title: Peripheral blood RNA from Dutch sample 1006


title: Peripheral blood RNA from Dutch sample 1004

status: Public on Feb 28 2010

type: RNA

city: Groningen

first: Lude

last: Franke

state: Groningen

department: Genetics

country: Netherlands

institute: University Medical Centre Groningen

description: Gene expression from whole peripheral blood from unrelated Dutch individuals

hyb_protocol: Complementary RNA was hybridized to Illumina HumanHT12 v3.0 Whole Genome BeadChips

scan_protocol: Illumina BeadArray Reader, data was handled through Illumina BeadStudio Gene Expression module v3

data_processing:
Quantile-quantile normalized log2 transformed expression intensity. Subsequently, per sample the intensities have been centered to zero and subsequently scaled such that each individual has a standard deviation of 1 in probe.

RAW intensity is provided in the supplementary file on the Sample record (below).

molecule: total RNA

organism: Homo sapiens

source_name: Total RNA from peripheral blood

label_protocol: 2.5 ml of peripheral blood was collected into a PAXgene tube (Becton Dickinson, UK, 762165). PAXgene vials were chosen to prevent density gradient centrifugation, immortalization or in vitro cell culture artifacts changing mRNA profiles. PAXgene tubes were mixed gently and incubated at room temperature for two hours. After collection, tubes were frozen at -20 degrees Celsius for at least 24 hours followed by storage at -80 degrees Celsius. RNA was isolated using the PAXgene Blood RNA isolation kit (Qiagen, UK, 762174). RNA was quantified using the Nanodrop (Nanodrop Technologies, USA). Total RNA integrity was analyzed using an Agilent Bioanalyzer (Agilent Technologies, USA).

extract_protocol: PAXgene Blood RNA isolation kit protocol (Qiagen, UK, 762174)

