title: M_U133A_51_DLPFC


title: M_U133A_46_DLPFC

status: Public on Nov 21 2006

type: RNA

city: Ann Arbor

first: Fan

last: Meng

state: MI

address: 205 Zina Pitcher Place

department: Psychiatry

country: USA

institute: U of Michigan

description: Gene expression data from postmorten brain regions

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with the GCRMA method using custom CDF file Hs133A_Hs_UG_3.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Postmorten human brain: Dorsal Lateral Prefrontal Cortex

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

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

value: M

value: Dorsal Lateral Prefrontal Cortex

tag: Redo

value: No

tag: Cohort


title: M_U133A_44_DLPFC


title: M_U133A_42_DLPFC


title: M_U133A_47_DLPFC


title: M_U133Plus_36_DLPFC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133Plus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

value: Outlier


title: M_U133A_31_DLPFC


title: M_U133A_31_DLPFC_R

value: Yes


title: M_U133A_29_DLPFC


title: M_U133A_33_DLPFC


title: M_U133A_40_DLPFC


title: M_U133A_35_DLPFC


title: M_U133A_32_DLPFC_R


title: M_U133A_41_DLPFC


title: M_U133A_34_DLPFC


title: M_U133A_37_DLPFC


title: M_U133A_30_DLPFC_R


title: M_U133Plus_38_DLPFC


title: M_U133A_30_DLPFC


title: M_U133A_32_DLPFC


title: M_U133A_26_DLPFC


title: M_U133A_23_DLPFC


title: M_U133A_27_DLPFC


title: M_U133A_25_DLPFC


title: M_U133A_24_DLPFC


title: M_U133A_22_DLPFC_R


title: M_U133A_28_DLPFC


title: M_U133A_18_DLPFC_R


title: M_U133A_19_DLPFC


title: M_U133A_20_DLPFC


title: M_U133Plus_110_DLPFC


title: M_U133A_21_DLPFC


title: M_U133Plus_16_DLPFC


title: M_U133A_13_DLPFC


title: M_U133A_22_DLPFC


title: M_U133A_15_DLPFC


title: M_U133A_12_DLPFC_R


title: M_U133A_7_DLPFC


title: M_U133A_13_DLPFC_R


title: M_U133A_11_DLPFC_R


title: M_U133A_14_DLPFC


title: M_U133A_15_DLPFC_R


title: M_U133A_6_DLPFC


title: M_U133A_50_DLPFC_R


title: M_U133A_18_DLPFC


title: M_U133A_11_DLPFC


title: M_U133A_9_DLPFC


title: M_U133A_5_DLPFC_R


title: M_U133A_14_DLPFC_R


title: M_U133A_5_DLPFC


title: M_U133A_12_DLPFC


title: M_U133A_3_DLPFC


title: M_U133A_9_DLPFC_R


title: M_U133A_10_DLPFC


title: M_U133A_2_DLPFC


title: M_U133A_8_DLPFC


title: M_U133A_17_DLPFC


title: I_U133A_37_DLPFC

value: I


title: M_U133A_4_DLPFC


title: I_U133A_75_DLPFC


title: M_U133A_7_DLPFC_R


title: I_U133A_71_DLPFC


title: M_U133A_1_DLPFC


title: I_U133A_34_DLPFC


title: I_U133A_1_DLPFC


title: I_U133A_2_DLPFC


title: I_U133A_17_DLPFC


title: I_U133A_6_DLPFC


title: I_U133A_33_DLPFC


title: D_U133Plus_123_DLPFC

value: D


title: D_U133Plus_121_DLPFC


title: D_U133Plus_125_DLPFC


title: I_U133A_19_DLPFC


title: I_U133A_3_DLPFC


title: D_U133Plus_119_DLPFC


title: I_U133A_26_DLPFC


title: D_U133A_118_DLPFC


title: D_U133Plus_116_DLPFC


title: D_U133Plus_126_DLPFC


title: D_U133Plus_124_DLPFC


title: I_U133A_28_DLPFC


title: I_U133A_20_DLPFC


title: D_U133Plus_120_DLPFC


title: D_U133Plus_122_DLPFC


title: I_U133A_10_DLPFC


title: D_U133A_117_DLPFC


title: I_U133A_21_DLPFC


title: D_U133Plus_115_DLPFC


title: D_U133A_112_DLPFC


title: D_U133Plus_113_DLPFC


title: D_U133A_114_DLPFC


title: D_U133A_111_DLPFC


title: D_U133Plus_110_DLPFC


title: D_U133A_102_DLPFC


title: D_U133A_103_DLPFC


title: D_U133A_109_DLPFC


title: D_U133A_106_DLPFC


title: D_U133A_96_DLPFC


title: D_U133A_101_DLPFC


title: D_U133A_97_DLPFC


title: D_U133A_93_DLPFC


title: D_U133A_95_DLPFC


title: D_U133A_92_DLPFC


title: D_U133Plus_94_DLPFC


title: D_U133A_91_DLPFC


title: D_U133A_90_DLPFC


title: D_U133A_89_DLPFC


title: D_U133A_83_DLPFC


title: D_U133A_100_DLPFC


title: D_U133A_85_DLPFC


title: D_U133A_87_DLPFC


title: D_U133A_86_DLPFC


title: D_U133A_84_DLPFC


title: D_U133A_79_DLPFC


title: D_U133A_82_DLPFC


title: D_U133A_81_DLPFC


title: D_U133A_80_DLPFC


title: D_U133A_78_DLPFC


title: D_U133A_76_DLPFC


title: D_U133A_77_DLPFC


title: D_U133Plus_73_DLPFC


title: D_U133A_70_DLPFC


title: D_U133A_71_DLPFC


title: D_U133A_68_DLPFC


title: D_U133A_72_DLPFC


title: D_U133A_74_DLPFC


title: D_U133A_69_DLPFC


title: D_U133A_63_DLPFC


title: D_U133A_66_DLPFC


title: D_U133A_67_DLPFC


title: D_U133A_60_DLPFC


title: D_U133A_64_DLPFC


title: D_U133A_65_DLPFC


title: D_U133A_75_DLPFC


title: D_U133A_58_DLPFC


title: D_U133Plus_59_DLPFC


title: D_U133A_61_DLPFC


title: D_U133A_62_DLPFC


title: D_U133A_55_DLPFC


title: D_U133A_56_DLPFC


title: D_U133A_54_DLPFC


title: D_U133A_53_DLPFC


title: D_U133A_104_DLPFC


title: D_U133A_51_DLPFC


title: D_U133A_50_DLPFC


title: D_U133A_44_DLPFC


title: D_U133A_107_DLPFC


title: D_U133A_52_DLPFC


title: D_U133A_43_DLPFC


title: D_U133A_40_DLPFC


title: D_U133A_45_DLPFC


title: D_U133A_49_DLPFC


title: D_U133Plus_38_DLPFC


title: D_U133A_46_DLPFC


title: D_U133A_47_DLPFC


title: D_U133A_41_DLPFC


title: D_U133A_48_DLPFC


title: D_U133Plus_37_DLPFC_R


title: D_U133A_37_DLPFC


title: I_U133A_23_DLPFC


title: D_U133A_39_DLPFC


title: D_U133A_42_DLPFC


title: D_U133Plus_37_DLPFC


title: D_U133A_57_DLPFC


title: D_U133Plus_36_DLPFC


title: D_U133Plus_34_DLPFC_R


title: I_U133A_27_DLPFC


title: D_U133Plus_34_DLPFC


title: D_U133A_35_DLPFC


title: D_U133A_34_DLPFC


title: D_U133A_30_DLPFC


title: D_U133A_33_DLPFC


title: D_U133A_32_DLPFC


title: D_U133A_28_DLPFC


title: D_U133A_31_DLPFC


title: D_U133A_25_DLPFC


title: D_U133A_29_DLPFC


title: D_U133A_27_DLPFC


title: D_U133Plus_33_DLPFC_R


title: D_U133A_26_DLPFC


title: D_U133Plus_23_DLPFC


title: D_U133Plus_26_DLPFC_R


title: D_U133Plus_26_DLPFC


title: D_U133Plus_19_DLPFC


title: D_U133A_98_DLPFC


title: D_U133A_23_DLPFC


title: D_U133Plus_33_DLPFC


title: D_U133Plus_17_DLPFC


title: D_U133A_19_DLPFC


title: D_U133A_20_DLPFC


title: D_U133Plus_19_DLPFC_R


title: D_U133A_24_DLPFC


title: D_U133Plus_23_DLPFC_R


title: D_U133A_105_DLPFC


title: D_U133A_88_DLPFC


title: D_U133A_18_DLPFC


title: D_U133Plus_16_DLPFC


title: D_U133A_17_DLPFC


title: D_U133A_14_DLPFC


title: D_U133A_13_DLPFC


title: D_U133A_21_DLPFC


title: D_U133Plus_17_DLPFC_R


title: D_U133A_99_DLPFC


title: D_U133A_15_DLPFC


title: D_U133A_11_DLPFC


title: D_U133A_12_DLPFC


title: D_U133A_10_DLPFC


title: D_U133A_7_DLPFC


title: D_U133A_5_DLPFC


title: D_U133A_1_DLPFC


title: D_U133A_8_DLPFC


title: D_U133A_9_DLPFC


title: M_U133Plus_126_CB

source_name: Postmorten human brain: Cerebellum

value: Cerebellum


title: D_U133Plus_1_DLPFC_R


title: D_U133A_3_DLPFC


title: D_U133A_2_DLPFC


title: D_U133Plus_1_DLPFC


title: M_U133Plus_123_CB


title: D_U133A_4_DLPFC


title: M_U133Plus_125_CB


title: D_U133A_6_DLPFC


title: M_U133Plus_124_CB


title: M_U133Plus_122_CB


title: M_U133Plus_120_CB


title: M_U133Plus_116_CB


title: M_U133Plus_110_CB


title: M_U133Plus_113_CB


title: M_U133Plus_115_CB


title: M_U133Plus_108_CB


title: M_U133A_71_CB


title: M_U133Plus_73_CB


title: M_U133Plus_59_CB


title: M_U133A_75_CB


title: M_U133A_26_CB


title: M_U133A_34_CB


title: M_U133Plus_38_CB


title: M_U133A_27_CB


title: M_U133A_21_CB


title: M_U133A_20_CB


title: M_U133Plus_94_CB


title: M_U133Plus_16_CB


title: M_U133A_33_CB


title: M_U133A_6_CB


title: M_U133Plus_36_CB


title: M_U133A_2_CB


title: M_U133A_3_CB


title: M_U133A_10_CB


title: M_U133A_28_CB


title: M_U133A_17_CB


title: M_U133A_19_CB


title: M_U133A_23_CB


title: M_U133A_37_CB


title: I_U133Plus_125_CB


title: M_U133A_1_CB


title: I_U133Plus_126_CB


title: I_U133Plus_124_CB


title: I_U133Plus_119_CB


title: I_U133Plus_115_CB


title: I_U133Plus_116_CB


title: I_U133Plus_121_CB


title: I_U133Plus_123_CB


title: I_U133Plus_113_CB


title: I_U133A_109_CB


title: I_U133A_98_CB


title: I_U133A_114_CB


title: I_U133Plus_120_CB


title: I_U133Plus_110_CB


title: I_U133A_107_CB


title: D_U133A_22_DLPFC


title: I_U133Plus_122_CB


title: I_U133A_106_CB


title: I_U133A_112_CB


title: I_U133A_102_CB


title: I_U133A_96_CB


title: I_U133A_101_CB


title: I_U133Plus_108_CB


title: I_U133A_77_CB


title: I_U133A_104_CB


title: I_U133Plus_94_CB


title: I_U133A_80_CB


title: I_U133A_92_CB


title: M_U133Plus_119_CB


title: I_U133A_75_CB


title: I_U133A_76_CB


title: I_U133A_71_CB


title: I_U133Plus_73_CB


title: I_U133A_91_CB


