title: Male Patient  487 - Cy3:16803:13108062-Male-Female

description: Analysis genomic DNA male patient 487

source_name: Male Patient  487 - Cy3


title: Male Patient  593 - Cy3:17243:13115081-Male-Female

status: Public on Jun 23 2007

type: genomic

city: Nijmegen

first: Joris

middle: Andre

last: Veltman

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: Analysis genomic DNA male patient 593

hyb_protocol: Test and reference samples were mixed with 120 µg human Cot-1 DNA, co-precipitated and resuspended in 120 µl of a hybridization solution containing 50% formamide, 10% dextran sulfate, 2X SCC, 4% SDS and 10 µg/µl yeast tRNA. Overnight hybridization and post-hybridization washing procedures were performed using a GeneTac Hybridization Station

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4200AL fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis software.

data_processing: The log2 transformed test over reference ratio for each clone was normalized by subtracting its local mean log2 test over reference ratio obtained by a weighted median filter (Yin and Yang 1996). This filter averages the log ratios of autosomal clones weighted by a Gaussian with its mean at the spot to be normalized and a standard deviation of one physical millimetre on the array.

molecule: genomic DNA

organism: Homo sapiens

source_name: Male Patient  593 - Cy3

label_protocol: Five hundred nanogram of genomic DNA was labelled by random priming with Cy3-dUTP

extract_protocol: Genomic DNA extracted from blood

tag: Genomic DNA isolated from blood

source_name: female ref pool - Cy5

label_protocol: Five hundred nanogram of genomic DNA was labelled by random priming with Cy5-dUTP