tag: tissue

value: Peripheral blood


title: Peripheral blood RNA from Dutch sample 1005


title: Peripheral blood RNA from Dutch sample 1001


title: Peripheral blood RNA from Dutch sample 1003


title: Peripheral blood RNA from Dutch sample 1000


title: Peripheral blood RNA from Dutch sample 1002


title: Peripheral blood RNA from Dutch sample 992


title: Peripheral blood RNA from Dutch sample 991


title: Peripheral blood RNA from Dutch sample 994


title: Peripheral blood RNA from Dutch sample 996


title: Peripheral blood RNA from Dutch sample 990


title: Peripheral blood RNA from Dutch sample 989


title: Peripheral blood RNA from Dutch sample 997


title: Peripheral blood RNA from Dutch sample 988


title: Peripheral blood RNA from Dutch sample 995


title: Peripheral blood RNA from Dutch sample 993


title: Peripheral blood RNA from Dutch sample 987


title: Peripheral blood RNA from Dutch sample 986


title: Peripheral blood RNA from Dutch sample 984


title: Peripheral blood RNA from Dutch sample 998


title: Peripheral blood RNA from Dutch sample 985


title: Peripheral blood RNA from Dutch sample 982


title: Peripheral blood RNA from Dutch sample 983


title: Peripheral blood RNA from Dutch sample 999


title: Peripheral blood RNA from Dutch sample 1012


title: Peripheral blood RNA from Dutch sample 979


title: Peripheral blood RNA from Dutch sample 981


title: Peripheral blood RNA from Dutch sample 975


title: Peripheral blood RNA from Dutch sample 978


title: Peripheral blood RNA from Dutch sample 977


title: Peripheral blood RNA from Dutch sample 974


title: Peripheral blood RNA from Dutch sample 976


title: Peripheral blood RNA from Dutch sample 980


title: Peripheral blood RNA from Dutch sample 973


title: Peripheral blood RNA from Dutch sample 972


title: Peripheral blood RNA from Dutch sample 966


title: Peripheral blood RNA from Dutch sample 965


title: Peripheral blood RNA from Dutch sample 971


title: Peripheral blood RNA from Dutch sample 969


title: Peripheral blood RNA from Dutch sample 964


title: Peripheral blood RNA from Dutch sample 967


title: Peripheral blood RNA from Dutch sample 970


title: Peripheral blood RNA from Dutch sample 963


title: Peripheral blood RNA from Dutch sample 962


title: Peripheral blood RNA from Dutch sample 960


title: Peripheral blood RNA from Dutch sample 961


title: Peripheral blood RNA from Dutch sample 959


title: Peripheral blood RNA from Dutch sample 968


title: Peripheral blood RNA from Dutch sample 957


title: Peripheral blood RNA from Dutch sample 958


title: Peripheral blood RNA from Dutch sample 953


title: Peripheral blood RNA from Dutch sample 956


title: Peripheral blood RNA from Dutch sample 955


title: Peripheral blood RNA from Dutch sample 946


title: Peripheral blood RNA from Dutch sample 951


title: Peripheral blood RNA from Dutch sample 950


title: Peripheral blood RNA from Dutch sample 942


title: Peripheral blood RNA from Dutch sample 945


title: Peripheral blood RNA from Dutch sample 948


title: Peripheral blood RNA from Dutch sample 949


title: Peripheral blood RNA from Dutch sample 943


title: Peripheral blood RNA from Dutch sample 944


title: Peripheral blood RNA from Dutch sample 954


title: Peripheral blood RNA from Dutch sample 952


title: Peripheral blood RNA from Dutch sample 937


title: Peripheral blood RNA from Dutch sample 939


title: Peripheral blood RNA from Dutch sample 940


title: Peripheral blood RNA from Dutch sample 935


title: Peripheral blood RNA from Dutch sample 932


title: Peripheral blood RNA from Dutch sample 947


title: Peripheral blood RNA from Dutch sample 941


title: Peripheral blood RNA from Dutch sample 938


title: Peripheral blood RNA from Dutch sample 930


title: Peripheral blood RNA from Dutch sample 931


title: Peripheral blood RNA from Dutch sample 933


title: Peripheral blood RNA from Dutch sample 934


title: Peripheral blood RNA from Dutch sample 936


title: Peripheral blood RNA from Dutch sample 928


title: Peripheral blood RNA from Dutch sample 929


title: Peripheral blood RNA from Dutch sample 927


title: Peripheral blood RNA from Dutch sample 926


title: Peripheral blood RNA from Dutch sample 917


title: Peripheral blood RNA from Dutch sample 919


title: Peripheral blood RNA from Dutch sample 924


title: Peripheral blood RNA from Dutch sample 921


title: Peripheral blood RNA from Dutch sample 925


title: Peripheral blood RNA from Dutch sample 912


title: Peripheral blood RNA from Dutch sample 914


title: Peripheral blood RNA from Dutch sample 913


title: Peripheral blood RNA from Dutch sample 922


title: Peripheral blood RNA from Dutch sample 915


title: Peripheral blood RNA from Dutch sample 923


title: Peripheral blood RNA from Dutch sample 920


title: Peripheral blood RNA from Dutch sample 916


title: Peripheral blood RNA from Dutch sample 908


title: Peripheral blood RNA from Dutch sample 910


title: Peripheral blood RNA from Dutch sample 918


title: Peripheral blood RNA from Dutch sample 904


title: Peripheral blood RNA from Dutch sample 909


title: Peripheral blood RNA from Dutch sample 911


title: Peripheral blood RNA from Dutch sample 902


title: Peripheral blood RNA from Dutch sample 900


title: Peripheral blood RNA from Dutch sample 905


title: Peripheral blood RNA from Dutch sample 901


title: Peripheral blood RNA from Dutch sample 903


title: Peripheral blood RNA from Dutch sample 896


title: Peripheral blood RNA from Dutch sample 907


title: Peripheral blood RNA from Dutch sample 898


title: Peripheral blood RNA from Dutch sample 897


title: Peripheral blood RNA from Dutch sample 895


title: Peripheral blood RNA from Dutch sample 906


title: Peripheral blood RNA from Dutch sample 894


title: Peripheral blood RNA from Dutch sample 892


title: Peripheral blood RNA from Dutch sample 890


title: Peripheral blood RNA from Dutch sample 899


title: Peripheral blood RNA from Dutch sample 886


title: Peripheral blood RNA from Dutch sample 884


title: Peripheral blood RNA from Dutch sample 891


title: Peripheral blood RNA from Dutch sample 888


title: Peripheral blood RNA from Dutch sample 893


title: Peripheral blood RNA from Dutch sample 887


title: Peripheral blood RNA from Dutch sample 889


title: Peripheral blood RNA from Dutch sample 882


title: Peripheral blood RNA from Dutch sample 880


title: Peripheral blood RNA from Dutch sample 881


title: Peripheral blood RNA from Dutch sample 883


title: Peripheral blood RNA from Dutch sample 877


title: Peripheral blood RNA from Dutch sample 873


title: Peripheral blood RNA from Dutch sample 867


title: Peripheral blood RNA from Dutch sample 870


title: Peripheral blood RNA from Dutch sample 876


title: Peripheral blood RNA from Dutch sample 878


title: Peripheral blood RNA from Dutch sample 885


title: Peripheral blood RNA from Dutch sample 879


title: Peripheral blood RNA from Dutch sample 868


title: Peripheral blood RNA from Dutch sample 871


title: Peripheral blood RNA from Dutch sample 874


title: Peripheral blood RNA from Dutch sample 864


title: Peripheral blood RNA from Dutch sample 875


title: Peripheral blood RNA from Dutch sample 865


title: Peripheral blood RNA from Dutch sample 869


title: Peripheral blood RNA from Dutch sample 863


title: Peripheral blood RNA from Dutch sample 866


title: Peripheral blood RNA from Dutch sample 860


title: Peripheral blood RNA from Dutch sample 862


title: Peripheral blood RNA from Dutch sample 858


title: Peripheral blood RNA from Dutch sample 861


title: Peripheral blood RNA from Dutch sample 856


title: Peripheral blood RNA from Dutch sample 857


title: Peripheral blood RNA from Dutch sample 859


title: Peripheral blood RNA from Dutch sample 872


title: Peripheral blood RNA from Dutch sample 853


title: Peripheral blood RNA from Dutch sample 852


title: Peripheral blood RNA from Dutch sample 848


title: Peripheral blood RNA from Dutch sample 849


title: Peripheral blood RNA from Dutch sample 847


title: Peripheral blood RNA from Dutch sample 844


title: Peripheral blood RNA from Dutch sample 845


title: Peripheral blood RNA from Dutch sample 842


title: Peripheral blood RNA from Dutch sample 846


title: Peripheral blood RNA from Dutch sample 834


title: Peripheral blood RNA from Dutch sample 837


title: Peripheral blood RNA from Dutch sample 855


title: Peripheral blood RNA from Dutch sample 840


title: Peripheral blood RNA from Dutch sample 841


title: Peripheral blood RNA from Dutch sample 830


title: Peripheral blood RNA from Dutch sample 843


title: Peripheral blood RNA from Dutch sample 827


title: Peripheral blood RNA from Dutch sample 831


title: Peripheral blood RNA from Dutch sample 854


title: Peripheral blood RNA from Dutch sample 839


title: Peripheral blood RNA from Dutch sample 836


title: Peripheral blood RNA from Dutch sample 851


title: Peripheral blood RNA from Dutch sample 828


title: Peripheral blood RNA from Dutch sample 832


title: Peripheral blood RNA from Dutch sample 833


title: Peripheral blood RNA from Dutch sample 829


title: Peripheral blood RNA from Dutch sample 826


title: Peripheral blood RNA from Dutch sample 850


title: Peripheral blood RNA from Dutch sample 825


title: Peripheral blood RNA from Dutch sample 824


title: Peripheral blood RNA from Dutch sample 822


title: Peripheral blood RNA from Dutch sample 823


title: Peripheral blood RNA from Dutch sample 816


title: Peripheral blood RNA from Dutch sample 820


title: Peripheral blood RNA from Dutch sample 819


title: Peripheral blood RNA from Dutch sample 813


title: Peripheral blood RNA from Dutch sample 815


title: Peripheral blood RNA from Dutch sample 817


title: Peripheral blood RNA from Dutch sample 806


title: Peripheral blood RNA from Dutch sample 808


title: Peripheral blood RNA from Dutch sample 821


title: Peripheral blood RNA from Dutch sample 810


title: Peripheral blood RNA from Dutch sample 805


title: Peripheral blood RNA from Dutch sample 800


title: Peripheral blood RNA from Dutch sample 818


title: Peripheral blood RNA from Dutch sample 801


title: Peripheral blood RNA from Dutch sample 809


title: Peripheral blood RNA from Dutch sample 804


title: Peripheral blood RNA from Dutch sample 802