title: I_U133A_87_CB


title: I_U133A_74_CB


title: M_U133Plus_121_CB


title: I_U133A_68_CB


title: I_U133A_57_CB


title: I_U133A_58_CB


title: I_U133A_66_CB


title: I_U133A_64_CB


title: I_U133A_47_CB


title: I_U133A_62_CB


title: I_U133A_65_CB


title: I_U133A_52_CB


title: I_U133Plus_59_CB


title: I_U133A_60_CB


title: I_U133A_48_CB


title: I_U133A_51_CB


title: I_U133A_56_CB


title: I_U133A_63_CB


title: I_U133A_37_CB


title: I_U133Plus_38_CB


title: I_U133A_34_CB


title: I_U133A_49_CB


title: I_U133A_42_CB


title: I_U133A_67_CB


title: I_U133A_31_CB


title: I_U133A_61_CB


title: I_U133A_35_CB


title: I_U133A_41_CB


title: I_U133Plus_36_CB


title: I_U133A_54_CB


title: I_U133A_50_CB


title: I_U133A_30_CB


title: I_U133A_29_CB


title: I_U133A_33_CB


title: I_U133A_15_CB


title: I_U133A_44_CB


title: I_U133A_28_CB


title: I_U133A_17_CB


title: I_U133A_18_CB


title: I_U133A_26_CB


title: I_U133A_27_CB


title: I_U133A_32_CB


title: I_U133A_21_CB


title: I_U133A_12_CB


title: I_U133A_23_CB


title: I_U133A_19_CB


title: I_U133A_22_CB


title: I_U133A_7_CB


title: I_U133A_14_CB


title: I_U133A_5_CB


title: I_U133A_20_CB


title: I_U133A_13_CB


title: I_U133A_9_CB


title: I_U133Plus_16_CB


title: D_U133Plus_111_CB


title: D_U133Plus_106_CB


title: D_U133Plus_104_CB


title: D_U133Plus_92_CB


title: D_U133A_103_CB


title: I_U133A_6_CB


title: D_U133A_102_CB


title: D_U133A_95_CB


title: D_U133Plus_107_CB


title: D_U133A_85_CB


title: D_U133A_90_CB


title: D_U133Plus_101_CB


title: D_U133Plus_109_CB


title: D_U133A_96_CB


title: D_U133Plus_97_CB


title: D_U133Plus_87_CB


title: D_U133A_82_CB


title: D_U133Plus_89_CB


title: D_U133A_91_CB


title: D_U133Plus_77_CB


title: D_U133A_79_CB


title: D_U133A_80_CB


title: D_U133Plus_83_CB


title: D_U133Plus_78_CB


title: D_U133A_81_CB


title: D_U133A_66_CB


title: D_U133Plus_70_CB


title: D_U133Plus_56_CB


title: D_U133Plus_61_CB


title: D_U133A_52_CB


title: D_U133A_62_CB


title: D_U133A_54_CB


title: D_U133A_41_CB


title: M_U133Plus_124_AnCg

source_name: Postmorten human brain: Anterior Cingulate

value: Anterior Cingulate


title: M_U133Plus_125_AnCg


title: I_U133A_10_CB


title: D_U133Plus_55_CB


title: M_U133Plus_121_AnCg


title: D_U133A_98_CB


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title: M_U133A_118_AnCg


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title: I_U133A_2_CB


title: I_U133A_3_CB


title: I_U133A_1_CB


title: M_U133Plus_119_AnCg


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title: D_U133A_86_CB


title: M_U133A_114_AnCg


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title: M_U133A_106_AnCg


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title: M_U133A_93_AnCg


title: M_U133A_91_AnCg


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title: M_U133A_52_AnCg


title: M_U133A_60_AnCg


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title: M_U133A_52_AnCg_redo


title: M_U133A_47_AnCg


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title: M_U133A_26_AnCg


title: M_U133A_29_AnCg


title: M_U133A_31_AnCg


title: M_U133A_27_AnCg


title: M_U133A_23_AnCg


title: M_U133A_18_AnCg


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title: M_U133A_21_AnCg


title: M_U133A_11_AnCg


title: M_U133A_12_AnCg


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title: M_U133A_15_AnCg


title: M_U133A_22_AnCg


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title: M_U133A_9_AnCg


title: M_U133A_1_AnCg


title: M_U133A_14_AnCg


title: M_U133A_13_AnCg


title: M_U133A_5_AnCg


title: M_U133A_10_AnCg


title: M_U133Plus_16_AnCg


title: M_U133A_3_AnCg


title: M_U133A_2_AnCg


title: I_U133Plus_124_AnCg


title: I_U133Plus_125_AnCg


title: I_U133Plus_120_AnCg


title: I_U133Plus_121_AnCg


title: I_U133Plus_126_AnCg


title: M_U133A_6_AnCg


title: I_U133A_118_AnCg


title: I_U133Plus_116_AnCg


title: I_U133Plus_123_AnCg


title: I_U133Plus_115_AnCg


title: I_U133A_111_AnCg


title: I_U133Plus_113_AnCg


title: I_U133A_112_AnCg


title: I_U133Plus_110_AnCg


title: I_U133Plus_119_AnCg


title: I_U133A_106_AnCg


title: I_U133A_114_AnCg


title: I_U133A_109_AnCg


title: I_U133A_107_AnCg


title: I_U133A_104_AnCg


title: I_U133A_92_AnCg


title: I_U133A_96_AnCg


title: I_U133Plus_108_AnCg


title: I_U133A_97_AnCg


title: I_U133Plus_94_AnCg


title: I_U133A_87_AnCg


title: I_U133Plus_122_AnCg


title: I_U133A_101_AnCg


title: I_U133A_102_AnCg


title: I_U133A_89_AnCg


title: I_U133A_80_AnCg


title: I_U133A_98_AnCg


title: I_U133A_77_AnCg


title: I_U133A_81_AnCg


title: I_U133A_74_AnCg


title: I_U133A_90_AnCg


title: I_U133A_63_AnCg


title: I_U133A_91_AnCg


title: I_U133A_67_AnCg


title: I_U133A_75_AnCg


title: I_U133Plus_73_AnCg


title: I_U133A_68_AnCg


title: I_U133A_76_AnCg


title: I_U133A_60_AnCg


title: I_U133A_65_AnCg


title: I_U133A_64_AnCg


title: I_U133A_71_AnCg


title: I_U133A_66_AnCg


title: I_U133A_55_AnCg


title: I_U133A_58_AnCg


title: I_U133A_52_AnCg


title: I_U133Plus_59_AnCg


title: I_U133A_57_AnCg


title: I_U133A_62_AnCg


title: I_U133A_47_AnCg


title: I_U133A_44_AnCg


title: I_U133A_49_AnCg


title: I_U133A_50_AnCg


title: I_U133A_42_AnCg


title: I_U133A_48_AnCg


title: I_U133A_54_AnCg


title: I_U133Plus_36_AnCg


title: I_U133A_31_AnCg


title: I_U133A_51_AnCg


title: I_U133A_34_AnCg


title: I_U133A_56_AnCg


title: I_U133A_32_AnCg


title: I_U133A_41_AnCg


title: I_U133A_27_AnCg


title: I_U133A_35_AnCg


title: I_U133A_28_AnCg


title: I_U133A_30_AnCg


title: I_U133A_23_AnCg


title: I_U133A_26_AnCg


title: I_U133A_33_AnCg


title: I_U133A_29_AnCg


title: I_U133A_21_AnCg


title: I_U133A_20_AnCg


title: I_U133A_37_AnCg


title: I_U133A_18_AnCg


title: I_U133A_19_AnCg


title: I_U133A_15_AnCg


title: I_U133A_13_AnCg


title: I_U133A_14_AnCg


title: I_U133Plus_16_AnCg


title: I_U133A_17_AnCg


title: I_U133A_10_AnCg


title: I_U133Plus_38_AnCg


title: I_U133A_5_AnCg


title: I_U133A_12_AnCg


title: I_U133A_22_AnCg


title: I_U133A_11_AnCg


title: I_U133A_3_AnCg


title: I_U133A_7_AnCg


title: I_U133A_6_AnCg


title: I_U133A_2_AnCg


title: I_U133A_9_AnCg


title: I_U133A_1_AnCg


title: child #13

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: child #13

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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: affected by congenital disease

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Stratagene Absolutely RNA Miniprep Kit

treatment_protocol: B-cells from human patients transduced with EBV

tag: genetic modification:

tag: tissue

value: B-cells


title: I_U133Plus_126_Amy

source_name: Postmorten human brain: Amygdala

value: Amygdala


title: Mother #2

description: Mother #2

source_name: healthy donor


title: Pol II Chip, BY4741 replicate 3

type: genomic

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: Cells were grown to mid-log at the indicated temperature and fixed with formaldehyde.  Chromatin was sheared by sonication, and RNA Pol II was immunoprecipitated.  Precipitated DNA was isolated, and amplified by PCR, as was input DNA (sonicated, no IP step).

hyb_protocol: Amplified ChIP and WCE were labeled using the Bioprime random primed Klenow labeling kit using Cy3 and Cy5-labeled dCTP.  Samples 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.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: PCR-amplified ChIP against Pol II

label_protocol: The DNA were labeled with direct incorporation of Cy5 or Cy3, using Klenow, from the Invitrogen BioPrime labeling kit.  The DNA samples were combined and purified with Microcon YM-30 spin columns 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 RNA Polymerase II was immunoprecipitated from sonicated whole cell extract, and amplified by PCR.

tag: Strain

source_name: PCR-amplified sonicated input DNA

extract_protocol: Sonictaed whole cell extract was amplified by PCR.


title: Pol II Chip, BY4741 replicate 2


title: Pol II ChIP, FY23, 23 degrees


title: Father #1

description: Father #1


title: I_U133Plus_124_Amy


title: I_U133Plus_125_Amy


title: Pol II ChIP, rat1ts, 23 degrees


title: I_U133Plus_123_Amy


title: large airways, non-smoker 2, MAS5

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: large airways, non-smoker 2, MAS5

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA.