title: Male Patient  504 - Cy3:16841:13108064-Male-Female

description: Analysis genomic DNA male patient 504

source_name: Male Patient  504 - Cy3


title: Male Patient  628 - Cy3:18262:13127179-Male-Female

description: Analysis genomic DNA male patient 628

source_name: Male Patient  628 - Cy3


title: Male Patient  477 - Cy3:15884:13107812-Male-Female

description: Analysis genomic DNA male patient 477

source_name: Male Patient  477 - Cy3


title: Male Patient  468 - Cy3:16394:13108001-Male-Female

description: Analysis genomic DNA male patient 468

source_name: Male Patient  468 - Cy3


title: Male Patient  473 - Cy3:18757:13127200-Male-Female

description: Analysis genomic DNA male patient 473

source_name: Male Patient  473 - Cy3


title: Male Patient  448 - Cy3:16670:13105958-Male-Female

description: Analysis genomic DNA male patient 448

source_name: Male Patient  448 - Cy3


title: Male Patient  478 - Cy3:16931:13108052-Male-Female

description: Analysis genomic DNA male patient 478

source_name: Male Patient  478 - Cy3


title: Male Patient  465 - Cy3:18276:13127178-Male-Female

description: Analysis genomic DNA male patient 465

source_name: Male Patient  465 - Cy3


title: Male Patient  493 - Cy3:17970:13123993-Male-Female

description: Analysis genomic DNA male patient 493

source_name: Male Patient  493 - Cy3


title: Male Patient  459 - Cy3:16323:13105405-Male-Female

description: Analysis genomic DNA male patient 459

source_name: Male Patient  459 - Cy3


title: Male Patient  415 - Cy3:18753:13127198-Male-Female

description: Analysis genomic DNA male patient 415

source_name: Male Patient  415 - Cy3


title: Male Patient  446 - Cy3:17978:13123994-Male-Female

description: Analysis genomic DNA male patient 446

source_name: Male Patient  446 - Cy3


title: Male Patient  418 - Cy3:21236:13300988-Male-Female

description: Analysis genomic DNA male patient 418

source_name: Male Patient  418 - Cy3


title: Male Patient  460 - Cy3:16940:13105893-Male-Female

description: Analysis genomic DNA male patient 460

source_name: Male Patient  460 - Cy3


title: Male Patient  436 - Cy3:16566:13108007-Male-Female

description: Analysis genomic DNA male patient 436

source_name: Male Patient  436 - Cy3


title: Male Patient  412 - Cy3:16666:13107995-Male-Female

description: Analysis genomic DNA male patient 412

source_name: Male Patient  412 - Cy3


title: Male Patient  431 - Cy3:15707:13068540-Male-Female

description: Analysis genomic DNA male patient 431

source_name: Male Patient  431 - Cy3

source_name: female ref pool - Cy5


title: Male Patient  352 - Cy3:17580:13115084-Male-Female

description: Analysis genomic DNA male patient 352

source_name: Male Patient  352 - Cy3


title: Male Patient  367 - Cy3:17952:13123992-Male-Female

description: Analysis genomic DNA male patient 367

source_name: Male Patient  367 - Cy3


title: Male Patient  440 - Cy3:16662:13105957-Male-Female

description: Analysis genomic DNA male patient 440

source_name: Male Patient  440 - Cy3


title: Male Patient  383 - Cy3:17573:13115085-Male-Female

description: Analysis genomic DNA male patient 383

source_name: Male Patient  383 - Cy3


title: Male Patient  409 - Cy3:18749:13126691-Male-Female

description: Analysis genomic DNA male patient 409

source_name: Male Patient  409 - Cy3


title: Male Patient  381 - Cy3:18296:13127177-Male-Female

description: Analysis genomic DNA male patient 381

source_name: Male Patient  381 - Cy3


title: Male Patient  334 - Cy3:17008:13108066-Male-Female

description: Analysis genomic DNA male patient 334

source_name: Male Patient  334 - Cy3


title: Male Patient  365 - Cy3:18266:13127202-Male-Female

description: Analysis genomic DNA male patient 365

source_name: Male Patient  365 - Cy3


title: Male Patient  035 - Cy5:19875:13231202-Male-Male

description: Analysis genomic DNA male patient 035

source_name: male ref pool - Cy3

source_name: Male Patient  035 - Cy5


title: Male Patient  390 - Cy3:16658:13107994-Male-Female

description: Analysis genomic DNA male patient 390

source_name: Male Patient  390 - Cy3


title: Male Patient  345 - Cy3:18741:13126690-Male-Female

description: Analysis genomic DNA male patient 345

source_name: Male Patient  345 - Cy3


title: Male Patient  345 - Cy3:16315:13105404-Male-Female

description: Analysis genomic DNA male patient 345


title: Male Patient  280 - Cy3:15551:13059561-Male-Female

description: Analysis genomic DNA male patient 280

source_name: Male Patient  280 - Cy3


title: Male Patient  366 - Cy3:17948:13123999-Male-Female

description: Analysis genomic DNA male patient 366

source_name: Male Patient  366 - Cy3


title: Male Patient  293 - Cy3:15862:13107817-Male-Female

description: Analysis genomic DNA male patient 293

source_name: Male Patient  293 - Cy3


title: Male Patient  338 - Cy3:16295:13108011-Male-Female

description: Analysis genomic DNA male patient 338

source_name: Male Patient  338 - Cy3


title: Male Patient  329 - Cy3:16303:13108010-Male-Female

description: Analysis genomic DNA male patient 329

source_name: Male Patient  329 - Cy3

source_name: female ref pool - Cy5


title: Male Patient  035 - Cy3:19243:13211877-Male-Males

description: Analysis genomic DNA male patient 035

source_name: Male Patient  035 - Cy3

source_name: male ref pool - Cy5


title: Male Patient  203 - Cy3:16205:13105963-Male-Female

description: Analysis genomic DNA male patient 203

source_name: Male Patient  203 - Cy3


title: Male Patient  221 - Cy3:20327:13207943-Male-Male

description: Analysis genomic DNA male patient 221

source_name: Male Patient  221 - Cy3


title: Male Patient  186 - Cy3:15539:13068544-Male-Female

description: Analysis genomic DNA male patient 186

source_name: Male Patient  186 - Cy3


title: Male Patient  332 - Cy3:17956:13123987-Male-Female

description: Analysis genomic DNA male patient 332

source_name: Male Patient  332 - Cy3


title: Male Patient  172 - Cy3:13565:13012271-Male-Female

description: Analysis genomic DNA male patient 172

source_name: Male Patient  172 - Cy3


title: Male Patient  180 - Cy3:16897:13108055-Male-Female

description: Analysis genomic DNA male patient 180

source_name: Male Patient  180 - Cy3


title: Male Patient  215 - Cy3:16901:13108058-Male-Female

description: Analysis genomic DNA male patient 215

source_name: Male Patient  215 - Cy3


title: Male Patient  165 - Cy3:13241:12964538-Male-Female

description: Analysis genomic DNA male patient 165

source_name: Male Patient  165 - Cy3


title: Male Patient  132 - Cy3:17982:13123996-Male-Female

description: Analysis genomic DNA male patient 132

source_name: Male Patient  132 - Cy3


title: Male Patient  099 - Cy3:15673:13105842-Male-Female

description: Analysis genomic DNA male patient 099

source_name: Male Patient  099 - Cy3


title: Male Patient  097 - Cy3:16311:13105401-Male-Female

description: Analysis genomic DNA male patient 097

source_name: Male Patient  097 - Cy3


title: Male Patient  091 - Cy3:18841:13126696-Male-Female

description: Analysis genomic DNA male patient 091

source_name: Male Patient  091 - Cy3


title: Male Patient  120 - Cy3:11836:12994249-Male-Female

description: Analysis genomic DNA male patient 120

source_name: Male Patient  120 - Cy3


title: Male Patient  059 - Cy3:16385:13108008-Male-Female

description: Analysis genomic DNA male patient 059

source_name: Male Patient  059 - Cy3


title: Male Patient  127 - Cy3:16381:13107998-Male-Female

description: Analysis genomic DNA male patient 127

source_name: Male Patient  127 - Cy3

source_name: female ref pool - Cy5


title: Male Patient  167 - Cy3:18957:13126708-Male-Female

description: Analysis genomic DNA male patient 167

source_name: Male Patient  167 - Cy3


title: Male Patient  151 - Cy3:17252:13105898-Male-Female

description: Analysis genomic DNA male patient 151

source_name: Male Patient  151 - Cy3


title: Male Patient  071 - Cy3:11181:12940494-Male-Female

description: Analysis genomic DNA male patient 071

source_name: Male Patient  071 - Cy3


title: Male Patient  043 - Cy3:19027:13126706-Male-Female

description: Analysis genomic DNA male patient 043

source_name: Male Patient  043 - Cy3


title: Male Patient  071 - Cy3:15816:13068557-Male-Female

description: Analysis genomic DNA male patient 071


title: Male Patient  011 - Cy3:17248:13115080-Male-Female

description: Analysis genomic DNA male patient 011

source_name: Male Patient  011 - Cy3


title: Male Patient  041 - Cy3:18949:13126711-Male-Female

description: Analysis genomic DNA male patient 041

source_name: Male Patient  041 - Cy3


title: Female Patient  684 - Cy3: 532:22241:13406040-Female-Female

description: Analysis genomic DNA male patient 684

source_name: Female Patient  684 - Cy3


title: Female Patient  777 - Cy3: 532:22285:13406046-Female-Female

description: Analysis genomic DNA male patient 777

source_name: Female Patient  777 - Cy3


title: Male Patient  065 - Cy3:11757:6695-Male-Female

description: Analysis genomic DNA male patient 065

source_name: Male Patient  065 - Cy3


title: Male Patient  043 - Cy3:18953:13126712-Male-Female

description: Analysis genomic DNA male patient 043


title: Female Patient  776 - Cy3: 532:22231:13406039-Female-Female

description: Analysis genomic DNA male patient 776

source_name: Female Patient  776 - Cy3


title: Male Patient  289 - Cy3:16307:13105400-Male-Female

description: Analysis genomic DNA male patient 289

source_name: Male Patient  289 - Cy3


title: Female Patient  782 - Cy3: 532:22265:13406048-Female-Female

description: Analysis genomic DNA male patient 782

source_name: Female Patient  782 - Cy3


title: Female Patient  790 - Cy3: 532:22294:13401516-Female-Female

description: Analysis genomic DNA male patient 790

source_name: Female Patient  790 - Cy3


title: Female Patient  762 - Cy3: 532:22141:13401528-Female-Female

description: Analysis genomic DNA male patient 762

source_name: Female Patient  762 - Cy3


title: Female Patient  579 - Cy3: 532:22145:13401533-Female-Female

description: Analysis genomic DNA male patient 579

source_name: Female Patient  579 - Cy3


title: Female Patient  783 - Cy3: 532:22275:13406052-Female-Female

description: Analysis genomic DNA male patient 783

source_name: Female Patient  783 - Cy3


title: Female Patient  634 - Cy3: 532:22117:13401531-Female-Female

description: Analysis genomic DNA male patient 634

source_name: Female Patient  634 - Cy3

source_name: female ref pool - Cy5


title: Female Patient  812 - Cy3: 532:22363:13390739-Female-Female

description: Analysis genomic DNA male patient 812

source_name: Female Patient  812 - Cy3


title: Female Patient  747 - Cy3: 532:21911:13302443-Female-Female

description: Analysis genomic DNA male patient 747

source_name: Female Patient  747 - Cy3


title: Female Patient  824 - Cy3: 532:22090:13401538-Female-Female

description: Analysis genomic DNA male patient 824

source_name: Female Patient  824 - Cy3


title: Female Patient  774 - Cy3: 532:22307:13390743-Female-Female

description: Analysis genomic DNA male patient 774

source_name: Female Patient  774 - Cy3


title: Female Patient  737 - Cy3: 532:21855:13302463-Female-Female

description: Analysis genomic DNA male patient 737

source_name: Female Patient  737 - Cy3


title: Female Patient  743 - Cy3: 532:21976:13302456-Female-Female

description: Analysis genomic DNA male patient 743

source_name: Female Patient  743 - Cy3


title: Female Patient  761 - Cy3: 532:21896:13302454-Female-Female

description: Analysis genomic DNA male patient 761

source_name: Female Patient  761 - Cy3


title: Female Patient  731 - Cy3: 532:21194:13301593-Female-Female

description: Analysis genomic DNA male patient 731

source_name: Female Patient  731 - Cy3


title: Female Patient  715 - Cy3: 532:21188:13302151-Female-Female

description: Analysis genomic DNA male patient 715

source_name: Female Patient  715 - Cy3


title: Female Patient  153 - Cy3: 532:21435:13302167-Female-Female

description: Analysis genomic DNA male patient 153

source_name: Female Patient  153 - Cy3


title: Female Patient  748 - Cy3: 532:21984:13302453-Female-Female

description: Analysis genomic DNA male patient 748

source_name: Female Patient  748 - Cy3


title: Female Patient  763 - Cy3: 532:21252:13300991-Female-Female

description: Analysis genomic DNA male patient 763

source_name: Female Patient  763 - Cy3


title: Female Patient  671 - Cy3: 532:21107:13302152-Female-Female

description: Analysis genomic DNA male patient 671

source_name: Female Patient  671 - Cy3


title: Female Patient  438 - Cy3: 532:21255:13300986-Female-Female

description: Analysis genomic DNA male patient 438

source_name: Female Patient  438 - Cy3


title: Female Patient  707 - Cy3: 532:20992:13301576-Female-Female

description: Analysis genomic DNA male patient 707

source_name: Female Patient  707 - Cy3


title: Female Patient  735 - Cy3: 532:21853:13301203-Female-Female

description: Analysis genomic DNA male patient 735

source_name: Female Patient  735 - Cy3


title: Female Patient  689 - Cy3: 532:21505:13301188-Female-Female

description: Analysis genomic DNA male patient 689

source_name: Female Patient  689 - Cy3

source_name: female ref pool - Cy5


title: Female Patient  741 - Cy3: 532:21859:13301202-Female-Female

description: Analysis genomic DNA male patient 741

source_name: Female Patient  741 - Cy3


title: Female Patient  740 - Cy3: 532:21857:13301200-Female-Female

description: Analysis genomic DNA male patient 740

source_name: Female Patient  740 - Cy3


title: Female Patient  083 - Cy5: 635:13341:12939907-Male-Female

description: Analysis genomic DNA male patient 083

source_name: male ref pool - Cy3

source_name: Female Patient  083 - Cy5


title: Female Patient  723 - Cy3: 532:21430:13301187-Female-Female

description: Analysis genomic DNA male patient 723

source_name: Female Patient  723 - Cy3


title: Female Patient  202 - Cy5: 635:13943:13011813-Female-Female

description: Analysis genomic DNA male patient 202

source_name: female ref pool - Cy3

source_name: Female Patient  202 - Cy5


title: Female Patient  121 - Cy5: 635:14020:13011828-Male-Female

description: Analysis genomic DNA male patient 121

source_name: Female Patient  121 - Cy5


title: Female Patient  419 - Cy3: 532:21254:13300989-Female-Female

description: Analysis genomic DNA male patient 419

source_name: Female Patient  419 - Cy3


title: Female Patient 157 - Cy5: 635:11951:12994256-Male-Female

description: Analysis genomic DNA male patient 157

source_name: Female Patient 157 - Cy5


title: Female Patient  069 - Cy5: 635:10440:12940336-Female-Female

description: Analysis genomic DNA male patient 069

source_name: Female Patient  069 - Cy5


title: Female Patient  131 - Cy3: 532:21417:13300973-Female-Female

description: Analysis genomic DNA male patient 131

source_name: Female Patient  131 - Cy3


title: Female Patient  PN01-0013 - Cy3: 532:21212:13300982-Female-Female

description: Analysis genomic DNA male patient PN01-0013

source_name: Female Patient  PN01-0013 - Cy3


title: Female Patient  067 - Cy5: 635:10500:12940197-Male-Female

description: Analysis genomic DNA male patient 067

source_name: Female Patient  067 - Cy5


title: Female Patient  679 - Cy3: 532:21451:13300967-Female-Female

description: Analysis genomic DNA male patient 679

source_name: Female Patient  679 - Cy3


title: Female Patient  394 - Cy3: 532:21447:13300968-Female-Female

description: Analysis genomic DNA male patient 394

source_name: Female Patient  394 - Cy3


title: Female Patient  320 - Cy3: 532:21170:13302154-Female-Female

description: Analysis genomic DNA male patient 320

source_name: Female Patient  320 - Cy3

source_name: female ref pool - Cy5


title: Female Patient  320 - Cy3: 532:20468:13231211-Female-Female

description: Analysis genomic DNA male patient 320


title: Female Patient  702 - Cy3: 532:21507:13300965-Female-Female

description: Analysis genomic DNA male patient 702

source_name: Female Patient  702 - Cy3


title: Female Patient  526 - Cy3: 532:19886:13231215-Female-Female

description: Analysis genomic DNA male patient 526

source_name: Female Patient  526 - Cy3


title: Female Patient  545 - Cy3: 532:20494:13231200-Female-Female

description: Analysis genomic DNA male patient 545

source_name: Female Patient  545 - Cy3


title: Female Patient  661 - Cy5: 635:17539:13115089-Male-Female

description: Analysis genomic DNA male patient 661