title: Peripheral blood RNA from Dutch sample 814


title: Peripheral blood RNA from Dutch sample 811


title: Peripheral blood RNA from Dutch sample 803


title: Peripheral blood RNA from Dutch sample 807


title: Peripheral blood RNA from Dutch sample 797


title: Peripheral blood RNA from Dutch sample 835


title: Peripheral blood RNA from Dutch sample 798


title: Peripheral blood RNA from Dutch sample 812


title: Peripheral blood RNA from Dutch sample 793


title: Peripheral blood RNA from Dutch sample 794


title: Peripheral blood RNA from Dutch sample 795


title: Peripheral blood RNA from Dutch sample 796


title: Peripheral blood RNA from Dutch sample 838


title: Peripheral blood RNA from Dutch sample 789


title: Peripheral blood RNA from Dutch sample 799


title: Peripheral blood RNA from Dutch sample 792


title: Peripheral blood RNA from Dutch sample 788


title: Peripheral blood RNA from Dutch sample 790


title: Peripheral blood RNA from Dutch sample 785


title: Peripheral blood RNA from Dutch sample 778


title: Peripheral blood RNA from Dutch sample 781


title: Peripheral blood RNA from Dutch sample 780


title: Peripheral blood RNA from Dutch sample 775


title: Peripheral blood RNA from Dutch sample 786


title: Peripheral blood RNA from Dutch sample 791


title: Peripheral blood RNA from Dutch sample 774


title: Peripheral blood RNA from Dutch sample 770


title: Peripheral blood RNA from Dutch sample 779


title: Peripheral blood RNA from Dutch sample 783


title: Peripheral blood RNA from Dutch sample 777


title: Peripheral blood RNA from Dutch sample 771


title: Peripheral blood RNA from Dutch sample 782


title: Peripheral blood RNA from Dutch sample 772


title: Peripheral blood RNA from Dutch sample 773


title: Peripheral blood RNA from Dutch sample 776


title: Peripheral blood RNA from Dutch sample 784


title: Peripheral blood RNA from Dutch sample 787


title: Peripheral blood RNA from Dutch sample 765


title: Peripheral blood RNA from Dutch sample 766


title: Peripheral blood RNA from Dutch sample 769


title: Peripheral blood RNA from Dutch sample 758


title: Peripheral blood RNA from Dutch sample 767


title: Peripheral blood RNA from Dutch sample 768


title: Peripheral blood RNA from Dutch sample 757


title: Peripheral blood RNA from Dutch sample 764


title: Peripheral blood RNA from Dutch sample 761


title: Peripheral blood RNA from Dutch sample 760


title: Peripheral blood RNA from Dutch sample 756


title: Peripheral blood RNA from Dutch sample 763


title: Peripheral blood RNA from Dutch sample 752


title: Peripheral blood RNA from Dutch sample 753


title: Peripheral blood RNA from Dutch sample 759


title: Peripheral blood RNA from Dutch sample 762


title: Peripheral blood RNA from Dutch sample 755


title: Peripheral blood RNA from Dutch sample 748


title: Peripheral blood RNA from Dutch sample 750


title: Peripheral blood RNA from Dutch sample 751


title: Peripheral blood RNA from Dutch sample 741


title: Peripheral blood RNA from Dutch sample 743


title: Peripheral blood RNA from Dutch sample 742


title: Peripheral blood RNA from Dutch sample 745


title: Peripheral blood RNA from Dutch sample 744


title: Peripheral blood RNA from Dutch sample 747


title: Peripheral blood RNA from Dutch sample 740


title: Peripheral blood RNA from Dutch sample 746


title: Peripheral blood RNA from Dutch sample 749


title: Peripheral blood RNA from Dutch sample 737


title: Peripheral blood RNA from Dutch sample 733


title: Peripheral blood RNA from Dutch sample 738


title: Peripheral blood RNA from Dutch sample 739


title: Peripheral blood RNA from Dutch sample 734


title: Peripheral blood RNA from Dutch sample 735


title: Peripheral blood RNA from Dutch sample 730


title: Peripheral blood RNA from Dutch sample 736


title: Peripheral blood RNA from Dutch sample 732


title: Peripheral blood RNA from Dutch sample 729


title: Peripheral blood RNA from Dutch sample 728


title: Peripheral blood RNA from Dutch sample 727


title: Peripheral blood RNA from Dutch sample 725


title: Peripheral blood RNA from Dutch sample 726


title: Peripheral blood RNA from Dutch sample 723


title: Peripheral blood RNA from Dutch sample 731


title: Peripheral blood RNA from Dutch sample 722


title: Peripheral blood RNA from Dutch sample 720


title: Peripheral blood RNA from Dutch sample 718


title: Peripheral blood RNA from Dutch sample 721


title: Peripheral blood RNA from Dutch sample 717


title: Peripheral blood RNA from Dutch sample 716


title: Peripheral blood RNA from Dutch sample 719


title: Peripheral blood RNA from Dutch sample 754


title: Peripheral blood RNA from Dutch sample 715


title: Peripheral blood RNA from Dutch sample 713


title: Peripheral blood RNA from Dutch sample 712


title: Peripheral blood RNA from Dutch sample 710


title: Peripheral blood RNA from Dutch sample 707


title: Peripheral blood RNA from Dutch sample 709


title: Peripheral blood RNA from Dutch sample 701


title: Peripheral blood RNA from Dutch sample 699


title: Peripheral blood RNA from Dutch sample 708


title: Peripheral blood RNA from Dutch sample 703


title: Peripheral blood RNA from Dutch sample 702


title: Peripheral blood RNA from Dutch sample 705


title: Peripheral blood RNA from Dutch sample 714


title: Peripheral blood RNA from Dutch sample 704


title: Peripheral blood RNA from Dutch sample 696


title: Peripheral blood RNA from Dutch sample 697


title: Peripheral blood RNA from Dutch sample 706


title: Peripheral blood RNA from Dutch sample 711


title: Peripheral blood RNA from Dutch sample 700


title: Peripheral blood RNA from Dutch sample 695


title: Peripheral blood RNA from Dutch sample 694


title: Peripheral blood RNA from Dutch sample 689


title: Peripheral blood RNA from Dutch sample 692


title: Peripheral blood RNA from Dutch sample 693


title: Peripheral blood RNA from Dutch sample 691


title: Peripheral blood RNA from Dutch sample 687


title: Peripheral blood RNA from Dutch sample 690


title: Peripheral blood RNA from Dutch sample 688


title: Peripheral blood RNA from Dutch sample 685


title: Peripheral blood RNA from Dutch sample 686


title: Peripheral blood RNA from Dutch sample 684


title: Peripheral blood RNA from Dutch sample 683


title: Peripheral blood RNA from Dutch sample 680


title: Peripheral blood RNA from Dutch sample 678


title: Peripheral blood RNA from Dutch sample 667


title: Peripheral blood RNA from Dutch sample 679


title: Peripheral blood RNA from Dutch sample 669


title: Peripheral blood RNA from Dutch sample 673


title: Peripheral blood RNA from Dutch sample 670


title: Peripheral blood RNA from Dutch sample 677


title: Peripheral blood RNA from Dutch sample 671


title: Peripheral blood RNA from Dutch sample 676


title: Peripheral blood RNA from Dutch sample 674


title: Peripheral blood RNA from Dutch sample 668


title: Peripheral blood RNA from Dutch sample 681


title: Peripheral blood RNA from Dutch sample 665


title: Peripheral blood RNA from Dutch sample 666


title: Peripheral blood RNA from Dutch sample 682


title: Peripheral blood RNA from Dutch sample 724


title: Peripheral blood RNA from Dutch sample 675


title: Peripheral blood RNA from Dutch sample 672


title: Peripheral blood RNA from Dutch sample 662


title: Peripheral blood RNA from Dutch sample 664


title: Peripheral blood RNA from Dutch sample 659


title: Peripheral blood RNA from Dutch sample 656


title: Peripheral blood RNA from Dutch sample 698


title: Peripheral blood RNA from Dutch sample 657


title: Peripheral blood RNA from Dutch sample 655


title: Peripheral blood RNA from Dutch sample 651


title: Peripheral blood RNA from Dutch sample 654


title: Peripheral blood RNA from Dutch sample 644


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title: Peripheral blood RNA from Dutch sample 648


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title: Peripheral blood RNA from Dutch sample 646


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title: Peripheral blood RNA from Dutch sample 635


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title: Peripheral blood RNA from Dutch sample 641


title: Peripheral blood RNA from Dutch sample 637


title: Peripheral blood RNA from Dutch sample 647


title: Peripheral blood RNA from Dutch sample 639


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title: Peripheral blood RNA from Dutch sample 631


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title: Peripheral blood RNA from Dutch sample 640


title: Peripheral blood RNA from Dutch sample 649


title: Peripheral blood RNA from Dutch sample 661


title: Peripheral blood RNA from Dutch sample 636


title: Peripheral blood RNA from Dutch sample 628


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title: Peripheral blood RNA from Dutch sample 617


title: Peripheral blood RNA from Dutch sample 622


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title: Peripheral blood RNA from Dutch sample 638


title: Peripheral blood RNA from Dutch sample 616


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title: Peripheral blood RNA from Dutch sample 625


title: Peripheral blood RNA from Dutch sample 598


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title: Peripheral blood RNA from Dutch sample 597


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title: Peripheral blood RNA from Dutch sample 593


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title: Peripheral blood RNA from Dutch sample 602


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title: Peripheral blood RNA from Dutch sample 589


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title: Peripheral blood RNA from Dutch sample 584


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title: Peripheral blood RNA from Dutch sample 594


title: Peripheral blood RNA from Dutch sample 591


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title: Peripheral blood RNA from Dutch sample 578


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title: Peripheral blood RNA from Dutch sample 590


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title: Peripheral blood RNA from Dutch sample 549


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title: Peripheral blood RNA from Dutch sample 412