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

tag: Ethnic group

value: black

tag: Smoking Status

value: non-smoker


title: I_U133Plus_119_Amy


title: I_U133Plus_120_Amy


title: large airways, non-smoker 3, MAS5

description: large airways, non-smoker 3, MAS5

value: white


title: large airways, non-smoker 5, MAS5

description: large airways, non-smoker 5, MAS5


title: I_U133Plus_121_Amy


title: Pol II Chip, BY4741 replicate 1


title: Pol II ChIP, FY23, 37 degrees


title: I_U133Plus_122_Amy


title: large airways, non-smoker 4, MAS5

description: large airways, non-smoker 4, MAS5

value: F


title: I_U133A_114_Amy


title: Pol II ChIP, rtt103D


title: I_U133Plus_116_Amy


title: I_U133A_61_AnCg


title: child #12

description: child #12


title: I_U133Plus_115_Amy


title: Pol II ChIP, rat1ts, 37 degrees


title: Pol II ChIP, rai1D


title: large airways, smoker 6, MAS5

description: large airways, smoker 6, MAS5

value: hispanic

value: smoker, 25 pack-years


title: large airways, non-smoker 1, MAS5

description: large airways, non-smoker 1, MAS5


title: large airways, smoker 3, MAS5

description: large airways, smoker 3, MAS5

value: M

value: smoker, 30 pack-years


title: I_U133A_118_Amy

value: No


title: large airways, smoker 4, MAS5

description: large airways, smoker 4, MAS5

value: smoker, 20 pack-years


title: I_U133Plus_113_Amy


title: large airways, smoker 5, MAS5

description: large airways, smoker 5, MAS5

value: smoker, 24 pack-years


title: large airways, smoker 2, MAS5

description: large airways, smoker 2, MAS5

value: smoker, 23 pack-years


title: I_U133A_111_Amy

value: I


title: I_U133A_109_Amy


title: I_U133Plus_110_Amy


title: I_U133A_106_Amy


title: large airways, smoker 1, MAS5

description: large airways, smoker 1, MAS5


title: HC MB 1 grape.juice

city: Basel

first: Florent

last: Baty

address: Petersgraben 4

department: Pneumology

country: Switzerland

institute: Universitätsspital Basel

description: Healthy controls; individual=MB; time=1; beverage=grape.juice

data_processing: R and Bioconductor

source_name: peripheral blood cell


title: I_U133Plus_108_Amy


title: I_U133A_107_Amy


title: I_U133Plus_94_Amy


title: HC MB 12 water

description: Healthy controls; individual=MB; time=12; beverage=water


title: I_U133A_112_Amy


title: I_U133A_96_Amy


title: HC MB 4 grape.juice

description: Healthy controls; individual=MB; time=4; beverage=grape.juice


title: HC MB 12 grape.juice

description: Healthy controls; individual=MB; time=12; beverage=grape.juice


title: HC MB 2 grape.juice

description: Healthy controls; individual=MB; time=2; beverage=grape.juice


title: HC MB 2 wine

description: Healthy controls; individual=MB; time=2; beverage=wine


title: I_U133A_98_Amy


title: HC MB 4 wine

description: Healthy controls; individual=MB; time=4; beverage=wine


title: HC MB 4 water

description: Healthy controls; individual=MB; time=4; beverage=water


title: HC MB 0 water

description: Healthy controls; individual=MB; time=0; beverage=water


title: I_U133A_101_Amy


title: HC MB 12 wine

description: Healthy controls; individual=MB; time=12; beverage=wine


title: HC MB 1 wine

description: Healthy controls; individual=MB; time=1; beverage=wine


title: HC MB 1 water

description: Healthy controls; individual=MB; time=1; beverage=water


title: I_U133A_102_Amy


title: HC MB 0 wine

description: Healthy controls; individual=MB; time=0; beverage=wine


title: I_U133A_104_Amy


title: I_U133A_92_Amy


title: I_U133A_91_Amy

value: Outlier


title: HC MB 12 alcohol

description: Healthy controls; individual=MB; time=12; beverage=alcohol


title: I_U133A_97_Amy


title: HC MB 4 alcohol

description: Healthy controls; individual=MB; time=4; beverage=alcohol


title: I_U133A_87_Amy

description: Gene expression data from postmorten brain regions


title: HC MB 2 alcohol

description: Healthy controls; individual=MB; time=2; beverage=alcohol


title: I_U133A_89_Amy


title: I_U133A_90_Amy


title: I_U133Plus_73_Amy


title: I_U133A_63_Amy


title: HC JR 0 water

description: Healthy controls; individual=JR; time=0; beverage=water


title: I_U133A_68_Amy


title: HC JR 1 water

description: Healthy controls; individual=JR; time=1; beverage=water


title: HC MB 0 alcohol

description: Healthy controls; individual=MB; time=0; beverage=alcohol


title: HC JR 2 water

description: Healthy controls; individual=JR; time=2; beverage=water


title: HC JR 1 alcohol

description: Healthy controls; individual=JR; time=1; beverage=alcohol


title: HC MB 1 alcohol

description: Healthy controls; individual=MB; time=1; beverage=alcohol


title: HC JR 12 water

description: Healthy controls; individual=JR; time=12; beverage=water


title: HC JR 4 alcohol

description: Healthy controls; individual=JR; time=4; beverage=alcohol


title: I_U133A_62_Amy


title: I_U133A_80_Amy


title: HC JR 4 wine

description: Healthy controls; individual=JR; time=4; beverage=wine


title: HC JR 4 water

description: Healthy controls; individual=JR; time=4; beverage=water


title: HC JR 0 alcohol

description: Healthy controls; individual=JR; time=0; beverage=alcohol


title: HC JR 2 alcohol

description: Healthy controls; individual=JR; time=2; beverage=alcohol


title: I_U133A_61_Amy


title: HC JR 12 wine

description: Healthy controls; individual=JR; time=12; beverage=wine


title: I_U133A_81_Amy


title: I_U133A_66_Amy


title: I_U133A_77_Amy


title: I_U133A_74_Amy


title: I_U133A_60_Amy


title: I_U133Plus_59_Amy


title: I_U133A_76_Amy


title: I_U133A_56_Amy


title: I_U133A_50_Amy


title: I_U133A_55_Amy


title: HC JR 12 grape.juice

description: Healthy controls; individual=JR; time=12; beverage=grape.juice


title: I_U133A_48_Amy


title: HC JR 4 grape.juice

description: Healthy controls; individual=JR; time=4; beverage=grape.juice


title: I_U133A_44_Amy

description: Gene expression data from postmorten brain regions


title: HC JR 2 wine

description: Healthy controls; individual=JR; time=2; beverage=wine


title: I_U133A_47_Amy


title: HC JR 1 grape.juice

description: Healthy controls; individual=JR; time=1; beverage=grape.juice


title: HC JR 1 wine

description: Healthy controls; individual=JR; time=1; beverage=wine


title: I_U133A_51_Amy


title: HC JL 4 grape.juice

description: Healthy controls; individual=JL; time=4; beverage=grape.juice


title: I_U133A_41_Amy


title: HC JL 2 grape.juice

description: Healthy controls; individual=JL; time=2; beverage=grape.juice


title: HC JL 0 wine

description: Healthy controls; individual=JL; time=0; beverage=wine


title: I_U133Plus_36_Amy


title: HC JR 0 wine

description: Healthy controls; individual=JR; time=0; beverage=wine


title: HC JR 0 grape.juice

description: Healthy controls; individual=JR; time=0; beverage=grape.juice


title: I_U133Plus_38_Amy


title: I_U133A_49_Amy


title: I_U133A_42_Amy


title: I_U133A_35_Amy


title: HC JL 0 grape.juice

description: Healthy controls; individual=JL; time=0; beverage=grape.juice


title: HC JL 12 wine

description: Healthy controls; individual=JL; time=12; beverage=wine


title: HC JL 1 grape.juice

description: Healthy controls; individual=JL; time=1; beverage=grape.juice


title: I_U133A_32_Amy


title: HC JL 2 wine

description: Healthy controls; individual=JL; time=2; beverage=wine


title: HC JR 2 grape.juice

description: Healthy controls; individual=JR; time=2; beverage=grape.juice


title: HC JL 12 alcohol

description: Healthy controls; individual=JL; time=12; beverage=alcohol


title: HC JL 2 alcohol

description: Healthy controls; individual=JL; time=2; beverage=alcohol


title: HC JL 12 water

description: Healthy controls; individual=JL; time=12; beverage=water


title: I_U133A_31_Amy

description: Gene expression data from postmorten brain regions


title: I_U133A_18_Amy


title: I_U133A_29_Amy


title: I_U133Plus_16_Amy


title: I_U133A_30_Amy


title: HC JL 0 water

description: Healthy controls; individual=JL; time=0; beverage=water


title: I_U133A_15_Amy


title: I_U133A_13_Amy


title: I_U133A_7_Amy


title: I_U133A_12_Amy


title: HC JL 1 water

description: Healthy controls; individual=JL; time=1; beverage=water


title: I_U133A_11_Amy


title: HC IF 1 grape.juice

description: Healthy controls; individual=IF; time=1; beverage=grape.juice


title: I_U133A_5_Amy


title: HC IF 12 grape.juice

description: Healthy controls; individual=IF; time=12; beverage=grape.juice


title: D_U133Plus_126_Amy

value: D


title: HC IF 12 water

description: Healthy controls; individual=IF; time=12; beverage=water


title: HC IF 2 water

description: Healthy controls; individual=IF; time=2; beverage=water


title: HC IF 0 water

description: Healthy controls; individual=IF; time=0; beverage=water


title: HC IF 0 grape.juice

description: Healthy controls; individual=IF; time=0; beverage=grape.juice


title: D_U133Plus_124_Amy


title: I_U133A_9_Amy


title: HC JL 4 water

description: Healthy controls; individual=JL; time=4; beverage=water


title: HC IF 4 grape.juice

description: Healthy controls; individual=IF; time=4; beverage=grape.juice


title: HC JL 2 water

description: Healthy controls; individual=JL; time=2; beverage=water


title: D_U133Plus_125_Amy


title: HC IF 1 water

description: Healthy controls; individual=IF; time=1; beverage=water


title: D_U133Plus_123_Amy


title: HC IF 4 alcohol

description: Healthy controls; individual=IF; time=4; beverage=alcohol


title: D_U133Plus_120_Amy


title: D_U133Plus_119_Amy


title: D_U133Plus_118_Amy


title: D_U133Plus_122_Amy


title: D_U133Plus_116_Amy


title: HC IF 12 alcohol

description: Healthy controls; individual=IF; time=12; beverage=alcohol


title: HC IF 4 water

description: Healthy controls; individual=IF; time=4; beverage=water


title: D_U133Plus_115_Amy


title: HC IF 1 alcohol

description: Healthy controls; individual=IF; time=1; beverage=alcohol


title: D_U133Plus_113_Amy

description: Gene expression data from postmorten brain regions


title: D_U133Plus_121_Amy


title: HC IF 0 alcohol

description: Healthy controls; individual=IF; time=0; beverage=alcohol


title: D_U133Plus_112_Amy


title: D_U133Plus_111_Amy


title: HC IF 12 wine

description: Healthy controls; individual=IF; time=12; beverage=wine


title: D_U133Plus_106_Amy


title: HC IF 2 wine

