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PMC:3333881 / 13346-13944 JSONTXT

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bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T7752 0-7 JJ denotes Primary
T7753 8-18 NNS denotes antibodies
T7754 19-23 VBD denotes were
T7755 23-24 : denotes :
T7756 25-33 JJ denotes anti-p65
T7757 34-35 -LRB- denotes (
T7758 35-41 JJ denotes sc-372
T7759 41-42 -RRB- denotes )
T7760 42-43 , denotes ,
T7761 44-53 JJ denotes anti-IκBα
T7762 54-55 -LRB- denotes (
T7763 55-61 JJ denotes sc-203
T7764 61-62 -RRB- denotes )
T7765 63-66 CC denotes and
T7766 67-73 NN denotes rabbit
T7767 74-77 NNP denotes IgG
T7768 78-79 -LRB- denotes (
T7769 79-86 JJ denotes sc-2027
T7770 86-87 -RRB- denotes )
T7771 88-92 IN denotes from
T7772 93-98 NNP denotes Santa
T7773 99-103 NNP denotes Cruz
T7774 104-117 NNP denotes Biotechnology
T7775 117-118 : denotes ;
T7776 119-128 NNP denotes anti-FLAG
T7777 129-131 NNP denotes M2
T7778 132-136 IN denotes from
T7779 137-142 NNP denotes Sigma
T7780 143-150 NNP denotes Aldrich
T7781 150-151 . denotes .
T7782 152-172 NNS denotes Immunoprecipitations
T7783 173-177 VBD denotes were
T7784 178-185 VBN denotes carried
T7785 186-189 RP denotes out
T7786 190-192 IN denotes at
T7787 193-194 CD denotes 4
T7788 194-195 CD denotes °
T7789 195-196 NNP denotes C
T7790 197-206 JJ denotes overnight
T7791 207-210 CC denotes and
T7792 211-217 JJ denotes immune
T7793 218-227 NNS denotes complexes
T7794 228-232 VBD denotes were
T7795 233-242 VBN denotes collected
T7796 243-247 IN denotes with
T7797 248-255 NN denotes protein
T7798 256-257 NNP denotes G
T7799 258-265 JJ denotes agarose
T7800 266-271 NNS denotes beads
T7801 271-272 , denotes ,
T7802 273-279 VBD denotes washed
T7803 280-284 CD denotes five
T7804 285-290 NNS denotes times
T7805 291-295 IN denotes with
T7806 296-299 JJ denotes low
T7807 300-304 NN denotes salt
T7808 305-311 NN denotes buffer
T7809 312-313 -LRB- denotes (
T7810 313-315 CD denotes 20
T7811 316-318 NNP denotes mM
T7812 319-323 NNP denotes Tris
T7813 324-327 NNP denotes HCl
T7814 328-330 NNP denotes pH
T7815 331-334 CD denotes 8.0
T7816 334-335 , denotes ,
T7817 336-339 CD denotes 0.1
T7818 339-340 NN denotes %
T7819 341-344 NNP denotes SDS
T7820 344-345 , denotes ,
T7821 346-347 CD denotes 1
T7822 347-348 NN denotes %
T7823 349-355 NNP denotes Triton
T7824 356-361 NNP denotes X-100
T7825 361-362 , denotes ,
T7826 363-364 CD denotes 2
T7827 365-367 NNP denotes mM
T7828 368-372 NNP denotes EDTA
T7829 372-373 , denotes ,
T7830 374-377 CD denotes 150
T7831 378-380 NNP denotes mM
T7832 381-385 NNP denotes NaCl
T7833 385-386 -RRB- denotes )
T7834 386-387 , denotes ,
T7835 388-392 CD denotes four
T7836 393-398 NNS denotes times
T7837 399-403 IN denotes with
T7838 404-408 JJ denotes high
T7839 409-413 NN denotes salt
T7840 414-420 NN denotes buffer
T7841 421-422 -LRB- denotes (
T7842 422-424 CD denotes 20
T7843 425-427 NNP denotes mM
T7844 428-432 NNP denotes Tris
T7845 433-436 NNP denotes HCl
T7846 437-439 NNP denotes pH
T7847 440-443 CD denotes 8.0
T7848 443-444 , denotes ,
T7849 445-448 CD denotes 0.1