title: Peripheral blood RNA from Dutch sample 396


title: Peripheral blood RNA from Dutch sample 385


title: Peripheral blood RNA from Dutch sample 495


title: Peripheral blood RNA from Dutch sample 386


title: Peripheral blood RNA from Dutch sample 390


title: Peripheral blood RNA from Dutch sample 387


title: Peripheral blood RNA from Dutch sample 379


title: Peripheral blood RNA from Dutch sample 383


title: Peripheral blood RNA from Dutch sample 381


title: Peripheral blood RNA from Dutch sample 378


title: Peripheral blood RNA from Dutch sample 380


title: Peripheral blood RNA from Dutch sample 376


title: Peripheral blood RNA from Dutch sample 377


title: Peripheral blood RNA from Dutch sample 372


title: Peripheral blood RNA from Dutch sample 374


title: Peripheral blood RNA from Dutch sample 370


title: Peripheral blood RNA from Dutch sample 382


title: Peripheral blood RNA from Dutch sample 371


title: Peripheral blood RNA from Dutch sample 369


title: Peripheral blood RNA from Dutch sample 373


title: Peripheral blood RNA from Dutch sample 441


title: Peripheral blood RNA from Dutch sample 368


title: Peripheral blood RNA from Dutch sample 360


title: Peripheral blood RNA from Dutch sample 375


title: Peripheral blood RNA from Dutch sample 363


title: Peripheral blood RNA from Dutch sample 366


title: Peripheral blood RNA from Dutch sample 361


title: Peripheral blood RNA from Dutch sample 362


title: Peripheral blood RNA from Dutch sample 359


title: Peripheral blood RNA from Dutch sample 364


title: Peripheral blood RNA from Dutch sample 358


title: Peripheral blood RNA from Dutch sample 356


title: Peripheral blood RNA from Dutch sample 365


title: Peripheral blood RNA from Dutch sample 354


title: Peripheral blood RNA from Dutch sample 355


title: Peripheral blood RNA from Dutch sample 353


title: Peripheral blood RNA from Dutch sample 367


title: Peripheral blood RNA from Dutch sample 352


title: Peripheral blood RNA from Dutch sample 345


title: Peripheral blood RNA from Dutch sample 347


title: Peripheral blood RNA from Dutch sample 350


title: Peripheral blood RNA from Dutch sample 349


title: Peripheral blood RNA from Dutch sample 351


title: Peripheral blood RNA from Dutch sample 357


title: Peripheral blood RNA from Dutch sample 348


title: Peripheral blood RNA from Dutch sample 342


title: Peripheral blood RNA from Dutch sample 346


title: Peripheral blood RNA from Dutch sample 344


title: Peripheral blood RNA from Dutch sample 384


title: Peripheral blood RNA from Dutch sample 339


title: Peripheral blood RNA from Dutch sample 331


title: Peripheral blood RNA from Dutch sample 325


title: Peripheral blood RNA from Dutch sample 320


title: Peripheral blood RNA from Dutch sample 333


title: Peripheral blood RNA from Dutch sample 319


title: Peripheral blood RNA from Dutch sample 336


title: Peripheral blood RNA from Dutch sample 322


title: Peripheral blood RNA from Dutch sample 323


title: Peripheral blood RNA from Dutch sample 315


title: Peripheral blood RNA from Dutch sample 337


title: Peripheral blood RNA from Dutch sample 327


title: Peripheral blood RNA from Dutch sample 340


title: Peripheral blood RNA from Dutch sample 338


title: Peripheral blood RNA from Dutch sample 316


title: Peripheral blood RNA from Dutch sample 330


title: Peripheral blood RNA from Dutch sample 314


title: Peripheral blood RNA from Dutch sample 334


title: Peripheral blood RNA from Dutch sample 313


title: Peripheral blood RNA from Dutch sample 341


title: Peripheral blood RNA from Dutch sample 326


title: Peripheral blood RNA from Dutch sample 343


title: Peripheral blood RNA from Dutch sample 328


title: Peripheral blood RNA from Dutch sample 312


title: Peripheral blood RNA from Dutch sample 329


title: Peripheral blood RNA from Dutch sample 308


title: Peripheral blood RNA from Dutch sample 335


title: Peripheral blood RNA from Dutch sample 307


title: Peripheral blood RNA from Dutch sample 311


title: Peripheral blood RNA from Dutch sample 306


title: Peripheral blood RNA from Dutch sample 318


title: Peripheral blood RNA from Dutch sample 332


title: Peripheral blood RNA from Dutch sample 324


title: Peripheral blood RNA from Dutch sample 309


title: Peripheral blood RNA from Dutch sample 321


title: Peripheral blood RNA from Dutch sample 302


title: Peripheral blood RNA from Dutch sample 304


title: Peripheral blood RNA from Dutch sample 305


title: Peripheral blood RNA from Dutch sample 301


title: Peripheral blood RNA from Dutch sample 296


title: Peripheral blood RNA from Dutch sample 298


title: Peripheral blood RNA from Dutch sample 310


title: Peripheral blood RNA from Dutch sample 300


title: Peripheral blood RNA from Dutch sample 291


title: Peripheral blood RNA from Dutch sample 293


title: Peripheral blood RNA from Dutch sample 303


title: Peripheral blood RNA from Dutch sample 299


title: Peripheral blood RNA from Dutch sample 294


title: Peripheral blood RNA from Dutch sample 297


title: Peripheral blood RNA from Dutch sample 295


title: Peripheral blood RNA from Dutch sample 289


title: Peripheral blood RNA from Dutch sample 290


title: Peripheral blood RNA from Dutch sample 317


title: Peripheral blood RNA from Dutch sample 292


title: Peripheral blood RNA from Dutch sample 283


title: Peripheral blood RNA from Dutch sample 286


title: Peripheral blood RNA from Dutch sample 282


title: Peripheral blood RNA from Dutch sample 285


title: Peripheral blood RNA from Dutch sample 288


title: Peripheral blood RNA from Dutch sample 276


title: Peripheral blood RNA from Dutch sample 278


title: Peripheral blood RNA from Dutch sample 279


title: Peripheral blood RNA from Dutch sample 272


title: Peripheral blood RNA from Dutch sample 280


title: Peripheral blood RNA from Dutch sample 275


title: Peripheral blood RNA from Dutch sample 274


title: Peripheral blood RNA from Dutch sample 277


title: Peripheral blood RNA from Dutch sample 267


title: Peripheral blood RNA from Dutch sample 271


title: Peripheral blood RNA from Dutch sample 273


title: Peripheral blood RNA from Dutch sample 268


title: Peripheral blood RNA from Dutch sample 266


title: Peripheral blood RNA from Dutch sample 262


title: Peripheral blood RNA from Dutch sample 270


title: Peripheral blood RNA from Dutch sample 264


title: Peripheral blood RNA from Dutch sample 284


title: Peripheral blood RNA from Dutch sample 261


title: Peripheral blood RNA from Dutch sample 263


title: Peripheral blood RNA from Dutch sample 281


title: Peripheral blood RNA from Dutch sample 287


title: Peripheral blood RNA from Dutch sample 265


title: Peripheral blood RNA from Dutch sample 269


title: Peripheral blood RNA from Dutch sample 258


title: Peripheral blood RNA from Dutch sample 257


title: Peripheral blood RNA from Dutch sample 259


title: Peripheral blood RNA from Dutch sample 252


title: Peripheral blood RNA from Dutch sample 255


title: Peripheral blood RNA from Dutch sample 254


title: Peripheral blood RNA from Dutch sample 256


title: Peripheral blood RNA from Dutch sample 247


title: Peripheral blood RNA from Dutch sample 243


title: Peripheral blood RNA from Dutch sample 253


title: Peripheral blood RNA from Dutch sample 248


title: Peripheral blood RNA from Dutch sample 245


title: Peripheral blood RNA from Dutch sample 244


title: Peripheral blood RNA from Dutch sample 250


title: Peripheral blood RNA from Dutch sample 239


title: Peripheral blood RNA from Dutch sample 251


title: Peripheral blood RNA from Dutch sample 249


title: Peripheral blood RNA from Dutch sample 242


title: Peripheral blood RNA from Dutch sample 238


title: Peripheral blood RNA from Dutch sample 240


title: Peripheral blood RNA from Dutch sample 236


title: Peripheral blood RNA from Dutch sample 234


title: Peripheral blood RNA from Dutch sample 235


title: Peripheral blood RNA from Dutch sample 241


title: Peripheral blood RNA from Dutch sample 230


title: Peripheral blood RNA from Dutch sample 232


title: Peripheral blood RNA from Dutch sample 229


title: Peripheral blood RNA from Dutch sample 225


title: Peripheral blood RNA from Dutch sample 224


title: Peripheral blood RNA from Dutch sample 231


title: Peripheral blood RNA from Dutch sample 216


title: Peripheral blood RNA from Dutch sample 226


title: Peripheral blood RNA from Dutch sample 227


title: Peripheral blood RNA from Dutch sample 221


title: Peripheral blood RNA from Dutch sample 220


title: Peripheral blood RNA from Dutch sample 218


title: Peripheral blood RNA from Dutch sample 215


title: Peripheral blood RNA from Dutch sample 228


title: Peripheral blood RNA from Dutch sample 212


title: Peripheral blood RNA from Dutch sample 214


title: Peripheral blood RNA from Dutch sample 222


title: Peripheral blood RNA from Dutch sample 217


title: Peripheral blood RNA from Dutch sample 213


title: Peripheral blood RNA from Dutch sample 219


title: Peripheral blood RNA from Dutch sample 223


title: Peripheral blood RNA from Dutch sample 233


title: Peripheral blood RNA from Dutch sample 209


title: Peripheral blood RNA from Dutch sample 211


title: Peripheral blood RNA from Dutch sample 208


title: Peripheral blood RNA from Dutch sample 206


title: Peripheral blood RNA from Dutch sample 210


title: Peripheral blood RNA from Dutch sample 207


title: Peripheral blood RNA from Dutch sample 202


title: Peripheral blood RNA from Dutch sample 200


title: Peripheral blood RNA from Dutch sample 203


title: Peripheral blood RNA from Dutch sample 199


title: Peripheral blood RNA from Dutch sample 192


title: Peripheral blood RNA from Dutch sample 198


title: Peripheral blood RNA from Dutch sample 201


title: Peripheral blood RNA from Dutch sample 193


title: Peripheral blood RNA from Dutch sample 237


title: Peripheral blood RNA from Dutch sample 190


title: Peripheral blood RNA from Dutch sample 184


title: Peripheral blood RNA from Dutch sample 186


title: Peripheral blood RNA from Dutch sample 189


title: Peripheral blood RNA from Dutch sample 188


title: Peripheral blood RNA from Dutch sample 195


title: Peripheral blood RNA from Dutch sample 205


title: Peripheral blood RNA from Dutch sample 196


title: Peripheral blood RNA from Dutch sample 197


title: Peripheral blood RNA from Dutch sample 204


title: Peripheral blood RNA from Dutch sample 187


title: Peripheral blood RNA from Dutch sample 185


title: Peripheral blood RNA from Dutch sample 191


title: Peripheral blood RNA from Dutch sample 194


title: Peripheral blood RNA from Dutch sample 183


title: Peripheral blood RNA from Dutch sample 182


title: Peripheral blood RNA from Dutch sample 177


title: Peripheral blood RNA from Dutch sample 181


title: Peripheral blood RNA from Dutch sample 180


title: Peripheral blood RNA from Dutch sample 246


title: Peripheral blood RNA from Dutch sample 178


title: Peripheral blood RNA from Dutch sample 176


title: Peripheral blood RNA from Dutch sample 260


title: Peripheral blood RNA from Dutch sample 179


title: Peripheral blood RNA from Dutch sample 175


title: Peripheral blood RNA from Dutch sample 174


title: Peripheral blood RNA from Dutch sample 173


title: Peripheral blood RNA from Dutch sample 168


title: Peripheral blood RNA from Dutch sample 169


title: Peripheral blood RNA from Dutch sample 170


title: Peripheral blood RNA from Dutch sample 162


title: Peripheral blood RNA from Dutch sample 171


title: Peripheral blood RNA from Dutch sample 165


title: Peripheral blood RNA from Dutch sample 163


title: Peripheral blood RNA from Dutch sample 161


title: Peripheral blood RNA from Dutch sample 172


title: Peripheral blood RNA from Dutch sample 160


title: Peripheral blood RNA from Dutch sample 158


title: Peripheral blood RNA from Dutch sample 166


title: Peripheral blood RNA from Dutch sample 164


title: Peripheral blood RNA from Dutch sample 157


title: Peripheral blood RNA from Dutch sample 156


title: Peripheral blood RNA from Dutch sample 154


title: Peripheral blood RNA from Dutch sample 155


title: Peripheral blood RNA from Dutch sample 148


title: Peripheral blood RNA from Dutch sample 149


title: Peripheral blood RNA from Dutch sample 150


title: Peripheral blood RNA from Dutch sample 159