source_name: male ref pool - Cy3

source_name: Female Patient  661 - Cy5


title: Female Patient  348 - Cy3: 532:20006:13231209-Female-Female

description: Analysis genomic DNA male patient 348

source_name: Female Patient  348 - Cy3


title: Female Patient  PN01-0011 - Cy3: 532:20516:13231106-Female-Female

description: Analysis genomic DNA male patient PN01-0011

source_name: Female Patient  PN01-0011 - Cy3


title: Female Patient  662 - Cy3: 532:19909:13211890-Female-Female

description: Analysis genomic DNA male patient 662

source_name: Female Patient  662 - Cy3


title: Female Patient  754 - Cy3: 532:20834:13231109-Female-Female

description: Analysis genomic DNA male patient 754

source_name: Female Patient  754 - Cy3


title: Female Patient  749 - Cy3: 532:20819:13231102-Female-Female

description: Analysis genomic DNA male patient 749

source_name: Female Patient  749 - Cy3


title: Male Patient  090 - Cy3:17897:13124002-Male-Female

description: Analysis genomic DNA male patient 090

source_name: Male Patient  090 - Cy3


title: Female Patient  667 - Cy3: 532:19904:13211902-Female-Female

description: Analysis genomic DNA male patient 667

source_name: Female Patient  667 - Cy3


title: Female Patient  680 - Cy3: 532:20343:13207931-Female-Female

description: Analysis genomic DNA male patient 680

source_name: Female Patient  680 - Cy3


title: Female Patient  733 - Cy3: 532:20796:13231105-Female-Female

description: Analysis genomic DNA male patient 733

source_name: Female Patient  733 - Cy3


title: Female Patient  686 - Cy3: 532:20521:13207950-Female-Female

description: Analysis genomic DNA male patient 686

source_name: Female Patient  686 - Cy3


title: Female Patient  668 - Cy3: 532:20347:13207944-Female-Female

description: Analysis genomic DNA male patient 668

source_name: Female Patient  668 - Cy3


title: Female Patient  586 - Cy3: 532:19795:13126798-Female-Female

description: Analysis genomic DNA male patient 586

source_name: Female Patient  586 - Cy3

source_name: female ref pool - Cy5


title: Female Patient PN01-0008 - Cy3:18272:13127205-Female-Male

description: Analysis genomic DNA male patient PN01-0008

source_name: Female Patient PN01-0008 - Cy3

source_name: male ref pool - Cy5


title: Female Patient 157 - Cy3:12176:12994261-Female-Male

description: Analysis genomic DNA male patient 157

source_name: Female Patient 157 - Cy3


title: Female Patient  682 - Cy3: 532:20420:13207940-Female-Female

description: Analysis genomic DNA male patient 682

source_name: Female Patient  682 - Cy3


title: Female Patient 020 - Cy3:12046:12994264-Female-Male

description: Analysis genomic DNA male patient 020

source_name: Female Patient 020 - Cy3


title: Female Patient  638 - Cy3:17874:13124004-Female-Male

description: Analysis genomic DNA male patient 638

source_name: Female Patient  638 - Cy3


title: Female Patient  658 - Cy3:17814:13118860-Female-Male

description: Analysis genomic DNA male patient 658

source_name: Female Patient  658 - Cy3


title: Female Patient  615 - Cy3:18861:13126714-Female-Male

description: Analysis genomic DNA male patient 615

source_name: Female Patient  615 - Cy3


title: Female Patient  620 - Cy3:18280:13127189-Female-Male

description: Analysis genomic DNA male patient 620

source_name: Female Patient  620 - Cy3


title: Female Patient 001 - Cy3:16238:13105315-Female-Male

description: Analysis genomic DNA male patient 001

source_name: Female Patient 001 - Cy3


title: Female Patient  154 - Cy3: 532:16531:13105367-Female-Female

description: Analysis genomic DNA male patient 154

source_name: Female Patient  154 - Cy3


title: Female Patient  642 - Cy3:17994:13127186-Female-Male

description: Analysis genomic DNA male patient 642

source_name: Female Patient  642 - Cy3


title: Female Patient  657 - Cy3:18294:13127199-Female-Male

description: Analysis genomic DNA male patient 657

source_name: Female Patient  657 - Cy3


title: Female Patient  658 - Cy3:17509:13105529-Female-Male

description: Analysis genomic DNA male patient 658


title: Female Patient  650 - Cy3:18318:13127193-Female-Male

description: Analysis genomic DNA male patient 650

source_name: Female Patient  650 - Cy3


title: Female Patient  630 - Cy3: 532:20543:13207955-Female-Female

description: Analysis genomic DNA male patient 630

source_name: Female Patient  630 - Cy3


title: Female Patient  625 - Cy3:18813:13126784-Female-Male

description: Analysis genomic DNA male patient 625

source_name: Female Patient  625 - Cy3


title: Female Patient  752 - Cy3: 532:20808:13231111-Female-Female

description: Analysis genomic DNA male patient 752

source_name: Female Patient  752 - Cy3

source_name: female ref pool - Cy5


title: Female Patient  620 - Cy3:17513:13105525-Female-Male

description: Analysis genomic DNA male patient 620

source_name: male ref pool - Cy5


title: Female Patient  596 - Cy3:17231:13105895-Female-Male

description: Analysis genomic DNA male patient 596

source_name: Female Patient  596 - Cy3


title: Female Patient  608 - Cy3:18765:13126697-Female-Male

description: Analysis genomic DNA male patient 608

source_name: Female Patient  608 - Cy3


title: Female Patient  562 - Cy3:16799:13107963-Female-Male

description: Analysis genomic DNA male patient 562

source_name: Female Patient  562 - Cy3


title: Female Patient  577 - Cy3:16935:13108053-Female-Male

description: Analysis genomic DNA male patient 577

source_name: Female Patient  577 - Cy3


title: Female Patient  561 - Cy3:16819:13107960-Female-Male

description: Analysis genomic DNA male patient 561

source_name: Female Patient  561 - Cy3


title: Female Patient  535 - Cy3:17910:13124007-Female-Male

description: Analysis genomic DNA male patient 535

source_name: Female Patient  535 - Cy3


title: Female Patient  557 - Cy3:17225:13115082-Female-Male

description: Analysis genomic DNA male patient 557

source_name: Female Patient  557 - Cy3


title: Female Patient  527 - Cy3:16811:13107958-Female-Male

description: Analysis genomic DNA male patient 527

source_name: Female Patient  527 - Cy3


title: Female Patient  475 - Cy3:17902:13124003-Female-Male

description: Analysis genomic DNA male patient 475

source_name: Female Patient  475 - Cy3


title: Female Patient  396 - Cy3:21667:13302467-Female-Male

description: Analysis genomic DNA male patient 396

source_name: Female Patient  396 - Cy3


title: Female Patient  584 - Cy3:18223:13123990-Female-Male

description: Analysis genomic DNA male patient 584

source_name: Female Patient  584 - Cy3


title: Female Patient  439 - Cy3:18821:13126787-Female-Male

description: Analysis genomic DNA male patient 439

source_name: Female Patient  439 - Cy3


title: Female Patient  447 - Cy3:18270:13123983-Female-Male

description: Analysis genomic DNA male patient 447

source_name: Female Patient  447 - Cy3


title: Female Patient  427 - Cy3:16651:13105956-Female-Male

description: Analysis genomic DNA male patient 427

source_name: Female Patient  427 - Cy3


title: Female Patient  519 - Cy3:16916:13108068-Female-Male

description: Analysis genomic DNA male patient 519

source_name: Female Patient  519 - Cy3


title: Female Patient  424 - Cy3:15609:13068535-Female-Male

description: Analysis genomic DNA male patient 424

source_name: Female Patient  424 - Cy3


title: Female Patient  496 - Cy3:21672:13302465-Female-Male

description: Analysis genomic DNA male patient 496

source_name: Female Patient  496 - Cy3

source_name: male ref pool - Cy5


title: Female Patient  053 - Cy3:21414:13302166-Female-Female

description: Analysis genomic DNA male patient 053

source_name: Female Patient  053 - Cy3

source_name: female ref pool - Cy5


title: Female Patient  472 - Cy3:21629:13302464-Female-Female

description: Analysis genomic DNA male patient 472

source_name: Female Patient  472 - Cy3


title: Female Patient  454 - Cy3:21256:13300987-Female-Female

description: Analysis genomic DNA male patient 454

source_name: Female Patient  454 - Cy3


title: Female Patient  447 - Cy3:16767:13062461-Female-Male

description: Analysis genomic DNA male patient 447


title: Female Patient  068 - Cy3: 532:20815:13231100-Female-Female

description: Analysis genomic DNA male patient 068

source_name: Female Patient  068 - Cy3


title: Female Patient  507 - Cy3:21829:13406034-Female-Female

description: Analysis genomic DNA male patient 507

source_name: Female Patient  507 - Cy3


title: Female Patient  594 - Cy3:16807:13107962-Female-Male

description: Analysis genomic DNA male patient 594

source_name: Female Patient  594 - Cy3


title: Female Patient  546 - Cy3:16815:13107961-Female-Male

description: Analysis genomic DNA male patient 546

source_name: Female Patient  546 - Cy3


title: Female Patient  064 - Cy3:19816:13301585-Female-Female

description: Analysis genomic DNA male patient 064

source_name: Female Patient  064 - Cy3


title: Female Patient  444 - Cy3:15641:13068549-Female-Male

description: Analysis genomic DNA male patient 444

source_name: Female Patient  444 - Cy3


title: Female Patient  025 - Cy3:22125:13401530-Female-Female

description: Analysis genomic DNA male patient 025

source_name: Female Patient  025 - Cy3


title: Female Patient  604 - Cy3:18286:13127190-Female-Male

description: Analysis genomic DNA male patient 604

source_name: Female Patient  604 - Cy3


title: Female Patient  156 - Cy3:19253:13211876-Female-Female

description: Analysis genomic DNA male patient 156

source_name: Female Patient  156 - Cy3


title: Female Patient  272 - Cy3:21148:13302150-Female-Female

description: Analysis genomic DNA male patient 272

source_name: Female Patient  272 - Cy3


title: Female Patient  160 - Cy3:21663:13302466-Female-Female

description: Analysis genomic DNA male patient 160

source_name: Female Patient  160 - Cy3


title: Female Patient  496 - Cy3:16190:13105393-Female-Male

description: Analysis genomic DNA male patient 496

source_name: Female Patient  496 - Cy3


title: Female Patient  181 - Cy3:21443:13300966-Female-Female

description: Analysis genomic DNA male patient 181

source_name: Female Patient  181 - Cy3


title: Female Patient  281 - Cy3:21503:13301186-Female-Female

description: Analysis genomic DNA male patient 281

source_name: Female Patient  281 - Cy3


title: Female Patient  006 - Cy3:21198:13302159-Female-Female

description: Analysis genomic DNA male patient 006

source_name: Female Patient  006 - Cy3

source_name: female ref pool - Cy5


title: Female Patient  191 - Cy3:19783:13126799-Female-Female

description: Analysis genomic DNA male patient 191

source_name: Female Patient  191 - Cy3


title: Female Patient  251 - Cy3:20551:13207957-Female-Female

description: Analysis genomic DNA male patient 251

source_name: Female Patient  251 - Cy3


title: Female Patient  162 - Cy3:19262:13126700-Female-Female

description: Analysis genomic DNA male patient 162

source_name: Female Patient  162 - Cy3


title: Female Patient  233 - Cy3:21499:13300963-Female-Female

description: Analysis genomic DNA male patient 233

source_name: Female Patient  233 - Cy3


title: Female Patient  396 - Cy3:16195:13105392-Female-Male

description: Analysis genomic DNA male patient 396

source_name: Female Patient  396 - Cy3

source_name: male ref pool - Cy5


title: Female Patient  370 - Cy3:17966:13123991-Female-Male

description: Analysis genomic DNA male patient 370

source_name: Female Patient  370 - Cy3


title: Female Patient  386 - Cy3:16554:13105949-Female-Male

description: Analysis genomic DNA male patient 386

source_name: Female Patient  386 - Cy3


title: Female Patient  110 - Cy3:20416:13207951-Female-Female

description: Analysis genomic DNA male patient 110

source_name: Female Patient  110 - Cy3


title: Female Patient  369 - Cy3:17986:13124000-Female-Male

description: Analysis genomic DNA male patient 369

source_name: Female Patient  369 - Cy3


title: Female Patient  377 - Cy3:17893:13124001-Female-Male

description: Analysis genomic DNA male patient 377

source_name: Female Patient  377 - Cy3


title: Female Patient  386 - Cy3:16546:13105948-Female-Male

description: Analysis genomic DNA male patient 386


title: Female Patient  376 - Cy3:18155:13124008-Female-Male

description: Analysis genomic DNA male patient 376

source_name: Female Patient  376 - Cy3


title: Female Patient  685 - Cy3:20002:13211881-Female-Male

description: Analysis genomic DNA male patient 685

source_name: Female Patient  685 - Cy3


title: Female Patient  394 - Cy3:16920:13108061-Female-Male

description: Analysis genomic DNA male patient 394

source_name: Female Patient  394 - Cy3


title: Female Patient  348 - Cy3:18745:13126692-Female-Male

description: Analysis genomic DNA male patient 348

source_name: Female Patient  348 - Cy3


title: Female Patient  348 - Cy3:15880:13107810-Female-Male

description: Analysis genomic DNA male patient 348


title: Female Patient  346 - Cy3:16538:13105947-Female-Male

description: Analysis genomic DNA male patient 346

source_name: Female Patient  346 - Cy3


title: Female Patient  328 - Cy3:15683:13105841-Female-Male

description: Analysis genomic DNA male patient 328

source_name: Female Patient  328 - Cy3


title: Female Patient  331 - Cy3:17990:13127185-Female-Male

description: Analysis genomic DNA male patient 331

source_name: Female Patient  331 - Cy3


title: Female Patient  325 - Cy3:16995:13107957-Female-Male

description: Analysis genomic DNA male patient 325

source_name: Female Patient  325 - Cy3


title: Female Patient  336 - Cy3:15867:13107815-Female-Male

description: Analysis genomic DNA male patient 336

source_name: Female Patient  336 - Cy3


title: Female Patient  252 - Cy3:15894:13107813-Female-Male

description: Analysis genomic DNA male patient 252

source_name: Female Patient  252 - Cy3


title: Female Patient  220 - Cy3:17974:13123997-Female-Male

description: Analysis genomic DNA male patient 220

source_name: Female Patient  220 - Cy3


title: Female Patient  251 - Cy3:18924:13126709-Female-Male

description: Analysis genomic DNA male patient 251

source_name: Female Patient  251 - Cy3

source_name: male ref pool - Cy5


title: Female Patient  233 - Cy3:18835:13126701-Female-Male

description: Analysis genomic DNA male patient 233

source_name: Female Patient  233 - Cy3


title: Female Patient  241 - Cy3:21465:13300962-Female-Male

description: Analysis genomic DNA male patient 241

source_name: Female Patient  241 - Cy3


title: Female Patient  16560 - Cy3:16246:13105390-Female-Male

description: Analysis genomic DNA male patient 16560

source_name: Female Patient  16560 - Cy3


title: Female Patient  202 - Cy3:13573:13012257-Female-Male

description: Analysis genomic DNA male patient 202

source_name: Female Patient  202 - Cy3


title: Female Patient  241 - Cy3:16200:13105312-Female-Male

description: Analysis genomic DNA male patient 241


title: Female Patient  368 - Cy3:18209:13123981-Female-Male

description: Analysis genomic DNA male patient 368

source_name: Female Patient  368 - Cy3


title: Female Patient  16560 - Cy3:15492:13068550-Female-Male

description: Analysis genomic DNA male patient 16560


title: Female Patient  067 - Cy3:10436:6696-Female-Male

description: Analysis genomic DNA male patient 067

source_name: Female Patient  067 - Cy3


title: Female Patient  16560 - Cy3:16259:13105317-Female-Male

description: Analysis genomic DNA male patient 16560


title: Female Patient  173 - Cy3:21223:13211892-Female-Male

description: Analysis genomic DNA male patient 173

source_name: Female Patient  173 - Cy3


title: Female Patient  121 - Cy3:13209:12964534-Female-Male

description: Analysis genomic DNA male patient 121

source_name: Female Patient  121 - Cy3


title: Female Patient  001 - Cy3:16251:13105318-Female-Male

description: Analysis genomic DNA male patient 001

source_name: Female Patient  001 - Cy3


title: Female Patient  001 - Cy3:16267:13105320-Female-Male

description: Analysis genomic DNA male patient 001


title: HeLa_TMPyP4 Treatment_24hrs_Dyeswap1

status: Public on Jun 20 2007

type: RNA

city: Delhi

first: Anjali

last: Verma

state: Delhi

address: Mall road

department: Structural Biology and Genome Informatics Division

country: India

institute: Institute of Genomics and Integrative Biology

description: HeLa S3 cells were grown in Dulbecco's modified eagle medium (DMEM), 3.7 g/L sodium bicarbonate, 90%; fetal bovine serum, 10%. Cells were washed twice with 1X PBS before RNA isolation.

