title: 0412_032_20 ckb1_ckb2 pre-treatment 0 vs. ckb1_ckb2 3AT 40

value: ckb1ckb2 double deletion

value: 50mM 3-Amino-1,2,4-triazole (3-AT)


title: 0825_024_20 wt 3AT 20 vs. ckb1ckb2 3AT 20

status: Public on Jul 01 2011

type: RNA

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

country: USA

institute: Washington and Lee Unversity

hyb_protocol: Competitive hybridization at 65oC for 15h

scan_protocol: images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 5.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

molecule: total RNA

organism: Saccharomyces cerevisiae

label_protocol: aa-dUTP incorporation during cDNA synthesis

extract_protocol: Acid phenol

tag: genotype

tag: treatment

tag: time (min)

value: wild-type


title: 0825_021_20 wt 3AT 5 vs. ckb1ckb2 3AT 5


title: 0412_031_20 ckb1_ckb2 pre-treatment 0 vs. ckb1_ckb2 3AT 20

value: pretreatment sample


title: 0527_028_20 wt pre-treatment 0 vs. wt TBB 10


title: 0825_022_20 wt 3AT 10 vs. ckb1ckb2 3AT 10


title: 0412_030_20 ckb1_ckb2 pre-treatment 0 vs. ckb1_ckb2 3AT 10


title: 0412_029_20 ckb1_ckb2 pre-treatment 0 vs. ckb1_ckb2 3AT 5


title: 0825_023_20 wt 3AT 15 vs. ckb1ckb2 3AT 15


title: 0527_027_20 wt pre-treatment 0 vs. wt TBB 5


title: 0412_028_20 ckb2 pre-treatment 0 vs. ckb2 3AT 40

value: ckb1 ORF deletion


title: 0412_048_20 wt mock treated 40 vs. wt phosphate 40

value: Phosphate depletion

value: untreated control


title: 0412_047_20 wt mock treated 20 vs. wt phosphate 20


title: 0412_046_20 wt mock treated 10 vs. wt phosphate 10


title: 0412_027_20 ckb2 pre-treatment 0 vs. ckb2 3AT 20


title: 0412_022_20 ckb1 pre-treatment 0 vs. ckb1 3AT 10


title: 0412_026_20 ckb2 pre-treatment 0 vs. ckb2 3AT 10


title: 0527_029_20 wt pre-treatment 0 vs. wt TBB 20


title: 0412_023_20 ckb1 pre-treatment 0 vs. ckb1 3AT 20


title: 0306_133_20 wt pre-treatment 0 vs. wt Rap 10

value: 200ng/mL Rapamycin


title: 0306_135_20 wt pre-treatment 0 vs. wt Rap 40


title: 0306_132_20 wt pre-treatment 0 vs. wt Rap 5


title: 0306_134_20 wt pre-treatment 0 vs. wt Rap 20


title: 0306_098_20 wt pre-treatment 0 vs. wt Rap 20


title: 0412_024_20 ckb1 pre-treatment 0 vs. ckb1 3AT 40


title: 0412_025_20 ckb2 pre-treatment 0 vs. ckb2 3AT 5


title: 0306_099_20 wt pre-treatment 0 vs. wt Rap 40


title: 0412_045_20 wt mock treated 5 vs. wt phosphate 5


title: 0412_021_20 ckb1 pre-treatment 0 vs. ckb1 3AT 5


title: 0306_096_20 wt pre-treatment 0 vs. wt Rap 5


title: 0306_026_20 wt Rap 40 vs. wt pre-treatment 0


title: 1103_036_20 wt mock treated 10 vs. wt LiCl 10

value: 300mM LiCl


title: 0306_097_20 wt pre-treatment 0 vs. wt Rap 10


title: 0306_024_20 wt Rap 10 vs. wt pre-treatment 0


title: 0306_023_20 wt Rap 5 vs. wt pre-treatment 0


title: 0527_025_20 wt mock treated 20 vs. wt KCl_TBB 20

value: 1M KCl + 20uM 4,5,6,7-Tetrabromo-2-azabenzimidazole (TBB)


title: 0527_026_20 wt mock treated 40 vs. wt KCl_TBB 40


title: 1103_007_20 wt mock treated 40 vs. wt KCl_TBB 40


title: 1103_006_20 wt mock treated 20 vs. wt KCl_TBB 20


title: 0527_050_20 wt KCl 40 vs. wt KCl_TBB 40

value: 1M KCl


title: 0527_024_20 wt mock treated 10 vs. wt KCl_TBB 10


title: 0527_049_20 wt KCl 20 vs. wt KCl_TBB 20


title: 0527_048_20 wt KCl 10 vs. wt KCl_TBB 10


title: 1103_005_20 wt mock treated 10 vs. wt KCl_TBB 10


title: 0527_023_20 wt mock treated 5 vs. wt KCl_TBB 5


title: 0825_056_20 wt mock treatment 0 vs. wt heat_shock 40

value: 42oC Heat shock


title: 0121_057_20 wt mock treated 5 vs. wt nitrogen_3AT 5

value: Nitrogen depletion + 50mM 3-Amino-1,2,4-triazole (3-AT)


title: 0121_059_20 wt mock treated 20 vs. wt nitrogen_3AT 20


title: 0306_025_20 wt Rap 20 vs. wt pre-treatment 0


title: 0825_055_20 wt mock treatment 0 vs. wt heat_shock 20


title: 0121_029_20 wt mock treatment 5 vs. wt heat_shock 5


title: 0825_053_20 wt mock treatment 0 vs. wt heat_shock 5


title: 0825_054_20 wt mock treatment 0 vs. wt heat_shock 10


title: 1103_004_20 wt mock treated 5 vs. wt KCl_TBB 5


title: 0121_058_20 wt mock treated 10 vs. wt nitrogen_3AT 10


title: 0121_060_20 wt mock treated 40 vs. wt nitrogen_3AT 40


title: 0306_146_20 wt mock treated 20 vs. wt nitrogen_3AT 20


title: 0825_031_20 wt KCl 15 vs. ckb1ckb2 KCl 15


title: 0412_052_20 ckb1_ckb2 mock treated 40 vs. ckb1_ckb2 KCl 40


title: 0825_029_20 wt KCl 5 vs. ckb1ckb2 KCl 5


title: 0306_144_20 wt mock treated 5 vs. wt nitrogen_3AT 5


title: 0306_147_20 wt mock treated 40 vs. wt nitrogen_3AT 40


title: 0306_145_20 wt mock treated 10 vs. wt nitrogen_3AT 10


title: 0412_049_20 ckb1_ckb2 mock treated 5 vs. ckb1_ckb2 KCl 5


title: 0412_051_20 ckb1_ckb2 mock treated 20 vs. ckb1_ckb2 KCl 20


title: 0306_152_20 wt mock treated 5 vs. wt nitrogen 5

value: Nitrogen depletion


title: 0412_061_20 wt pre-treatment 0 vs. ckb1_ckb2 pre-treatment 0


title: 0306_153_20 wt mock treated 10 vs. wt nitrogen 10


title: 0306_154_20 wt mock treated 20 vs. wt nitrogen 20


title: 0412_038_20 wt pre-treatment 0 vs. ckb2 pre-treatment 0


title: 0825_032_20 wt KCl 20 vs. ckb1ckb2 KCl 20


title: 0825_030_20 wt KCl 10 vs. ckb1ckb2 KCl 10


title: 0306_016_20 wt mock treated 10 vs. wt nitrogen 10


title: 0306_155_20 wt mock treated 40 vs. wt nitrogen 40


title: 0825_052_20 wt mock treated 40 vs. wt inositol 40

value: Inositol depletion


title: 0825_051_20 wt mock treated 20 vs. wt inositol 20


title: 0412_044_20 wt mock treated 40 vs. wt inositol 40


title: 0306_017_20 wt nitrogen 20 vs. wt mock treated 20


title: 0412_043_20 wt mock treated 20 vs. wt inositol 20


title: 0825_050_20 wt mock treated 10 vs. wt inositol 10


title: 0825_049_20 wt mock treated 5 vs. wt inositol 5


title: 0412_042_20 wt mock treated 10 vs. wt inositol 10


title: 0412_050_20 ckb1_ckb2 mock treated 10 vs. ckb1_ckb2 KCl 10


title: 0306_018_20 wt nitrogen 40 vs. wt mock treated 40


title: 0121_052_20 hog1 mock treated 40 vs. hog1 KCl 40

value: hog1 ORF deletion


title: 0121_050_20 hog1 mock treated 10 vs. hog1 KCl 10


title: 0121_051_20 hog1 mock treated 20 vs. hog1 KCl 20


title: 1021_029_20 hog1 mock treated 40 vs. hog1 KCl 40


title: 0306_015_20 wt mock treated 5 vs. wt nitrogen 5


title: 1021_027_20 hog1 mock treated 10 vs. hog1 KCl 10


title: 1021_026_20 hog1 mock treated 5 vs. hog1 KCl 5


title: 1021_028_20 hog1 mock treated 20 vs. hog1 KCl 20


title: 0412_041_20 wt mock treated 5 vs. wt inositol 5


title: 0527_047_20 wt KCl 5 vs. wt KCl_TBB 5


title: 0306_143_20 his- mock treated 40 vs. his- hisdeplete 40

value: his3 ORF deletion

value: Histidine depletion


title: 0306_142_20 his- mock treated 20 vs. his- hisdeplete 20


title: 0306_141_20 his- mock treated 10 vs. his- hisdeplete 10


title: 1103_054_20 edc2 mock treated 40 vs. edc2 kcl 40

value: edc2 ORF deletion


title: 0306_139_20 HIS+ mock treated 40 vs. HIS+ hisdeplete 40

value: HIS3 (repair of parental deletion)


title: 0306_136_20 HIS+ mock treated 5 vs. HIS+ hisdeplete 5


title: 0306_140_20 his- mock treated 5 vs. his- hisdeplete 5


title: 0121_028_20 his- mock treated 40 vs. his- hisdeplete 40


title: 0121_023_20 HIS+ mock treated 20 vs. HIS+ hisdeplete 20


title: 0121_049_20 hog1 mock treated 5 vs. hog1 KCl 5


title: 0121_025_20 his- mock treated 5 vs. his- hisdeplete 5


title: 0121_021_20 HIS+ mock treated 5 vs. HIS+ hisdeplete 5


title: 0306_138_20 HIS+ mock treated 20 vs. HIS+ hisdeplete 20


title: 0121_024_20 HIS+ mock treated 40 vs. HIS+ hisdeplete 40


title: 1021_037_20 his- mock treated 40 vs. his- hisdeplete 40


title: 0306_137_20 HIS+ mock treated 10 vs. HIS+ hisdeplete 10


title: 1021_036_20 his- mock treated 20 vs. his- hisdeplete 20


title: 0306_127_20 HIS+ mock treated 40 vs. HIS+ hisdeplete 40


title: 1021_035_20 his- mock treated 10 vs. his- hisdeplete 10


title: 0121_027_20 his- mock treated 20 vs. his- hisdeplete 20


title: 1021_034_20 his- mock treated 5 vs. his- hisdeplete 5


title: 0306_122_20 his- mock treated 20 vs. his- hisdeplete 20


title: 0306_125_20 HIS+ mock treated 10 vs. HIS+ hisdeplete 10


title: 1021_030_20 HIS+ mock treated 5 vs. HIS+ hisdeplete 5


title: 1021_032_20 HIS+ mock treated 20 vs. HIS+ hisdeplete 20


title: 1021_033_20 HIS+ mock treated 40 vs. HIS+ hisdeplete 40


title: 0306_123_20 his- mock treated 40 vs. his- hisdeplete 40


title: 1021_031_20 HIS+ mock treated 10 vs. HIS+ hisdeplete 10


title: 0121_026_20 his- mock treated 10 vs. his- hisdeplete 10


title: 0306_124_20 HIS+ mock treated 5 vs. HIS+ hisdeplete 5


title: 0825_062_20 wt pre-treatment 0 vs. wt DTT_10mm 10

value: wild-type

value: 10mM dithiothreitol (DTT)

value: pretreatment sample


title: 0825_063_20 wt pre-treatment 0 vs. wt DTT_10mm 20


title: 0121_022_20 HIS+ mock treated 10 vs. HIS+ hisdeplete 10

value: untreated control


title: 0825_064_20 wt pre-treatment 0 vs. wt DTT_10mm 40


title: 0825_060_20 wt pre-treatment 0 vs. wt DTT_1mm 40

value: 1mM dithiothreitol (DTT)


