
R11424 T15990 T15987 prep for,incubated
R11425 T15991 T15992 nummod 10,min
R11426 T15992 T15990 pobj min,for
R11427 T15993 T15987 punct ",",incubated
R11428 T15994 T15987 cc and,incubated
R11429 T15995 T15996 advmod then,centrifuged
R11430 T15996 T15987 conj centrifuged,incubated
R11431 T15997 T15996 prep at,centrifuged
R11432 T15998 T15999 nummod 15000,rpm
R11433 T15999 T15997 pobj rpm,at
R11434 T16000 T15996 prep for,centrifuged
R11435 T16001 T16002 nummod 15,min
R11436 T16002 T16000 pobj min,for
R11437 T16003 T15987 punct .,incubated
R11438 T16004 T16006 det The,nuclei
R11439 T16005 T16006 amod pelleted,nuclei
R11440 T16006 T16008 nsubjpass nuclei,resuspended
R11441 T16007 T16008 auxpass were,resuspended
R11442 T16008 T16008 ROOT resuspended,resuspended
R11443 T16009 T16008 prep in,resuspended
R11444 T16010 T16009 pobj solution,in
R11445 T16011 T16008 npadvmod C,resuspended
R11446 T16012 T16015 punct (,supplemented
R11447 T16013 T16014 compound solution,A
R11448 T16014 T16015 nsubj A,supplemented
R11449 T16015 T16011 parataxis supplemented,C
R11450 T16016 T16015 prep with,supplemented
R11451 T16017 T16019 nummod 420,NaCl
R11452 T16018 T16019 compound mM,NaCl
R11453 T16019 T16016 pobj NaCl,with
R11454 T16020 T16019 cc and,NaCl
R11455 T16021 T16022 nummod 20,%
R11456 T16022 T16023 compound %,glycerol
R11457 T16023 T16019 conj glycerol,NaCl
R11458 T16024 T16015 punct ),supplemented
R11459 T16025 T16011 punct ",",C
R11460 T16026 T16011 cc and,C
R11461 T16027 T16011 conj incubated,C
R11462 T16028 T16027 prep on,incubated
R11463 T16029 T16028 pobj ice,on
R11464 T16030 T16027 prep for,incubated
R11465 T16031 T16032 nummod 20,min
R11466 T16032 T16030 pobj min,for
R11467 T16033 T16008 punct .,resuspended
R11468 T16034 T16036 det The,pellet
R11469 T16035 T16036 amod resuspended,pellet
R11470 T16036 T16038 nsubjpass pellet,centrifuged
R11471 T16037 T16038 auxpass was,centrifuged
R11472 T16038 T16038 ROOT centrifuged,centrifuged
R11473 T16039 T16038 prep at,centrifuged
R11474 T16040 T16041 nummod 15000,rpm
R11475 T16041 T16039 pobj rpm,at
R11476 T16042 T16038 prep for,centrifuged
R11477 T16043 T16044 nummod 15,min
R11478 T16044 T16042 pobj min,for
R11479 T16045 T16038 punct ",",centrifuged
R11480 T16046 T16038 cc and,centrifuged
R11481 T16047 T16050 det the,extracts
R11482 T16048 T16050 amod resulting,extracts
R11483 T16049 T16050 amod nuclear,extracts
R11484 T16050 T16053 nsubjpass extracts,collected
R11485 T16051 T16050 amod supernatant,extracts
R11486 T16052 T16053 auxpass were,collected
R11487 T16053 T16038 conj collected,centrifuged
R11488 T16054 T16053 prep in,collected
R11489 T16055 T16058 det a,tube
R11490 T16056 T16058 amod chilled,tube
R11491 T16057 T16058 compound Eppendorf,tube
R11492 T16058 T16054 pobj tube,in
R11493 T16059 T16053 punct .,collected
R11494 T16060 T16061 compound Consensus,oligonucleotides
R11495 T16061 T16064 nsubj oligonucleotides,using
R11496 T16062 T16064 aux were,using
R11497 T16063 T16064 advmod end-labeled,using
R11498 T16064 T16064 ROOT using,using
R11499 T16065 T16067 nummod T4,kinase
R11500 T16066 T16067 compound polynucleotide,kinase
R11501 T16067 T16064 dobj kinase,using
R11502 T16068 T16067 cc and,kinase
R11503 T16069 T16073 compound [,ATP