hyb_protocol: Hybridization was done in DigEasy hybridization buffer (Roche). To prevent non-specific hybridizations single stranded DNA from salmon testes and yeast transfer RNA were used. Hybridizations were performed at 37ºC for 16hrs.

scan_protocol: Slides were scanned at 10um resolution with Genepix pro 6.0 scanner using two different lasers, for Cy5 (635nm) and for Cy3 (532 nm).

data_processing: GenePixPro 6.0

molecule: total RNA

source_name: HeLa S3 cell culture

label_protocol: Labeling was done with the help of cRNA target synthesis and labeling kit provided by Roche, as per manufacturer protocol.

growth_protocol: Cells were grown in 25cm2 canted flasks in the presence of air, 95%, 5% CO2 at 37ºC. The cells were grown in Dulbecco's modified eagle medium (DMEM), 3.7 g/L sodium bicarbonate, 90%; fetal bovine serum, 10%. After treatments the cells were grown in minimum exposure to light

extract_protocol: Total RNA was isolated with Trizol reagent as per manufacturer protocol(SIGMA).

treatment_protocol: Cells were grown to 50% confluency before TMPyP4 treatments (100 uM final concentration in complete medium), in minimum exposure to light

tag: HeLa S3 cell line is a subclone of HeLa cells which is derived from cervix cancer epithelial cells (ADENOCARCINOMA)

label: Cy3, treated


title: Female Patient  004 - Cy3:16379:13108006-Female-Male

description: Analysis genomic DNA male patient 004

source_name: Female Patient  004 - Cy3


title: Female Patient  001 - Cy3:16264:13105391-Female-Male

description: Analysis genomic DNA male patient 001


title: HeLa_TMPyP4 Treatment_24hrs_Dyeswap2


title: hsa_hippocamp-adult vs. synthetic miRNA pool

status: Public on Jun 17 2007

city: COLOGNE

first: Frank

last: Huebel

state: NRW

address: Stoeckheimer Weg 1

department: MACS Molecular 9

country: Germany

institute: Miltenyi Biotec GmbH, MACS Molecular Business Unit

description: PMID

hyb_protocol: 5 µg of respective total RNA were mixed with 2.5 fmol of each of four RNA oligonucleotides reverse complement to miRControl 1 probes and 5 fmol of each of 20 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The sy

scan_protocol: Image capture was done with Agilent DNA-Microarray Scanner (Agilent, Santa Clara, CA)

data_processing: Signal processing and quantification was done with ImaGene software version 5.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the ratio of both fluorescent labels. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity in of the miRNAs derived from the samples of interest was two-fold the mean background value (2bkg dataset). The mean ratios of all probes were normalized to the median of the ratios detected for the spiked 20 synthetic RNA oligonucleotides reverse complement to miRControl 3 probes.

organism: synthetic construct

source_name: synthetic miRNA pool

label_protocol: 5 µg total RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array labeling kit, Exiqon) following the instructions of the manufacturer

extract_protocol: Total RNA was extracted as described in: Pfeffer, S., Lagos-Quintana, M., and Tuschl, T. (2003). Cloning of small RNA molecules. In Current Protocols in Molecular Biology, F. M. Ausubel, R. Brent, R. E. Kingston , D. D. Moore, J. G. Seidmann, J. A. Smith, and K. Struhl, eds. (New York, John Wiley and Sons), pp. 26.24.21-26.24.18.

tag: 5 fmol of each of 816 synthetic miRNAs were pooled and labelled.

source_name: nervous system, central nervous system, brain


title: hsa_T-cell-CD4-A301 vs. synthetic miRNA pool rep1

description: PMID

source_name: hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4

tag: CD4+ T-cell line provided by F.A. Grässer, graesser@med-rz.uni-sb.de


title: hsa_T-cell-CD4-A301 vs. synthetic miRNA pool rep2

description: PMID

hyb_protocol: 10 µg of respective total RNA were mixed with 2.5 fmol of each of four RNA oligonucleotides reverse complement to miRControl 1 probes and 5 fmol of each of 20 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The s


title: Female Patient  037 - Cy3:18945:13126710-Female-Male

description: Analysis genomic DNA male patient 037

source_name: Female Patient  037 - Cy3


title: HeLa_TMPyP4 Treatment_24hrs_Replicate1

source_name: Hela Cell culture

label: Cy5, treated


title: hsa_Gliobl-SNb19 vs. synthetic miRNA pool

description: PMID

source_name: nervous system, central nervous system, brain, glioblastoma cell

tag: Human glioblastoma cell line obtained from DSMZ (DSMZ no

value: ACC 325) established from the surgical resection of a left parieto-occipital glioblastoma from a 47-year-old man in 1980; cells were described to secrete plasminogen activator, to be clonogenic in soft agar and to be tumorigenic in nude mice


title: hsa_Hepatoma_PLC vs. synthetic miRNA pool

description: PMID

source_name: liver, hepatoma cell

tag: Hepatoma cell line, HBV infected, Source ATCC (ATCC no


title: HeLa_TMPyP4 Treatment_24hrs_Replicate2


title: hsa_hepatocell-carcinoma-Huh7-mock vs. synthetic miRNA pool

description: PMID

source_name: liver, hepatocellular carcinoma cell

tag: Huh7.5, not infected. Source

value: kind gift of C.Rice (Blight, K. J., McKeating, J. A. & Rice, C. M. (2002) J. Virol. 76, 13001–13014. ).  This strain has a single nucleotide substitution of RIG-I rendering an amino acid change in codon 55 (T55I) leading to permissiveness for HCV RNA replication ( Sumpter, R., Jr., Loo, Y. M., Foy, E., Li, K., Yoneyama, M., Fujita, T., Lemon, S. M. & Gale, M., Jr. (2005) J. Virol. 79, 2689–2699)


title: i3ERbeta30h+tet+E2(5)UHR(3)array94 T47D cells with inducible ERbeta

status: Public on Jun 01 2007

city: Provo

first: Chin-Yo

last: Lin

state: UT

address: 753 WIDB

department: Microbiology and Molecular Biology

country: USA

institute: Brigham Young University

description: uninduced and treated at 30 hour following E2 treatment

hyb_protocol: Brown Lab protocol

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using GenePix Pro Software.

data_processing: Signal calculation: mean intensity minus median background and normalized by median value of all spot filtered genes.

source_name: T-47D cells with inducible ERbeta construct

label_protocol: 25 ug each of sample total RNA and human universal reference RNA (Stratagene, La Jolla, CA, USA) were labeled with Cy5-conjugated dUTP and Cy3-conjugated dUTP (PerkinElmer, Boston, MA, USA), respectively, and hybridized to the arrays using protocols established by the Patrick O. Brown Laboratory (Stanford University, USA) accessible at http://cmgm.stanford.edu/pbrown/protocols/index.html.

growth_protocol: Cells were added to 150 mm plates at a confluency of 40%; after one day, the normal medium was replaced by the medium described above, supplemented with 5% dextran coated charcoal treated FBS (DCCFBS). After 24h, 10 nM ICI 182,780 was added to the cultures and incubation proceeded for an additional 48h. For expression of ERb, tetracycline was removed 12 h before initiation of treatment with 17b-estradiol. At time 0 h the medium was changed to 0.5% DCCFBS and 10 nM of 17b-estradiol or equivalent volume of DMSO for mock-treated controls were added.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: T-47D breast cancer cell line

tag: Tissue

value: breast cancer cell line

source_name: Universal human reference RNA (Stratagene)

tag: Purchased from Stratagene


title: h4ERbeta16h-tet+E2(5)UHR(3)array87 T47D cells with inducible ERbeta

description: induced and treated at 16 hour following E2 treatment


title: i4ERbeta30h-tet+E2(5)UHR(3)array95 T47D cells with inducible ERbeta

description: induced and treated at 30 hour following E2 treatment


title: i2ERbeta30h-tet(5)UHR(3)array93 T47D cells with inducible ERbeta

description: induced and untreated at 30 hour following E2 treatment


title: h3ERbeta16h+tet+E2(5)UHR(3)array86 T47D cells with inducible ERbeta

description: uninduced and treated at 16 hour following E2 treatment


title: h1ERbeta16h+tet(5)UHR(3)array84 T47D cells with inducible ERbeta

description: uninduced and untreated at 16 hour following E2 treatment


title: i1ERbeta30h+tet(5)UHR(3)array92 T47D cells with inducible ERbeta

description: uninduced and untreated at 30 hour following E2 treatment


title: h2ERbeta16h-tet(5)UHR(3)array85 T47D cells with inducible ERbeta

description: induced and untreated at 16 hour following E2 treatment


title: g3ERbeta12h+tet+E2(5)UHR(3)array108 T47D cells with inducible ERbeta

description: uninduced and treated at 12 hour following E2 treatment


title: d3ERbeta6h+tet+E2(5)UHR(3)array69 T47D cells with inducible ERbeta

description: uninduced and treated at 6 hour following E2 treatment


title: g2ERbeta12h-tet(5)UHR(3)array107 T47D cells with inducible ERbeta

description: induced and untreated at 12 hour following E2 treatment


title: g4ERbeta12h-tet+E2(5)UHR(3)array109 T47D cells with inducible ERbeta

description: induced and treated at 12 hour following E2 treatment


title: a4ERbeta1h-tet+E2(5)UHR(3)array99 T47D cells with inducible ERbeta

description: induced and treated at 1 hour following E2 treatment


title: g1ERbeta12h+tet(5)UHR(3)array106 T47D cells with inducible ERbeta

description: uninduced and untreated at 12 hour following E2 treatment


title: d1ERbeta6h+tet(5)UHR(3)array67 T47D cells with inducible ERbeta

description: uninduced and untreated at 6 hour following E2 treatment


title: a2ERbeta1h-tet(5)UHR(3)array97 T47D cells with inducible ERbeta

description: induced and untreated at 1 hour following E2 treatment


title: d2ERbeta6h-tet(5)UHR(3)array68 T47D cells with inducible ERbeta

description: induced and untreated at 6 hour following E2 treatment


title: d4ERbeta6h-tet+E2(5)UHR(3)array70 T47D cells with inducible ERbeta

description: induced and treated at 6 hour following E2 treatment


title: Embryo5_Replicate4

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description: Identification of in vivo CTCF binding sites in the Drosophila genome.