title: Peripheral blood RNA from Dutch sample 152


title: Peripheral blood RNA from Dutch sample 145


title: Peripheral blood RNA from Dutch sample 151


title: Peripheral blood RNA from Dutch sample 146


title: Peripheral blood RNA from Dutch sample 147


title: Peripheral blood RNA from Dutch sample 144


title: Peripheral blood RNA from Dutch sample 140


title: Peripheral blood RNA from Dutch sample 167


title: Peripheral blood RNA from Dutch sample 139


title: Peripheral blood RNA from Dutch sample 142


title: Peripheral blood RNA from Dutch sample 133


title: Peripheral blood RNA from Dutch sample 143


title: Peripheral blood RNA from Dutch sample 135


title: Peripheral blood RNA from Dutch sample 130


title: Peripheral blood RNA from Dutch sample 136


title: Peripheral blood RNA from Dutch sample 137


title: Peripheral blood RNA from Dutch sample 124


title: Peripheral blood RNA from Dutch sample 127


title: Peripheral blood RNA from Dutch sample 126


title: Peripheral blood RNA from Dutch sample 141


title: Peripheral blood RNA from Dutch sample 134


title: Peripheral blood RNA from Dutch sample 128


title: Peripheral blood RNA from Dutch sample 129


title: Peripheral blood RNA from Dutch sample 120


title: Peripheral blood RNA from Dutch sample 131


title: Peripheral blood RNA from Dutch sample 122


title: Peripheral blood RNA from Dutch sample 125


title: Peripheral blood RNA from Dutch sample 123


title: Peripheral blood RNA from Dutch sample 121


title: Peripheral blood RNA from Dutch sample 117


title: Peripheral blood RNA from Dutch sample 119


title: Peripheral blood RNA from Dutch sample 116


title: Peripheral blood RNA from Dutch sample 118


title: Peripheral blood RNA from Dutch sample 132


title: Peripheral blood RNA from Dutch sample 115


title: Peripheral blood RNA from Dutch sample 113


title: Peripheral blood RNA from Dutch sample 153


title: Peripheral blood RNA from Dutch sample 110


title: Peripheral blood RNA from Dutch sample 112


title: Peripheral blood RNA from Dutch sample 108


title: Peripheral blood RNA from Dutch sample 114


title: Peripheral blood RNA from Dutch sample 109


title: Peripheral blood RNA from Dutch sample 111


title: Peripheral blood RNA from Dutch sample 107


title: Peripheral blood RNA from Dutch sample 106


title: Peripheral blood RNA from Dutch sample 105


title: Peripheral blood RNA from Dutch sample 104


title: Peripheral blood RNA from Dutch sample 96


title: Peripheral blood RNA from Dutch sample 103


title: Peripheral blood RNA from Dutch sample 99


title: Peripheral blood RNA from Dutch sample 101


title: Peripheral blood RNA from Dutch sample 100


title: Peripheral blood RNA from Dutch sample 88


title: Peripheral blood RNA from Dutch sample 85


title: Peripheral blood RNA from Dutch sample 86


title: Peripheral blood RNA from Dutch sample 98


title: Peripheral blood RNA from Dutch sample 102


title: Peripheral blood RNA from Dutch sample 93


title: Peripheral blood RNA from Dutch sample 90


title: Peripheral blood RNA from Dutch sample 89


title: Peripheral blood RNA from Dutch sample 83


title: Peripheral blood RNA from Dutch sample 97


title: Peripheral blood RNA from Dutch sample 95


title: Peripheral blood RNA from Dutch sample 84


title: Peripheral blood RNA from Dutch sample 91


title: Peripheral blood RNA from Dutch sample 87


title: Peripheral blood RNA from Dutch sample 92


title: Peripheral blood RNA from Dutch sample 80


title: Peripheral blood RNA from Dutch sample 79


title: Peripheral blood RNA from Dutch sample 82


title: Peripheral blood RNA from Dutch sample 77


title: Peripheral blood RNA from Dutch sample 76


title: Peripheral blood RNA from Dutch sample 81


title: Peripheral blood RNA from Dutch sample 78


title: Peripheral blood RNA from Dutch sample 75


title: Peripheral blood RNA from Dutch sample 94


title: Peripheral blood RNA from Dutch sample 73


title: Peripheral blood RNA from Dutch sample 71


title: Peripheral blood RNA from Dutch sample 72


title: Peripheral blood RNA from Dutch sample 74


title: Peripheral blood RNA from Dutch sample 61


title: Peripheral blood RNA from Dutch sample 138


title: Peripheral blood RNA from Dutch sample 69


title: Peripheral blood RNA from Dutch sample 70


title: Peripheral blood RNA from Dutch sample 63


title: Peripheral blood RNA from Dutch sample 60


title: Peripheral blood RNA from Dutch sample 66


title: Peripheral blood RNA from Dutch sample 67


title: Peripheral blood RNA from Dutch sample 68


title: Peripheral blood RNA from Dutch sample 64


title: Peripheral blood RNA from Dutch sample 65


title: Peripheral blood RNA from Dutch sample 59


title: Peripheral blood RNA from Dutch sample 62


title: Peripheral blood RNA from Dutch sample 53


title: Peripheral blood RNA from Dutch sample 51


title: Peripheral blood RNA from Dutch sample 55


title: Peripheral blood RNA from Dutch sample 49


title: Peripheral blood RNA from Dutch sample 57


title: Peripheral blood RNA from Dutch sample 50


title: Peripheral blood RNA from Dutch sample 58


title: Peripheral blood RNA from Dutch sample 54


title: Peripheral blood RNA from Dutch sample 52


title: Peripheral blood RNA from Dutch sample 47


title: Peripheral blood RNA from Dutch sample 46


title: Peripheral blood RNA from Dutch sample 48


title: Peripheral blood RNA from Dutch sample 44


title: Ash1_mES_rep1 (mouse promoter array 2)

type: genomic

city: Cambridge

first: Mike

last: Kagey

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute

description: V6.5 murine ES cells were cultured as described in Boyer et al., Nature 2006 (PMID: 16625203).

hyb_protocol: Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006). In brief, mouse Cot1 DNA, Agilent blocking buffer (1X final conc.), Agilent hybridization buffer (1X final conc.), was added to Cy5- and Cy3-labeled DNA. Mixture was incubated at 95C for 3 minutes, followed by 37C for 30 minutes. Sample was centrifuged for 1 min and sample was hybridized to Agilent mouse promoter array set (2x244k feature set).

scan_protocol: Agilent DNA microarray scanner BA. PMT settings were set manually to normalize bulk signal in the Cy3 and Cy5 channel.

data_processing: Data was processed as described in Lee TI et al. Cell 2006 (PMID: 16630818) to calculated enrichment ratios and determine bound regions.

molecule: genomic DNA

organism: Mus musculus

source_name: Ash1 IP

label_protocol: LM-PCR immunoprecipitated DNA was labeled with Cy5. Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006).

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates. Mouse embryonic fibroblasts were prepared and cultured from NeoR strain mice.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using Ash1 antibody. Purified immunoprecipitated DNA were amplified using two rounds of ligated mediated PCR, as described in Lee et al., Nature Protocols 2006 (PMID: 17406303).

tag: cell type

value: embryonic stem cells (V6.5)

tag: antibody

source_name: Ash1 input

label_protocol: LM-PCR input DNA was labeled with Cy3 using Invitrogen Bioprime random primer labeling kit. Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006).

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were extracted as described in Lee et al., Nature Protocols 2006 (PMID: 17406303).


title: Peripheral blood RNA from Dutch sample 41


title: Ash1_mES_rep2 (mouse promoter array 1)


title: Peripheral blood RNA from Dutch sample 42


title: Peripheral blood RNA from Dutch sample 35


title: Peripheral blood RNA from Dutch sample 37


title: Peripheral blood RNA from Dutch sample 38


title: Peripheral blood RNA from Dutch sample 45


title: Peripheral blood RNA from Dutch sample 36


title: Peripheral blood RNA from Dutch sample 43


title: Peripheral blood RNA from Dutch sample 40


title: Ash1_mES_rep2 (mouse promoter array 2)


title: Ash1_mES_rep1 (mouse promoter array 1)

hyb_protocol: Agilent Mammalian ChIP-on-chip protocol (version 9.1, Nov 2006).  In brief, mouse Cot1 DNA, Agilent blocking buffer (1X final conc.), Agilent hybridization buffer (1X final conc.), was added to Cy5- and Cy3-labeled DNA.  Mixture was incubated at 95C for 3 minutes, followed by 37C for 30 minutes.  Sample was centrifuged for 1 min and sample was hybridized to Agilent mouse promoter array set (2x244k feature set).


title: Peripheral blood RNA from Dutch sample 29


title: Peripheral blood RNA from Dutch sample 34


title: Peripheral blood RNA from Dutch sample 25


title: Peripheral blood RNA from Dutch sample 32


title: Peripheral blood RNA from Dutch sample 26


title: Peripheral blood RNA from Dutch sample 31


title: Peripheral blood RNA from Dutch sample 27


title: Peripheral blood RNA from Dutch sample 23


title: Peripheral blood RNA from Dutch sample 28


title: Peripheral blood RNA from Dutch sample 24


title: Peripheral blood RNA from Dutch sample 30


title: Peripheral blood RNA from Dutch sample 20


title: Peripheral blood RNA from Dutch sample 22


title: Peripheral blood RNA from Dutch sample 33


title: Peripheral blood RNA from Dutch sample 18


title: Peripheral blood RNA from Dutch sample 21


title: Peripheral blood RNA from Dutch sample 15


title: Peripheral blood RNA from Dutch sample 13


title: Peripheral blood RNA from Dutch sample 19


title: Peripheral blood RNA from Dutch sample 10


title: Peripheral blood RNA from Dutch sample 12


title: Peripheral blood RNA from Dutch sample 11


title: Peripheral blood RNA from Dutch sample 14


title: Peripheral blood RNA from Dutch sample 9


title: Peripheral blood RNA from Dutch sample 16


title: Peripheral blood RNA from Dutch sample 5


title: Peripheral blood RNA from Dutch sample 17


title: Peripheral blood RNA from Dutch sample 4


title: Peripheral blood RNA from Dutch sample 1


title: Peripheral blood RNA from Dutch sample 7


title: Peripheral blood RNA from Dutch sample 39


title: Peripheral blood RNA from Dutch sample 3


title: Peripheral blood RNA from Dutch sample 56


title: ES cells + control microRNA replicate 3

status: Public on Feb 27 2010

first: Sophie

middle: Alexandra

last: Hanina

state: Cambridgeshire

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: control replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were transformed with a variance-stabilising algorithm and normalised using quantile normalisation in lumi in R. The selection of the data aims at removing non-expressed genes or data that are too close to the background to be distinguished. Not removing those genes will add noise to the data. The selection was done using the following criteria:

- Threshold for selection: detection p-value inferior to 0.01 for a measurement to be selected.
- A gene must be present in at least one sample.

label: biotin

source_name: ES cells + control microRNA

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: ES cells grown in feeder-free conditions, in ES-cell medium containing 15% FCS, DMEM/F-12 and 2000U/ml LIF.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini kit with on-column DNaseI digestion in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were co-transfected (Amaxa nucleofection) with 300pmol of microRNA and 1microgram of pEGFP-1, which served as a control for transfection efficiency.  GFP-positive cells were sorted 24 hours after transfection.

tag: strain

value: Mouse ES cells, Dicer1-null


title: Peripheral blood RNA from Dutch sample 8


title: Peripheral blood RNA from Dutch sample 6


title: ES cells + control microRNA replicate 2

description: control replicate 2


title: Dye swapped controlt2hvsCDt2h rep6

city: chongup

first: sun

middle: wook

last: Jeong

state: Chonbuk

address: Sinjeongdong 1266

department: Radiation biotechnology

country: South Korea

institute: Korea atomic energy research institute

hyb_protocol: The labeled cDNA pools were mixed, dried, and dissolved with hybridization buffer. The probes were denatured by heating and hybridized simultaneously to a prehybridized DNA microarray slide for 16 h at 42°C in a MAUI Hybridization System (BioMicro Systems, Salt Lake City, UT, USA) with gentle mixing, After hybridization, slides were washed sequential

scan_protocol: Scanned on an Genepix Pro 4000B scanner. Images were quantified using Genepix Pro Software (version 6.0).

data_processing: LOWESS normalized, performed in GeneSpringGX 11 software, Agilent.