title: 0825_059_20 wt pre-treatment 0 vs. wt DTT_1mm 20


title: 0306_121_20 his- mock treated 10 vs. his- hisdeplete 10


title: 0412_006_20 wt mock treated 10 vs. wt sorbitol 10

value: 1M Sorbitol


title: 0412_007_20 wt mock treated 20 vs. wt sorbitol 20


title: 0825_057_20 wt pre-treatment 0 vs. wt DTT_1mm 5


title: 0306_120_20 his- mock treated 5 vs. his- hisdeplete 5


title: 0412_008_20 wt mock treated 40 vs. wt sorbitol 40


title: 0825_058_20 wt pre-treatment 0 vs. wt DTT_1mm 10


title: 0412_005_20 wt mock treated 5 vs. wt sorbitol 5


title: 0825_061_20 wt pre-treatment 0 vs. wt DTT_10mm 5


title: 0121_036_20 wt mock treated 40 vs. wt SMM 40

value: 5ug/mL sulfometuron methyl (SMM)


title: 0121_035_20 wt mock treated 20 vs. wt SMM 20


title: 0121_034_20 wt mock treated 10 vs. wt SMM 10


title: 0121_033_20 wt mock treated 5 vs. wt SMM 5


title: 0825_027_20 wt rapamycin 15 vs. ckb1ckb2 rapamycin 15

value: ckb1ckb2 double deletion

value: 200ng/mL Rapamycin


title: 0825_028_20 wt rapamycin 20 vs. ckb1ckb2 rapamycin 20


title: 0412_054_20 ckb1_ckb2 mock treated 10 vs. ckb1_ckb2 rapamycin 10


title: 0412_053_20 ckb1_ckb2 mock treated 5 vs. ckb1_ckb2 rapamycin 5


title: 0825_017_20 wt pre-treatment 0 vs. wt 3AT 5

value: 50mM 3-Amino-1,2,4-triazole (3-AT)


title: 0825_020_20 wt pre-treatment 0 vs. wt 3AT 20


title: 0306_126_20 HIS+ mock treated 20 vs. HIS+ hisdeplete 20


title: 0412_056_20 ckb1_ckb2 mock treated 40 vs. ckb1_ckb2 rapamycin 40


title: 0412_055_20 ckb1_ckb2 mock treated 20 vs. ckb1_ckb2 rapamycin 20


title: 0412_019_20 wt pre-treatment 0 vs. wt 3AT 20


title: 0825_018_20 wt pre-treatment 0 vs. wt 3AT 10


title: 0825_019_20 wt pre-treatment 0 vs. wt 3AT 15


title: 0412_020_20 wt pre-treatment 0 vs. wt 3AT 40


title: 0527_038_20 wt pre-treatment 0 vs. wt 3AT 40


title: 0825_025_20 wt rapamycin 5 vs. ckb1ckb2 rapamycin 5


title: 0825_026_20 wt rapamycin 10 vs. ckb1ckb2 rapamycin 10


title: 0412_018_20 wt pre-treatment 0 vs. wt 3AT 10


title: 0527_035_20 wt pre-treatment 0 vs. wt 3AT 5


title: 1103_009_20 wt mock treated 10 vs. wt nacl 10

value: 0.5M NaCl


title: 0527_036_20 wt pre-treatment 0 vs. wt 3AT 10


title: 1103_033_20 wt mock treated 20 vs. wt nacl 20


title: 1103_034_20 wt mock treated 40 vs. wt nacl 40


title: 1103_008_20 wt mock treated 5 vs. wt nacl 5


title: 0527_018_20 wt TBB 0 vs. wt rap_TBB 40

value: 200ng/mL Rapamycin + 20uM 4,5,6,7-Tetrabromo-2-azabenzimidazol (TBB)


title: 1103_043_20 rrp6 mock treated 40 vs. rrp6 kcl 40

value: rrp6 ORF deletion

value: 1M KCl


title: 1103_039_20 rrp6 mock treated 5 vs. rrp6 kcl 5


title: 0527_017_20 wt TBB 0 vs. wt rap_TBB 20


title: 1103_041_20 rrp6 mock treated 20 vs. rrp6 kcl 20


title: 0412_017_20 wt pre-treatment 0 vs. wt 3AT 5


title: 0527_043_20 wt rap 5 vs. wt rap_TBB 5


title: 1103_040_20 rrp6 mock treated 10 vs. rrp6 kcl 10


title: 0412_001_20 wt mock treated 5 vs. wt NaCl 5


title: 1103_002_20 wt mock treated 40 vs. wt kcl 40


title: 1103_001_20 wt mock treated 20 vs. wt kcl 20


title: 0527_045_20 wt rap 20 vs. wt rap_TBB 20


title: 0825_096_20 wt mock treated 10 vs. wt kcl 10


title: 1021_024_20 wt mock treated 20 vs. wt KCl 20


title: 0527_015_20 wt TBB 0 vs. wt rap_TBB 5


title: 1021_023_20 wt mock treated 10 vs. wt KCl 10


title: 0527_016_20 wt TBB 0 vs. wt rap_TBB 10


title: 1021_025_20 wt mock treated 40 vs. wt KCl 40


title: 1021_022_20 wt mock treated 5 vs. wt KCl 5


title: 0527_044_20 wt rap 10 vs. wt rap_TBB 10


title: 0527_046_20 wt rap 40 vs. wt rap_TBB 40


title: 1021_063_20 wt mock treated 40 vs. wt KCl 40


title: 0121_044_20 wt mock treated 40 vs. wt KCl 40


title: 1021_061_20 wt mock treated 10 vs. wt KCl 10


title: 1021_060_20 wt mock treated 5 vs. wt KCl 5


title: 1021_062_20 wt mock treated 20 vs. wt KCl 20


title: 1103_003_20 wt mock treated 60 vs. wt kcl 60


title: 0121_042_20 wt mock treated 10 vs. wt KCl 10


title: 0121_043_20 wt mock treated 20 vs. wt KCl 20


title: 0121_041_20 wt mock treated 5 vs. wt KCl 5


title: 0121_056_20 wt mock treated 40 vs. wt amino_acid_deplete 40

value: Complete amino acid depletion


title: 0121_055_20 wt mock treated 20 vs. wt amino_acid_deplete 20


title: 0121_054_20 wt mock treated 10 vs. wt amino_acid_deplete 10


title: 0306_049_20 wt pre-treatment 0 vs. wt Wort 10

value: 1mg/mL Wortmannin


title: 0306_100_20 wt pre-treatment 0 vs. wt Wort 5


title: 0306_050_20 wt pre-treatment 0 vs. wt Wort 20


title: 0306_051_20 wt pre-treatment 0 vs. wt Wort 40


title: 0306_102_20 wt pre-treatment 0 vs. wt Wort 20


title: 0306_103_20 wt pre-treatment 0 vs. wt Wort 40


title: 0306_101_20 wt pre-treatment 0 vs. wt Wort 10


title: 0121_031_20 wt mock treatment 20 vs. wt heat_shock 20

value: 42oC Heat shock


title: 0306_048_20 wt Wort 5 vs. wt pre-treatment 0

value: wild-type


title: 0121_032_20 wt mock treatment 40 vs. wt heat_shock 40


title: 0825_036_20 wt pre-treatment 0 vs. wt 3AT_TBB 15

value: 50mM 3-Amino-1,2,4-triazole (3-AT) + 20uM 4,5,6,7-Tetrabromo-2-azabenzimidazole (TBB)