description: Healthy controls; individual=IF; time=2; beverage=wine


title: D_U133Plus_110_Amy


title: HC IF 4 wine

description: Healthy controls; individual=IF; time=4; beverage=wine


title: D_U133Plus_108_Amy


title: D_U133A_102_Amy


title: HC IF 1 wine

description: Healthy controls; individual=IF; time=1; beverage=wine


title: D_U133Plus_109_Amy


title: D_U133Plus_104_Amy


title: D_U133Plus_101_Amy


title: D_U133A_98_Amy


title: D_U133Plus_92_Amy


title: HC IF 0 wine

description: Healthy controls; individual=IF; time=0; beverage=wine


title: HC CM 1 alcohol

description: Healthy controls; individual=CM; time=1; beverage=alcohol


title: HC CM 12 alcohol

description: Healthy controls; individual=CM; time=12; beverage=alcohol


title: D_U133A_96_Amy


title: D_U133Plus_94_Amy


title: D_U133Plus_77_Amy


title: HC CM 4 wine

description: Healthy controls; individual=CM; time=4; beverage=wine


title: D_U133A_91_Amy


title: D_U133Plus_89_Amy


title: D_U133A_80_Amy


title: HC CM 12 wine

description: Healthy controls; individual=CM; time=12; beverage=wine


title: D_U133Plus_87_Amy


title: HC CM 0 alcohol

description: Healthy controls; individual=CM; time=0; beverage=alcohol


title: HC IF 2 alcohol

description: Healthy controls; individual=IF; time=2; beverage=alcohol


title: HC CM 2 wine

description: Healthy controls; individual=CM; time=2; beverage=wine


title: D_U133A_76_Amy


title: D_U133A_74_Amy


title: HC CM 1 wine

description: Healthy controls; individual=CM; time=1; beverage=wine


title: D_U133Plus_107_Amy


title: D_U133A_63_Amy


title: D_U133A_66_Amy


title: D_U133A_62_Amy


title: HC CM 0 wine

description: Healthy controls; individual=CM; time=0; beverage=wine


title: D_U133A_60_Amy


title: D_U133Plus_61_Amy


title: D_U133Plus_59_Amy


title: HC CM 12 grape.juice

description: Healthy controls; individual=CM; time=12; beverage=grape.juice


title: D_U133Plus_56_Amy

description: Gene expression data from postmorten brain regions


title: HC CM 4 water

description: Healthy controls; individual=CM; time=4; beverage=water


title: HC CM 12 water

description: Healthy controls; individual=CM; time=12; beverage=water


title: HC CM 4 grape.juice

description: Healthy controls; individual=CM; time=4; beverage=grape.juice


title: D_U133Plus_55_Amy


title: D_U133A_68_Amy


title: 3T3-L1 Adipocytes_Glc_c8a

city: Wageningen

first: ping

last: wang

address: bornsesteeg 45

country: Netherlands

institute: RIKILT / Maastricht University

description: 3T3-L1 adipocytes

hyb_protocol: Before hybridization, the Cy5- and Cy3- labeled cDNAs were mixed 1:1(v/v). The cDNA hybridization was performed at 42°C in a Geneframe of a volume of 140 µl as described previously in Pellis L, et al. (2003) Physiol Genomics 16: 99-106

scan_protocol: The signals were captured by Scanarray Express HT (Perkin Elmer). Both channels were recorded with a laser power of 90% and a PMT of 60%.

data_processing: The signal were extracted using ArrayVision. The intensity of each spot was measured as median density. Data were exported into GeneMaths XT for analysis. Spots with an average intensity, over all arrays, of either Cy5 or Cy3 lower than 2-fold above average background were cleaned up. Then, the Cy5 intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

organism: Mus musculus

source_name: 3T3-L1 Adipocytes, treated with Glc, replicate:c8a

label_protocol: 45 µg of total RNA was mixed with 5 µg T21 primer, heated at 65°C for 3 min followed by 25°C for 10 min. cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy5-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42°C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of  96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37°C for 10 minutes. The reaction was neutralized with Tris-HCl, pH 6.8 and 1M HCl. The Cy5- and Cy3- labelled cDNAs were purified with the Qiaquick PCR purification kit and precipitated overnight at -20°C using NaAc/ EtOH. The cDNAs were resolved in 80 µl hybridization buffer (5x SSC, 0.4% SDS, 5X Denhardt's buffer, 0.5v/v formamid, 0.2 mg/ml herringsperm DNA).

extract_protocol: using Trizol (Invitrogen) according to the manufacturer's instruction, and after the chloroform extraction a phenol/chloroform/isoamylalcohol (25:24:1) extraction followed by a chloroform extraction was added.

tag: experiment sample

source_name: reference RNA

label_protocol: 45 µg of total RNA was mixed with 5 µg T21 primer, heated at 65°C for 3 min followed by 25°C for 10 min. cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy3-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42°C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of  96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37°C for 10 minutes. The reaction was neutralized with Tris-HCl, pH 6.8 and 1M HCl. The Cy5- and Cy3- labelled cDNAs were purified with the Qiaquick PCR purification kit and precipitated overnight at -20°C using NaAc/ EtOH. The cDNAs were resolved in 80 µl hybridization buffer (5x SSC, 0.4% SDS, 5X Denhardt's buffer, 0.5v/v formamid, 0.2 mg/ml herringsperm DNA).

tag: A reference sample, consisting of a pool of total RNA extracted from all samples


title: HC CM 1 grape.juice

description: Healthy controls; individual=CM; time=1; beverage=grape.juice


title: 3T3-L1 Adipocytes_Glc_d8a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Glc, replicate:d8a


title: D_U133A_51_Amy


title: HC CM 2 grape.juice

description: Healthy controls; individual=CM; time=2; beverage=grape.juice


title: 3T3-L1 Adipocytes_Glc_c8b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Glc, replicate:c8b


title: 3T3-L1 Adipocytes_Glc_b8b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Glc, replicate:b8b


title: D_U133A_50_Amy


title: D_U133Plus_97_Amy


title: D_U133A_49_Amy


title: HC CM 1 water

description: Healthy controls; individual=CM; time=1; beverage=water


title: 3T3-L1 Adipocytes_Glc_b8a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Glc, replicate:b8a


title: D_U133A_48_Amy


title: large airways, non-smoker 020510R, MAS5

description: large airways, non-smoker 020510R, MAS5

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HuGeneFL. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray 2500.

tag: Lung

value: right


title: HC CM 2 water

description: Healthy controls; individual=CM; time=2; beverage=water


title: D_U133A_42_Amy

value: Amygdala


title: HC CM 0 water

description: Healthy controls; individual=CM; time=0; beverage=water


title: 3T3-L1 Adipocytes_Rosi_b7b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi, replicate:b7b


title: 3T3-L1 Adipocytes_Rosi_d7a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi, replicate:d7a


title: D_U133A_47_Amy


title: HC CJ 2 water

description: Healthy controls; individual=CJ; time=2; beverage=water


title: 3T3-L1 Adipocytes_Rosi_c7b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi, replicate:c7b


title: 3T3-L1 Adipocytes_Rosi_b7a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi, replicate:b7a


title: HC CJ 4 water

description: Healthy controls; individual=CJ; time=4; beverage=water


title: D_U133Plus_38_Amy


title: HC CM 2 alcohol

description: Healthy controls; individual=CM; time=2; beverage=alcohol


title: D_U133A_41_Amy


title: HC CJ 1 water

description: Healthy controls; individual=CJ; time=1; beverage=water


title: large airways, non-smoker 020501L, MAS5

description: large airways, non-smoker 020501L, MAS5

value: black

value: left


title: HC CJ 0 water

description: Healthy controls; individual=CJ; time=0; beverage=water


title: 3T3-L1 Adipocytes_Rosi_c7a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi, replicate:c7a


title: 3T3-L1 Adipocytes_Ins_c6b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins, replicate:c6b


title: 3T3-L1 Adipocytes_Ins_d6a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins, replicate:d6a


title: D_U133Plus_36_Amy

source_name: Postmorten human brain: Amygdala


title: D_U133A_44_Amy


title: large airways, non-smoker 020501R, MAS5

description: large airways, non-smoker 020501R, MAS5

value: non-smoker


title: 3T3-L1 Adipocytes_Ins_c6a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins, replicate:c6a


title: HC CJ 12 water

description: Healthy controls; individual=CJ; time=12; beverage=water


title: HC CJ 4 alcohol

description: Healthy controls; individual=CJ; time=4; beverage=alcohol


title: large airways, non-smoker 011128R, MAS5

description: large airways, non-smoker 011128R, MAS5

source_name: airway epithelial cells obtained by bronchoscopy and brushing


title: large airways, non-smoker 011128L, MAS5

description: large airways, non-smoker 011128L, MAS5


title: D_U133A_32_Amy


title: HC CJ 12 alcohol

description: Healthy controls; individual=CJ; time=12; beverage=alcohol

source_name: peripheral blood cell


title: large airways, non-smoker 020510L, MAS5

description: large airways, non-smoker 020510L, MAS5


title: large airways, non-smoker 011102R, MAS5

description: large airways, non-smoker 011102R, MAS5

value: white


title: HC CJ 1 alcohol

description: Healthy controls; individual=CJ; time=1; beverage=alcohol


title: 3T3-L1 Adipocytes_Basal_d5a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Basal, replicate:d5a


title: HC CJ 0 alcohol

description: Healthy controls; individual=CJ; time=0; beverage=alcohol


title: 3T3-L1 Adipocytes_Basal_c5a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Basal, replicate:c5a

source_name: reference RNA


title: HC CJ 2 alcohol

description: Healthy controls; individual=CJ; time=2; beverage=alcohol


title: D_U133A_35_Amy

description: Gene expression data from postmorten brain regions


title: 3T3-L1 Adipocytes_Basal_c5b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Basal, replicate:c5b


title: large airways, non-smoker 010823R, MAS5

description: large airways, non-smoker 010823R, MAS5


title: D_U133A_29_Amy


title: 3T3-L1 Adipocytes_Basal_b5b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Basal, replicate:b5b


title: D_U133A_30_Amy


title: large airways, non-smoker 010823L, MAS5

description: large airways, non-smoker 010823L, MAS5


title: D_U133Plus_16_Amy


title: 3T3-L1 Adipocytes_Rosi+Ins+Glc_d4a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi+Ins+Glc, replicate:d4a