T7850 448-449 NN denotes %
T7851 450-453 NNP denotes SDS
T7852 453-454 , denotes ,
T7853 455-456 CD denotes 1
T7854 456-457 NN denotes %
T7855 458-464 NNP denotes Triton
T7856 465-470 NNP denotes X-100
T7857 470-471 , denotes ,
T7858 472-473 CD denotes 2
T7859 474-476 NNP denotes mM
T7860 477-481 NNP denotes EDTA
T7861 481-482 , denotes ,
T7862 483-486 CD denotes 500
T7863 487-489 NNP denotes mM
T7864 490-494 NNP denotes NaCl
T7865 494-495 -RRB- denotes )
T7866 495-496 , denotes ,
T7867 497-501 RB denotes once
T7868 502-506 IN denotes with
T7869 507-509 NNP denotes TE
T7870 510-516 NN denotes buffer
T7871 517-518 -LRB- denotes (
T7872 518-520 CD denotes 10
T7873 521-523 NNP denotes mM
T7874 524-528 NNP denotes Tris
T7875 529-532 NNP denotes HCl
T7876 533-535 NNP denotes pH
T7877 536-539 CD denotes 8.0
T7878 539-540 , denotes ,
T7879 541-542 CD denotes 1
T7880 543-545 NNP denotes mM
T7881 546-550 NNP denotes EDTA
T7882 550-551 -RRB- denotes )
T7883 551-552 , denotes ,
T7884 553-556 CC denotes and
T7885 557-566 VBN denotes extracted
T7886 567-569 IN denotes in
T7887 570-572 NNP denotes TE
T7888 573-579 NN denotes buffer
T7889 580-590 VBG denotes containing
T7890 591-592 CD denotes 2
T7891 592-593 NN denotes %
T7892 594-597 NNP denotes SDS
T7893 597-598 . denotes .
R6473 T7752 T7753 amod Primary,antibodies
R6474 T7753 T7754 nsubj antibodies,were
R6475 T7754 T7754 ROOT were,were
R6476 T7755 T7754 punct :,were
R6477 T7756 T7767 amod anti-p65,IgG
R6478 T7757 T7767 punct (,IgG
R6479 T7758 T7767 amod sc-372,IgG
R6480 T7759 T7758 punct ),sc-372
R6481 T7760 T7758 punct ",",sc-372
R6482 T7761 T7758 conj anti-IκBα,sc-372
R6483 T7762 T7763 punct (,sc-203
R6484 T7763 T7767 amod sc-203,IgG
R6485 T7764 T7763 punct ),sc-203
R6486 T7765 T7763 cc and,sc-203
R6487 T7766 T7763 conj rabbit,sc-203
R6488 T7767 T7754 attr IgG,were
R6489 T7768 T7769 punct (,sc-2027
R6490 T7769 T7767 appos sc-2027,IgG
R6491 T7770 T7769 punct ),sc-2027
R6492 T7771 T7769 prep from,sc-2027
R6493 T7772 T7773 compound Santa,Cruz
R6494 T7773 T7774 compound Cruz,Biotechnology
R6495 T7774 T7771 pobj Biotechnology,from
R6496 T7775 T7767 punct ;,IgG
R6497 T7776 T7777 compound anti-FLAG,M2
R6498 T7777 T7767 conj M2,IgG
R6499 T7778 T7767 prep from,IgG
R6500 T7779 T7778 pobj Sigma,from
R6501 T7780 T7767 conj Aldrich,IgG
R6502 T7781 T7767 punct .,IgG
R6503 T7782 T7784 nsubjpass Immunoprecipitations,carried
R6504 T7783 T7784 auxpass were,carried
R6505 T7784 T7784 ROOT carried,carried
R6506 T7785 T7784 prt out,carried
R6507 T7786 T7784 prep at,carried
R6508 T7787 T7788 nummod 4,°
R6509 T7788 T7790 nummod °,overnight
R6510 T7789 T7790 compound C,overnight
R6511 T7790 T7786 pobj overnight,at
R6512 T7791 T7790 cc and,overnight
R6513 T7792 T7790 conj immune,overnight
R6514 T7793 T7795 nsubjpass complexes,collected
R6515 T7794 T7795 auxpass were,collected
R6516 T7795 T7784 conj collected,carried
R6517 T7796 T7795 prep with,collected
R6518 T7797 T7800 nmod protein,beads
R6519 T7798 T7800 nmod G,beads
R6520 T7799 T7800 amod agarose,beads
R6521 T7800 T7796 pobj beads,with
R6522 T7801 T7802 punct ",",washed