title: 1103_065_20 wt pre-treatment 0 vs. wt 3AT_TBB 10

value: pretreatment sample


title: 0121_030_20 wt mock treatment 10 vs. wt heat_shock 10

value: untreated control


title: 0825_033_20 wt pre-treatment 0 vs. wt 3AT_TBB 0


title: 0825_034_20 wt pre-treatment 0 vs. wt 3AT_TBB 5


title: 0412_058_20 wt pre-treatment 0 vs. wt 3AT_TBB 10


title: 1103_032_20 wt pre-treatment 0 vs. wt 3AT_TBB 5


title: 1103_010_20 wt pre-treatment 0 vs. wt 3AT_TBB 0


title: 0412_060_20 wt pre-treatment 0 vs. wt 3AT_TBB 40


title: 0121_053_20 wt mock treated 5 vs. wt amino_acid_deplete 5


title: 1103_070_20 wt 3AT 20 vs. wt 3AT_TBB 20


title: 0412_057_20 wt pre-treatment 0 vs. wt 3AT_TBB 5


title: 1103_068_20 wt 3AT 10 vs. wt 3AT_TBB 10


title: 0825_035_20 wt pre-treatment 0 vs. wt 3AT_TBB 10


title: 1103_069_20 wt 3AT 15 vs. wt 3AT_TBB 15


title: 1103_066_20 wt pre-treatment 0 vs. wt 3AT_TBB 15


title: 0527_037_20 wt pre-treatment 0 vs. wt 3AT 20


title: 0412_059_20 wt pre-treatment 0 vs. wt 3AT_TBB 20


title: 0527_032_20 wt TBB 0 vs. wt 3AT_TBB 10


title: 0527_034_20 wt TBB 0 vs. wt 3AT_TBB 40


title: 0527_039_20 wt 3AT_TBB 5 vs. wt 3AT 5


title: 0412_004_20 wt mock treated 40 vs. wt NaCl 40


title: 0527_033_20 wt TBB 0 vs. wt 3AT_TBB 20


title: 0527_040_20 wt 3AT_TBB 10 vs. wt 3AT 10


title: 1103_067_20 wt 3AT 5 vs. wt 3AT_TBB 5


title: 0412_002_20 wt mock treated 10 vs. wt NaCl 10


title: 0527_041_20 wt 3AT_TBB 20 vs. wt 3AT 20


title: 1114_016_10 wt rapamycin 20 vs. wt pre-treatment 0


title: 1114_013_10 rrp6 rapamycin 40 vs. wt rapamycin 40


title: 1114_012_10 rrp6 rapamycin 20 vs. wt rapamycin 20


title: 1114_015_10 wt LiCl 20 vs. wt pre-treatment 0

value: 300mM LiCl


title: 1114_008_10 rrp6 LiCl 40 vs. wt LiCl 40


title: 1114_014_10 wt KCl 20 vs. wt pre-treatment 0


title: 1114_011_10 rrp6 rapamycin 10 vs. wt rapamycin 10


title: 0527_031_20 wt TBB 0 vs. wt 3AT_TBB 5


title: 1114_007_10 rrp6 LiCl 20 vs. wt LiCl 20


title: 1114_010_10 rrp6 rapamycin 5 vs. wt rapamycin 5


title: 1114_009_10 rrp6 pre-treatment 0 vs. wt pre-treatment 0


title: 1114_006_10 rrp6 LiCl 10 vs. wt LiCl 10


title: 1114_005_10 rrp6 LiCl 5 vs. wt LiCl 5


title: 1114_003_10 rrp6 KCl 20 vs. wt KCl 20


title: 0412_003_20 wt mock treated 20 vs. wt NaCl 20


title: 1114_004_10 rrp6 KCl 40 vs. wt KCl 40


title: 0527_042_20 wt 3AT_TBB 40 vs. wt 3AT 40


title: 0527_013_10 wt 3AT_rap 20 vs. wt pre-treatment 0

value: 50mM 3-Amino-1,2,4-triazole (3-AT) + 200ng/mL Rapamycin


title: 0527_014_10 wt 3AT_rap 40 vs. wt pre-treatment 0


title: 1114_001_10 rrp6 KCl 5 vs. wt KCl 5


title: 0527_012_10 wt 3AT_rap 10 vs. wt pre-treatment 0


title: 0527_011_10 wt 3AT_rap 5 vs. wt pre-treatment 0


title: 0412_037_10 ckb1 pre-treatment 0 vs. wt pre-treatment 0

value: ckb1 ORF deletion


title: 0224_028_10 wt 3AT_KCl 40 vs. wt mock treated 40

value: 50mM 3-Amino-1,2,4-triazole (3-AT) + 1M KCl


title: 0527_019_10 wt 3AT_KCl 5 vs. wt mock treated 5


title: 0527_022_10 wt 3AT_KCl 40 vs. wt mock treated 40


title: 0825_044_10 wt LiCl 40 vs. wt mock treated 40


title: 0224_027_10 wt 3AT_KCl 20 vs. wt mock treated 20


title: 1114_002_10 rrp6 KCl 10 vs. wt KCl 10


title: 0224_026_10 wt 3AT_KCl 10 vs. wt mock treated 10


title: 0527_020_10 wt 3AT_KCl 10 vs. wt mock treated 10


title: 0224_025_10 wt 3AT_KCl 5 vs. wt mock treated 5


title: 1103_074_10 wt LiCl 40 vs. wt mock treated 40


title: 1103_073_10 wt LiCl 20 vs. wt mock treated 20


title: 0527_021_10 wt 3AT_KCl 20 vs. wt mock treated 20


title: 0825_042_10 wt LiCl 10 vs. wt mock treated 10


title: 0825_041_10 wt LiCl 5 vs. wt mock treated 5


title: 0825_043_10 wt LiCl 20 vs. wt mock treated 20


title: 1103_072_10 wt LiCl 10 vs. wt mock treated 10


title: 1103_035_10 wt LiCl 5 vs. wt mock treated 5


title: 0825_048_10 wt carbon 40 vs. wt mock treated 40

value: Glucose depletion


title: 1103_036_10 wt LiCl 10 vs. wt mock treated 10


title: 0825_047_10 wt carbon 20 vs. wt mock treated 20


title: 1103_038_10 wt LiCl 40 vs. wt mock treated 40


title: 1103_037_10 wt LiCl 20 vs. wt mock treated 20


title: 0224_031_10 wt carbon 20 vs. wt mock treated 20


title: 1103_071_10 wt LiCl 5 vs. wt mock treated 5


title: 0825_046_10 wt carbon 10 vs. wt mock treated 10


title: 0224_032_10 wt carbon 40 vs. wt mock treated 40


title: 0825_045_10 wt carbon 5 vs. wt mock treated 5


title: 0224_030_10 wt carbon 10 vs. wt mock treated 10


title: 0224_029_10 wt carbon 5 vs. wt mock treated 5


title: 1103_052_10 edc2 kcl 20 vs. edc2 mock treated 20

value: edc2 ORF deletion


title: 1103_044_10 edc2 kcl 5 vs. edc2 mock treated 5


title: 0527_029_10 wt TBB 20 vs. wt pre-treatment 0


title: 0527_030_10 wt TBB 40 vs. wt pre-treatment 0


title: 0412_032_10 ckb1_ckb2 3AT 40 vs. ckb1_ckb2 pre-treatment 0

value: ckb1ckb2 double deletion

value: 50mM 3-Amino-1,2,4-triazole (3-AT)


title: 0412_029_10 ckb1_ckb2 3AT 5 vs. ckb1_ckb2 pre-treatment 0


title: 0825_021_10 ckb1ckb2 3AT 5 vs. wt 3AT 5


title: 0825_022_10 ckb1ckb2 3AT 10 vs. wt 3AT 10


title: 0412_031_10 ckb1_ckb2 3AT 20 vs. ckb1_ckb2 pre-treatment 0


title: 0412_027_10 ckb2 3AT 20 vs. ckb2 pre-treatment 0


title: 0412_028_10 ckb2 3AT 40 vs. ckb2 pre-treatment 0


title: 0412_030_10 ckb1_ckb2 3AT 10 vs. ckb1_ckb2 pre-treatment 0


title: 0412_025_10 ckb2 3AT 5 vs. ckb2 pre-treatment 0


title: 0527_027_10 wt TBB 5 vs. wt pre-treatment 0


title: 0527_028_10 wt TBB 10 vs. wt pre-treatment 0


title: 0412_026_10 ckb2 3AT 10 vs. ckb2 pre-treatment 0


title: 0412_023_10 ckb1 3AT 20 vs. ckb1 pre-treatment 0


title: 0825_023_10 ckb1ckb2 3AT 15 vs. wt 3AT 15


title: 0825_024_10 ckb1ckb2 3AT 20 vs. wt 3AT 20


title: 0412_022_10 ckb1 3AT 10 vs. ckb1 pre-treatment 0


title: 0412_024_10 ckb1 3AT 40 vs. ckb1 pre-treatment 0


title: 1103_050_10 edc2 kcl 10 vs. edc2 mock treated 10


title: 0412_048_10 wt phosphate 40 vs. wt mock treated 40

value: Phosphate depletion


title: 0412_021_10 ckb1 3AT 5 vs. ckb1 pre-treatment 0


title: 0412_047_10 wt phosphate 20 vs. wt mock treated 20


title: 0412_046_10 wt phosphate 10 vs. wt mock treated 10


title: 0412_045_10 wt phosphate 5 vs. wt mock treated 5


title: 0306_133_10 wt Rap 10 vs. wt pre-treatment 0

value: 200ng/mL Rapamycin


title: 0306_134_10 wt Rap 20 vs. wt pre-treatment 0


title: 0306_135_10 wt Rap 40 vs. wt pre-treatment 0


title: 0306_132_10 wt Rap 5 vs. wt pre-treatment 0


title: 0306_098_10 wt Rap 20 vs. wt pre-treatment 0


title: 0306_097_10 wt Rap 10 vs. wt pre-treatment 0


title: 0306_096_10 wt Rap 5 vs. wt pre-treatment 0


title: 0306_023_10 wt pre-treatment 0 vs. wt Rap 5


title: 0306_026_10 wt pre-treatment 0 vs. wt Rap 40


title: 0306_025_10 wt pre-treatment 0 vs. wt Rap 20


title: 1103_005_10 wt KCl_TBB 10 vs. wt mock treated 10

value: 1M KCl + 20uM 4,5,6,7-Tetrabromo-2-azabenzimidazole (TBB)


title: 0306_024_10 wt pre-treatment 0 vs. wt Rap 10


title: 1103_007_10 wt KCl_TBB 40 vs. wt mock treated 40


title: 0527_026_10 wt KCl_TBB 40 vs. wt mock treated 40


title: 1103_004_10 wt KCl_TBB 5 vs. wt mock treated 5


title: 0527_023_10 wt KCl_TBB 5 vs. wt mock treated 5


title: 0527_024_10 wt KCl_TBB 10 vs. wt mock treated 10


title: 0306_099_10 wt Rap 40 vs. wt pre-treatment 0


title: 0825_056_10 wt heat_shock 40 vs. wt mock treatment 0


title: 0527_025_10 wt KCl_TBB 20 vs. wt mock treated 20


title: 0527_050_10 wt KCl_TBB 40 vs. wt KCl 40

value: 1M KCl


title: 0527_049_10 wt KCl_TBB 20 vs. wt KCl 20


title: 0825_053_10 wt heat_shock 5 vs. wt mock treatment 0

value: 42oC Heat shock


title: 0121_029_10 wt heat_shock 5 vs. wt mock treatment 5

value: wild-type


title: 0825_054_10 wt heat_shock 10 vs. wt mock treatment 0


title: 0825_055_10 wt heat_shock 20 vs. wt mock treatment 0


title: 0224_016_10 wt heat_shock 40 vs. wt mock treatment 40


title: 0224_013_10 wt heat_shock 5 vs. wt mock treatment 5


title: 0224_015_10 wt heat_shock 20 vs. wt mock treatment 20


title: 1103_006_10 wt KCl_TBB 20 vs. wt mock treated 20


title: 0527_048_10 wt KCl_TBB 10 vs. wt KCl 10


title: 0121_059_10 wt nitrogen_3AT 20 vs. wt mock treated 20

value: Nitrogen depletion + 50mM 3-Amino-1,2,4-triazole (3-AT)


title: 0224_014_10 wt heat_shock 10 vs. wt mock treatment 10


title: 0121_060_10 wt nitrogen_3AT 40 vs. wt mock treated 40


title: 0121_057_10 wt nitrogen_3AT 5 vs. wt mock treated 5


title: 0825_029_10 ckb1ckb2 KCl 5 vs. wt KCl 5


title: 0306_146_10 wt nitrogen_3AT 20 vs. wt mock treated 20


title: 0121_058_10 wt nitrogen_3AT 10 vs. wt mock treated 10


title: 0412_052_10 ckb1_ckb2 KCl 40 vs. ckb1_ckb2 mock treated 40


title: 0412_049_10 ckb1_ckb2 KCl 5 vs. ckb1_ckb2 mock treated 5


title: 0306_147_10 wt nitrogen_3AT 40 vs. wt mock treated 40


title: 0412_050_10 ckb1_ckb2 KCl 10 vs. ckb1_ckb2 mock treated 10


title: 0412_061_10 ckb1_ckb2 pre-treatment 0 vs. wt pre-treatment 0

value: pretreatment sample


title: 0825_031_10 ckb1ckb2 KCl 15 vs. wt KCl 15


title: 0306_145_10 wt nitrogen_3AT 10 vs. wt mock treated 10

value: untreated control


title: 0306_155_10 wt nitrogen 40 vs. wt mock treated 40

value: Nitrogen depletion


title: 0306_018_10 wt mock treated 40 vs. wt nitrogen 40


title: 0306_144_10 wt nitrogen_3AT 5 vs. wt mock treated 5


title: 0306_154_10 wt nitrogen 20 vs. wt mock treated 20


title: 0825_052_10 wt inositol 40 vs. wt mock treated 40

value: Inositol depletion


title: 0412_051_10 ckb1_ckb2 KCl 20 vs. ckb1_ckb2 mock treated 20


title: 0306_153_10 wt nitrogen 10 vs. wt mock treated 10


title: 0306_017_10 wt mock treated 20 vs. wt nitrogen 20


title: 0825_030_10 ckb1ckb2 KCl 10 vs. wt KCl 10


title: 0825_032_10 ckb1ckb2 KCl 20 vs. wt KCl 20


title: 0306_016_10 wt nitrogen 10 vs. wt mock treated 10


title: 0825_051_10 wt inositol 20 vs. wt mock treated 20


title: 0306_015_10 wt nitrogen 5 vs. wt mock treated 5


title: 0412_038_10 ckb2 pre-treatment 0 vs. wt pre-treatment 0

value: ckb1 ORF deletion


title: 0825_050_10 wt inositol 10 vs. wt mock treated 10


title: 0306_152_10 wt nitrogen 5 vs. wt mock treated 5


title: 0825_049_10 wt inositol 5 vs. wt mock treated 5


title: 0412_044_10 wt inositol 40 vs. wt mock treated 40


title: 0121_052_10 hog1 KCl 40 vs. hog1 mock treated 40

value: hog1 ORF deletion


title: 0121_049_10 hog1 KCl 5 vs. hog1 mock treated 5


title: 0412_041_10 wt inositol 5 vs. wt mock treated 5


title: 1021_028_10 hog1 KCl 20 vs. hog1 mock treated 20


title: 0412_042_10 wt inositol 10 vs. wt mock treated 10


title: 1021_026_10 hog1 KCl 5 vs. hog1 mock treated 5


title: 1021_029_10 hog1 KCl 40 vs. hog1 mock treated 40


title: 1021_027_10 hog1 KCl 10 vs. hog1 mock treated 10


title: 0412_043_10 wt inositol 20 vs. wt mock treated 20


title: 0306_138_10 HIS+ hisdeplete 20 vs. HIS+ mock treated 20

value: HIS3 (repair of parental deletion)

value: Histidine depletion


title: 0306_141_10 his- hisdeplete 10 vs. his- mock treated 10

value: his3 ORF deletion


title: 0306_140_10 his- hisdeplete 5 vs. his- mock treated 5


title: 1103_054_10 edc2 kcl 40 vs. edc2 mock treated 40

value: edc2 ORF deletion


title: 0306_136_10 HIS+ hisdeplete 5 vs. HIS+ mock treated 5


title: 0121_051_10 hog1 KCl 20 vs. hog1 mock treated 20


title: 0121_050_10 hog1 KCl 10 vs. hog1 mock treated 10


title: 0121_025_10 his- hisdeplete 5 vs. his- mock treated 5


title: 0306_137_10 HIS+ hisdeplete 10 vs. HIS+ mock treated 10


title: 0121_026_10 his- hisdeplete 10 vs. his- mock treated 10


title: 0527_047_10 wt KCl_TBB 5 vs. wt KCl 5


title: 0121_028_10 his- hisdeplete 40 vs. his- mock treated 40


title: 0121_024_10 HIS+ hisdeplete 40 vs. HIS+ mock treated 40


title: 0121_023_10 HIS+ hisdeplete 20 vs. HIS+ mock treated 20


title: 0306_143_10 his- hisdeplete 40 vs. his- mock treated 40


title: 0306_142_10 his- hisdeplete 20 vs. his- mock treated 20


title: 0121_022_10 HIS+ hisdeplete 10 vs. HIS+ mock treated 10


title: 0306_139_10 HIS+ hisdeplete 40 vs. HIS+ mock treated 40


title: 0121_027_10 his- hisdeplete 20 vs. his- mock treated 20


title: 0121_021_10 HIS+ hisdeplete 5 vs. HIS+ mock treated 5


title: 1021_037_10 his- hisdeplete 40 vs. his- mock treated 40


title: 1021_036_10 his- hisdeplete 20 vs. his- mock treated 20


title: 1021_030_10 HIS+ hisdeplete 5 vs. HIS+ mock treated 5


title: 0306_125_10 HIS+ hisdeplete 10 vs. HIS+ mock treated 10


title: 1021_035_10 his- hisdeplete 10 vs. his- mock treated 10


title: 0825_063_10 wt DTT_10mm 20 vs. wt pre-treatment 0

value: 10mM dithiothreitol (DTT)