title: HC CJ 4 wine

description: Healthy controls; individual=CJ; time=4; beverage=wine


title: HC CJ 12 wine

description: Healthy controls; individual=CJ; time=12; beverage=wine


title: HC CJ 2 wine

description: Healthy controls; individual=CJ; time=2; beverage=wine


title: large airways, non-smoker 010511R, MAS5

description: large airways, non-smoker 010511R, MAS5

value: F


title: D_U133A_18_Amy


title: large airways, non-smoker 011102L, MAS5

description: large airways, non-smoker 011102L, MAS5


title: 3T3-L1 Adipocytes_Basal_b5a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Basal, replicate:b5a


title: D_U133A_31_Amy


title: 3T3-L1 Adipocytes_Rosi+Ins+Glc_c4b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi+Ins+Glc, replicate:c4b


title: HC CJ 0 wine

description: Healthy controls; individual=CJ; time=0; beverage=wine


title: D_U133A_15_Amy


title: large airways, non-smoker 010430L, MAS5

description: large airways, non-smoker 010430L, MAS5


title: D_U133A_13_Amy


title: 3T3-L1 Adipocytes_Rosi+Ins+Glc_c4a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi+Ins+Glc, replicate:c4a


title: large airways, non-smoker 010430R, MAS5

description: large airways, non-smoker 010430R, MAS5


title: large airways, non-smoker 010316R, MAS5

description: large airways, non-smoker 010316R, MAS5


title: HC CJ 4 grape.juice

description: Healthy controls; individual=CJ; time=4; beverage=grape.juice


title: large airways, non-smoker 010511L, MAS5

description: large airways, non-smoker 010511L, MAS5


title: D_U133A_12_Amy


title: HC CJ 1 wine

description: Healthy controls; individual=CJ; time=1; beverage=wine


title: 3T3-L1 Adipocytes_Rosi+Ins+Glc_b4a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi+Ins+Glc, replicate:b4a


title: 3T3-L1 Adipocytes_Ins_b6b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins, replicate:b6b


title: D_U133A_11_Amy


title: large airways, non-smoker 010316L, MAS5

description: large airways, non-smoker 010316L, MAS5


title: D_U133Plus_73_Amy


title: D_U133A_9_Amy


title: large airways, non-smoker 010119R, MAS5

description: large airways, non-smoker 010119R, MAS5


title: 3T3-L1 Adipocytes_Ins+Glc_c3b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins+Glc, replicate:c3b


title: HC CJ 2 grape.juice

description: Healthy controls; individual=CJ; time=2; beverage=grape.juice


title: large airways, non-smoker 010119L, MAS5

description: large airways, non-smoker 010119L, MAS5


title: D_U133A_7_Amy


title: 3T3-L1 Adipocytes_Rosi+Ins+Glc_b4b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Rosi+Ins+Glc, replicate:b4b


title: HC CJ 1 grape.juice

description: Healthy controls; individual=CJ; time=1; beverage=grape.juice


title: HC CJ 12 grape.juice

description: Healthy controls; individual=CJ; time=12; beverage=grape.juice


title: infected HCT116 tumor replicate 1

status: Public on Nov 20 2006

city: Baltimore

first: Xin

last: Huang

state: MD

address: 1650 Orleans Street, CRB I, Room 520

department: Oncology

institute: Johns Hopkins University

description: The features were extracted by using the NimbleScan software.

hyb_protocol: Hybridization with the end-labeled samples was carried out at 45°C for 16 hours in 100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20 and 10.5% glycerol.

scan_protocol: After washing, the arrays were stained with Cy3-Streptavidin, followed by scanning with an Axon 4000B scanner.

data_processing: Data was analyzed with the Bioconductor project using quantile normalization (see:Bolstad B, Irizarry R, Astrand M, Speed T (2003) A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19 (2), p185-193) and gene calls generated using the RMA algorithm (Robust multichip average described in Biostatistics 2003 Apr;4(2):249-64 ).

organism:
Homo sapiens
Clostridium novyi NT

source_name: infected HCT116 tumor

label_protocol: total RNA was reverse transcribed with SuperScript II Reverse Transcriptase (Invitrogen). The first-strand cDNA was fragmented by DNase I (Promega, Madison WI) and labeled with biotinylated ddATP through a terminal transferase end-labeling reaction.

growth_protocol: Six- to 8-week-old athymic nu/nu  mice (Harlan, Indianapolis, IN) were inoculated subcutaneously with five million HCT116 human cancer cells.  Three hundred million C. novyi-NT spores were administered by tail-vein injection once the tumor volumes reached ~500 mm3. Germination was generally observed to initiate within 12 hours and RNA isolated eighteen hours later, just after germination became evident.

extract_protocol:
Vegetative bacteria or spores were collected by centrifugation and homogenized by vortexing in RNAwiz buffer (RiboPureTM-Bacteria kit, Ambion, Austin, TX) containing 250 µL of Zirconia beads (Biospec, Bartlesville, OK) for 10 minutes at 4°C, followed by a 5-min break. This cycle was repeated 12 times to ensure disruption of the spores (as assessed by phase contrast microscopy and RNA yield). RNA was purified with the RiboPureTM-Bacteria kit (Ambion) following the manufacturer’s instructions.
         RNA was prepared from infected or uninfected tumors by homogenizing (50 strokes) the dissected tumors in a glass homogenizer containing a 10-fold volume of the RNAwiz buffer on ice.  The homogenate was aliquoted into 0.5-mL RNase-free tubes. The samples were then processed exactly as described above, using a 12-cycle homogenization with Zirconia beads.

tag: infected HCT116 tumor


title: infected HCT116 tumor replicate 2


title: infected HCT116 tumor replicate 3


title: 3T3-L1 Adipocytes_Ins+Glc_b3b

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins+Glc, replicate:b3b


title: infected HCT116 tumor replicate 5


title: D_U133A_5_Amy

source_name: Postmorten human brain: Amygdala


title: infected CT26 tumor replicate 2

organism:
Mus musculus
Clostridium novyi NT

source_name: infected CT26 tumor

growth_protocol: Six- to 8-week-old BALB/c mice (Harlan, Indianapolis, IN) were inoculated subcutaneously with five million CT26 murine colon cancer cells.  Three hundred million C. novyi-NT spores were administered by tail-vein injection once the tumor volumes reached ~500 mm3. Germination was generally observed to initiate within 12 hours and RNA isolated eighteen hours later, just after germination became evident.

tag: infected CT26 tumor


title: HC CJ 0 grape.juice

description: Healthy controls; individual=CJ; time=0; beverage=grape.juice

source_name: peripheral blood cell


title: infected CT26 tumor replicate 5


title: infected CT26 tumor replicate 3


title: Uninfected HCT116 tumor replicate 1

source_name: Uninfected HCT116 tumor

growth_protocol: Six- to 8-week-old athymic nu/nu mice (Harlan, Indianapolis, IN) were inoculated subcutaneously with five million HCT116 human colon cancer cells.  The tumor was harvested once the tumor volumes reached ~500 mm3.

tag: Uninfected HCT116 tumor


title: infected CT26 tumor replicate 4


title: Uninfected CT26 tumor replicate 2

source_name: Uninfected CT26 tumor

growth_protocol: Six- to 8-week-old BALB/c mice (Harlan, Indianapolis, IN) were inoculated subcutaneously with five million CT26 murine colon cancer cells.  Tumor was harvested once the tumor volumes reached ~500 mm3.

tag: Uninfected CT26 tumor


title: Uninfected HCT116 tumor replicate 2


title: infected CT26 tumor replicate 1


title: 3T3-L1 Adipocytes_Ins+Glc_c3a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins+Glc, replicate:c3a

source_name: reference RNA


title: infected HCT116 tumor replicate 4


title: Uninfected CT26 tumor replicate 1


title: C. novyi-NT spore Replicate 1

organism: Clostridium novyi NT

source_name: C. novyi-NT spore

growth_protocol: The bacteria were cultured in sporulation medium for at least two weeks to ensure maximum yield of mature spores.  Mature spores were purified through two consecutive continuous Percoll gradients followed by four washes and resuspensions in phosphate-buffered saline (PBS).  Purity of the spore preparations was determined to be >99.9% using phase contrast microscopy as well as by staining with malachite green and eosin Y (http://pb.merck.de/servlet/PB/show/ 1235100/115942en.pdf).

extract_protocol: Vegetative bacteria or spores were collected by centrifugation and homogenized by vortexing in RNAwiz buffer (RiboPureTM-Bacteria kit, Ambion, Austin, TX) containing 250 µL of Zirconia beads (Biospec, Bartlesville, OK) for 10 minutes at 4°C, followed by a 5-min break. This cycle was repeated 12 times to ensure disruption of the spores (as assessed by phase contrast microscopy and RNA yield). RNA was purified with the RiboPureTM-Bacteria kit (Ambion) following the manufacturer’s instructions.

tag: C. novyi-NT spore


title: C. novyi-NT spore Replicate 4


title: C. novyi-NT spore Replicate 5


title: C. novyi-NT spore Replicate 2


title: C. novyi-NT Mid Log Replicate 3

source_name: C. novyi-NT in Mid Log Phase

growth_protocol: Overnight cultures were diluted into fresh deoxygenated culture medium and anaerobic incubation continued until bacteria entered mid (OD600 = 0.6) log phase.

tag: C. novyi-NT in Mid Log Phase


title: C. novyi-NT Mid Log Replicate 1


title: C. novyi-NT Mid Log Replicate 2


title: C. novyi-NT spore Replicate 3


title: LuCap 23.1

status: Public on Nov 18 2006

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description: Fresh frozen tumor sample was obtained from four different mice bearing the LuCaP 23.1 xenograft

hyb_protocol: Filters were pre-hybridized for 6 hours at 68°C in hybridization buffer containing 100 µg/ml denaturated (10 min at 100°C) herring sperm DNA. Buffer was then removed and filters were hybridized with the labeled samples for 48 hours. Filters were then washed in 0.1X SSC/0.1% SDS solution for 3 hours. Finally, membranes were rinsed in 2x SSC and air-dried before exposure.

scan_protocol: After hybridizations and washes, arrays were exposed for 48 hours to phosphoimaging plates (FUJIFILM), which were then scanned with a BAS-5000 (FUJIFILM) machine (25 µm resolution, dynamic range: L5/S10000). After image acquisition, hybridization signals were quantified using ArrayGauge software. For each array a result file containing raw data was generated. Furthermore, all images were carefully inspected and spots with overestimated intensities due to neighbourhood effects were manually excluded. For each array, background intensity was calculated on the basis of the average of the 400 lowest values and substracted.