R6523 T7802 T7784 conj washed,carried
R6524 T7803 T7804 nummod five,times
R6525 T7804 T7802 npadvmod times,washed
R6526 T7805 T7802 prep with,washed
R6527 T7806 T7808 amod low,buffer
R6528 T7807 T7808 compound salt,buffer
R6529 T7808 T7805 pobj buffer,with
R6530 T7809 T7808 punct (,buffer
R6531 T7810 T7812 nummod 20,Tris
R6532 T7811 T7812 compound mM,Tris
R6533 T7812 T7808 appos Tris,buffer
R6534 T7813 T7814 compound HCl,pH
R6535 T7814 T7808 appos pH,buffer
R6536 T7815 T7814 nummod 8.0,pH
R6537 T7816 T7814 punct ",",pH
R6538 T7817 T7818 nummod 0.1,%
R6539 T7818 T7819 npadvmod %,SDS
R6540 T7819 T7814 appos SDS,pH
R6541 T7820 T7819 punct ",",SDS
R6542 T7821 T7822 nummod 1,%
R6543 T7822 T7824 compound %,X-100
R6544 T7823 T7824 compound Triton,X-100
R6545 T7824 T7819 conj X-100,SDS
R6546 T7825 T7824 punct ",",X-100
R6547 T7826 T7828 nummod 2,EDTA
R6548 T7827 T7828 compound mM,EDTA
R6549 T7828 T7824 conj EDTA,X-100
R6550 T7829 T7828 punct ",",EDTA
R6551 T7830 T7832 nummod 150,NaCl
R6552 T7831 T7832 compound mM,NaCl
R6553 T7832 T7828 appos NaCl,EDTA
R6554 T7833 T7828 punct ),EDTA
R6555 T7834 T7819 punct ",",SDS
R6556 T7835 T7836 nummod four,times
R6557 T7836 T7819 npadvmod times,SDS
R6558 T7837 T7819 prep with,SDS
R6559 T7838 T7840 amod high,buffer
R6560 T7839 T7840 compound salt,buffer
R6561 T7840 T7837 pobj buffer,with
R6562 T7841 T7844 punct (,Tris
R6563 T7842 T7844 nummod 20,Tris
R6564 T7843 T7844 compound mM,Tris
R6565 T7844 T7840 appos Tris,buffer
R6566 T7845 T7846 compound HCl,pH
R6567 T7846 T7885 nsubj pH,extracted
R6568 T7847 T7846 nummod 8.0,pH
R6569 T7848 T7846 punct ",",pH
R6570 T7849 T7850 nummod 0.1,%
R6571 T7850 T7851 npadvmod %,SDS
R6572 T7851 T7846 npadvmod SDS,pH
R6573 T7852 T7851 punct ",",SDS
R6574 T7853 T7854 nummod 1,%
R6575 T7854 T7856 compound %,X-100
R6576 T7855 T7856 compound Triton,X-100
R6577 T7856 T7851 appos X-100,SDS
R6578 T7857 T7856 punct ",",X-100
R6579 T7858 T7860 nummod 2,EDTA
R6580 T7859 T7860 compound mM,EDTA
R6581 T7860 T7856 conj EDTA,X-100
R6582 T7861 T7860 punct ",",EDTA
R6583 T7862 T7864 nummod 500,NaCl
R6584 T7863 T7864 compound mM,NaCl
R6585 T7864 T7860 appos NaCl,EDTA
R6586 T7865 T7860 punct ),EDTA
R6587 T7866 T7851 punct ",",SDS
R6588 T7867 T7868 advmod once,with
R6589 T7868 T7851 prep with,SDS
R6590 T7869 T7870 compound TE,buffer
R6591 T7870 T7868 pobj buffer,with
R6592 T7871 T7851 punct (,SDS
R6593 T7872 T7874 nummod 10,Tris
R6594 T7873 T7874 compound mM,Tris
R6595 T7874 T7851 appos Tris,SDS
R6596 T7875 T7876 compound HCl,pH
R6597 T7876 T7851 appos pH,SDS
R6598 T7877 T7876 nummod 8.0,pH
R6599 T7878 T7876 punct ",",pH
R6600 T7879 T7881 nummod 1,EDTA
R6601 T7880 T7881 compound mM,EDTA
R6602 T7881 T7876 appos EDTA,pH
R6603 T7882 T7876 punct ),pH
R6604 T7883 T7851 punct ",",SDS
R6605 T7884 T7846 cc and,pH
R6606 T7885 T7885 ROOT extracted,extracted
R6607 T7886 T7885 prep in,extracted
R6608 T7887 T7888 compound TE,buffer
R6609 T7888 T7886 pobj buffer,in
R6610 T7889 T7888 acl containing,buffer
R6611 T7890 T7891 nummod 2,%
R6612 T7891 T7889 dobj %,containing
R6613 T7892 T7889 npadvmod SDS,containing
R6614 T7893 T7885 punct .,extracted