title: 0306_127_10 HIS+ hisdeplete 40 vs. HIS+ mock treated 40


title: 0306_122_10 his- hisdeplete 20 vs. his- mock treated 20


title: 0306_126_10 HIS+ hisdeplete 20 vs. HIS+ mock treated 20


title: 1021_034_10 his- hisdeplete 5 vs. his- mock treated 5


title: 0306_121_10 his- hisdeplete 10 vs. his- mock treated 10


title: 0306_120_10 his- hisdeplete 5 vs. his- mock treated 5


title: 0306_123_10 his- hisdeplete 40 vs. his- mock treated 40


title: 0825_064_10 wt DTT_10mm 40 vs. wt pre-treatment 0


title: 0306_124_10 HIS+ hisdeplete 5 vs. HIS+ mock treated 5


title: 1021_033_10 HIS+ hisdeplete 40 vs. HIS+ mock treated 40


title: 0825_062_10 wt DTT_10mm 10 vs. wt pre-treatment 0


title: 0412_007_10 wt sorbitol 20 vs. wt mock treated 20

value: 1M Sorbitol


title: 0412_008_10 wt sorbitol 40 vs. wt mock treated 40


title: 0412_006_10 wt sorbitol 10 vs. wt mock treated 10


title: 0825_060_10 wt DTT_1mm 40 vs. wt pre-treatment 0

value: 1mM dithiothreitol (DTT)


title: 0825_061_10 wt DTT_10mm 5 vs. wt pre-treatment 0


title: 0825_059_10 wt DTT_1mm 20 vs. wt pre-treatment 0


title: 1021_031_10 HIS+ hisdeplete 10 vs. HIS+ mock treated 10


title: 0412_005_10 wt sorbitol 5 vs. wt mock treated 5


title: 0121_036_10 wt SMM 40 vs. wt mock treated 40

value: 5ug/mL sulfometuron methyl (SMM)


title: 0825_057_10 wt DTT_1mm 5 vs. wt pre-treatment 0


title: 0121_034_10 wt SMM 10 vs. wt mock treated 10


title: 0224_052_10 ckb2 SMM 20 vs. ckb2 pre-treatment 0


title: 0224_050_10 ckb1 SMM 20 vs. ckb1 pre-treatment 0


title: 0121_035_10 wt SMM 20 vs. wt mock treated 20


title: 0121_033_10 wt SMM 5 vs. wt mock treated 5


title: 0224_045_10 cka1 SMM 10 vs. cka1 pre-treatment 0

value: cka1 ORF deletion


title: 0224_048_10 cka2 SMM 20 vs. cka2 pre-treatment 0

value: cka2 ORF deletion


title: 0224_049_10 ckb1 SMM 10 vs. ckb1 pre-treatment 0


title: 0224_020_10 wt SMM 40 vs. wt mock treated 40

value: wild-type


title: 0825_058_10 wt DTT_1mm 10 vs. wt pre-treatment 0

value: pretreatment sample


title: 0224_051_10 ckb2 SMM 10 vs. ckb2 pre-treatment 0


title: 0825_025_10 ckb1ckb2 rapamycin 5 vs. wt rapamycin 5

value: ckb1ckb2 double deletion

value: 200ng/mL Rapamycin


title: 0825_026_10 ckb1ckb2 rapamycin 10 vs. wt rapamycin 10


title: 0224_019_10 wt SMM 20 vs. wt mock treated 20

value: untreated control


title: 0825_027_10 ckb1ckb2 rapamycin 15 vs. wt rapamycin 15


title: 0224_017_10 wt SMM 5 vs. wt mock treated 5


title: 0224_018_10 wt SMM 10 vs. wt mock treated 10


title: 0412_055_10 ckb1_ckb2 rapamycin 20 vs. ckb1_ckb2 mock treated 20


title: 0412_056_10 ckb1_ckb2 rapamycin 40 vs. ckb1_ckb2 mock treated 40


title: 0825_028_10 ckb1ckb2 rapamycin 20 vs. wt rapamycin 20


title: 0412_054_10 ckb1_ckb2 rapamycin 10 vs. ckb1_ckb2 mock treated 10


title: 0412_053_10 ckb1_ckb2 rapamycin 5 vs. ckb1_ckb2 mock treated 5


title: 0825_020_10 wt 3AT 20 vs. wt pre-treatment 0

value: 50mM 3-Amino-1,2,4-triazole (3-AT)


title: 0825_019_10 wt 3AT 15 vs. wt pre-treatment 0


title: 0224_047_10 cka2 SMM 10 vs. cka2 pre-treatment 0


title: 0825_017_10 wt 3AT 5 vs. wt pre-treatment 0


title: 0412_020_10 wt 3AT 40 vs. wt pre-treatment 0


title: 0224_046_10 cka1 SMM 20 vs. cka1 pre-treatment 0


title: 0825_018_10 wt 3AT 10 vs. wt pre-treatment 0


title: 0412_019_10 wt 3AT 20 vs. wt pre-treatment 0


title: 0412_018_10 wt 3AT 10 vs. wt pre-treatment 0


title: 0527_037_10 wt 3AT 20 vs. wt pre-treatment 0


title: 0527_038_10 wt 3AT 40 vs. wt pre-treatment 0


title: 0412_017_10 wt 3AT 5 vs. wt pre-treatment 0


title: 0527_036_10 wt 3AT 10 vs. wt pre-treatment 0


title: 1021_023_10 wt KCl 10 vs. wt mock treated 10

value: 1M KCl


title: 1103_009_10 wt nacl 10 vs. wt mock treated 10

value: 0.5M NaCl


title: 0527_018_10 wt rap_TBB 40 vs. wt TBB 0

value: 200ng/mL Rapamycin + 20uM 4,5,6,7-Tetrabromo-2-azabenzimidazol (TBB)


title: 1103_033_10 wt nacl 20 vs. wt mock treated 20


title: 1021_024_10 wt KCl 20 vs. wt mock treated 20


title: 0527_017_10 wt rap_TBB 20 vs. wt TBB 0


title: 0527_044_10 wt rap_TBB 10 vs. wt rap 10


title: 0825_096_10 wt kcl 10 vs. wt mock treated 10


title: 1021_060_10 wt KCl 5 vs. wt mock treated 5


title: 0527_016_10 wt rap_TBB 10 vs. wt TBB 0


title: 1103_041_10 rrp6 kcl 20 vs. rrp6 mock treated 20

value: rrp6 ORF deletion


title: 1103_040_10 rrp6 kcl 10 vs. rrp6 mock treated 10


title: 0527_015_10 wt rap_TBB 5 vs. wt TBB 0


title: 1021_022_10 wt KCl 5 vs. wt mock treated 5


title: 1103_039_10 rrp6 kcl 5 vs. rrp6 mock treated 5


title: 0527_046_10 wt rap_TBB 40 vs. wt rap 40


title: 0527_035_10 wt 3AT 5 vs. wt pre-treatment 0


title: 1103_001_10 wt kcl 20 vs. wt mock treated 20


title: 0412_001_10 wt NaCl 5 vs. wt mock treated 5


title: 1021_063_10 wt KCl 40 vs. wt mock treated 40


title: 1021_025_10 wt KCl 40 vs. wt mock treated 40


title: 0121_041_10 wt KCl 5 vs. wt mock treated 5


title: 0121_056_10 wt amino_acid_deplete 40 vs. wt mock treated 40

value: Complete amino acid depletion


title: 0224_023_10 wt amino_acid_deplete 20 vs. wt mock treated 20


title: 0224_024_10 wt amino_acid_deplete 40 vs. wt mock treated 40


title: 0224_021_10 wt amino_acid_deplete 5 vs. wt mock treated 5


title: 0121_042_10 wt KCl 10 vs. wt mock treated 10


title: 0224_022_10 wt amino_acid_deplete 10 vs. wt mock treated 10


title: 0306_051_10 wt Wort 40 vs. wt pre-treatment 0

value: 1mg/mL Wortmannin


title: 0527_043_10 wt rap_TBB 5 vs. wt rap 5


title: 0306_100_10 wt Wort 5 vs. wt pre-treatment 0


title: 0306_103_10 wt Wort 40 vs. wt pre-treatment 0


title: 0121_032_10 wt heat_shock 40 vs. wt mock treatment 40

value: 42oC Heat shock


title: 0306_049_10 wt Wort 10 vs. wt pre-treatment 0


title: 0306_050_10 wt Wort 20 vs. wt pre-treatment 0


title: 1103_043_10 rrp6 kcl 40 vs. rrp6 mock treated 40


title: 0306_048_10 wt pre-treatment 0 vs. wt Wort 5


title: 1103_002_10 wt kcl 40 vs. wt mock treated 40


title: 0121_055_10 wt amino_acid_deplete 20 vs. wt mock treated 20


title: 0527_045_10 wt rap_TBB 20 vs. wt rap 20


title: 0121_043_10 wt KCl 20 vs. wt mock treated 20


title: 1021_061_10 wt KCl 10 vs. wt mock treated 10


title: 1103_034_10 wt nacl 40 vs. wt mock treated 40


title: 1103_008_10 wt nacl 5 vs. wt mock treated 5


title: 1103_003_10 wt kcl 60 vs. wt mock treated 60


title: 1021_062_10 wt KCl 20 vs. wt mock treated 20


title: 0121_044_10 wt KCl 40 vs. wt mock treated 40


title: 0306_102_10 wt Wort 20 vs. wt pre-treatment 0


title: 0121_031_10 wt heat_shock 20 vs. wt mock treatment 20


title: 0121_053_10 wt amino_acid_deplete 5 vs. wt mock treated 5


title: 0121_054_10 wt amino_acid_deplete 10 vs. wt mock treated 10


title: 0121_030_10 wt heat_shock 10 vs. wt mock treatment 10


title: 1103_032_10 wt 3AT_TBB 5 vs. wt pre-treatment 0

value: 50mM 3-Amino-1,2,4-triazole (3-AT) + 20uM 4,5,6,7-Tetrabromo-2-azabenzimidazole (TBB)


title: NA_C12

type: genomic

city: Baltimore

first: Scott

middle: E.

last: Devine

state: MD

address: 801 W. Baltimore Street

institute: Institute for Genome Sciences

hyb_protocol: Standard Affymetrix 6.0 kits and protocols were used.

data_processing: Affymetrix APT software with BRLMM-P.  The APT select_probes routine was used to identify probes with AIC values <325 and FLDAB >3.  INDELs with >60 no calls also were eliminated.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: control

extract_protocol: Genomic DNA was purchased from Coriell.

tag: sample type

value: control


title: NA_B12

scan_protocol: Standard Affymetrix 6.0 kits and protocols were used.


title: 0306_101_10 wt Wort 10 vs. wt pre-treatment 0


title: 1103_066_10 wt 3AT_TBB 15 vs. wt pre-treatment 0


title: 0825_036_10 wt 3AT_TBB 15 vs. wt pre-treatment 0


title: 0825_035_10 wt 3AT_TBB 10 vs. wt pre-treatment 0


title: 1103_065_10 wt 3AT_TBB 10 vs. wt pre-treatment 0


title: 1103_010_10 wt 3AT_TBB 0 vs. wt pre-treatment 0


title: NA19132, technical replicate 1

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19132b.CEL

source_name: YRI

label_protocol: Standard Affymetrix 6.0 kits and protocols were used.

tag: population

value: YRI


title: NA19119, technical replicate 1

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19119b.CEL


title: 0412_058_10 wt 3AT_TBB 10 vs. wt pre-treatment 0


title: 0412_059_10 wt 3AT_TBB 20 vs. wt pre-treatment 0


title: 0825_034_10 wt 3AT_TBB 5 vs. wt pre-treatment 0


title: 0412_060_10 wt 3AT_TBB 40 vs. wt pre-treatment 0


title: 0412_057_10 wt 3AT_TBB 5 vs. wt pre-treatment 0


title: 0825_033_10 wt 3AT_TBB 0 vs. wt pre-treatment 0


title: NA19130

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19130b.CEL


title: NA19119, duplicate of NA19119b

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19119V3.CEL


title: 1103_070_10 wt 3AT_TBB 20 vs. wt 3AT 20


title: 0527_031_10 wt 3AT_TBB 5 vs. wt TBB 0


title: 1103_069_10 wt 3AT_TBB 15 vs. wt 3AT 15


title: 0527_034_10 wt 3AT_TBB 40 vs. wt TBB 0


title: NA19132, technical replicate 2

description:
Yoruban HapMap trios (YRI; The International HapMap Consortium, Nature 437,1299-1320, 2005).