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

source_name: Cadmium untreated cells and incubation for 2h

label_protocol: 50 µg of total RNA were primed with 2 µl of 3 µg/µl random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 2 µl of 50X aminoallyl-dNTP mix, 25 µM Cy3-labeling dye

extract_protocol: Total RNA extracted using RiboEX (GeneAll biotechnology, Korea) following manufacturer's instructions

tag: stress treatment

value: none (reference)

source_name: Cadmium treated cells and incubated for 2h

value: D.radiodurans R1 exposed to 100 µM CdCl2 and incubated 2 h (test)


title: ES cells + control microRNA replicate 1

description: control replicate 1


title: ES cells + miR-294 replicate 1

description: experimental replicate 1

source_name: ES cells + miR-294


title: Dye swapped controlt2hvsCDt2h rep8


title: Peripheral blood RNA from Dutch sample 2


title: ES cells + miR-294 replicate 2

description: experimental replicate 2


title: CDt2hvscontrolt2h rep4


title: ES cells + miR-294 replicate 3

description: experimental replicate 3


title: Dye swapped controlt1hvsCDt1h rep5

source_name: Cadmium untreated cells and incubated for 1h

source_name: Cadmium treated cells and incubated for 1h

value: D.radiodurans R1 exposed to 100 µM CdCl2 and incubated for 1h (test)


title: Dye swapped controlt1hvsCDt1h rep6


title: Dye swapped controlt2hvsCDt2h rep7


title: Dye swapped controlt2hvsCDt2h rep5


title: CDt2hvscontrolt2h rep1


title: Dye swapped controlt1hvsCDt1h rep7


title: CDt2hvscontrolt2h rep3


title: CDt2hvscontrolt2h rep2


title: Dye swapped controlt1hvsCDt1h rep8


title: CDt1hvscontrolt1h rep4


title: CDt1hvscontrolt1h rep3


title: CDt1hvscontrolt1h rep2


title: CDt0.5hvscontrolt0.5h rep2

source_name: Cadmium treated cells and incubated for 0.5h

value: D.radiodurans R1 exposed to 100 µM CdCl2 and incubated 0.5 h (test)

source_name: Cadmium untreated cells and incubation for 0.5h


title: CDt1hvscontrolt1h rep1


title: Dye swapped controlt0.5hvsCDt0.5h rep6


title: CDt0.5hvscontrolt0.5h rep3


title: CDt0.5hvscontrolt0.5h rep4


title: Dye swapped controlt0.25hvsCDt0.25h rep7

source_name: Cadmium untreated cells and incubation for 0.25h

source_name: Cadmium treated cells and incubated for 0.25h

value: D.radiodurans R1 exposed to 100 µM CdCl2 and incubated 0.25 h (test)


title: Dye swapped controlt0.5hvsCDt0.5h rep7


title: Dye swapped controlt0.25hvsCDt0.25h rep8


title: CDt0.25hvscontrolt0.25h rep1


title: CDt0.25hvscontrolt0.25h rep2


title: Dye swapped controlt0.5hvsCDt0.5h rep8


title: Dye swapped controlt0.25hvsCDt0.25h rep5


title: CDt0.25hvscontrolt0.25h rep4


title: CDt0.25hvscontrolt0.25h rep3


title: CDt0.5hvscontrolt0.5h rep1


title: IFNAR MAC S.t._2

status: Public on Feb 26 2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: IFNAR MAC S.t._2

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: Signal Intensities were calculated using RMA algorithm and for statistical analysis we applied GeneSpring GX 10 software suite (Agilent Technologies, Waldbronn, Germany).

source_name: Bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: with MCSF

extract_protocol: Qiagen RNAeasy

treatment_protocol: 6 hours with S.typhimurium MOI: 5

tag: genetic modification

value: IFNAR knockout

value: bone marrow

value: macrophages


title: IFNAR MAC cntr_2

description: IFNAR MAC cntr_2

treatment_protocol: Untreated control


title: wt MAC VSV-AV2_2

description: wt MAC VSV-AV2_2

treatment_protocol: 6 hours with VSV-AV2 MOI: 2


title: MC cntr_3

description: MC cntr_3

growth_protocol: with IL-3

value: mast cells


title: IFNAR MAC L.m._2

description: IFNAR MAC L.m._2

treatment_protocol: 6 hours with L.monocytogenes MOI: 5


title: MC VSV-AV2_2

description: MC VSV-AV2_2


title: Dye swapped controlt0.25hvsCDt0.25h rep6


title: IFNAR MAC S.t._1

description: IFNAR MAC S.t._1


title: IFNAR MAC L.m._1

description: IFNAR MAC L.m._1


title: wt MAC cntr_3

description: wt MAC cntr_3


title: MC VSV-AV2_1

description: MC VSV-AV2_1


title: MC S.t._2

description: MC S.t._2

treatment_protocol: 6 hours with S.typhimurium MOI: 50


title: IFNAR MAC cntr_1

description: IFNAR MAC cntr_1


title: MC L.m._2

description: MC L.m._2

treatment_protocol: 6 hours with L.monocytogenes, MOI: 50


title: wt MAC S.t._2

description: wt MAC S.t._2


title: wt MAC L.m._2

description: wt MAC L.m._2


title: wt MAC VSV-AV2_1

description: wt MAC VSV-AV2_1


title: MC cntr_2

description: MC cntr_2


title: wt MAC S.t._1

description: wt MAC S.t._1


title: wt MAC cntr_2

description: wt MAC cntr_2


title: Dye swapped controlt0.5hvsCDt0.5h rep5


title: Series 3: H3k4me3 IP from cdc7ts cells 90min after release from arrest in 24C replicate 1

type: other

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

description: CYM36 cells bearing a cdc7 ts mutant were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDmedia prewarmed to 24C containing 20ug/ml pronase (SIGMA).Cells were grown at 24C and harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

hyb_protocol: Amplified ChIP and ChIP input were mixed, purified by microcon, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 55 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios were calculated to produce the values given in the data table.

organism: Saccharomyces cerevisiae

source_name: H3K4me3 IP

label_protocol: The cDNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

extract_protocol: Chromatin associated with the target epitope was immunoprecipitated from mononucleosomal cell extract and amplified by TLAD.

value: CYM36 (cdc7ts)

source_name: input

extract_protocol: DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.


title: Series 3: H3k4me3 IP from cdc7ts cells 90min after release from arrest in 24C replicate 2


title: Series 3: H3k4me3 IP from cdc7ts cells 135min after release from arrest in 24C


title: Series 3: H3k4me3 IP from cdc7ts cells 90min after release from arrest in 37C replicate 1

description: CYM36 cells bearing a cdc7 ts mutant were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDmedia prewarmed to 37C containing 20ug/ml pronase (SIGMA).Cells were grown at 37C and harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: Series 1: H3k4me3 IP from wt cells 45min after release from arrest

description: BY4741 cells bearing a deletion in bar1  were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDmedia containing 20ug/ml pronase (SIGMA).Cells were harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

value: BY4741 bar1del


title: Series 3: H3k4me3 IP from cdc7ts cells 90min after release from arrest in 37C replicate 2


title: wt MAC L.m._1

description: wt MAC L.m._1


title: Series 3: H3k4me3 IP from alpha factor arrested cdc7ts cells at 24C replicate 1


title: Series 3: H3k4me3 IP from alpha factor arrested cdc7ts cells at 24C replicate2


title: Series 1: H3k4me3 IP from wt cells 60min after release from arrest


title: wt MAC cntr_1

description: wt MAC cntr_1


title: MC S.t._1

description: MC S.t._1


title: Series 1: H3k4me3 IP from wt cells 15min after release from arrest


title: Series 1: H3k4me3 IP from midlog wt cells


title: Series 3: H3k4me3 IP from cdc7ts cells 180min after release from arrest in 37C


title: Series 2: H3k4me3 IP from jhd2 delete cells 60min after release from arrest

description: BY4741 cells bearing a deletion in bar1 and jhd2 were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDmedia containing 20ug/ml pronase (SIGMA).Cells were harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

value: BY4741 bar1del jhd2del


title: Series 1: H3k4me3 IP from wt cells 90min after release from arrest


title: Series 1: H3k4me3 IP from alpha factor arrested wt cells


title: MC cntr_1

description: MC cntr_1


title: Series 3: H3k4me3 IP from cdc7ts cells 30min after release from arrest in 37C


title: mut ARX 14

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: Three timed-pregnant Arx heterozygous dams crossed with C57Bl/6 males were sacrificed at E14.5, the embryos harvested and placed into cold PBS. After brain isolarion, meninges and olfactory bulbs were removed, and the ventral telencephalon separated from the overlying cerebral cortex. The same procedure was repeated for 5 wt and 5 Arx mutant embryos.

hyb_protocol: Hybridization was done according to Affymetrix standard protocol.

scan_protocol: GeneChips scanning was done according to Affymetrix standard protocol.

data_processing: Microarray quality control and statistical validation were performed using Bioconductor. Background correction, normalization, and probe set intensities were obtained by means of RMA and quantile normalization.