hyb_protocol: As described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/

data_processing:
Spotfinding performed with Dapple (Buhler J. et al (2000). Dapple: improved techniques for finding spots on DNA microarrays. University of Washington technical report, UWTR 2000-08-05).
VSN normalisation of 4 slides in an experimental group - VALUE is the VSN normalised ratio of experimental (anti-CTCF-enriched to control). All other data are raw un-normalised values.
See www.flychip.org.uk for full details

organism: Drosophila melanogaster

source_name: Normal Rabbit Serum immunopurification

label_protocol: Enriched chromatin labelling as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/

extract_protocol: Chromatin purified as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/

tag: Control Chromatin from 0-20hr immunopurified with noraml rabit serum. Immunopurification as described in Birch-Machin et al (2005) Genome Biology 6:R63. Detailed protocol from http://www.flychip.org.uk/protocols/chip/

source_name: Anti-CTCF immunopurification

tag: Experimental Chromatin from 0-20hr immunopurified with rabbit anti-CTCF (Moon et al, 2005, EMBO Reports, 6:p165). Immunopurification as described in Birch-Machin et al (2005) Genome Biology 6:R63. Detailed protocol from http://www.flychip.org.uk/protocols/chip/


title: Female Patient  036 - Cy3:21207:13300977-Female-Female

description: Analysis genomic DNA male patient 036

source_name: Female Patient  036 - Cy3

source_name: female ref pool - Cy5


title: Embryo6_Replicate3

scan_protocol: As described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/


title: Embryo6_Replicate2


title: a1ERbeta1h+tet(5)UHR(3)array96 T47D cells with inducible ERbeta

description: uninduced and untreated at 1 hour following E2 treatment


title: Embryo6_Replicate4


title: a3ERbeta1h+tet+E2(5)UHR(3)array98 T47D cells with inducible ERbeta

description: uninduced and treated at 1 hour following E2 treatment


title: Embryo5_Replicate3


title: Embryo5_Replicate1


title: Embryo6_Replicate1


title: Female Patient  309 - Cy3:18274:13124358-Female-Male

description: Analysis genomic DNA male patient 309

source_name: Female Patient  309 - Cy3

source_name: male ref pool - Cy5


title: Embryo1_Replicate1

tag: Experimental Chromatin from 0-20hr immunopurified with rabbit anti-CTCF (Moon et al, 2005, EMBO Reports, 6:p165).  Immunopurification as described in  Birch-Machin et al (2005) Genome Biology 6:R63.  Detailed protocol from http://www.flychip.org.uk/protocols/chip/

tag: Control Chromatin from 0-20hr immunopurified with noraml rabit serum.  Immunopurification as described in  Birch-Machin et al (2005) Genome Biology 6:R63.  Detailed protocol from http://www.flychip.org.uk/protocols/chip/


title: brain at T96, T4_40.3nM, biological rep2

status: Public on May 12 2007

city: Victoria

first: Caren

middle: C

last: Helbing

state: British Columbia

address: PO Box 3055 Stn CSC

department: Biochemistry and Microbiology

country: Canada

institute: University of Victoria

description: Gene expression data sets obtained from three biological replicate arrays for each treatment and time point were analyzed for consistency and absolute agreement using intra-class correlation with a 2-way random effects model (SPSS Version 12.0, Chicago, IL, USA). The averages of the intra-class correlation coefficients over the replicate sets was not less than 0.82 with most values greater than 0.9 (Supplementary Table 3). Fold change response to each treatment was determined for each gene relative to the control and genes exhibiting fold change values greater than or equal to two were identified. As an additional quality measure and to reduce the chance of making a type I error, we omitted genes which displayed large variability over the replicate sets.  For each gene/replicate set, variability was measured using the equation:  (maximum value-minimum value)/2 which is appropriate for samples up to 5 per group (Montgomery, 1991). If the variation estimate for the gene/replicate set was greater than 1.1-1.7 (depending on the data set), the gene was removed from the final list of genes affected following chemical treatment for that time point. If less than 4 observations were available for a given time point and treatment, that gene was also removed from the final list of genes.

hyb_protocol: Prehybridization, hybridization, and posthybridization washes were performed at 65°C. The radiolabeled cDNA targets from MMI-, PTU-, and PER-exposed animals and their time-matched experimental controls were each divided into 3 pools of (n=3, 3, and 4) for each treatment time point such that three arrays were probed per treatment and time point. The radiolabeled cDNA targets from T3 and T4-exposed animals with their respective time-matched control animals, were derived from 3 individual animals such that one array was used for each individual. Hybridizations were carried out in 20 ml of hybridization solution containing 4x SSC, 10% (w/v) dextran sulfate, 1.0% (w/v) SDS, and 0.5% (w/v) Blotto. Prewarmed hybridization solution was added to each hybridization tube (35 mm internal diameter x 150 mm length; Amersham) containing the array membrane and prehybridization was allowed to continue for 2 h. Radiolabeled cDNA samples were then added to a final concentration of 5 x 105 cpm/ml and allowed to hybridize overnight. After hybridization, the membranes were rinsed briefly with 50 ml 2x SSC, then washed twice with 50 ml 2x SSC/0.1% SDS for 15 min, once with 50 ml 0.1x SSC/1.0% SDS for 25 min, and rinsed with 50 ml 0.1x SSC. The arrays were placed on 3MM filter paper (Rose Scientific Ltd, Edmonton, AB, Canada) soaked with ddH20 and wrapped with plastic wrap. Each processed membrane was exposed to a phosphorimager screen (Molecular Dynamics Inc., Sunnyvale, CA, USA) for five days.

scan_protocol: Hybridization signals were collected using a Storm 820 Gel and Blot Imaging System (Amersham) at 50 µm resolution.

data_processing: The resulting image data were converted to a standard 8-bit TIFF file using Photoshop V5.0 (Adobe Systems Inc, San Jose, CA, USA). Both non-auto- and auto-level images were prepared for analysis in order to account for signal saturation. Non-autoleveled images provide a linear range of strong signal intensities (such as b-actin) while auto-leveled images allow for analysis of the remaining signals.  Relative expression for each gene target was collected from the image data using ImaGene Version 5.6.1 (BioDiscovery Inc, El Segundo, CA, USA). Signal intensities for each gene and blank position were determined from the median spot pixel intensities and corrected by subtracting the local median background pixel intensities. Signal intensities that were derived from areas of non-specific hybridization on the arrays were not included in the final analysis. A non-signal background was determined from the median intensity value plus one standard deviation of blank positions across the auto-leveled data set, and signal intensities for gene positions exhibiting values below the no signal were adjusted to this value. Saturated gene positions identified in auto-level data were replaced across all data sets by the corresponding values obtained in the non-auto-level analysis.  Data for the three sets were analyzed by time point. Both non-auto- and auto-leveled data for each array were normalized using a geometric mean derived from the median signal intensities from the following genes: ribosomal proteins L8 and S10, GAPDH, ferritin, ubiquitin, NM23/dinucleotide phosphate kinase, cytoplasmic b-actin, and elongation factor-1 a chain. The choice of which of these transcripts were used for normalization within a time point was dictated by spot quality and consistency (see Statistics below). The gene transcripts used for normalization across a time point are indicated in Supplementary Table 1.

organism: Xenopus laevis

source_name: NF stage 54 tadpoles at 96 h of exposure

label_protocol: Amplified RNA (aRNA) was produced using the MessageAmp aRNA Kit as per the manufacturer’s protocol (Ambion) from one microgram brain total RNA isolated from an individual (for the T3 and T4 experimental sets) or from three separate pools of total RNA from individuals (for the inhibitor experimental set). This aRNA (500 ng) was annealed with 500 ng random hexamer oligonucleotide (Amersham Biosciences Inc, Baie d’Urfé, QC, Canada), and cDNA was prepared using MMLV RNase H- Superscript II reverse transcriptase as described by the manufacturer (Invitrogen) with the following modifications: the dNTP mix consisted of 500 µM each of dGTP, dTTP, and dCTP, 4 µM dATP, and 50 µCi [?-32P] dATP (PerkinElmer Life Sciences, Inc, Boston, MA, USA). RNA was removed from the radiolabeled cDNA by addition of 10 ?L 1M NaOH and incubation at 70 °C for 10 min. Samples were cooled to room temperature and 10 ?L of 1M HCl were added to neutralize the reactions. The radiolabeled cDNA was purified using a QIAquick PCR purification kit (Qiagen) and, immediately prior to hybridization, was heat denatured for 5 min at 95°C and then quickly cooled on ice for 5 min.

extract_protocol: Brain tissue was collected from each individual tadpole and total RNA was isolated using TRIzol reagent as described by the manufacturer (Invitrogen Canada Inc., Burlington, Ontario, Canada).

treatment_protocol:
Experiment 1 (T4 and T3)
Twenty-eight early prometamorphic (NF stage 54;(Nieuwkoop and Faber, 1956; Shi, 2000)) tadpoles were continuously exposed to three separate T4 concentrations (10, 20.1, and 40.3 nM), and a LSW control in one exposure set, or five different T3 concentrations (0.48, 0.97, 1.92, 3.84, and 7.68 nM), and a LSW control in the second exposure set as described in detail in Zhang et al (2006). Each chemical exposure concentration was replicated twice along with the associated LSW control. At 24 h, 48 h and 96 h two animals per exposure replicate (four animals total per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.  On exposure day 14, all remaining organisms were euthanized in MS-222, weighed, and developmentally staged in a blind evaluation. Animals exposed to either chemical showed an acceleration of metamorphosis which was published previously (Zhang et al., 2006).
Experiment 2 (MMI, PTU and PER)
NF stage 54 tadpoles were continuously exposed to a single concentration of PTU (20 mg/L), MMI (100 mg/L) or PER (4 mg/L).  We have previously shown that exposure to these concentrations resulted in an increase in thyroid gland size at day 8 and significantly delayed metamorphosis at 14 days (Degitz et al., 2005; Tietge et al., 2005). The exposure regimen details are recorded elsewhere (Zhang et al., 2006). Briefly, tadpoles were randomly placed into 24 tanks (20 tadpoles/tank) and exposed (six tanks/chemical) to a single concentration of each chemical. At 24 h, 48 h and 96 h 5 tadpoles from two of the 6 tanks (10 tadpoles per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.