SED00001_NA19132V3.CEL


title: 0527_033_10 wt 3AT_TBB 20 vs. wt TBB 0


title: 1103_067_10 wt 3AT_TBB 5 vs. wt 3AT 5


title: 0527_032_10 wt 3AT_TBB 10 vs. wt TBB 0


title: 1103_068_10 wt 3AT_TBB 10 vs. wt 3AT 10


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_s9-1

city: New York

first: Victor

middle: Piana

last: Andrade

state: NY

address: 408E 69th Street z427E

department: Breast Surgery

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina BeadStudio used to generate the non-normalized data.  No normalization was used in our analysis (using R software) as numbers looked similar before and after normalization.

source_name: Invasive breast cancer, surgical excision, anastrozole group (Formalin-fixed/paraffin-embeded)

label_protocol: DASL GoldenGate Assay Kit with UDG (96 samples); catalog number DA-95-205

extract_protocol: RNA was extracted from macrodissected areas on 10 micron unstained slides from FFPE blocks using the protocol described in High-Pure RNA Paraffin Kit Roche

tag: gender

value: Female

tag: patient hormone status

value: Post-menopausal

tag: tumor er status

value: ER Positive

tag: sampling technique

value: Surgical excision; FFPE; Tissue Macrodissection

tag: time biopsy to surgery (days)

tag: sample name

tag: paired sample

tag: treatment before sampling

value: Anastrozole 1mg/d for 10 days


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_sx2-121


title: 0527_041_10 wt 3AT 20 vs. wt 3AT_TBB 20

value: wild-type


title: 0527_040_10 wt 3AT 10 vs. wt 3AT_TBB 10

value: 50mM 3-Amino-1,2,4-triazole (3-AT)


title: 0527_042_10 wt 3AT 40 vs. wt 3AT_TBB 40


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_sx2-82


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_sx2-101


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_sx2-91


title: 0412_002_10 wt NaCl 10 vs. wt mock treated 10

value: untreated control


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_s18-1


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_s7-1


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_s23-1


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_s6-1


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_s19-1


title: 0412_003_10 wt NaCl 20 vs. wt mock treated 20

value: 0.5M NaCl


title: Invasivebreastca_surgicalexcision_anastrozoletreatedgroup_s22-1


title: 0527_039_10 wt 3AT 5 vs. wt 3AT_TBB 5


title: 0412_004_10 wt NaCl 40 vs. wt mock treated 40


title: longissimus dorsi muscle 120d, biological rep3

city: Wuhan

first: Xiaoting

last: Feng

address: 1 Shizishan Street

country: China

institute: Huazhong Agricultural University

description: Gene expression data from longissimus dorsi muscle at 120 days afterbirth

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

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

data_processing: The expression values for each gene were acquired using the GeneChip Operating System (GCOS 1.4, Affymetrix). Data normalization and filtering were carried out with DNA-Chip Analyzer (dChip).

organism: Sus scrofa

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

growth_protocol: Meishan pigs were all fed using standard commercial practices. Pig fetuses were collected from Meishan pregnant females at 65dpc and fetuses of the same female pigs were seen as an individual. All pigs were sacrificed at slaughterhouse (Center of Quality Test and Supervision for Breeding Swine, Wuhan, MOA ), the longissimus dorsi muscles (LM) were harvested according to the four developmental stages

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

treatment_protocol: Longissimus dorsi muscles (LM) were frozen in liquid nitrogen immediately and stored at -80 ℃ until further use.

tag: tissue

value: longissimus dorsi muscle

tag: breed

value: Meishan

tag: age


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_cx2-8

source_name: Invasive breast cancer, core biopsy, anastrozole group, before treatment (Formalin-fixed/paraffin-embeded)

value: Core Biopsy; FFPE;Tissue Macrodissection

value: Before Anastrozole Treatment


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_c9


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_c8


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_cx2-12


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_c6


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_cx2-9


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_cx2-10


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_c23


title: longissimus dorsi muscle 120d, biological rep2

source_name: longissimus dorsi muscle at 120 days afterbirth


title: longissimus dorsi muscle 120d, biological rep1

value: longissimus dorsi muscle at 120 days afterbirth


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_c22


title: Invasivebreastca_surgicalexcision_notreatment_s2-72

source_name: Invasive breast cancer, surgical excision, no treatment (Formalin-fixed/paraffin-embeded)

value: No Treatment


title: longissimus dorsi muscle 60d, biological rep2

description: Gene expression data from longissimus dorsi muscle at 60 days afterbirth


title: longissimus dorsi muscle 60d, biological rep3

source_name: longissimus dorsi muscle at 60 days afterbirth


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_c18-2


title: Invasivebreastca_corebiopsy_anastrozoletreatedgroup_c19-2


title: Invasivebreastca_surgicalexcision_notreatment_sx2-62


title: longissimus dorsi muscle 60d, biological rep1

value: longissimus dorsi muscle at 60 days afterbirth


title: Invasivebreastca_surgicalexcision_notreatment_s13-1


title: Invasivebreastca_surgicalexcision_notreatment_s10-1


title: longissimus dorsi muscle 3d, biological rep3

description: Gene expression data from longissimus dorsi muscle at 3 days afterbirth


title: longissimus dorsi muscle 3d, biological rep2

source_name: longissimus dorsi muscle at 3 days afterbirth


title: Invasivebreastca_corebiopsy_notreatment_cx2-71

source_name: Invasive breast cancer, core biopsy, no treatment (Formalin-fixed/paraffin-embeded)


title: longissimus dorsi muscle 65dpc, biological rep1

description: Gene expression data from longissimus dorsi muscle at 65 days post coitus


title: Invasivebreastca_surgicalexcision_notreatment_sx2-52


title: Invasivebreastca_surgicalexcision_notreatment_sx2-42


title: Invasivebreastca_surgicalexcision_notreatment_sx2-31


title: Invasivebreastca_surgicalexcision_notreatment_sx2-21


title: longissimus dorsi muscle 65dpc, biological rep3

source_name: longissimus dorsi muscle at 65 days post coitus


title: Invasivebreastca_corebiopsy_notreatment_cx2-62


title: longissimus dorsi muscle 3d, biological rep1

value: longissimus dorsi muscle at 3 days afterbirth


title: Invasivebreastca_corebiopsy_notreatment_cx2-52

value: Female


title: Invasivebreastca_corebiopsy_notreatment_cx2-4

value: Post-menopausal


title: Invasivebreastca_corebiopsy_notreatment_cx2-2

value: ER Positive


title: Invasivebreastca_corebiopsy_notreatment_c10


title: longissimus dorsi muscle 65dpc, biological rep2

value: longissimus dorsi muscle at 65 days post coitus


title: Invasivebreastca_corebiopsy_notreatment_c13-1


title: Invasivebreastca_corebiopsy_notreatment_cx2-3


title: Normal_cortex_frozen_tissue_3

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

description: Gene expression profile of tuberculous meningitis

hyb_protocol: The samples with specific activity >9 pmol Cy3 per ug and yield > 1600 ug were selected for hybridization.  Cy-3 labeled cRNA was fragmented and hybridized onto oligonucleotide based whole human genome DNA microarrays (G4112F, 4 X 44 K, Agilent Technologies) for 16 hours at 65 0C with constant rotation at 10 rpm.

scan_protocol: The arrays were washed with gene expression wash buffers kit (Agilent Technologies) and scanned with Agilent DNA microarray scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The images were processed with Agilent feature extraction software.

source_name: Normal cortex

label_protocol: cDNA synthesized from total mRNA was used to synthesize cRNA.  Simultaneous amplification and Cy3 dye was used for labeling of cRNA  as per manufacturer’s protocol (Agilent Quick Amp Labeling Kit (Catalog #.51900442, Agilent technologies).  Labelled cRNA reaction mixture was then cleaned to remove unlabelled cRNA.  Labelling efficiency and yield of labeled RNA was then carried out using nanodrop (NanoDrop® ND-1000).

extract_protocol: Approximately 100 mg of tissue from the normal and infected groups were used for RNA isolation. The tissues were pulverized in 1 ml of QIAzol lysis reagent using homogenizer. Total RNA extraction and purification was carried out using RNeasy Lipid Tissue Mini kit (Catalog # 74804, QIAGEN, CA 91355, USA) as per manufacturer’s protocol.  RNA yield was calculated by measuring the absorbance at 260 nm.  Purity of the isolated total RNA was checked by calculating the ratio of absorbance at 260 nm to absorbance at 280 nm.  Integrity of the isolated RNA was checked either by agarose gel electrophoresis or by 2100 Bioanalyzer (Agilent Technologies) that measures the ratio of 28S and 18S ribosomal RNAs to compute the integrity of total mRNA.

value: Frontal cortex frozen tissue

tag: postmortem delay

value: 20 hrs


title: Normal_cortex_frozen_tissue_4

value: 6 hrs


title: breast cancer 585

city: Houston

first: TAKAYUKI

last: IWAMOTO

state: TX

address: 1515 Holcombe Blvd

department: Breast medical Oncology

institute: UT MD Anderson

description: Gene expression data from breast cancer FNA biopsy, pre-treatment

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized to affymetrix U133A arrays overnight at 42C. Microarrays were washed and stained in Microarray Suite 5.0.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.

data_processing: The data were normalized using dChip version 1.3 followed by logrithm-base-2 sc600 transformation. The dChip version 1.3 was used to calculate Model Based Expression Index (MBEI) values of the arrays using the digital standard microarray MDA-BCNorm.CEL and the probe sensitivity index file UTMDACC-BreastCancerNormalizer.psi as described in Hess, et. al, Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and 5-Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer, Journal of Clinical Oncology, 24 (26), 2006.

source_name: breast cancer FNA biopsy, pre-treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 ug total RNA using the BioArray High Yield RNA transcript labeling kit (Enzo Laboratories).

extract_protocol: total RNA was extracted from the FNA specimens using Qiagen RNeasy kit following the manufacturer’s instructions (http://www.qiagen.com).

tag: ibc vs non-ibc

value: Not-IBC

value: Pass

tag: er positive vs negative

value: ER neg

tag: her2 positive vs negative

tag: grade

value: III

tag: prechemo tumor size

tag: prechemo t stage

tag: prechemo nodal status

value: Positive


title: breast cancer 592

value: ER pos


title: breast cancer 618


title: TBM_cortex_frozen_tissue_6

source_name: TBM cortex

tag: gender

value: Male

value: 3 h 20min


title: HCT116_pre-miR-1_48h

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description:
HCT116-miR-1
Gene expression in human colorectal cancer cells with miR-1 precursor molecule

hyb_protocol: Hybridization was performed using an Gene Expression Hybridization Kit (Agilent technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction.

source_name: HCT116 cells transfected with miR-1 precursor molecule

label_protocol: Total RNA (700 ng) was amplified and labeled using a Quick Amp Labeling Kit one-color (Agilent Technologies).

growth_protocol: HCT116 cells were cultured in McCoy 5A medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: HCT116 cells (1.0E+6 cells) were transfected with 100 pmol of a Pre-miR-1 miRNA Precursor Molecule (Ambion) or a Pre-miR miRNA Molecule Negative Control #1 (Ambion) using a Cell Line Nucleofector kit V (Lonza, Basel, Switzerland) with a Nucleofector I electroporation device (Lonza) according to the manufacturer’s instructions.  Forty-eight hours after transfection, total RNA extraction were carried out.