data_processing: Global normalization

source_name: XENOGRAFT MOUSE

label_protocol: Total RNA was mixed with 8 µg oligodT(25) and 0.3 ng cytochrome CG03 mRNA. Samples were heated at 70°C to remove secondary structure and progressively cooled to 42°C to ensure annealing of oligo(dT) with the poly(A) tail. Then, 17 µl of labeling mix (1 µl RNasin, 6 µl 5x first strand buffer, 2 µl 0.1 M DTT, 0.6 µl of 20 mM (each) dATP dGTP dTTP, 0.6 µl of 120 µM dCTP, 3 µl of alpha-33P-dCTP, 1 µl SuperScript II reverse transcriptase, 2.8 µl water) were added and reverse transcription was performed at 42°C for one hour. To improve reverse transcription, 1 µl SuperScript II reverse transcriptase was subsequently added and reaction was carried on for one hour. RNA was removed by treatment at 68°C for 30 min with 1 µl 1% SDS, 1 µl 0.5 M EDTA and 3µl 3 M NaOH. After equilibration (15 min at room temperature) samples were neutralized using 10 µl 1 M Tris-HCl and 3 µl 2N HCl. Next, 2 µg of polyA(80) and 2 µg of mouse COT-1 (InVitrogen) were added and samples were heated at 100°C for 5 min. Volume was then adjusted to 500 ULwith hybridization buffer (5x SSC, 5x Denhardt's, 0.5% SDS) and samples were heated for 2 hr 30 at 68°C.

extract_protocol: Total RNA was extracted from HR, Hs and LuCap 23.1 mouse xenograft samples by lysis in guanidium isothiocyanate and centrifugation over a cesium chloride cushion following standard protocols (Theillet Chromosomes Cancer 1993). RNA quality was assessed by denaturing formaldehyde agarose gel electrophoresis and reverse-transcribed PCR (RT-PCR) amplification of the ß2-microglobulin transcript. RNA extracts were pooled according to the three distinct stages of tumor progression in the LuCaP 23.1 model (4 samples / tumor stage).

tag: LOCAL CANCER tumor samples

tag: male NOD-SCID mouse

tag: prostate gland


title: C. novyi-NT Late Log Replicate 1

source_name: C. novyi-NT in Late Log Phase

growth_protocol: Overnight cultures were diluted into fresh deoxygenated culture medium and anaerobic incubation continued until bacteria entered late (OD600 = 0.8) log phase.

tag: C. novyi-NT in Late Log Phase


title: C. novyi-NT Late Log Replicate 4


title: HR

source_name: MOUSE XENOGRAFT

tag: hormone refractory (HR) tumor samples

tag: (day 114 post- transplantation)


title: HS

tag: hormone sensitivity prostate cancer sample

tag: (day 7 post- transplantation)


title: C. novyi-NT Early Log Replicate 4

source_name: C. novyi-NT in Early Log Phase

growth_protocol: Overnight cultures were diluted into fresh deoxygenated culture medium and anaerobic incubation continued until bacteria entered early (OD600 = 0.2) log phases.

tag: C. novyi-NT in Early Log Phase


title: C. novyi-NT Late Log Replicate 3


title: C. novyi-NT Late Log Replicate 2


title: C. novyi-NT Early Log Replicate 1

data_processing: Data was analyzed with the Bioconductor project using quantile normalization (see:Bolstad B, Irizarry R, Astrand M, Speed T (2003) A comparison of normalization  methods for high density oligonucleotide array data based on bias and variance.  Bioinformatics 19 (2), p185-193) and gene calls generated using the RMA algorithm (Robust multichip average described in Biostatistics 2003 Apr;4(2):249-64 ).


title: C. novyi-NT Early Log Replicate 2


title: C. novyi-NT Early Log Replicate 3


title: salinity stress, biological rep1

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

description: Gene expression data

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Barley1 Gene Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with GCOS 1.2 using Affymetrix default analysis settings and global scaling as normalization method

organism: Hordeum vulgare

source_name: barley crown and growing point tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA

extract_protocol: Trizol extraction of total RNA

treatment_protocol: salt stress growth condition

tag: genotype Golden Promise


title: Breast Cancer Post-Treatment 3

city: México

first: Carlos

last: Pérez-Plasencia

address: Av. San Fernando 22

department: BASIC RESEARCH

country: Mexico

institute: INSTITUTO NACIONAL DE CANCEROLOGIA

description: Gene expression data from a primary breast tumor after 7 days of treatment with hydralazine and magnesium valproate prior to the first course of doxorubicin plus cyclophosphamide.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 37C on Human Whole Genome CodeLink Bioarray. Stain and post-hybridization washes were performed according to the manufacturer's instructions.

scan_protocol: Bioarrays were scanned with a GenePix Personal 4100A scanner.

data_processing: Expression values were globally normalized to the median expression value of the whole array spots.  To circumvent division by zero, values below three times background value were taken as 5.

label: Biotin

source_name: Tumor mammary tissue 1 after treatment

label_protocol: Biotinylated cRNA was prepared according to the standard CodeLink protocol from 2 ug total RNA

tag: Core-needle biopsy was taken from primary breast tumors after 7 days of treatment with hydralazine and magnesium valproate prior to the first course of doxorubicin plus cyclophosphamide.


title: control, biological rep2

description: Gene expression data

treatment_protocol: unstressed growth condition


title: JA, biological rep1

description: Gene expression data

treatment_protocol: JA treatment


title: Breast Cancer Post-Treatment 2

source_name: Tumor mammary tissue 2 after treatment


title: salinity stress, biological rep2

description: Gene expression data

treatment_protocol: salt stressed growth condition


title: Breast Cancer Pre-Treatment 1

description: Gene expression data from a primary breast tumor previous to receive hydralazine and magnesium valproate prior to the first course of doxorubicin plus cyclophosphamide.

source_name: Tumor mammary tissue 1 previous to treatment.

tag: Core-needle biopsy was taken from primary breast tumors at diagnosis day prior to the first course of doxorubicin plus cyclophosphamide.


title: control, biological rep1

description: Gene expression data


title: Breast Cancer Post-Treatment 1

source_name: Tumor mammary tissue 1 after treatment.


title: JA, biological rep2

description: Gene expression data


title: JA and salinity stress, biological rep1

description: Gene expression data

treatment_protocol: JA pretreatment before salt stress


title: JA and salinity stress, biological rep2

description: Gene expression data


title: J1a12 (40oC) vs rpoE- (40oC)- 3000115475L

status: Public on Nov 17 2006

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)]

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization

organism: Xylella fastidiosa

label_protocol: 20ug of total RNA was reverse transcribed and labeled using Superscript Plus Indirect cDNA Labeling System (Invitrogen). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

growth_protocol: Xylella fastidiosa strain J1a12 was grown in Periwinkle wilt broth plus 0.5% glucose (PWG) at 25oC for 7 days.

extract_protocol: Total RNA was isolated with Trizol and residual DNA was removed by treatment with 0.03U of RQ1 RNAse-free DNAse I (Promega) and 40U RNAse inhibitor RNAsin (Promega). The integrity of the RNA was checked by agarose gel electrophoresis and the lack of residual DNA was checked by PCR.

treatment_protocol: Heat shock at 40oC was applied to 7 days old cultures for 25 minutes.

source_name: rpoE- 40oC (cy5)

label_protocol: 20ug of total RNA was reverse transcribed and labeled using Superscript Plus Indirect cDNA Labeling System (Invitrogne). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

growth_protocol: Xylella fastidiosa strain J1a12 rpoE- was grown in Periwinkle wilt broth plus 0.5% glucose (PWG) containing 10 ug/mL ampicillin at 25oC for 7 days.

tag: rpoE- 40oC (cy5)


title: J1a12 (40oC) vs rpoE- (40oC)- 3000188435R


title: J1a12 (40oC) vs rpoE- (40oC)- 3000115669L

source_name: rpoE- 40oC (cy3)

growth_protocol: Xylella fastidiosa strain J1a12 rpoE- was grown in Periwinkle wilt broth plus 0.5% glucose(PWG) containing 10 ug/mL ampicillin at 25oC for 7 days.

tag: rpoE- 40oC (cy3)


title: J1a12 (40oC) vs rpoE- (40oC)- 3000188430L


title: J1a12 (40oC) vs rpoE- (40oC)- 3000188435L


title: J1a12 (40oC) vs rpoE- (40oC)- 3000188436R


title: J1a12 (40oC) vs rpoE- (40oC)- 3000188436L


title: J1a12 (40oC) vs rpoE- (40oC)- 3000188430R


title: MRC5_UV exposure_M10_4H/16H

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: Data processing will be described in detail in our website http://140.114.106.30/publication/kuchang/

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer’s instruction of 3DNA array 350 kit.

scan_protocol: Barcode=12766812 "PMTGain=710	600" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.89	3.09" Temperature=31.25 "ScanPower=100	100"

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 1 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

source_name: Sample harvested at 4 hours after UV irradiation

label_protocol: 3DNA Array 350 kit was used for fluorescence labeling on cDNA. Each total RNA (5μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA was then purified by microcon YM-30 column and was blocked by addictive 0.5μg of Cot1 human DNA.

growth_protocol: The MRC-5 cell, obtained from the American Type Culture Collection (ATCC, MA, USA) was grown in the complete growth medium and was incubated at 37 oC and 5 % CO2 in air atmosphere. The complete growth medium was the α-MEM medium supplemented with antibiotic (100 U/ml penicillin plus 10ug/ml streptomycin), and 10% heat-inactivated fetal bovine serum. The medium was replenished every 48 h after cell passage. Cells were routinely subcultivated in cell culture petri dishes of 100 mm2 every 3-4 days with 1:3 subcultivation ratio. In the beginning of subcultivation, the cell layer was briefly rinsed with 2 ml of 0.25% (w/v) trypsin-0.53 mM EDTA in 15 ~ 20 seconds after removal of whole medium with serum. Then we incubated the culture dish at 37 oC to facilitate dispersal in 1.5~2 min. We add fresh complete growth medium 10 ml per petri dish and aspirate cells by gently pipeting. Finally we add appropriate aliquots of the cell suspension to new petri dishes. The entire experiments were performed at passages 21 to 28.

extract_protocol: Total RNA was extracte by lying directly in the 100mm petri dish with 1.0 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).

tag: Cell strain, Gender

value: male, Age:14 weeks, Tissue: hung fibroblast,


title: J1a12 (40oC) vs rpoE- (40oC)- 3000115668R


title: MRC5_UV exposure_M09_24H/8H

scan_protocol: Barcode=12766810 "PMTGain=710	600" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.87	3.09" Temperature=31.25 "ScanPower=100	100"

source_name: Sample harvested at 24 hours after UV irradiation

source_name: Sample harvested at 8 hours after UV irradiation


title: MRC5_16 hours_UV exposure_M05_16H/16C

scan_protocol: Barcode=12767257 "PMTGain=750	560" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.94	3.06" Temperature=29.3 "ScanPower=100	100"

source_name: Sample harvested at 16 hours after UV irradiation

source_name: Control samples corresponding to 16H

treatment_protocol: No


title: J1a12 (40oC) vs rpoE- (40oC)- 3000115669R


title: J1a12 (40oC) vs rpoE- (40oC)- 3000115668L


title: MRC5_24 hours_UV exposure_M07_24H/24C

scan_protocol: Barcode=12766193 "PMTGain=700	520" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.91	3.07" Temperature=29.3 "ScanPower=100	100"

treatment_protocol: Sample harvested at 24 hours after UV irradiation

source_name: Control samples corresponding to 24H


title: J1a12 vs rpoE- - 3000115489R

growth_protocol: Xylella fastidiosa strain J1a12 was grown in Periwinkle wilt broth plus 0.5% glucose(PWG) at 25oC for 7 days.