tag: NF stage 54 tadpoles from US Environmental Protection Agency, Mid-Continent Ecology Division in house culture


title: brain at T96, T4_20.1nM, biological rep3


title: brain at T96, T4_40.3nM, biological rep3


title: brain at T96, T4_20.1nM, biological rep2


title: brain at T96, T4_40.3nM, biological rep1


title: brain at T96, T4_20.1nM, biological rep1


title: Female Patient  083 - Cy3:17962:13123985-Female-Male

description: Analysis genomic DNA male patient 083

source_name: Female Patient  083 - Cy3


title: brain at T96, T4_10nM, biological rep2


title: brain at T96, T4_10nM, biological rep3


title: Embryo2_Replicate2

source_name: normal Rabbit Serum immunopurification


title: brain at T96, T4_control, biological rep2


title: brain at T48, T4_40.3nM, biological rep3

source_name: NF stage 54 tadpoles at 24 h of exposure


title: brain at T96, T4_control, biological rep1


title: Embryo1_Replicate2


title: brain at T48, T4_20.1nM, biological rep2


title: brain at T48, T4_40.3nM, biological rep1


title: brain at T48, T4_20.1nM, biological rep1


title: brain at T48, T4_40.3nM, biological rep2


title: brain at T96, T4_10nM, biological rep1


title: Embryo2_Replicate3


title: brain at T96, T4_control, biological rep3


title: Embryo1_Replicate3


title: brain at T48, T4_10nM, biological rep1


title: brain at T48, T4_10nM, biological rep3


title: brain at T48, T4_control, biological rep3


title: Embryo5_Replicate2


title: Embryo2_Replicate4


title: brain at T48, T4_control, biological rep2


title: brain at T48, T4_10nM, biological rep2


title: brain at T48, T4_20.1nM, biological rep3


title: brain at T24, T4_40.3nM, biological rep2


title: brain at T24, T4_20.1nM, biological rep3


title: brain at T24, T4_40.3nM, biological rep1


title: brain at T24, T4_20.1nM, biological rep1


title: Stroma free hESC derived mesenchymal precursors (SF_hESC_MPC)

status: Public on May 17 2007

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: according to manufacturer

data_processing: GCOS 1.4

label: biotin

source_name: stroma free hESC derived mesenchymal precursors

label_protocol: Ambion message Amp. labeling kit

extract_protocol: trizol


title: brain at T24, T4_40.3nM, biological rep3


title: brain at T24, T4_10nM, biological rep3


title: brain at T24, T4_20.1nM, biological rep2


title: OP9 feeder induced hESC derivec mesenchymal precursors (OP9_hESC_MPC)


title: NA_passage_15 times_rep2

status: Public on May 30 2007

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: NA is an EBV-positive NPC cell line previously generated by in vitro infection of NPC-TW01 cells with recombinant Akata EBV.

hyb_protocol: To prepare the hybridization mixture, the experimental and reference samples were subsequently pooled, purified and concentrated with a Centricon YM-30 column (Millipore), resuspended to a final volume of 150 μl, and then mixed with 50 μg of human Cot-1 DNA (Invitrogen), 50 μl of 10× blocking buffer (Agilent), and 250 μl of 2× aCGH hybrixization buffer (Agilent). Before hybridization, the 500 μl hybridization mixtures were denatured at 95℃ for 3 min and incubated at 37℃ for 30 min. Array hybridizations were carried out for 40 h at 65℃, then washed for 5 min at room temperature in Oligo aCGH Wash Buffer 1 (Agilent), followed by 1 min at 37℃ in Oligo aCGH Wash Buffer 2 (Agilent).

scan_protocol: Hardware: Agilent G2565BA DNA microarray scanner (Agilent Technologies) Software: ScanControl Software (Agilent Technologies) The scanning and image acquisition protocols: the arrays were imaged at a resolution of 10 μm. Excitation of Cy3 and Cy5 was performed at a wavelength of 532 and 635 nm, respectively. A laser power of 100% was used. Each arrays was subjected to a series of scans. The signals were digitized into 16 bit/pixel, yielding a maximum detection range from 1 to 65536; i.e., almost five orders of magnitude.

data_processing: The data in VALUE column were generated by using Linear Normalization Method with rank consistent probes. The data was transformed into Log10-based scale.

source_name: NP1: EBV-positive cell lines derived from nasopharyngeal carcinoma, without EBV reactivation, low-number-passage

label_protocol: After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer’s instructions. In brief, Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy5-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated and the labeled experimental and reference targets were pooled and filtered by using a Centricon YM-30 column (Millipore).

growth_protocol: Cells were all maintained in Dulbecco's modified Eagle's medium supplemented with 10% FBS and 400 microgram per ml of G418

extract_protocol: Genomic DNA was isolated with DNeasy Tissue Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Without any treatment.

tag: Cell line

value: an EBV-positive NPC cell line

tag: Gender

value: male

value: Nasopharyngeal carcinoma

source_name: NP15: EBV-positive cell lines derived from nasopharyngeal carcinoma, without EBV reactivation, experienced 15 times passage from NP1

label_protocol: After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer’s instructions. In brief, Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy3-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated and the labeled experimental and reference targets were pooled and filtered by using a Centricon YM-30 column (Millipore).

growth_protocol: NA cells were all maintained in Dulbecco's modified Eagle's medium supplemented with 10% FBS and 400 microgram per ml of G418

treatment_protocol: without any treatment except regular passage during cell culture.


title: NA_passage_15 time_rep1

growth_protocol: Cells were all maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 400 microgram per ml of G418

extract_protocol: Genomic DNA was isolated with DNeasy Tissue Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: Without any treatment except regular passage during cell culture.

growth_protocol: NA cells were all maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 400 microgram per ml of G418

treatment_protocol: without any treatment


title: brain at T48, T4_control, biological rep1


title: Undifferentiated human embryonic stem cells (hESC_UNDIFF2)

source_name: undifferentiated human embryonic stem cells


title: brain at T24, T4_10nM, biological rep2


title: NA_reactivation_15 time_rep1

source_name: EBV-positive cell lines derived from nasopharyngeal carcinoma, recurrent EBV reactivation, 15 times

label_protocol: Genomic DNA labeling was performed according to the standard array-CGH protocol provided by Agilent Technologies. After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer's instructions. Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy5-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated.

growth_protocol: NA cells were all maintained in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 400 microgram/ml of G418

extract_protocol: Genomic DNA was isolated from NPC cells harboring 15 times of EBV-reactivation with DNeasy Tissue Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol:
Induction of EBV reactivation was performed 15 times, once per passage.
      Induction of EBV reactivation was established by combinational use of 12-O-tetradecanoylphorbol -13-acetate (TPA) and sodium n-butyrate (SB). Briefly, NA cells seeded in cultured medium and allow adhering overnight before treatment. TPA and SB were dissolved in medium at final concentration of 20 ng/ml and 3 mM, respectively. Twenty four hours post incubation, medium containing TPA and SB was removed following by incubation in normal culture medium for 24 hours prior next passage or genomic DNA extraction.

source_name: EBV-positive cell lines derived fromnasopharyngeal carcinoma, without EBV reactivation, low-number-passage

label_protocol: Genomic DNA labeling was performed according to the standard array-CGH protocol provided by Agilent Technologies. After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer's instructions. Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy3-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated.

growth_protocol: NA cells were all maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 400 microgran/ml of G418.

treatment_protocol: without any treatment.


title: NA_reactivation_15 time_rep2

source_name: EBV-positive cell lines derived from nasopharyngeal carcinoma, without EBV reactivation, low-number-passage

label_protocol: Genomic DNA labeling was performed according to the standard array-CGH protocol provided by Agilent Technologies. After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer’s instructions. Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy5-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated.

label_protocol: Genomic DNA labeling was performed according to the standard array-CGH protocol provided by Agilent Technologies. After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer’s instructions. Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy3-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated.

treatment_protocol:
Induction of EBV reactivation was performed 15 times, once per passage.
      Induction of EBV reactivation was established by combinational use of 12-O-tetradecanoylphorbol -13-acetate (TPA) and sodium n-butyrate (SB). Briefly, NA cells seeded in cultured medium and allow adhering overnight before treatment. TPA and SB were dissolved in medium at final concentration of 20 ng/ml and 3 mM, respectively. Twenty four hours post incubation, medium containing TPA and SB was removed following by incubation in normal medium for 24 hours prior next passage


title: brain at T24, T4_control, biological rep1


title: brain at T24, T4_control, biological rep2


title: brain at T24, T4_10nM, biological rep1


title: Bone marrow derived mesenchymal precursors (BM_MPC)

source_name: bone marrow derived mesenchymal precursors


title: brain at T96, T3_3.84nM, biological rep3


title: brain at T96, T3_7.68nM, biological rep2


title: brain at T96, T3_0.97nM, biological rep1


title: brain at T96, T3_3.84nM, biological rep2


title: brain at T96, T3_0.97nM, biological rep3


title: brain at T24, T4_control, biological rep3


title: brain at T96, T3_1.92nM, biological rep2


title: brain at T96, T3_3.84nM, biological rep1


title: NA_reactivation_1 time_rep1

hyb_protocol: To prepare the hybridization mixture, the experimental and reference samples were subsequently pooled, purified and concentrated with a Centricon YM-30 column (Millipore), resuspended to a final volume of 150 μl, and then mixed with 50 μg of human Cot-1 DNA (Invitrogen), 50 μl of 10× blocking buffer (Agilent), and 250 μl of 2× aCGH hybrixization buffer (Agilent). Before hybridization, the 500 μl hybridization mixtures were denatured at 95℃ for 3 min and incubated at 37℃ for 30 min. Array hybridizations were carried out for 40 h at 65℃, then washed for 5 min at room temperature in Oligo aCGH Wash Buffer 1 (Agilent), followed by 1 min at 37 in Oligo aCGH Wash Buffer 2 (Agilent).

source_name: EBV-positive cell lines derived from nasopharyngeal carcinoma, EBV reactivation, one time

treatment_protocol:
Induction of EBV reactivation once.
Induction of EBV reactivation by combinational use of 12-O-tetradecanoylphorbol -13-acetate (TPA) and sodium n-butyrate (SB). Briefly, NA cells seeded in cultured medium and allow adhering overnight before treatment. TPA and SB were dissolved in medium at final concentration of 20 ng/ml and 3 mM, respectively. Twenty four hours post incubation, medium containing TPA and SB was removed following by incubation in normal medium for 24 hours prior genomic DNA extraction .


title: brain at T96, T3_1.92nM, biological rep1


title: Undifferentiated hESC (hESC_UNDIFF1)

source_name: undifferentiated hESC

tag: undifferentiated hESC


title: Embryo1_Replicate4

source_name: Normal Rabbit Serum immunopurification

source_name: Anti-CTCF immunopurification


title: brain at T96, T3_7.68nM, biological rep3


title: brain at T96, T3_7.68nM, biological rep1


title: Embryo2_Replicate1


title: brain at T96, T3_0.48nM, biological rep3


title: brain at T96, T3_0.48nM, biological rep1


title: brain at T96, T3_0.97nM, biological rep2


title: brain at T96, T3_control, rep1


title: Undifferentiated human embryonic stem cells (hESC_UNDIFF3)

tag: undifferentiated human embryonic stem cells


title: brain at T96, T3_control, rep2


title: NA_reactivation_1 time_rep2

source_name: EBV-positive cell lines derived from nasopharyngeal carcinoma, without EBV reactivation, low-passage-number

growth_protocol: NA cells were all maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 400 microgram/ml of G418

treatment_protocol: without and treatment

growth_protocol: NA cells were all maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 400 microgran/ml of G418

treatment_protocol: Induction of EBV reactivation was established by combinational use of 12-O-tetradecanoylphorbol -13-acetate (TPA) and sodium n-butyrate (SB). Briefly, NA cells seeded in cultured medium and allow adhering overnight before treatment. TPA and SB were dissolved in medium at final concentration of 20 ng/ml and 3 mM, respectively. Twenty four hours post incubation, medium containing TPA and SB was removed following by incubation in normal medium for 24 hours prior genomic DNA extraction.