tag: cell line

value: colorectal cancer cell line HCT116

tag: transfection

value: Pre-miR-1 miRNA Precursor Molecule


title: normal lung tissue

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

description: normal lung tissue

hyb_protocol: standard affymetrix hybridisation protocol

scan_protocol: standard affymetrix scanning protocol with affymetrix 3000 7G Scanner

data_processing: The data were analyzed with GCOS version 1.1.1.052 using Affymetrix default analysis settings. Scaling was performed using Mask Files provided by Affymetrix (HGU133Anorm.msk for U133A arrays, HGU133_plus_2norm.msk for U133 Plus 2.0 arrays). The mean target intensity was arbitrarily set to 1200 (U133A) or 850 (U133 Plus 2.0). All samples were normalized with RMA algorithm.

label: Biotin

source_name: normal lung tissue

label_protocol: standard affymetrix labeling protocol

extract_protocol: standard qiagen isolation protocol

tag: tissue type

value: normal lung tissue


title: breast cancer 624


title: Normal_cortex_frozen_tissue_1

value: 13 h 30min


title: HCT116_pre-miR-control_48h

description:
HCT116-cont
Gene expression in human colorectal cancer cells with miR precursor molecule negative control

source_name: HCT116 cells transfected with miR precursor molecule negative control

value: control


title: TBM_cortex_frozen_tissue_5

value: 18 hrs


title: breast cancer 640

value: IBC

value: II


title: breast cancer 644

value: Negative


title: normal kidney tissue

description: normal kidney tissue

source_name: normal kidney tissue

value: normal kidney tissue


title: breast cancer 650

value: Not-IBC

value: Pass


title: breast cancer 594

value: ER neg

value: III


title: TBM_cortex_frozen_tissue_3

value: Frontal cortex frozen tissue

value: 9 hrs


title: breast cancer 570

value: Positive


title: breast cancer 595


title: FAIRE_CHRF_8min

city: Hinxton

first: Dirk

middle: Stefan

last: Paul

address: Wellcome Trust Genome Campus

department: Human Genetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

description: FAIRE-chip in CHRF-288-11 cells (8 min formaldehyde cross-linking time)

hyb_protocol: Labeled samples were co-hybridized to the tiling arrays according to the manufacturer’s protocol (NimbleGen Arrays User’s Guide, ChIP-chip Analysis v4.1).

scan_protocol: Array washing and scanning were performed using the dual-channel microarray platform by Roche NimbleGen, according to the manufacturer’s protocol (NimbleGen Arrays User’s Guide, ChIP-chip Analysis v4.1).

data_processing: Experimental data were analyzed using the software NimbleScan v2.5 (Roche NimbleGen). The two-channel raw signal intensities were scaled between channels by subtracting the Tukey bi-weight mean for the log2-ratio values for all features from each log2-ratio value.

source_name: FAIRE DNA from CHRF-288-11 cells, 8 min cross-linking (Exp. A1)

label_protocol: DNA extracted from cross-linked cells (FAIRE, input sample) and uncross-linked cells (reference sample) were labeled with Cy5 and Cy3 dye, respectively, according to the manufacturer’s protocol (NimbleGen Arrays User’s Guide, ChIP-chip Analysis v4.1).

extract_protocol: FAIRE experiments were carried out as previously described (P. Giresi et al, 2009, Methods 48, 233-239). Briefly, for each cell type, 20 million cells were cross-linked with 1% formaldehyde for 8 or 12 min (as indicated). Chromatin was extracted and subjected to 12 sonication cycles (30 sec of high pulse, 30 sec of rest) using the Bioruptor UCD-200 (Diagenode). DNA fragments depleted of proteins (‘open chromatin’) were phenol-chloroform extracted and ethanol precipitated. The samples were treated with RNase A and cleaned-up using the MinElute PCR Purification Kit (QIAGEN). A DNA amplification step was not applied.

tag: cross-linking time

value: 8 min

tag: cell type

source_name: Reference DNA from CHRF-288-11 cells (Exp. A1)


title: TBM_cortex_frozen_tissue_4

tag: tissue

value: Male

value: 14 hrs


title: breast cancer 537

value: ER pos


title: breast cancer 485


title: breast cancer 553


title: breast cancer 472


title: FAIRE_CHRF_12min

description: FAIRE-chip in CHRF-288-11 cells (12 min formaldehyde cross-linking time)

source_name: FAIRE DNA from CHRF-288-11 cells, 12 min cross-linking (Exp. A2)

value: 12 min

source_name: Reference DNA from CHRF-288-11 cells (Exp. A2)


title: FAIRE_K562_12min

description: FAIRE-chip in K562 cells (12 min formaldehyde cross-linking time)

source_name: FAIRE DNA from K562 cells, 12 min cross-linking (Exp. B2)

source_name: Reference DNA from K562 cells (Exp. B2)


title: FGFR-4 Arg388 PNT1a cells, sample 1

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: FGFR-4 Arg388 PNT1a cells, compared to universal reference RNA

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Human Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.

label: Alexa Fluor 647

source_name: PNT1a prostate cell line

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: PNT1a cells were maintained in RPMI-1640 medium (Invitrogen) containing 10% fetal bovine serum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

tag: expressing

value: FGFR-4 Arg388

label: Alexa Fluor 555

source_name: human, universal reference RNA

tag: sample type

value: Universal Human Reference RNA (Stratagene Catalog #740000)


title: FGFR-4 Gly388 PNT1a cells, sample 2

description: FGFR-4 Gly388 PNT1a cells, compared to universal reference RNA

value: FGFR-4 Gly388


title: FGFR-4 Arg388 PNT1a cells, sample 2


title: Normal_cortex_frozen_tissue_2

tag: age

tag: postmortem delay

value: 10 hrs


title: TBM_cortex_frozen_tissue_1

value: 1 h 15min


title: breast cancer 564

tag: ibc vs non-ibc

value: Not-IBC

tag: er positive vs negative


title: breast cancer 441

value: Pass

tag: her2 positive vs negative

tag: grade


title: FAIRE_K562_8min

description: FAIRE-chip in K562 cells (8 min formaldehyde cross-linking time)

source_name: FAIRE DNA from K562 cells, 8 min cross-linking (Exp. B1)

source_name: Reference DNA from K562 cells (Exp. B1)


title: breast cancer 419

tag: prechemo tumor size

tag: prechemo t stage


title: breast cancer 504

value: II

tag: prechemo nodal status


title: Msgn1_48hMinDox-biological rep3

city: Frederick

first: Ravindra B

last: Chalamalasetty

address: 1050 Boyles St, Bldg 539,Rm205

department: Cancer and Developmental Biology

institute: National Cancer Institute-Frederick

description: Gene expression data of Day2 embryoid bodies cultured for another 48h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix GCOS software. Statistical and clustering analysis was done using BRB array tools and Genespring GX11 software.

organism: Mus musculus

source_name: Embryoid bodies, 48h,Min Dox

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

growth_protocol: A2loxFMsgn1 ES cells were grown in DMEM, 15%FBS, Pen/Strep and LIF on mitomycin treated mouse embryonic fibroblasts. For EB differentiation, ESC were plated on 10cm Petri dishes at a density of 2.5 million cells per plate in 15ml of DMEM, 10% FBS, 1x NEAA, Pen/Strep, 2-Mercaptoethanol and 50ug/ml ascorbic acid (Sigma).

extract_protocol: Cells were lysed in RLT buffer (Qiagen) according to manufacturers instructions. Total RNA was purified using RNeasy mini kit (Qiagen). RNA quality was checked on the Agilent Bioanalyzer.  All samples used for microarray analysis had high quality scores (RIN >9).

treatment_protocol: After 2 days of differentiation, EBs were then transferred to 6 well ultra low attachment dishes (Corning) and expression of FLAG-Msgn1 was induced using 1ug/ml Dox. Samples were collected at 12h interval up to 48h. Using this protocol, the expression of endogenous markers of the PSM lineage initiate on day 3 of in vitro differentiation. Thus induction of F-Msgn1 expression after 2 days of differentiation results in premature, ectopic Msgn1 expression.

tag: strain

value: 129P2 (formerly called 129/Ola)

value: embryoid bodies

tag: treatment

value: Day2 EBs cultured for another 48h


title: breast cancer 403

source_name: breast cancer FNA biopsy, pre-treatment

value: ER neg

value: III

value: Positive


title: breast cancer 464


title: Msgn1_48hPlusDox-biological rep2

description: Gene expression data of Day2 embryoid bodies induced with doxycycline and cultured for another 48h

source_name: Embryoid bodies, 48h,Plus Dox

value: Day2 EBs induced with doxycycline and cultured for another 48h


title: breast cancer 519

value: Negative


title: breast cancer 398


title: breast cancer 510

value: ER pos


title: Msgn1_48hMinDox-biological rep1


title: Msgn1_48hPlusDox-biological rep3


title: Msgn1_48hPlusDox-biological rep1


title: FGFR-4 Gly388 PNT1a cells, sample 1

tag: cell line


title: breast cancer 391


title: breast cancer 482


title: breast cancer 463


title: breast cancer 562


title: Msgn1_48hMinDox-biological rep2


title: MP-positive ACs-1

city: Cambridge

first: Jeremy

middle: N

last: Kay

state: MA

address: 52 Oxford Street

institute: Harvard University

hyb_protocol: 20ug of aRNA were fragmented and hybridized according to standard Affymetrix protocols for 16 h at 45 degrees C. Arrays were washed and stained in Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used for scanning.

data_processing: Data were analyized in dChip.

source_name: CFP+VC1.1+ retinal neurons

label_protocol: MessageAmp II-biotin system (Ambion). Two rounds of amplification were used.

growth_protocol: Male mice carrying the MP transgene were crossed to non-carrier females, and the progeny were sacrificed at postnatal day 6.

extract_protocol: PicoPure RNA Isolation Kit (MDS)

treatment_protocol: To purify MP-expressing ACs, the VC1.1+CFP+ fraction was collected by flow cytometry. To purify MP-expressing bipolar cells, VC1.1+ cells were removed by a magnetic column, and then the VC1.1–CFP+ fraction was collected by flow cytometry. ~1000 cells were collected for each biological replicate.

value: Mixed C57Bl6 x CD1

tag: origin

value: Papain-dissociated retinal cell suspension

value: CFP+VC1.1+ retinal neurons


title: breast cancer 578


title: breast cancer 390


title: MP-positive bipolars-1

source_name: CFP+VC1.1– retinal neurons

tag: cell type

value: CFP+VC1.1– retinal neurons


title: MP-positive ACs-2


title: breast cancer 379


title: MP-positive bipolars-2


title: breast cancer 367


title: Msgn1_24hPlusDox-biological rep1

description: Gene expression data of Day2 embryoid bodies induced with doxycycline and cultured for another 24h

source_name: Embryoid bodies, 24h,Plus Dox

tag: tissue

value: Day2 EBs induced with doxycycline and cultured for another 24h


title: Msgn1_24hPlusDox-biological rep3


title: Msgn1_24hMinDox-biological rep2

description: Gene expression data of Day2 embryoid bodies cultured for another 24h

source_name: Embryoid bodies, 24h,Min Dox

value: Day2 EBs cultured for another 24h


title: breast cancer 387

value: Not-IBC

value: Pass


title: breast cancer 297

value: II


title: Msgn1_24hPlusDox-biological rep2

value: 129P2 (formerly called 129/Ola)

value: embryoid bodies


title: breast cancer 340


title: Msgn1_24hMinDox-biological rep3


title: breast cancer 335


title: Msgn1_12hPlusDox-biological rep3

description: Gene expression data of Day2 embryoid bodies induced with doxycycline and cultured for another 12h

source_name: Embryoid bodies, 12h,Plus Dox

value: Day2 EBs induced with doxycycline and cultured for another 12h


title: breast cancer 345

value: ER neg

value: III


title: breast cancer 346

value: Positive


title: breast cancer 378

value: Negative


title: breast cancer 299

value: ER pos


title: Msgn1_12hPlusDox-biological rep1


title: breast cancer 284


title: Msgn1_24hMinDox-biological rep1


title: Msgn1_12hMinDox-biological rep3

description: Gene expression data of Day2 embryoid bodies cultured for another 12h

source_name: Embryoid bodies, 12h,Min Dox

value: Day2 EBs cultured for another 12h


title: Msgn1_12hPlusDox-biological rep2


title: Msgn1_12hMinDox-biological rep1


title: breast cancer 270


title: Msgn1_12hMinDox-biological rep2


title: breast cancer 258


title: Wildtype_XY_2

city: Oobu

first: Yuko

last: Katoh-Fukui

address: 35genngo ,moriokamachi

institute: National Inastitute for Longevity Sciences

description:
Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.