label: Biotin

source_name: ventral telencephalon

label_protocol: Biotin labeled cRNAs were generated with Affymetrix kit according to manufacturer protocol

extract_protocol: Qiagen RNA micro kit (Qiagen, Valencia, CA)

tag: Arx heterozygous dams crossed with C57Bl/6 males sacrificed at E14.5


title: mut ARX 13


title: Series 2: H3k4me3 IP from jhd2 delete cells 15min after release from arrest


title: Series 3: H3k4me3 IP from cdc7ts cells 180min after release from arrest in 24C


title: Series 2: H3k4me3 IP from alpha factor arrested jhd2 delete cells


title: mut ARX 15


title: Series 3: H3k4me3 IP from cdc7ts cells 45min after release from arrest in 24C


title: Series 3: H3k4me3 IP from cdc7ts cells 15min after release from arrest in 24C


title: Series 2: H3k4me3 IP from midlog jhd2 delete cells

description: BY4741 cells bearing a deletion in bar1 and jhd2 were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPD media containing 20ug/ml pronase (SIGMA). Cells were harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: Series 3: H3k4me3 IP from cdc7ts cells 60min after release from arrest in 37C


title: Series 3: H3k4me3 IP from cdc7ts cells 15min after release from arrest in 37C


title: Series 3: H3k4me3 IP from cdc7ts cells 60min after release from arrest in 24C


title: Series 3: H3k4me3 IP from jhd2 delete cells 45min after release from arrest


title: Series 3: H3k4me3 IP from cdc7ts cells 135min after release from arrest in 37C


title: Series 3: H3k4me3 IP from cdc7ts cells 30min after release from arrest in 24C


title: Series 2: H3k4me3 IP from jhd2 delete cells 90min after release from arrest


title: Series 3: H3k4me3 IP from cdc7ts cells 45min after release from arrest in 37C


title: mut ARX 11


title: wt ARX 5


title: wt ARX 2


title: case 11 microRNA

city: Taipei

first: Yu Hsuan

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

description: miRNA expression data from CNS GCT patient

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GCT patient case

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: primary intracranial pediatric germ cell tumor (GCT)

tag: diagnosis

value: immature teratoma predominant + embryonal carcinoma + yolk sac tumor

tag: age

value: 7.7 years


title: case 12 microRNA

value: yolk sac tumor + germinoma

value: 14.5 years


title: case 10 microRNA

value: yolk sac tumor predominant + immature teratoma

value: 10.6 years


title: case 9 microRNA

value: germinoma + immature teratoma

value: 10.25 years


title: wt ARX 21


title: MC L.m._1

description: MC L.m._1


title: mut ARX 12


title: case 8 microRNA

value: immature teratoma

value: 10 days


title: case 7 microRNA

value: immature teratoma predominant + germinoma

value: 4.3 years


title: case 6 microRNA

value: germinoma

value: 14 years


title: wt ARX 1


title: case 5 microRNA

value: 11.5 years


title: wt ARX 22


title: case 4 microRNA

value: 10.4 years


title: case 3 microRNA

value: primary intracranial pediatric germ cell tumor (GCT)

value: 14.2 years


title: Series 4: H3k4me3 IP from alpha factor arrested wt cells in galactose

description: BY4741 cells bearing a deletion in bar1  were grown to an OD of 0.3 in YPgalactose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were filtered on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDextrose media containing 20ug/ml pronase (SIGMA) or 1ug/ml alfa factor. Cells were harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 agilent S.cerevisiae whole genome arrays.

value: BY4741 bar1del


title: Series 4: H3k4me3 IP from midlog wt cells in galactose


title: case 2 microRNA


title: Series 2: H3k4me3 IP from jhd2 delete cells 60min after release from arrest

description: BY4741 cells bearing a deletion in bar1 and jhd2 were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPD media containing 20ug/ml pronase (SIGMA). Cells were harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 agilent S.cerevisiae whole genome arrays.

value: BY4741 bar1del jhd2del


title: Series 3: H3k4me3 IP from cdc7ts cells 90min after release from arrest in 24C

description: CYM36 cells bearing a cdc7 ts mutant were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDmedia prewarmed to 24C containing 20ug/ml pronase (SIGMA).Cells were grown at 24C and harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 agilent S.cerevisiae whole genome arrays .

value: CYM36 (cdc7ts)


title: Series 3: H3k4me3 IP from cdc7ts cells 90min after release from arrest in 37C


title: Series 2: H3k4me3 IP from alpha factor arrested jhd2 delete cells


title: Series 4: H3k4me3 IP from wt cells 75min after switch to dextrose and release from arrest


title: Series 3: H3k4me3 IP from alpha factor arrested cdc7ts cells at 24C


title: KAR1_rep2

status: Public on Feb 25 2010

city: Stellenbosch

first: Paul

last: Hills

state: Western Cape

address: Natural Sciences Building, Merriman Avenue

country: South Africa

institute: Stelllenbosch University

description: Gene expression of KAR1 treated 21DAG seedlings

hyb_protocol: Cy3-labelled samples were loaded on the array (44K Nicotiana tabacum microarray, Agilent, www.agilent.com) and hybridised overnight (17 h at 65°C).

scan_protocol: Slides were washed as recommended by manufacturer’s protocol and scanned on the Agilent Microarray Scanner with extended dynamic range (XDR) at high resolution (5 µm).

data_processing: Data sets were extracted by use of the feature extraction software (v9.5.3.1/Agilent Technologies) using a standard protocol. Each hybridised Agilent array was normalised and analysed via the embedded R scripts in GeneSpringGX (Version 10.0, Agilent Technologies Inc., Santa Clara, California, USA). In brief, global normalization and scaling was achieved by normalization to the median of all probe sets for all the arrays using the MAS5.0 algorithm and absolute calls for each probe set were obtained using a lower critical cut-off value of 0.05 and higher critical cut-off value of 0.065. Gene selections based on an asymptotic one-way ANOVA were made to filter those genes whose residuals between the compared sample pairs are significantly higher than the measured noise level and considered to be differentially expressed. The residual P-value obtained by the one-way ANOVA was corrected for multiple testing by the Benjamini and Hochberg (1995) algorithm and these false discovery rate (FDR) corrected P-values (P < 0.05) and an associated 2.0-fold change cut-off value in at least one of the gene pairs normalised to the control treatment were considered significant.

organism: Nicotiana benthamiana

source_name: Whole seedling, 21DAG, 10-7M KAR1, replicate 2

label_protocol: Synthesis of cDNA was performed as described in the one-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006; Agilent Technologies, Santa Clara, www.agilent.com).

growth_protocol: Nicotiana benthamiana seeds were surface sterilized and allowed to germinate on half-strength Murashige and Skoog (MS) nutrient medium (pH 5.9) solidified with 8 g l-1 bacteriological agar containing the relevant growth promoting substances. All test compounds were added to the media prior to autoclaving.  Plates were grown under cool fluorescent light (Osram L 58V/740) in a growth room using a 16/8 h light/dark regime with a photosynthetic photon flux density of 50 µmol photons m-2 s-1. All data was collected three weeks post germination, in three independent experimental trials.

extract_protocol: Homogenised plant material (200 mg) was extracted with 1 ml CTAB buffer (2% (w/v) CTAB, 2% (w/v) PVP, 100 mM Tris-HCl (pH 8.0), 25 mM EDTA, 2 M NaCl, 0.5 g l-1 spermidine). Samples were vortexed immediately and incubated for 15 min at 65°C. Thereafter, they were centrifuged at 13000 g for 10 min after which the supernatant was transferred to a new tube. Samples were extracted twice with chloroform:isoamylalcohol (24:1, v.v) and the supernatant again transferred to a new tube. Total RNA was precipitated overnight at 4°C by adding 8 M LiCl2 to a final concentration of 2 M LiCl2 per sample. RNA was collected by centrifugation at 13000 g for 60 min at 4°C. RNA was washed twice with ice cold 70% ethanol and once with 100% ethanol. RNA was resuspended in 50 μl dH2O and kept at -80°C until use.

treatment_protocol: Applications of control (untreated), GR24 (10-7M), smoke water (1:1000 dilution) and butenolide (10-7M) were applied in the 0.5 MS/agar medium

value: seedling


title: KAR1_rep1

source_name: Whole seedling, 21DAG, 10-7M KAR1, replicate 1


title: smoke_rep2

description: Gene expression of smoke treated 21DAG seedlings

source_name: Whole seedling, 21DAG, 1:1000 smoke, replicate 2


title: Series 1: H3k4me3 IP from wt cells 60min after release from arrest

description: BY4741 cells bearing a deletion in bar1  were grown to an OD of 0.3 in YPDextrose and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hrs. Cells were released from arrest by filtering on 0.8um filter paper and washing with doubly distilled water. The filters were then placed in fresh YPDmedia containing 20ug/ml pronase (SIGMA).Cells were harvested at indicated times, crosslinked with formaldehyde (2%), washed with water and zymolyase treated.    Cells were then digested with MNase, and subjected to immunoprecipitation with with 6.5ul Millipore rabbit anti-H3K4Me3 monoclonal antibody.  As a reference, DNA was obtained from the input MNAse digested chromatin prior to antibody addition.  The ChIP and reference samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 agilent S.cerevisiae whole genome arrays.