title: brain at T96, T3_control, rep3

source_name: NF stage 54 tadpoles at 96 h of exposure


title: brain at T48, T3_3.84nM, biological rep3

source_name: NF stage 54 tadpoles at 48 h of exposure

treatment_protocol:
Experiment 1 (T4 and T3)
Twenty-eight early prometamorphic (NF stage 54;(Nieuwkoop and Faber, 1956; Shi, 2000)) tadpoles were continuously exposed to three separate T4 concentrations (10, 20.1, and 40.3 nM), and a LSW control in one exposure set, or five different T3 concentrations (0.48, 0.97, 1.92, 3.84, and 7.68 nM), and a LSW control in the second exposure set as described in detail in Zhang et al (2006). Each chemical exposure concentration was replicated twice along with the associated LSW control. At 24h, 48h and 96h two animals per exposure replicate (four animals total per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.  On exposure day 14, all remaining organisms were euthanized in MS-222, weighed, and developmentally staged in a blind evaluation. Animals exposed to either chemical showed an acceleration of metamorphosis which was published previously (Zhang et al., 2006).
Experiment 2 (MMI, PTU and PER)
NF stage 54 tadpoles were continuously exposed to a single concentration of PTU (20 mg/L), MMI (100 mg/L) or PER (4 mg/L).  We have previously shown that exposure to these concentrations resulted in an increase in thyroid gland size at day 8 and significantly delayed metamorphosis at 14 days (Degitz et al., 2005; Tietge et al., 2005). The exposure regimen details are recorded elsewhere (Zhang et al., 2006). Briefly, tadpoles were randomly placed into 24 tanks (20 tadpoles/tank) and exposed (six tanks/chemical) to a single concentration of each chemical. At 24h, 48h and 96h 5 tadpoles from two of the 6 tanks (10 tadpoles per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater  for analysis of gene expression.


title: brain at T48, T3_7.68nM, biological rep2


title: brain at T96, T3_0.48nM, biological rep2


title: brain at T48, T3_7.68nM, biological rep3


title: brain at T48, T3_7.68nM, biological rep1


title: brain at T48, T3_3.84nM, biological rep2


title: tail at T48, T4, biological rep3

description: Tissue-specific gene expression data sets obtained from the biological replicate arrays for each treatment and time point were analyzed for consistency and absolute agreement using intra-class correlation with a 2-way random effects model (SPSS Version 12.0, Chicago, IL, USA). The averages of the intra-class correlation coefficients over the replicate sets was not less than 0.78 with most values greater than 0.9 (Supplementary Table 3). Fold change response to each treatment was determined for each gene relative to the control and genes exhibiting fold change values greater than or equal to two were identified. As an additional quality measure and to reduce the chance of making a type I error, we omitted genes which displayed large variability over the replicate sets.  For each gene/replicate set, variability was measured using the equation:  (maximum value-minimum value)/2 which is appropriate for samples up to 5 per group (Montgomery, 1991). If the variation estimate for the gene/replicate set was greater than 1.1, the gene was removed from the final list of genes affected following chemical treatment for that time point. If less than 4 observations were available for a given time point and treatment, that gene was also removed from the final list of genes.

hyb_protocol: Prehybridization, hybridization, and posthybridization washes were performed at 65°C. Hybridizations were carried out in 20 ml of hybridization solution containing 4x SSC, 10% (w/v) dextran sulfate, 1.0% (w/v) SDS, and 0.5% (w/v) Blotto. Prewarmed hybridization solution was added to each hybridization tube (35 mm internal diameter x 150 mm length; Amersham) containing the array membrane and prehybridization was allowed to continue for 2 h. To standardize subsequent exposure times to the phosphorimager screens, equal counts of radiolabeled cDNA samples (final concentration of 5 x 105 cpm/ml) were then added and allowed to hybridize for 18 h. After hybridization, the membranes were rinsed briefly with 50 ml 2x SSC, then washed twice with 50 ml 2x SSC/0.1% SDS for 15 min, once with 50 ml 0.1x SSC/1.0% SDS for 25 min, and rinsed with 50 ml 0.1x SSC. The arrays were placed on 3MM filter paper (Rose Scientific Ltd, Edmonton, AB, Canada) soaked with ddH20 and wrapped with plastic wrap. Each processed membrane was exposed to a phosphorimager screen (Molecular Dynamics Inc., Sunnyvale, CA, USA) for five days.

data_processing: The resulting image data were converted to a standard 8-bit TIFF file using Photoshop Version 5.0 (Adobe Systems Inc, San Jose, CA, USA). Both non-auto- and auto-level images were prepared for analysis in order to account for signal saturation. Non-auto-leveled images provide a linear range of strong signal intensities (such as b-actin) while auto-leveled images allow for analysis of the remaining signals. Relative expression for each gene target was collected from the image data using ImaGene Version 5.6.1 (BioDiscovery Inc, El Segundo, CA, USA). Signal intensities for each gene and blank position were determined from the median spot pixel intensities and corrected by subtracting the local median background pixel intensities. Signal intensities that were derived from areas of non-specific hybridization on the arrays were not included in the final analysis. A non-signal background was determined from the median intensity value plus one standard deviation of blank positions across the auto-level data set, and signal intensities for gene positions exhibiting values below the non signal were adjusted to this value. Saturated gene positions identified in auto-level data were replaced across all data sets by the corresponding values obtained in the non-auto-level analysis. Data for the treatment sets were analyzed by time point. Both non-auto- and auto-leveled data for each array were normalized using a geometric mean derived from the median signal intensities of the following genes: ribosomal proteins L8, L32, and S10, GAPDH, ferritin, NM23/dinucleotide phosphate kinase, skeletal a-actin, cytoplasmic b-actin, and elongation factor-1 a chain. The choice of which of these transcripts were used for normalization within a time point was dictated by spot quality and consistency (see Statistics below). The gene transcripts used for normalization within a given time point are indicated in Supplementary Table 1. After normalization, relative expression values for each gene were determined from the median of signal intensities across the replicate array membranes for each treatment time point. Genes with less than four signal intensity values were not included in further analyses.

label_protocol: Amplified RNA (aRNA) was produced using the MessageAmp aRNA Kit as per the manufacturer’s protocol (Ambion) from one microgram total RNA from individual animals of a subset of the exposures tested. We focused on 48 h for the tail and 24 h for the hindlimb based upon previous work indicating that these time points were appropriate for examining gene expression changes (Zhang et al., 2006). For the THs, we initially examined tadpole tissues exposed to either 1.92 nM T3 or 10 nM T4 (n=4 for each) with arrays and compared the expression profiles to those obtained from time- and experiment-matched controls (n=3 each). These concentrations evoke equivalent responses in the acceleration of metamorphosis and in the induction of TR? and BTEB transcripts in the tail (Zhang et al., 2006). For MMI, PTU, and PER, tissues from three individuals were examined for each chemical tested along with time- and experiment-matched controls. For this experimental set, we examined both 24 h and 96 h time points. Once candidate gene transcripts were identified, we then performed QPCR analysis on these and additional concentrations on a gene-by-gene basis.

extract_protocol: Tails and hindlimbs were collected from each individual tadpole and total RNA was isolated using TRIzol reagent as described by the manufacturer (Invitrogen Canada Inc., Burlington, Ontario, Canada). Mechanical disruption of each tissue utilized 300 µl (hindlimbs) or 700 ul (tail) TRIzol reagent, a 3 mm diameter tungsten-carbide bead, and safe-lock Eppendorf 1.5 ml microcentrifuge tubes in a Retsch MM301 Mixer Mill (Fisher Scientific Ltd, Ottawa, ON) at 20 Hz for six minutes. Mixing chambers were rotated 180 degrees halfway through the homogenization procedure. Twenty micrograms of glycogen (Roche Diagnostics, Laval, PQ) was added prior to isopropanol precipitation to maximize RNA yield. Isolated RNA was subsequently resuspended in 20 ul (hindlimb) or 40 ul (tail) diethyl pyrocarbonate (DEPC)-treated water and stored at -70°C.


title: tail at T48, T4, biological rep4


title: tail at T48, T4, biological rep2


title: brain at T48, T3_1.92nM, biological rep2


title: brain at T48, T3_3.84nM, biological rep1


title: brain at T48, T3_1.92nM, biological rep3


title: tail at T48, T4, control, biological rep3


title: tail at T48, T4, control, biological rep1


title: tail at T48, T4, biological rep1


title: tail at T48, T4, control, biological rep2


title: brain at T48, T3_1.92nM, biological rep1


title: brain at T48, T3_0.97nM, biological rep3


title: brain at T48, T3_0.97nM, biological rep2


title: brain at T48, T3_0.48nM, biological rep3


title: brain at T48, T3_0.97nM, biological rep1


title: tail at T48, T3, biological rep4

treatment_protocol:
Experiment 1 (T4 and T3)
Twenty-eight early prometamorphic (NF stage 54;(Nieuwkoop and Faber, 1956; Shi, 2000)) tadpoles were continuously exposed to three separate T4 concentrations (10, 20.1, and 40.3 nM), and a LSW control in one exposure set, or five different T3 concentrations (0.48, 0.97, 1.92, 3.84, and 7.68 nM), and a LSW control in the second exposure set as described in detail in Zhang et al (2006). Each chemical exposure concentration was replicated twice along with the associated LSW control. At 24h, 48h and 96h two animals per exposure replicate (four animals total per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.  On exposure day 14, all remaining organisms were euthanized in MS-222, weighed, and developmentally staged in a blind evaluation. Animals exposed to either chemical showed an acceleration of metamorphosis which was published previously (Zhang et al., 2006).
Experiment 2 (MMI, PTU and PER)
NF stage 54 tadpoles were continuously exposed to a single concentration of PTU (20 mg/L), MMI (100 mg/L) or PER (4 mg/L).  We have previously shown that exposure to these concentrations resulted in an increase in thyroid gland size at day 8 and significantly delayed metamorphosis at 14 days (Degitz et al., 2005; Tietge et al., 2005). The exposure regimen details are recorded elsewhere (Zhang et al., 2006). Briefly, tadpoles were randomly placed into 24 tanks (20 tadpoles/tank) and exposed (six tanks/chemical) to a single concentration of each chemical. At 24h, 48h and 96h 5 tadpoles from two of the 6 tanks (10 tadpoles per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater  for analysis of gene expression


title: brain at T48, T3_0.48nM, biological rep2


title: tail at T48, T3, biological rep1


title: brain at T48, T3_control, rep1


title: brain at T48, T3_control, rep2


title: brain at T48, T3_control, rep3


title: tail at T48, T3, control, biological rep3


title: tail at T48, T3, biological rep3


title: brain at T48, T3_0.48nM, biological rep1


title: tail at T48, T3, biological rep2


title: brain at T24, T3_7.68nM, biological rep1

data_processing: The resulting image data were converted to a standard 8-bit TIFF file using Photoshop V5.0 (Adobe Systems Inc, San Jose, CA, USA). Both non-auto- and auto-level images were prepared for analysis in order to account for signal saturation. Non-autoleveled images provide a linear range of strong signal intensities (such as b-actin) while auto-leveled images allow for analysis of the remaining signals. Relative expression for each gene target was collected from the image data using ImaGene Version 5.6.1 (BioDiscovery Inc, El Segundo, CA, USA). Signal intensities for each gene and blank position were determined from the median spot pixel intensities and corrected by subtracting the local median background pixel intensities. Signal intensities that were derived from areas of non-specific hybridization on the arrays were not included in the final analysis. A non-signal background was determined from the median intensity value plus one standard deviation of blank positions across the auto-level data set, and signal intensities for gene positions exhibiting values below the no signal were adjusted to this value. Saturated gene positions identified in auto-level data were replaced across all data sets by the corresponding values obtained in the non-auto-level analysis.  Data for the treatment sets were analyzed by time point. Both non-auto- and auto-leveled data for each array were normalized using a geometric mean derived from the median signal intensities from the following genes: ribosomal proteins L8 and S10, GAPDH, ferritin, ubiquitin, NM23/dinucleotide phosphate kinase, cytoplasmic b-actin, and elongation factor-1 a chain. The choice of which of these transcripts were used for normalization within a time point was dictated by spot quality and consistency (see Statistics below). The gene transcripts used for normalization across a time point are indicated in Supplementary Table 1.