hyb_protocol: Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

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

data_processing: Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.

source_name: Cbx2_KO_XX gonads at E11.5

label_protocol: Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.

growth_protocol: Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.

extract_protocol: RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.

tag: genotype/variation

value: gonads


title: breast cancer 255


title: Wildtype_XY_3


title: breast cancer 274


title: breast cancer 283


title: Wildtype_XX_2


title: breast cancer 220


title: breast cancer 228


title: Wildtype_XY_1


title: breast cancer 233


title: breast cancer 176


title: Cbx2_KO_XX_3


title: breast cancer 226


title: Cbx2_KO_XY_3

source_name: Cbx2_KO_XY gonads at E11.5


title: Tet2 KO CFU 5th rep1

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description:
Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat1
Gene expression data from Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat1

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.

source_name: Total RNA, Tet2 KO LSK 5th plating

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

extract_protocol: Qiagen RNEasy Plus Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: LSK and CMP cells were sorted from Tet2+/+ Mx+, Tet-/-Mx+ littermate mice 4 weeks post deletion via pIC injection. Additionally cells were obtained from serial replating of CD150+ sorted Tet2 deficient cells.

tag: genetic background

tag: genotype

value: Tet2 KO

value: Tet2 deficient CD150+ sorted LSKs


title: breast cancer 227

description: Gene expression data from breast cancer FNA biopsy, pre-treatment

tag: age


title: Wildtype_XX_1


title: Cbx2_KO_XX_2


title: breast cancer 642

tag: ibc vs non-ibc

value: IBC


title: breast cancer 108

tag: er positive vs negative


title: breast cancer 151

tag: her2 positive vs negative


title: Tet2 KO GMP rep2

description:
Tet2 deficient  Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2

source_name: Total RNA, Tet2 KO GMP

value: Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors GMP


title: breast cancer 603

tag: grade


title: Cbx2_KO_XY_2


title: breast cancer 125

value: Not-IBC

tag: prechemo tumor size


title: breast cancer 574

value: Pass

tag: prechemo t stage


title: Tet2 KO CFU 5th rep2

description:
Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat2
Gene expression data from Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat2


title: Cbx2_KO_XX_1


title: breast cancer 126

tag: prechemo nodal status


title: Tet2 KO GMP rep1

description:
Tet2 deficient  Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1


title: Cbx2_KO_XY_1


title: breast cancer 219


title: breast cancer 144


title: Tet2 KO CMP rep1

description:
Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1

source_name: Total RNA, Tet2 KO CMP

value: Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors CMP


title: WT GMP rep2

description:
WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2

source_name: Total RNA, WT GMP

value: WT


title: breast cancer 518


title: Tet2 KO LSK rep1

description:
Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1
Gene expression data from Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1

source_name: Total RNA, Tet2 KO LSK


title: breast cancer 558


title: breast cancer 534

value: II


title: breast cancer 454


title: breast cancer 455


title: breast cancer 531


title: WT CMP rep2

description:
WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2

source_name: Total RNA, WT CMP


title: breast cancer 526


title: breast cancer 514


title: Tet2 KO CMP rep2

description:
Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2


title: WT GMP rep1

description:
WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1


title: Tet2 KO LSK rep2

description:
Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2
Gene expression data from Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2


title: WT CMP rep1

description:
WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1


title: breast cancer 402


title: WT LSK rep2

description:
WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2
Gene expression data from WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2

source_name: Total RNA, WT LSK


title: WT LSK rep1

description:
WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1
Gene expression data from WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1


title: KO_Jej_0h_4

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

hyb_protocol: The Mouse 430_2 GeneChip probe arrays were pre-hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol. 15 ug of labeled cRNA was fragmented in 30 uL 1X fragmentation buffer 100 mM KOAc, 30 mM MgOAc at 95°C for 35 minutes. The fragmented labeled cRNA was resuspended in 300 ?L 1X hybridization buffer containing 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20, 0.5 mg/mL Aceylated BSA, 0.1 mg/mL herring sperm DNA, control oligo B2, and control transcripts bioB 1.5 pM, bioC 5 pM, bioD 25 pM, and cre 100 pM, and hybridized to Genechip probe arrays according to manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip probe arrays were scanned using GeneArray Scanner (Hewlett Packard, Corvallis, OR).

data_processing: CEL files were subjected to GC-content-based Robust Multi-array Average (GCRMA) normalization. Colon and Jejunum tissue data were processed separately. Expression levels were log (base 2) transformed. All calculations and analyses were carried out using R and Bioconductor computational tools. Analyses were applied to discover genes that were differentially expressed between specific sets of tissue. First, to identify differentially expressed genes between groups of samples, we applied the linear modeling approach (MANOVA) to fit gene expression levels (log2 transformed) according to the defined groups of samples and Bayesian posterior error analysis. Genes that exhibited a log-odds score greater than zero and fold change greater then 1.5 were considered significantly different.

source_name: Jejunum

label_protocol: Five ug of purified total RNA was used in a 20 uL first strand reaction with 200U SuperScript II (Invitrogen, Carlsbad,CA) and 0.5ug (dT) T7primer[5’GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(T)24] in 1X first strand buffer (Invitrogen Life Technologies, Carlsbad, CA) with a 42°C incubation for 1 hour. Second strand synthesis was carried out by the addition of 40 U E. coli DNA Polymerase, 2 U E. coli RNase H, 10 U E. coli DNA Ligase in 1X second strand buffer (Invitrogen Life Technologies, Carlsbad, CA) followed by incubation at 16°C for 2 hrs. The second strand synthesis reaction was purified using the Genechip Sample Cleanup Module according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA). The purified cDNA was amplified using BioArray high yield RNA transcription labeling kit (Enzo Life Sciences, Inc., Parmingdale, NY) according to manufacturer’s protocol to produce 70-120 ug of biotin labeled cRNA (compliment RNA).

extract_protocol: At 6h and 24h post-ionizing radiation mice were sacrificed, and whole colon and jejunum were harvested, and total RNA was isolated from these  tissues. Samples were homogenized using an Ultra-Turrax T8 (IKA-Werke, Staufen, Germany) in TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA) according to manufacturer's protocol. 100 ìg of total RNA was further purified using an RNeasy Mini column (QIAGEN, Valencia, CA) according to manufacturer's protocol.

treatment_protocol: Mice were treated with 3 Gy of ionizing radiation.

tag: strain

value: BALB/C

value: Jejunum

value: 3 Gy ionizing radiation 0h


title: KO_Jej_0h_5

tag: treatment


title: breast cancer 371

source_name: breast cancer FNA biopsy, pre-treatment

value: ER neg

value: III

value: Positive


title: breast cancer 287


title: breast cancer 325

value: ER pos


title: breast cancer 318


title: KO_Jej_0h_2


title: breast cancer 347


title: breast cancer 252


title: breast cancer 230


title: KO_Jej_6h_1

value: 3 Gy ionizing radiation 6h


title: KO_Jej_0h_3


title: Wildtype_XX_3

value: gonads


title: KO_Jej_24h_1

value: 3 Gy ionizing radiation 24h


title: breast cancer 499

value: IBC


title: KO_Jej_24h_3


title: KO_Jej_24h_4


title: KO_Jej_6h_3


title: KO_Jej_24h_2


title: KO_Jej_6h_4


title: KO_Jej_24h_5


title: WT_Jej_6h_5


title: KO_Jej_6h_5


title: breast cancer 279


title: KO_Jej_0h_1


title: WT_Jej_0h_5


title: breast cancer 292


title: breast cancer 572


title: nontransgenic seedlings, normal conditions

city: Shanghai

first: weiwei

last: qi

address: 220#Handan road

institute: Fudan university

description: Gene expression data from leaf tissues of 4-leaf-old seedlings (10 plants each).

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: 4-leaf-old nontransgenic seedlings

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: OsEATB transgenic 9311 and nontransgenic control 9311 plants were grown in half-strength Murashige and Skoog medium under white ﬂuorescent light (a 14/10h light/dark cycle) at 28℃.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

value: leaf tissue

value: nontransgenic

tag: cultivar

value: indica 9311


title: WT_Jej_0h_2


title: WT_Jej_0h_3


title: prion infected vs normal endpoint, rep6 (printrun 9.1)

city: Winnipeg

first: Rhiannon

middle: LCH

last: Huzarewich

state: MB

address: 1015 Arlington St.

department: Molecular PathoBiology

country: Canada

institute: Public Health Agency of Canada

hyb_protocol: Pre-hybridization of the slides was performed to reduce background signal by incubating them in a slide rack containing pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42ºC for 45 min. Once the pre-hybridization was complete, the slides were washed in nuclease-free water for 5 min. in a slide rack shaking at 100 rpm and then dipped once into isopropanol and spin dried in a slide spinner. The 22x60I mm Lifterslips (Erie Scientific Company) were also dipped once into isopropanol and wiped dry with a kimwipe. The Lifterslip (Erie Scientific Company) was placed on top of the slide silica gel side down, and the whole assembly was placed at 55°C until it was ready for hybridization. Slides were used within 5 min. of prehybridization. Samples were prepared for hybridization by drying down 5 µg of each labeled aRNA sample using a DNA speed vac (Savant, model DNA 110). Each sample was then resuspended in 30 µl of DIG Easy Hyb hybridization buffer (Roche, Cat. 1034946) and the two samples (control and infected) that were being hybridized together onto one slide for a competitive hybridization experiment were mixed together for total of 60 µl, and 1 µl of mouse specific COT1-DNA (20 µg/µl) (Invitrogen, Cat. 18440016) and 1 µl of Poly(A)-DNA (20 µg/µl) (Invitrogen, Cat. polyA.gf) was added to prevent non-specific binding during hybridization. Once the samples were mixed well, they were placed at 95°C for 3 min. to denature any secondary structures and snap cooled on ice for 30 secs. The denatured samples from above were added to each prehybridized slide by pipetting the labeled probe mixture (60 μl) underneath the Lifterslip (Erie Scientific Company) slowly until the mixture spread uniformly across the array via capillary action. About 4 ml of DIG Easy Hyb buffer (Roche, Cat. 1034946) was added to the bottom reservoir in the hybridization chamber (Genetix) to provide a humid environment during hybridization. The hybridization chambers were sealed and incubated overnight (14-16 hrs.) at 42°C. Once hybridization was complete, the Lifterslips were removed by gently dipping the slide into pre-warmed (42°C) low stringency wash buffer (1X SSC and 0.2% SDS) repeatedly until it dislodged. The arrays were subsequently washed once each for 5 min. at 100 rpm in a slide rack on a shaker in low stringency wash buffer (pre-warmed to 42°C), high stringency wash buffer (0.1X SSC and 0.2% SDS), and 0.1X SSC buffer (Ambion, 20x SSC buffer, Cat. 9763). After the third and final wash, the slides were dried immediately in a slide spinner and placed in a light tight slide container until they could be scanned.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3).

data_processing: Microarray .TIFF images were uploaded into Array-Pro (MediaCybernetics, version 4.5) and spots were identified and grids constructed. To construct grids, the different grid options that were specifically selected for were whole cell area to measure the raw signal intensity of the spot, local corners for the background calculations, trimmed background subtracted from raw intensity for the net intensity measurement, and finally, normalization was not enabled in this program as this was done in subsequent programs. The data obtained was stored in and normalized using the GeneTraffic Microarray Database and Analysis System (version 2.6, Iobion Informatics). Normalization of raw intensities was performed using a linear regression smoothing algorithm (Loess best-fit) over the individual array subgrids and the subsequent normalized gene list containing log2 ratios were obtained.

label: AlexaFluor 555

source_name: Prion Infected Splenic cells, endpoint

label_protocol: Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Ambion) following manufacturer's instructions. Each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen)

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer's instructions

tag: strain of mouse

value: VM

tag: inoculum

value: 22A (scrapie)

tag: inoculation type

value: IP

tag: date of inoculation

label: AlexaFluor 647

source_name: Normal Splenic cells, endpoint

value: PBS


title: breast cancer 116

value: Pass


title: prion infected vs normal endpoint, rep1 (printrun 9.1)


title: prion infected vs normal endpoint, rep5 (printrun 9.1)


title: WT_Jej_6h_1

value: BALB/C

tag: tissue

value: Jejunum

value: WT


title: WT_Jej_0h_1

tag: genotype

value: 3 Gy ionizing radiation 0h


title: prion infected vs normal endpoint, rep4 (printrun 9.1)


title: WT_Jej_6h_2


title: WT_Jej_0h_4


title: WT_Jej_24h_2


title: WT_Jej_24h_3


title: WT_Jej_24h_4


title: prion infected vs normal endpoint, rep1 (printrun 7.1)

description: Dyeswap_1of2. 13176736_C#3(555)_I#13(647).