R11504 T16070 T16073 compound P32,ATP
R11505 T16071 T16073 compound ],ATP
R11506 T16072 T16073 punct -,ATP
R11507 T16073 T16067 conj ATP,kinase
R11508 T16074 T16073 prep for,ATP
R11509 T16075 T16076 nummod 10,min
R11510 T16076 T16074 pobj min,for
R11511 T16077 T16073 prep at,ATP
R11512 T16078 T16079 nummod 37,°
R11513 T16079 T16077 pobj °,at
R11514 T16080 T16073 npadvmod C,ATP
R11515 T16081 T16064 punct .,using
R11516 T16082 T16085 det The,reactions
R11517 T16083 T16084 compound gel,shift
R11518 T16084 T16085 compound shift,reactions
R11519 T16085 T16087 nsubjpass reactions,assembled
R11520 T16086 T16087 auxpass were,assembled
R11521 T16087 T16087 ROOT assembled,assembled
R11522 T16088 T16087 cc and,assembled
R11523 T16089 T16087 conj incubated,assembled
R11524 T16090 T16089 prep at,incubated
R11525 T16091 T16092 compound room,temperature
R11526 T16092 T16090 pobj temperature,at
R11527 T16093 T16087 punct .,assembled
R11528 T16094 T16103 advmod Subsequently,added
R11529 T16095 T16103 punct ",",added
R11530 T16096 T16097 nummod 1,ml
R11531 T16097 T16101 nmod ml,buffer
R11532 T16098 T16097 prep of,ml
R11533 T16099 T16098 pobj gel,of
R11534 T16100 T16101 compound loading,buffer
R11535 T16101 T16103 nsubjpass buffer,added
R11536 T16102 T16103 auxpass was,added
R11537 T16103 T16103 ROOT added,added
R11538 T16104 T16103 prep to,added
R11539 T16105 T16106 det each,reaction
R11540 T16106 T16104 pobj reaction,to
R11541 T16107 T16103 cc and,added
R11542 T16108 T16103 conj loaded,added
R11543 T16109 T16108 prep onto,loaded
R11544 T16110 T16114 det a,gel
R11545 T16111 T16112 nummod 6,%
R11546 T16112 T16114 nmod %,gel
R11547 T16113 T16114 amod non-denaturating,gel
R11548 T16114 T16109 pobj gel,onto
R11549 T16115 T16103 punct .,added
R11550 T16116 T16117 det The,gel
R11551 T16117 T16119 nsubjpass gel,subjected
R11552 T16118 T16119 auxpass was,subjected
R11553 T16119 T16119 ROOT subjected,subjected
R11554 T16120 T16119 prep to,subjected
R11555 T16121 T16120 pobj electrophoresis,to
R11556 T16122 T16125 mark until,was
R11557 T16123 T16124 det the,dye
R11558 T16124 T16125 nsubj dye,was
R11559 T16125 T16119 advcl was,subjected
R11560 T16126 T16125 attr four-fifths,was
R11561 T16127 T16126 prep of,four-fifths
R11562 T16128 T16129 det the,way
R11563 T16129 T16127 pobj way,of
R11564 T16130 T16129 prep down,way
R11565 T16131 T16132 det the,gel
R11566 T16132 T16130 pobj gel,down
R11567 T16133 T16119 punct .,subjected
R11568 T16134 T16135 det The,gel
R11569 T16135 T16137 nsubjpass gel,dried
R11570 T16136 T16137 auxpass was,dried
R11571 T16137 T16137 ROOT dried,dried
R11572 T16138 T16137 prep for,dried
R11573 T16139 T16140 nummod 1,h
R11574 T16140 T16138 pobj h,for
R11575 T16141 T16137 prep at,dried
R11576 T16142 T16144 nummod 80,C
R11577 T16143 T16144 nummod °,C
R11578 T16144 T16141 pobj C,at
R11579 T16145 T16137 cc and,dried
R11580 T16146 T16137 conj exposed,dried
R11581 T16147 T16146 prep to,exposed
R11582 T16148 T16149 compound film,overnight
R11583 T16149 T16147 pobj overnight,to
R11584 T16150 T16146 prep at,exposed
R11585 T16151 T16152 nummod -70,°
R11586 T16152 T16153 nummod °,C.
R11587 T16153 T16150 pobj C.,at

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T15917 749-773 Protein denotes T4 polynucleotide kinase