title: brain at T24, T3_7.68nM, biological rep3


title: brain at T24, T3_7.68nM, biological rep2


title: tail at T48, T3, control, biological rep1


title: tail at T48, T3, control, biological rep2


title: brain at T24, T3_3.84nM, biological rep3


title: brain at T24, T3_3.84nM, biological rep2


title: tail at T48, PER, biological rep3


title: brain at T24, T3_1.92nM, biological rep2


title: brain at T24, T3_3.84nM, biological rep1


title: brain at T24, T3_1.92nM, biological rep3


title: brain at T24, T3_1.92nM, biological rep1


title: tail at T48, MMI, biological rep1


title: tail at T48, MMI, biological rep2


title: tail at T48, PTU, biological rep2


title: tail at T48, PER, biological rep1


title: tail at T48, PER, biological rep2


title: brain at T24, T3_control, rep3


title: brain at T24, T3_0.48nM, biological rep1


title: brain at T24, T3_0.97nM, biological rep3


title: brain at T24, T3_0.97nM, biological rep2


title: tail at T48, control, biological rep3


title: brain at T24, T3_0.97nM, biological rep1


title: tail at T48, PTU, biological rep3


title: tail at T48, MMI, biological rep3


title: tail at T48, control, biological rep2


title: tail at T48, PTU, biological rep1


title: brain at T24, T3_0.48nM, biological rep2


title: brain at T24, T3_0.48nM, biological rep3


title: brain at T24, T3_control, rep2


title: tail at T48, control, biological rep1


title: hindlimb at T24, T4, biological rep3


title: hindlimb at T24, T4, biological rep2


title: hindlimb at T24, T4, biological rep4


title: brain at T24, T3_control, rep1


title: hindlimb at T24, T4, biological rep1


title: hindlimb at T24, T4, control, biological rep3


title: hindlimb at T24, T4, control, biological rep2


title: hindlimb at T24, T3, biological rep3


title: hindlimb at T24, T4, control, biological rep1


title: hindlimb at T24, T3, biological rep2


title: hindlimb at T96, MMI, biological rep3


title: hindlimb at T24, T3, control, biological rep1


title: hindlimb at T24, T3, biological rep4


title: hindlimb at T96, PER, biological rep2


title: hindlimb at T96, MMI, biological rep2


title: hindlimb at T96, control, biological rep2


title: hindlimb at T96, control, biological rep3


title: hindlimb at T24, T3, biological rep1


title: hindlimb at T96, PTU, biological rep1


title: hindlimb at T96, PTU, biological rep2


title: hindlimb at T24, MMI, biological rep3


title: hindlimb at T96, PER, biological rep3


title: hindlimb at T96, PER, biological rep1


title: hindlimb at T96, PTU, biological rep3


title: hindlimb at T24, MMI, biological rep1


title: hindlimb at T96, MMI, biological rep1


title: hindlimb at T24, T3, control, biological rep3


title: hindlimb at T24, T3, control, biological rep2


title: hindlimb at T96, control, biological rep1


title: hindlimb at T24, MMI, biological rep2


title: hindlimb at T24, PER, biological rep2


title: hindlimb at T24, PER, biological rep3


title: hindlimb at T24, control, biological rep3


title: hindlimb at T24, PTU, biological rep2


title: hindlimb at T24, PER, biological rep1


title: hindlimb at T24, PTU, biological rep3


title: hindlimb at T24, control, biological rep1


title: hindlimb at T24, control, biological rep2

treatment_protocol:
Experiment 1 (T4 and T3)
Twenty-eight early prometamorphic (NF stage 54;(Nieuwkoop and Faber, 1956; Shi, 2000)) tadpoles were continuously exposed to three separate T4 concentrations (10, 20.1, and 40.3 nM), and a LSW control in one exposure set, or five different T3 concentrations (0.48, 0.97, 1.92, 3.84, and 7.68 nM), and a LSW control in the second exposure set as described in detail in Zhang et al (2006). Each chemical exposure concentration was replicated twice along with the associated LSW control. At 24h, 48h and 96h two animals per exposure replicate (four animals total per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.  On exposure day 14, all remaining organisms were euthanized in MS-222, weighed, and developmentally staged in a blind evaluation. Animals exposed to either chemical showed an acceleration of metamorphosis which was published previously (Zhang et al., 2006).
Twenty-eight early prometamorphic (NF stage 54;(Nieuwkoop and Faber, 1956; Shi, 2000)) tadpoles were continuously exposed to three separate T4 concentrations (10, 20.1, and 40.3 nM), and a LSW control in one exposure set, or five different T3 concentrations (0.48, 0.97, 1.92, 3.84, and 7.68 nM), and a LSW control in the second exposure set as described in detail in Zhang et al (2006). Each chemical exposure concentration was replicated twice along with the associated LSW control. At 24h, 48h and 96h two animals per exposure replicate (four animals total per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater (Ambion Inc., Austin, Texas, USA) for analysis of gene expression.  On exposure day 14, all remaining organisms were euthanized in MS-222, weighed, and developmentally staged in a blind evaluation. Animals exposed to either chemical showed an acceleration of metamorphosis which was published previously (Zhang et al., 2006).
NF stage 54 tadpoles were continuously exposed to a single concentration of PTU (20 mg/L), MMI (100 mg/L) or PER (4 mg/L).  We have previously shown that exposure to these concentrations resulted in an increase in thyroid gland size at day 8 and significantly delayed metamorphosis at 14 days (Degitz et al., 2005; Tietge et al., 2005). The exposure regimen details are recorded elsewhere (Zhang et al., 2006). Briefly, tadpoles were randomly placed into 24 tanks (20 tadpoles/tank) and exposed (six tanks/chemical) to a single concentration of each chemical. At 24h, 48h and 96h 5 tadpoles from two of the 6 tanks (10 tadpoles per each individual treatment) were randomly selected, euthanized in MS-222, and preserved in RNAlater  for analysis of gene expression.


title: hindlimb at T24, PTU, biological rep1


title: E16.5 Top2b+/+ brain

status: Public on May 02 2007

city: Piscataway

first: Yi Lisa

last: Lyu

state: NJ

address: 675 Hoes Lane

department: Pharmacology

institute: UMDNJ-Robert Wood Johnson Medical School

data_processing: Rosetta Resolver system for gene expression data analysis (Rosetta Inpharmatics, Inc.)

label: Biotin

organism: Mus musculus

source_name: E16.5 Top2b+/+ brain

tag: Strain

value: Top2b+/+ in 129SvEv (minor 129SvJ) background;

tag: Age

value: E16.5 embryo;

value: male;

value: whole brain


title: E14.5 top2b-/- brain

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

source_name: E14.5 top2b-/- brain

label_protocol: in vitro transcription

extract_protocol: Trizol/RNeasy

value: top2b-/- in 129SvEv (minor 129SvJ) background;

value: E14.5 embryo;


title: E18.5 top2b-/- brain

source_name: E18.5 top2b-/- brain

value: E18.5 embryo;


title: E16.5 top2b-/- brain

source_name: E16.5 top2b-/- brain

value: female;


title: E14.5 Top2b+/+ brain

source_name: E14.5 Top2b+/+ brain


title: E18.5 Top2b+/+ brain

source_name: E18.5 Top2b+/+ brain

tag: strain


title: 9234

status: Public on May 01 2007

first: Roland

middle: P.

last: Kuiper

description: primary ALL diagnosis sample

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: copy number detection using CNAG2.0 software (http://www.genome.umin.jp/)

source_name: Bone marrow with 97% blasts

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

tag: Immunotype

value: T-ALL; Age:9.4 yrs; Gender:F


title: 9306

description: primary ALL diagnosis sample

source_name: Bone marrow with 82% blasts

value: pre-B ALL; Age:14.8 yrs; Gender:M


title: 9318

description: primary ALL diagnosis sample

source_name: Bone marrow with 34% blasts

value: T-ALL; Age:5.1 yrs; Gender:M


title: 9420

description: primary ALL diagnosis sample

source_name: Bone marrow with 90% blasts

value: pre-B ALL; Age:3.9 yrs; Gender:M


title: 9418

description: primary ALL diagnosis sample

source_name: Bone marrow with 94% blasts

value: common ALL; Age:3 yrs; Gender:F


title: 9390

description: primary ALL diagnosis sample

source_name: Peripheral blood with 30% blasts

value: pro-B ALL; Age:17.6 yrs; Gender:M


title: 9345

description: primary ALL diagnosis sample

source_name: Bone marrow with 96% blasts

value: pre-B ALL; Age:1.9 yrs; Gender:F


title: 9333

description: primary ALL diagnosis sample

source_name: Peripheral blood with 96% blasts

value: common ALL; Age:16.9 yrs; Gender:F


title: 9348

description: primary ALL diagnosis sample

source_name: Peripheral blood with 87% blasts

value: T-ALL; Age:5.3 yrs; Gender:F


title: 9255

description: primary ALL diagnosis sample

source_name: Bone marrow with 87% blasts

value: T-ALL; Age:11.9 yrs; Gender:M


title: 9365

description: primary ALL diagnosis sample

source_name: Bone marrow with 91% blasts

value: common ALL; Age:3.4 yrs; Gender:M


title: 9112

description: primary ALL diagnosis sample

source_name: Bone marrow with 95% blasts

value: pre-B ALL; Age:2.2 yrs; Gender:F


title: 9367

description: primary ALL diagnosis sample

source_name: Bone marrow with 98% blasts

value: pre-B ALL; Age:3 yrs; Gender:M


title: 9274

description: primary ALL diagnosis sample

source_name: Bone marrow with 85% blasts

value: common ALL; Age:8.4 yrs; Gender:F


title: 9419

description: primary ALL diagnosis sample

value: common ALL; Age:12.1 yrs; Gender:F


title: male ref pool_250kNsp

description: pool of 10 male individuals

source_name: Peripheral blood

tag: control sample


title: 9393

description: primary ALL diagnosis sample

value: pre-B ALL; Age:2.7 yrs; Gender:M


title: 9361

description: primary ALL diagnosis sample

value: common ALL; Age:2.5 yrs; Gender:M


title: 9394

description: primary ALL diagnosis sample

source_name: Bone marrow with 92% blasts

value: pre-B ALL; Age:3.4 yrs; Gender:F


title: 9410

description: primary ALL diagnosis sample

source_name: Bone marrow with 89% blasts

value: pre-B ALL; Age:2.5 yrs; Gender:M


title: 9258

description: primary ALL diagnosis sample

value: pre-B ALL; Age:6 yrs; Gender:M


title: female ref pool_250kNsp

description: pool of 10 female individuals


title: 9386

description: primary ALL diagnosis sample

value: common ALL; Age:2 yrs; Gender:M


title: 9162

description: primary ALL diagnosis sample

source_name: Bone marrow with 97% blasts

value: pre-B ALL; Age:2.8 yrs; Gender:M


title: 9264

description: primary ALL diagnosis sample

value: pre-B ALL; Age:9.3 yrs; Gender:F


title: 9228

description: primary ALL diagnosis sample

source_name: Bone marrow with 93% blasts

value: T-ALL; Age:13.2 yrs; Gender:M


title: 9383

description: primary ALL diagnosis sample

source_name: Bone marrow with 73% blasts

value: T-ALL; Age:1.8 yrs; Gender:M


title: female ref pool_50kHind

description: pool of 10 female individuals