GO-MF

Id Subject Object Predicate Lexical cue
T8082 8-18 http://purl.obolibrary.org/obo/GO_0003823 denotes antibodies

GO-CC

Id Subject Object Predicate Lexical cue
T8077 8-18 http://purl.obolibrary.org/obo/GO_0019815 denotes antibodies
T8079 8-18 http://purl.obolibrary.org/obo/GO_0042571 denotes antibodies

sentences

Id Subject Object Predicate Lexical cue
T7522 0-598 Sentence denotes Primary antibodies were: anti-p65 (sc-372), anti-IκBα (sc-203) and rabbit IgG (sc-2027) from Santa Cruz Biotechnology; anti-FLAG M2 from Sigma–Aldrich. Immunoprecipitations were carried out at 4°C overnight and immune complexes were collected with protein G agarose beads, washed five times with low salt buffer (20 mM Tris–HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), four times with high salt buffer (20 mM Tris–HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), once with TE buffer (10 mM Tris–HCl pH 8.0, 1 mM EDTA), and extracted in TE buffer containing 2% SDS.
T90 0-151 Sentence denotes Primary antibodies were: anti-p65 (sc-372), anti-IκBα (sc-203) and rabbit IgG (sc-2027) from Santa Cruz Biotechnology; anti-FLAG M2 from Sigma–Aldrich.
T91 152-598 Sentence denotes Immunoprecipitations were carried out at 4°C overnight and immune complexes were collected with protein G agarose beads, washed five times with low salt buffer (20 mM Tris–HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl), four times with high salt buffer (20 mM Tris–HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl), once with TE buffer (10 mM Tris–HCl pH 8.0, 1 mM EDTA), and extracted in TE buffer containing 2% SDS.

events-check-again

Id Subject Object Predicate Lexical cue
T8129 248-257 Protein denotes protein G

bionlp-st-ge-2016-reference-tees

Id Subject Object Predicate Lexical cue
T8141 30-33 Protein denotes p65
T8142 44-62 Protein denotes anti-IκBα (sc-203)
T8143 74-77 Protein denotes IgG

test2

Id Subject Object Predicate Lexical cue
T7497 248-257 Protein denotes protein G

bionlp-st-ge-2016-reference

Id Subject Object Predicate Lexical cue
T7507 248-257 Protein denotes protein G

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T7533 30-33 Q04206 denotes p65
T7534 30-33 P21579 denotes p65
T7535 49-53 P25963 denotes IκBα
T7536 328-330 P0A7Z4 denotes pH
T7537 437-439 P0A7Z4 denotes pH
T7538 533-535 P0A7Z4 denotes pH