title: Series 1: H3k4me3 IP from alpha factor arrested wt cells


title: Series 4: H3k4me3 IP from wt cells 30min after switch to dextrose and release from arrest


title: Series 1: H3k4me3 IP from midlog wt cells


title: GR24_rep1

description: Gene expression of GR24 treated 21DAG seedlings

source_name: Whole seedling, 21DAG, 10-7M GR24, replicate 1


title: GR24_rep2

source_name: Whole seedling, 21DAG, 10-7M GR24, replicate 2


title: untreated_control_rep1

description: Gene expression of untreated 21DAG seedlings

source_name: Whole seedling, 21DAG, untreated control, replicate 1


title: MN160_2 (untreated)

first: Gerben

last: Duns

address: Oostersingel, ingang 47, 2nd floor, room E2.036

institute: Genetics Department, Groningen University

hyb_protocol: Transcript abundance in treated and untreated cells was measured using Human HT-12_V3_Beadchips (48K) (Ilumina)following the manufacturer's protocol

scan_protocol: Arrays were scanned using an Illumina scanner

data_processing: Microarray data normalization was performed using the Lumi package implemented in R. Data were transformed and normalized using variance-stabilizing transformation followed by robust spline normalization.

source_name: Proximal tubular epithelial cells

label_protocol: Total RNA was labeled using the Illumina ® TotalPrep™-96 RNA amplification kit following the manufacturer's instructions.

growth_protocol: The cell lines were maintained in RPMI 1640 (Sigma) supplemented with 10 % fetal calf serum (Gibco), penicillin (1.0 U/l) (Gibco), streptomycin (1 μg/ul) (Gibco), glutamin (2.0 mM) (Gibco). Cells were grown in an incubator at 37˚C, 5% CO2.

extract_protocol: Total RNA was isolated using RNEasy miniKIT (Qiagen) following the manufacturer's protocol

treatment_protocol: Cells were grown to approximately 90 % confluence in 75 cm flasks, cells were trypsinized and harvested

tag: cell line

tag: sample type

value: proximal tubular epithelium


title: PTEC_1 (untreated)

value: PTEC


title: case 1 microRNA

value: 15.9 years


title: untreated_control_rep2

source_name: Whole seedling, 21DAG, untreated control, replicate 2


title: PTEC_2 (untreated)


title: Series 4: H3k4me3 IP from alpha factor arrested wt cells 30min after switch to dextrose


title: RCC-MF_not-treated_2 (untreated)

source_name: cell line derived from clear cell renal cell carcinoma tumor

treatment_protocol: Cells were grown to approximately 70 % confluence in 75 cm flasks, medium was refreshed.Following 8 hrs of incubation (37 °C, 5% CO2), cells were trypsinized and harvested

value: RCC-MF (KTCTL-1M )

tag: depositor

value: Cell Lines Service, www.cellbank.de

tag: gender

value: Male

value: clear cell renal cell carcinoma (lung metastasis)

tag: tumor stage

value: pT2,N1,Mx/GII-III (lung-metastasis)

tag: age of diagnosis


title: MN160_1 (untreated)


title: RCC-MF_not-treated_1 (untreated)


title: smoke_rep1

source_name: Whole seedling, 21DAG, 1:1000 smoke, replicate 1


title: RCC-JW_not-treated_2 (untreated)

value: RCC-JW (KTCTL-195)

value: clear cell renal cell carcinoma primary tumour


title: RCC-JW_not-treated_1 (untreated)


title: RCC-JF_not-treated_emetine_2 (untreated)

value: RCC-JF (KTCTL-140 )

value: Female


title: RCC-JF_not-treated_emetine_1 (untreated)


title: RCC-JF_not-treated_caffeine exp_2 (untreated)


title: RCC-HS_not-treated_2 (untreated)

value: RCC-HS (KTCTL-30)


title: RCC-JF_not-treated_caffeine exp_1 (untreated)


title: RCC-HS_not-treated_1 (untreated)


title: RCC-ER_not-treated_emetine exp_2 (untreated)

value: RCC-ER (KTCTL-13)

value: pT3a, N1,Mx/GIII


title: RCC-ER_not-treated_caffeine exp_2 (untreated)


title: RCC-FG2_not-treated_1 (untreated)

value: RCC-FG2 (KTCTL-26A)


title: case 15 genotype

description: Genomic DNA extracted from germ cell tumors was genotyped using Infinium Human610_Quad Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from breast tumors was genotyped using Infinium Human610_Quad Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: primary intracranial pediatric germ cell tumor (GCT)

value: immature teratoma predominant + embryonal carcinoma + yolk sac tumor

value: 7.7 years


title: case 16 genotype

value: yolk sac tumor

value: 14.5 years


title: case 11 genotype

value: campatible with mature teratoma

value: 11.5 years


title: case 13 genotype

value: immature teratoma

value: 10 days


title: case 8 genotype

value: (spinal tumor) mature teratoma

value: 4 months


title: RCC-ER_not-treated_caffeine exp_1 (untreated)

value: Cell Lines Service, www.cellbank.de

value: Male

value: clear cell renal cell carcinoma primary tumour


title: Series 4: H3k4me3 IP from alpha factor arrested wt cells 75min after switch to dextrose

value: BY4741 bar1del


title: RCC-AB_not-treated_emetine exp_2 (untreated)

value: RCC-AB (KTCTL-21)

value: pT2, N0, MX/GII


title: case 14 genotype

value: primary intracranial pediatric germ cell tumor (GCT)

value: yolk sac tumor predominant + immature teratoma

value: 10.6 years


title: RCC-FG2_not-treated_2 (untreated)

value: RCC-FG2 (KTCTL-26A)


title: case 10 genotype

value: mature teratoma + germinoma

value: 4.6 years


title: case 9 genotype

value: 9.7 years


title: case 5 genotype

value: germinoma

value: 10.4 years


title: RCC-AB_not-treated_emetine exp_1 (untreated)


title: case 3 genotype

value: 12.2 years


title: RCC-AB_not-treated_caffeine exp_2 (untreated)


title: RCC5_not-treated_2 (untreated)

value: Gerharz and Gabbert (Virchows Archiv (1994) 424:403-409)

value: clear cell renal cell carcinoma

value: unknown


title: RCC4_not-treated_emetine exp_1 (untreated)


title: case 4 genotype

value: 14.2 years


title: RCC4_not-treated_caffeine exp_2 (untreated)


title: RCC4_not-treated_emetine exp_2 (untreated)


title: RCC4_not-treated_caffeine exp_1 (untreated)


title: case 12 genotype

value: germinoma + immature teratoma

value: 11.5 years


title: RCC5_not-treated_1 (untreated)


title: RCC1_not-treated_1 (untreated)


title: Daoy_Biologicalreplicate2_2

city: san antonio

first: raquel

last: abreu

state: TX

address: 8403 Floyd Curl Drive

institute: CCRI

description: Biological Replicate 2

hyb_protocol: Labeled products were precipitated with isopropanol and resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit.

scan_protocol: Microarrays were scanned with the Agilent Microarray Scanner G2565AA.

data_processing: Gene expression values were generated using NimbleScan expression RMA (Robust Multi-array Analysis). Report files were further analyzed in the R Project for Statistical Computing using the Bioconductor package limma. First to assess quality control (one microarray was eliminated) and then to achieve the same empirical distribution on the single channel microarray intensities of the two biological replicates. Finally, we averaged gene expression values to obtain the final values.

source_name: Daoy medulloblastoma cells

label_protocol: Samples were labeled with Cy3-9mer primers using Klenow enzyme.

growth_protocol: MEM Richter’s modification medium (Gibco), supplemented with 10% fetal bovine serum (Atlanta Biologicals Inc., Lawrenceville, GA), 100 units/ml penicillin, and 100microg/ml streptomycin (Herndon, VA).

extract_protocol: RNA was purified using TRIzol as recommended by Invitrogen and re-purified with the RNeasy kit from Qiagen.

tag: genotype/variation

value: WT

value: Daoy medulloblastoma cell line


title: RCC-MF_caffeine_2 (GINI)

treatment_protocol: Cells were grown to approximately 70 % confluence in 75 cm flasks, medium was refreshed, caffeine was added (10 mM).Following 8 hrs of incubation (37 °C, 5% CO2), cells were trypsinized and harvested

value: RCC-MF (KTCTL-1M )

value: Cell Lines Service, www.cellbank.de

value: Male

value: clear cell renal cell carcinoma (lung metastasis)

value: pT2,N1,Mx/GII-III (lung-metastasis)

tag: treatment

value: Caffeine


title: RCC1_not-treated_2 (untreated)


title: RCC-MF_emetine_2 (GINI)

treatment_protocol: Cells were grown to approximately 70 % confluence in 75 cm flasks, medium was refreshed, emetine dihydrochloride hydrate was added (100 μg/ml).Following 8 hrs of incubation (37 °C, 5% CO2), cells were trypsinized and harvested

value: emetine


title: Daoy_Biologicalreplicate2_3

description: Biological Replicate 2


title: RCC-MF_emetine_1 (GINI)


title: Daoy_Biologicalreplicate2_1

description: Biological Replicate 2


title: case 6 genotype

tag: tissue

value: primary intracranial pediatric germ cell tumor (GCT)

value: germinoma


title: RCC-ER_not-treated_emetine exp_1 (untreated)

value: RCC-ER (KTCTL-13)

value: clear cell renal cell carcinoma primary tumour

value: pT3a, N1,Mx/GIII


title: RCC-MF_not-treated_2 (GINI)


title: RCC-MF_caffeine_1 (GINI)


title: Daoy_Biologicalreplicate1_4

description: Biological Replicate 1


title: Daoy_Biologicalreplicate2_4

description: Biological Replicate 2


title: Daoy_Biologicalreplicate1_2

description: Biological Replicate 1


title: RCC-JW_emetine_2 (GINI)

value: RCC-JW (KTCTL-195)


title: RCC-AB_not-treated_caffeine exp_1 (untreated)

value: RCC-AB (KTCTL-21)

value: pT2, N0, MX/GII


title: RCC-MF_not-treated_1 (GINI)