treatment_protocol: wild type strain J1a12

source_name: rpoE- (cy5)

growth_protocol: Xylella fastidiosa strain J1a12 rpoE- was grown in Periwinkle wilt broth plus 0.5% glucose (PWG) containing 10 ug/ml ampicillin at 25oC for 7 days.

treatment_protocol: mutant rpoE-

tag: rpoE- (cy5)


title: MRC5_4 hours_UV exposure_M02_8C/4H

scan_protocol: Barcode=12766152 "PMTGain=650	600" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.88	3.11" Temperature=30.76 "ScanPower=100	100"

source_name: Control samples corresponding to 8H

treatment_protocol: Sample harvested at 4 hours after UV irradiation


title: J1a12 vs rpoE- - 3000115489L


title: MRC5_24 hours_UV exposure_Mo8_4C/24H

scan_protocol: Barcode=12767255 "PMTGain=690	640" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.88	3.1" Temperature=30.76 "ScanPower=100	100"

source_name: Control samples corresponding to 4H


title: 3T3-L1 Adipocytes_Ins+Glc_b3a

description: 3T3-L1 adipocytes

source_name: 3T3-L1 Adipocytes, treated with Ins+Glc, replicate:b3a

tag: experiment sample

source_name: reference RNA

tag: A reference sample, consisting of a pool of total RNA extracted from all samples


title: MRC5_8 hours_UV exposure_M04_16C/8H

scan_protocol: Barcode=12766192 "PMTGain=630	600" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.91	3.07" Temperature=30.76 "ScanPower=100	100"

treatment_protocol: Sample harvested at 8 hours after UV irradiation


title: MRC5_8 hours_UV exposure_M03_8H/8C

scan_protocol: Barcode=12766191 "PMTGain=700	540" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.94	3.05" Temperature=29.3 "ScanPower=100	100"


title: J1a12 vs rpoE- - 3000137030R


title: J1a12 vs rpoE- - 3000137031R


title: J1a12 vs rpoE- - 3000137030L


title: Ronghe 062205 13

status: Public on Nov 16 2006

city: Tuxedo Park

first: Ronghe

last: Zhang

address: 57 Old Forge Rd

department: Environmental Medicine

institute: New York University School of Medicine

description: An immortalized rat keratinocyte cell line,originally isolated from the dorsal skin of neonatal male weanling Sprague_Dawley rats(CD)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with BRB-ArraYTools version 3.5.0-Beta-1

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Rat skin keratynocyte with radiation treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5-2ug polyA RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: 3Gy 56 Fe radiation treatment

tag: Dorsal skin of neonatal male weanling Sprague_Dawley rats(CD)


title: MRC5_16 hours_UV exposure_M06_24C/16H

scan_protocol: Barcode=12766809 "PMTGain=700	650" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.9	3.09" Temperature=30.76 "ScanPower=100	100"

treatment_protocol: Sample harvested at 16 hours after UV irradiation


title: J1a12 vs rpoE- - 3000137031L


title: Ronghe 062205 11


title: Ronghe 062205 3

source_name: Rat skin keratinocyte without treatment

treatment_protocol: No treatment


title: Ronghe 062205 2


title: Ronghe 062205 1


title: HCT116-Neo124 PTEN +/+

status: Public on Nov 15 2006

city: Washington

first: JUNGSIK

last: KIM

state: DC

address: 3970 Reservoir Road

institute: GEORGETOWN UNIVERSITY

description: Cells were grown in McCoy’s 5A medium with 10% FBS

hyb_protocol: Hybridization and washing steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Protocol	EukGE-WS2v4 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	1 Hybridize Date	11/06/02  16:49

scan_protocol: Imaging steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Pixel Size	 3 Filter	570 Scan Date	11/06/02  16:56 Number of Scans	2

source_name: HCT116-Neo124 human colon cancer cells with intact PTEN

label_protocol: Genechip IVT labeling kit

extract_protocol: Total RNA was prepared using standard TRIZOL-based techniques.


title: PTEN-22 (-/-)

hyb_protocol: Hybridization and washing steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Protocol	EukGE-WS2v4 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	2 Hybridize Date	11/06/02  14:21

scan_protocol: Imaging steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Pixel Size	 3 Filter	570 Scan Date	11/06/02  15:10 Number of Scans	2

source_name: HCT116 human colon cancer cells with PTEN -/-


title: HCT116 PTEN +/+

hyb_protocol: Hybridization and washing steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Protocol	EukGE-WS2v4 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	1 Hybridize Date	11/06/02  14:22

scan_protocol: Imaging steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Pixel Size	 3 Filter	570 Scan Date	11/06/02  14:59 Number of Scans	2

source_name: HCT116 human colon cancer cells with intact PTEN


title: PTEN 121 (-/-)

hyb_protocol: Hybridization and washing steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Protocol	EukGE-WS2v4 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	4 Hybridize Date	11/06/02  14:21

scan_protocol: Imaging steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Pixel Size	 3 Filter	570 Scan Date	11/06/02  15:33 Number of Scans	2

source_name: HCT116 human colon cancer cells with PTEn -/-


title: Ronghe 062205 12


title: Caenorhabditis elegans small RNA sequences from wild type animals fed on sel-1 dsRNA producing bacteria

type: other

city: Stanford

first: Andrew

last: Fire

state: CA

address: 300 Pasteur Drive RML235 M5324

department: Pathology and Genetics

institute: Stanford University

description: Raw data files (e.g. on Science Magazine website) may be preferred source for analysis.

data_processing:
Tags are complete (in most cases linker-containing) cDNA sequence. Value indicates number of instances in library.
FASTA nucleic acid file available in supplementary data link below.

molecule: other

organism: Caenorhabditis elegans

source_name: sel-1 RNAi (feeding)


title: PTEN-111 (-/-)

hyb_protocol: Hybridization and washing steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Protocol	EukGE-WS2v4 Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	25 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	4 Mixes per Wash B Cycle	15 Stain Temperature (C)	25 First Stain Time (seconds)	600 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	25 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	600 Third Stain Time (seconds)	600 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	30 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25 Station	1 Module	3 Hybridize Date	11/06/02  14:21

scan_protocol: Imaging steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource. Pixel Size	 3 Filter	570 Scan Date	11/06/02  15:22 Number of Scans	2

tag: HCT116 human colon cancer cells with PTEN -/-


title: For Figure 5; SK1; Ty4LTR vs Ty3LTR

first: Maitreya

middle: J.

last: Dunham

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: For Figure 5; SK1; Ty4LTR vs Ty3LTR

hyb_protocol: Description : Mix 500 ng of Cy5 DNA, 500 ng Cy3 DNA, and water to 200 ?l.  Prepare 10X control targets (Agilent) per kit directions.  Add 50 ?l 10X control targets to each tube. Mix.  Incubate 95C 5 min.  Cool RT 5 min.  Add 250 ?l 2X hybridization buffer.  Set up hybe according to Agilent protocol.  Hybe 60C for 17 hours in Agilent hybe oven.

scan_protocol: Pixel Size : 10 Scan Date : 2006-06-16 Scan Time : 12:11:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : A.7.5.1
Datafile type : Agilent result file

source_name: SK1-Ty4 LTR probe

label_protocol: Description : DNA labeling is done per Bio-Prime array CGH kit instructions using 21 ?L extracted DNA.  Purify labeled DNA with Zymo DNA Clean and Concentrator 5 columns.  Elute in 21 ?L water.

extract_protocol: Description : Mix 500/2000 ng of pooled restriction digested DNA, 15 ?L HSE buffer (Qiagen), 1.5 ?L probe mix (Qiagen), and water to bring to 30 ?L total.  Heat for 15 minutes at 95C, then transfer to a Qiagen EZ-1-6 robot and allow to re-nature and extend for 20 minutes at 65C.  Use Qiagen Haploprep Cartridge (Catalog #4340001/H100.C-48) to wash and capture.  Elute by heating to 80C 20 minutes. Collect supernatant.

tag: Strain Name

tag: Description

value: Prep DNA from 100 ml culture using the Qiagen Genomic DNA kit.  Measure starting DNA concentration with a fluorometer.  Digest 2-3 ?g DNA using appropriate enzyme and buffers.  Ethanol precipitate. Mix equal amounts of DNA from each digest if multiple digests required.

source_name: SK1-Ty3 LTR probe


title: mouse brain sense 430A

city: Newcastle

first: Andreas

last: Werner

address: Framlington Place

department: Cell and Molecular Biosciences

country: United Kingdom

institute: Newcastle University

description: Sense transcriptome

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: total mouse brain

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: The brain was dissected, rinsed in ice cold PBS and directly used for RNA extraction with TRIzol (Invitrogen).

tag: Strain 129SvJ

tag: Male, age 5 weeks


title: For Figure 4;  CEN.PK; Ty1 vs Ty2

description: For Figure 4;  CEN.PK; Ty1 vs Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-06-16 Scan Time : 12:43:20 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: mouse brain sense 430B

description: Sense transcriptome


title: For Figure 5; SK1 vs S288c; Ty1/Ty2

description: For Figure 5; SK1 vs S288c; Ty1/Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-01 Scan Time : 10:56:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: SK1 digested and extracted DNA

source_name: FY digested and extracted DNA


title: For figure 6; pooled Stu1 digested Tn7; 5' URA3 probes vs 3' URA3 probes

scan_protocol: Pixel Size : 10 Scan Date : 2006-08-24 Scan Time : 10:50:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 5' URA3 probes

source_name: 3' URA3 probes


title: For Figure 4; W303; Ty1 vs Ty2

description: For Figure 4; W303; Ty1 vs Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-06-16 Scan Time : 12:35:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: For Figure 3B;  S288c; Ty1 vs Ty2

description: For Figure 3B;  S288c; Ty1 vs Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-13 Scan Time : 11:10:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 11070-Ty1 probe

source_name: 11070-Ty2 probe


title: For Figure 4; CEN.PK vs S288c; Ty1/Ty2

description: For Figure 4; CEN.PK vs S288c; Ty1/Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-04-01 Scan Time : 11:28:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: CenPK digested and labeled

source_name: FY digested and labeled


title: For Figure 5;  SK1; Ty1 vs Ty2

description: For Figure 5;  SK1; Ty1 vs Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-07-11 Scan Time : 18:39:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: sk1-ty1 probe

source_name: sk1-ty2 probe


title: Tobacco_abuse_5

status: Public on Nov 14 2006

city: Iowa City

first: Gi-yung

last: Ryu

state: IA

address: EMRB 200A

department: Neurosurgery

institute: University of Iowa

description: Tobacco abuse in the Iowa Adoption Studies

hyb_protocol: Array hybridization was performed for 16 hrs at 55 oC. Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391).

label: DIG-UTP

source_name: lymphoblast cell line

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 μg of total RNA from each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 1.0 (P/N 4340472) according to the manufacturer’s protocol (P/N 4339629).

extract_protocol: RNA was extracted from the cell lines using our standard procedures using an Invitrogen RNA purification kit (Invitrogen, Carlsbad, CA) according to the instructions provided by the manufacturer and stored in Ambion RNA storage solution at –80o

tag: Tobacco abuse


title: For Figure 4; W303 vs S288c; Ty1/Ty2

description: For Figure 4; W303 vs S288c; Ty1/Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-28 Scan Time : 16:44:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: For Figure 3A; RM11 vs S288c; Ty1/Ty2

description: For Figure 3A; RM11 vs S288c; Ty1/Ty2

scan_protocol: Pixel Size : 10 Scan Date : 2006-03-07 Scan Time : 09:57:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Hypoxic adrenal rep4

city: Milwaukee

first: Eric

middle: David

last: Bruder

state: WI

address: 2801 W. KK River Parkway, Suite 245

department: Endocrine Research

institute: Aurora St. Luke's Medical Center

description: PD7 adrenal subcapsule

hyb_protocol: Fragmented, biotinylated cRNA (10 mg), along with hybrid controls (Affymetrix; Santa Clara, CA), were hybridized to the Affymetrix Rat Genome U34A GeneChip array containing probes for 15,923 transcripts.

scan_protocol: Arrays were washed and stained and then scanned at 488 nm in a G2500A GeneArray Scanner (Agilent; Palo Alto, CA).

data_processing: Evaluation of data from microarray analysis was performed as described in detail previously (15).  Briefly, scanned images were quantified by GeneChip Operating Software 1.1 (Affymetrix).  Signal intensities were used to determine overall expression level and a detection confidence score.  Fold-change in expression was calculated from the average signal intensity of each group.  A modified version of the false-discovery rate (FDR) method was used to assess significance of results (15).  To identify genes significantly affected by hypoxia, genes with a FDR £ 0.25 and a minimum fold-change of ± 1.3 were selected.  Functional categories used to sort genes according to biological function were derived from the Expression Analysis Systematic Explorer (EASE) software.  More specific descriptions of gene function were obtained from the National Center for Biotechnology Information Entrez Gene Database (http://www.ncbi.nlm.nih.gov).

source_name: rat hypoxic adrenals at PD7

label_protocol: double-stranded DNA was synthesized from 10 mg total RNA using a Superscript cDNA Synthesis Kit (Invitrogen).  Biotin-labeled cRNA was generated by transcription with T7 polymerase and purified on RNeasy affinity columns (Qiagen).

extract_protocol: TRIzol reagent and column purified.  RNA quality was assessed spectrophotometrically on the basis of the A260/A280 ratio.  All RNA samples were checked for integrity of 18S and 28S RNA by gel electrophoresis.

treatment_protocol: hypoxia @ 12 % O2 from birth to PD7 (or control at room air); adrenals quickly removed and decapsulated; frozen on dry ice and pooled (24 glands/sample)

tag: adrenal subcapsules; Hsd:SD rats; male/female; PD7


title: Tobacco_abuse_6

scan_protocol: image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).


title: Hypoxic adrenal rep2

description: PD7 adrenal subcapsule


title: Hypoxic adrenal rep3

description: PD7 adrenal subcapsule


title: Tobacco_abuse_2


title: Tobacco_abuse_1


title: No_abuse_3

description: No abuse in the Iowa Adoption Studies

tag: No abuse


title: Tobacco_abuse_3


title: No_abuse_5

description: No abuse in the Iowa Adoption Studies


title: No_abuse_8

description: No abuse in the Iowa Adoption Studies


title: No_abuse_2

description: No abuse in the Iowa Adoption Studies


title: No_abuse_6

description: No abuse in the Iowa Adoption Studies


title: Normoxic adrenal rep4

description: PD7 adrenal subcapsule

source_name: rat normoxic adrenals at PD7


title: Tobacco_abuse_4


title: No_abuse_1

description: No abuse in the Iowa Adoption Studies


title: Identification of the off-target genes induced by Smad2-RNAi

city: Beijing

first: yu

last: jian

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: Confirmation of the off-target genes of Smad2-RNAi in Hep3B cells

hyb_protocol: Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 80 µL hybridization solution (3×SSC, 0.2% SDS, 25% formamide and 5×Denhart’s). DNA in hybridization solution was denatured at 95℃ for 3 min prior loading on a microarray. Hybridization was performed under LifterSlipTM (Erie Company), which allows for even dispersal of hybridization solutions between the microarray and coverslip. The hybridization chamber was placed on a 3D-Tilting Agitator (CapitalBio Corp.) to facilitate the microfluidic circulation under the coverslip. The array was hybridized at 42℃ overnight and washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42℃ for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Microarrays were scanned with a confocal LuxScanTM scanner (CapitalBio Corp.), and the data of obtained images were extracted with SpotData Software (CapitalBio Corp.).

data_processing: The raw data was normalized using a space and intensity-dependant LOWESS program (Yang et al., 2002). The data from faint spots was removed, in which the intensity was lower than the average intensity plus 2 standard deviations of the negative controls on the array.

source_name: S2KD (Smad2 knockdown) cells without TGFb stimulation

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA).

treatment_protocol: The cells were stimulated by incubation in the absence(-) of 5 ng/ml of TGF-β for 12 h

tag: stable Smad2 knockdown Hep3B cells

source_name: WT (control) cells without TGFb stimulation

label_protocol: Fluorescent dye (Cy3 and Cy5-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with RNeasy Mini Kit (Qiagen). Because sense oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

tag: stable transfetcted with RNAi vector in Hep3B cells


title: Identification of the off-target genes induced by Smad3-RNAi

description: Confirmation of the off-target genes of Smad3-RNAi in Hep3B cells

source_name: S3KD (Smad3 knockdown) cells without TGFb stimulation

tag: stable Smad3 knockdown Hep3B cells


title: Normoxic adrenal rep3

description: PD7 adrenal subcapsule


title: Identification of the off-target genes induced by Smad4-RNAi

description: Confirmation of the off-target genes of Smad4-RNAi in Hep3B cells

source_name: S4KD (Smad4 knockdown) cells without TGFb stimulation

tag: stable Smad4 knockdown Hep3B cells


title: No_abuse_4

description: No abuse in the Iowa Adoption Studies


title: No_abuse_7

description: No abuse in the Iowa Adoption Studies


title: For Figure 2; FY2 vs FY5; Ty1/Ty2

description: chip on chip array with fy2 vs fy5 ty related fgts

scan_protocol: Pixel Size : 10 Scan Date : 2006-02-20 Scan Time : 09:32:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: No_abuse_9

description: No abuse in the Iowa Adoption Studies


title: Normoxic adrenal rep2

description: PD7 adrenal subcapsule


title: J1a12 (40oC) vs rpoE- (40oC)- 3000115475R

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

source_name: rpoE- 40oC (cy5)

tag: rpoE- 40oC (cy5)


title: Normoxic adrenal rep1

description: PD7 adrenal subcapsule


title: Identification of Smad3-dependent genes in Hep3B cells

description: Confirmation of the Smad3-dependent genes in the TGFb pathway in Hep3B cells

source_name: S3KD (Smad3 knockdown) cells with TGFb stimulation

treatment_protocol: The cells were stimulated by incubation in the presence (+) of 5 ng/ml of TGF-β for 12 h

source_name: WT (control) cells with TGFb stimulation


title: Identification of Smad2-dependent genes in Hep3B cells

description: Confirmation of the Smad2-dependent genes in the TGFb pathway in Hep3B cells

source_name: S2KD (Smad2 knockdown) cells with TGFb stimulation

treatment_protocol: The cells were stimulated by incubation in the presence (+) of 5 ng/ml of TGF-β for 12 h.


title: Cdc25a_CGH_expt_rep2

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

hyb_protocol: Followed Agilent aCGH hybridization protocol  v2.0 (August 2005) with wash procedure B (no ozone protection)

scan_protocol: Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution

data_processing: Agilent Feature Extraction software (v.8.5) was used to assess spot quality, extract feature intensity statistics, and perform normalization

source_name: MMTV-cdc25a;MMTV-neu #1852 CELL LINE

label_protocol: Invitrogen BioPrime Array CGH Genomic Labeling Module

extract_protocol: Dneasy Tissue kit (Qiagen Cat# 69504) per manufacturer's instructions

tag: Derived from tumor of

value: Strain:FVB/N , Gender:female , Age:26 weeks, Tissue:mammary, Tumor Stage:T1 (<1cm, early stage)

source_name: Normal FVBN Mouse mammary gland DNA

tag: Strain


title: Cdc25a_CGH_expt_rep1

value: FVB/N , Gender:female , Age:26 weeks, Tissue:mammary


title: Identification of Smad4-dependent genes in Hep3B cells

description: Confirmation of the Smad4-dependent genes in the TGFb pathway in Hep3B cells

source_name: S4KD (Smad4 knockdown) cells with TGFb stimulation


title: Identification of TGFb-responsive genes in Hep3B cells

description: Confirmation of the TGFb signaling-dependent genes in Hep3B cells

source_name: WT cells with TGFb stimulation

source_name: WT cells without TGFb stimulation

treatment_protocol: The cells were stimulated by incubation in the absence (-) of 5 ng/ml of TGF-β for 12 h


title: Cdc25a_expt_pair1_rep1

status: Public on Nov 13 2006

hyb_protocol: Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying

data_processing: Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)

source_name: FvBn-MMTV-neu #5

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)

extract_protocol: Agilent RNA isolation mini-kit

value: FVB/N , Gender:female , Age:26 weeks, Tissue:mammary, Tumor Stage:T1 (<1cm, early stage)

source_name: MMTV-cdc25a;MMTV-neu #1868


title: Cdc25a_expt_pair1_rep2


title: Cdc25a_expt_pair2_rep2

source_name: MMTV-cdc25a;MMTV-neu #1869

source_name: FvBn-MMTV-neu #6


title: Cdc25a_expt_pair2_rep1


title: Hypoxic adrenal rep1

description: PD7 adrenal subcapsule

source_name: rat hypoxic adrenals at PD7


title: Squamous cell carcinoma 86043_B

status: Public on Nov 10 2006

city: st louis

first: Yan

last: Lu

state: MO

address: 660 s. euclid ave

institute: washington univ.

description: Squamous cell carcinoma

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Robust Multichip Average

source_name: Squamous cell carcinoma

label_protocol: Approximately 1 to 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: standard Affymetrix procedures

tag: Gender

value: F; age:59; stage:T1N0


title: Squamous cell carcinoma 86011_B

description: Squamous cell carcinoma

value: F; age:78; stage:T1N0