title: WT_Jej_6h_4


title: prion infected vs normal endpoint, rep2 (printrun 9.1)


title: KO_Col_6h_5

source_name: Colon

value: Colon


title: transgenic seedlings, normal conditions

source_name: 4-leaf-old transgenic seedlings

value: OsEATB transgenic

tag: age


title: WT_Jej_6h_3

value: 3 Gy ionizing radiation 6h


title: KO_Col_24h_5

value: 3 Gy ionizing radiation 24h


title: WT_Jej_24h_1


title: prion infected vs normal endpoint, rep2 (printrun 7.1)

description: Dyeswap_2of2. 13176735_C#3(647)_I#13(555).

value: IC


title: prion infected vs normal endpoint, rep3 (printrun 9.1)


title: KO_Col_6h_4


title: KO_Col_0h_5


title: KO_Col_0h_3


title: KO_Col_6h_2


title: KO_Col_0h_2


title: KO_Col_24h_1


title: OXA treated SW480 colon cancer cells

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

hyb_protocol: The microarrays used in our study were the Human 19K Oligo Array from Center for Applied Genomics (University of Medicine of New Jersey). Microarray slides were prehybridized in buffer containing 5x SSC, 25% formamide and 0.1% SDS at 42 °C for 45min and washed by dipping in isopropanol. The slides were then dipped in distilled water and dried with compressed air.  The Final Hybridization Mix was added to the prehybridized slide. A 22 x 60 mm coverslip was cleaned with compressed air and then gradually placed on the slide to form a thin layer of labeled targets. To maintain humidity inside the chamber, 20 ul 2x SSC was added to the two reservoir wells. The chamber was then tightly sealed and incubated at 55°C water bath overnight for 16-20 h. Slide was then removed from the chamber, washed for 10 min sequentially at 42C in 2x SSC/0.2% SDS buffer, at room temperature in 2x SSC buffer and at room temperature in 0.2x SSC buffer, rinsed in distilled water for 5 s, and dried by compressed air.  Then, we prepare the 3DNA Array 350 Capture Reagent (Vial 1) by thawing the vial in the dark at room temperature for 20 minutes, vortexing at the maximum setting for 3 seconds and microfuge briefly and incubating at 50-55°C for 10 minutes. Simultaneously we resuspended the 2X Hybridization Buffer (Vial 6) by heating to 70°C for at least 10 minutes. For each array, we prepare a 3DNA Hybridization Mix containing 2.5ul of 3DNA Array 350 Capture Reagent-1 (Vial 1),  2.5ul of 3DNA Array 350 Capture Reagent-2 (Vial 1) , 25ul of 2X Hybridization Buffer (Vial 6) and 20 ul of water. Gently vortex and briefly microfuge the 3DNA Hybridization Mix. We incubate the 3DNA Hybridization Mix first at 75-80°C for 10 minutes, and then we add the 3DNA Hybridization Mix to a prewarmed microarray, taking care to leave behind any precipitate at the bottom of the tube. To maintain humidity inside the chamber, 20ul 2x SSC was added to the two reservoir wells. The chamber was then tightly sealed and incubated at 60 °C water bath for 4 h.   Slide was then removed from the chamber, washed for 10 min sequentially at 65C in 2x SSC/0.2% SDS buffer, at room temperature in 2x SSC buffer and at room temperature in 0.2x SSC buffer, rinsed in distilled water for 5 s, and dried by compressed air.

scan_protocol: All slides were scanned immediately with an Affymetrix GMS 418 Array Scanner using appropriate gains on the photomultiplier tube to obtain the highest intensity without saturation. A 16 bit TIFF image was generated for each channel, Cy3 and Cy5. The image analysis was performed with Imagene 4.1 software (BioDiscovery) to quantify the signal intensities. Data from spots not recognized by the Imagene analysis software were excluded from further considerations (empty, poor and negative spots). Data from the spots visually identified as flawed (<15% in all arrays) were also removed. Only the spots with flag value equal to 0 were included in the analysis.

data_processing: The data sets were imported into Microsoft Excel in order to analyze the quality for each feature. Two parameters were used to asses the data filtration: difference between median and mean under 20% for each feature and intensity feature median greater than background mean plus 2 standard deviation. Normalization data was performed with ArrayNorm 1.7.2 software by using Lowess and Dye Swap Sim Fix Filter methods. Visualization of results was performed with the normalized data using average linkage and Euclidean distance as a measurement of similarity using GENESIS 1.5.0 Software (Alexander Sturn, Institute for Genomics and Bioinformatics, Graz University of Technology). ANOVA was used as statistical function to determine gene expression differences between resistant (cluster R) and sensitive (cluster S) cell groups. The differences were considered statistically significant when two-sided p-values were less than 0.01.

label: Cy5, Cy3

source_name: Total RNA from human OXA treated SW480 colorectal cancer cells

label_protocol: Labeling of total RNA was performed using 3DNA Array-350 Detection kit according to manufacturer's protocol (Genisphere, Hatfield, PA). Total RNA was reverse transcribed using reverse transcription (RT) primers. Briefly, 5 µg of total RNA and 1 µl of Cy3 or Cy5 capture sequence were brought to 11 µl with RNase free water and incubated for 10 min at 80°C. In a separate microtube 4 µl of 5x RT buffer, 1 µl dNTP mix, 2 µl 0.1M DTT, 1 ul of Superase In TM Rnase inhibitor and 1µl of Superscript II reverse transcriptase were combined and the reaction was incubated 2 h at 42°C. The reaction was terminated by adding 3.5 µl of 0.5 M NaOH/50 mM EDTA and incubating it at 65°C for 10 min. The reaction was neutralized with 5 µl 1 M Tris-Cl, pH 7.5. The Cy3 and Cy5 reactions were then combined and precipitated with 15 µg of linear acrylamide, 250 µl 3 M ammonium acetate, and 875 µl 100% ethanol at -20 °C for 1 hour. Following precipitation the pellet was dried with speed-vac. In preparation for hybridization the cDNA pellet was resuspended in 29 µl RNase free water deionized distilled water. Then, 29 µl hybridization buffer (vial 12) were added to the mix and incubated at 80 °C for 10 min, followed by 55 °C for 45 min. This is the Final Hybridization Mix for loading on the array.

growth_protocol: Cell lines were grown as monolayer in RPMI-1640 (Invitrogen) medium (DLD1, LS513, HCT116, HCT15, LS411N, SW1417 and SW48) and DMEM (Invitrogen) medium (HT29, CACO2, LS174T, SW1116, SW480 and SW948) supplemented with 10% of heat-inactivated fetal calf serum (Biological Industries), 400 U/ml of penicillin, 40 ug/ml of gemtamicine, 2 mM of L-glutamine (Sigma) and 10 mM of Hepes (Sigma). LoVo was grown in HAM’S F12 (Invitrogen) with 20% of FBS, 200 U/ml of penicillin and 20ug/ml of gemtamicine. All cell lines were cultured at 37C in a humidified atmosphere of 5% CO2.

extract_protocol: All cell lines were grown in P60 dishes and total RNA from each sample isolated by using the RNeasy Mini kit (Qiagen) and were exhaustively treated with RNase-free DNAse I. RNA quantification were performed using NanoDrop spectophotometer (Nucliber).

treatment_protocol: For assessment of OXA sensitivity, we treated the cells with different concetrations of OXA during 24 hours and analyzed them by MTT colorimetric assay to determine the IC50 for each cell line. We considered OXA highly sensitive cells those with IC50 under 1 microM. All cell lines were grown in P60 dishes, one aliquot treated with IC50 OXA and another for untreated control.

tag: cell type

value: colorectal cancer cells

tag: oxa sensitivity

source_name: Reference RNA (Human Reference RNA, Stratagene)

tag: sample type

value: Human Reference RNA from Stratagene


title: KO_Col_24h_3


title: OXA treated  SW948 colon cancer cells

source_name: Total RNA from human OXA treated SW948 colorectal cancer cells


title: OXA treated CACO2 colon cancer cells

source_name: Total RNA from human OXA treated CACO2 colorectal cancer cells


title: WT_Col_6h_4


title: OXA treated SW1417 colon cancer cells

source_name: Total RNA from human OXA treated SW1417 colorectal cancer cells


title: WT_Col_6h_5


title: OXA treated HCT15 colon cancer cells

source_name: Total RNA from human OXA treated HCT15 colorectal cancer cells


title: WT_Col_24h_5


title: KO_Col_0h_1


title: KO_Col_6h_1


title: WT_Col_0h_5


title: WT_Col_0h_4


title: KO_Col_24h_2


title: WT_Col_24h_3


title: OXA treated SW1116 colon cancer cells

source_name: Total RNA from human OXA treated SW1116 colorectal cancer cells


title: OXA treated SW48 colon cancer cells

source_name: Total RNA from human OXA treated SW48 colorectal cancer cells


title: OXA treated LS13 colon cancer cells

source_name: Total RNA from human OXA treated LS513 colorectal cancer cells


title: KO_Col_24h_4


title: WT_Col_0h_3


title: OXA treated HCT116 colon cancer cells

source_name: Total RNA from human OXA treated HCT116 colorectal cancer cells


title: breast cancer 154

description: Gene expression data from breast cancer FNA biopsy, pre-treatment

tag: ibc vs non-ibc

value: IBC

tag: er positive vs negative

value: ER neg

tag: her2 positive vs negative

tag: grade

value: III

value: Positive


title: OXA treated LS411N colon cancer cells

source_name: Total RNA from human OXA treated LS411N colorectal cancer cells


title: OXA treated LS174T colon cancer cells

source_name: Total RNA from human OXA treated LS174T colorectal cancer cells


title: OXA treated LoVo colon cancer cells

source_name: Total RNA from human OXA treated LoVo colorectal cancer cells


title: WT_Col_0h_2

tag: strain


title: Control CACO2 colon cancer cells

source_name: Total RNA from human CACO2 colorectal cancer cells


title: Control HCT116 colon cancer cells

source_name: Total RNA from human HCT116 colorectal cancer cells


title: WT_Col_0h_1

source_name: Colon

extract_protocol: At 6h and 24h post-ionizing radiation mice were sacrificed, and whole colon and jejunum were harvested, and total RNA was isolated from these tissues. Samples were homogenized using an Ultra-Turrax T8 (IKA-Werke, Staufen, Germany) in TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA) according to manufacturer's protocol. 100 ìg of total RNA was further purified using an RNeasy Mini column (QIAGEN, Valencia, CA) according to manufacturer's protocol.

tag: treatment


title: WT_Col_6h_1


title: Control  SW948 colon cancer cells

source_name: Total RNA from human SW948 colorectal cancer cells


title: WT_Col_24h_2


title: OXA treated HT29 colon cancer cells

source_name: Total RNA from human OXA treated HT29 colorectal cancer cells


title: OXA treated DLD11 colon cancer cells

source_name: Total RNA from human OXA treated DLD11 colorectal cancer cells

source_name: Reference RNA (Human Reference RNA, Stratagene)


title: Fresh-frozen tissue 5M5

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

institute: The Hospital for Sick Children

description:
This Sample represents 2 dye-swapped samples.

Cy5=tumor, Cy3=normal control:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_4.txt
Cy5=normal control, Cy3=tumor:
US22502683_251485043231_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: Agilent hybridization protocol following the manufacturer’s instructions. Dye-swap design.

scan_protocol: Scanned on Agilent Scanner G25505B.

data_processing: Array raw data were generated using Feature Extraction 9.1 Software. Feature signals had to fulfill the following criteria to be considered for further analysis: a minimal signal to background ratio ≥ 1.5 in at least one channel; a minimal raw signal of 200; a mean to median spot intensity ≤ the 75% quantile + 3 times the interquartile range of all features on the array; and a feature replicate standard deviation ≤ 0.25 per array. Normalization of raw signals was performed using vsn (Huber et al., 2002). Dye-swap experiments were averaged. Probes with more than 80% missing values across all samples were removed. Based on BLASTing the probes sequence information against the genome, biological annotations were retrieved from EnsEMBL (version 54, NCBI Build 36 of the human genome reference sequence).

source_name: tumoral tissue (medulloblastoma), WNT

label_protocol: Agilent labeling protocol following the manufacturer’s instructions.

growth_protocol: Fresh frozen material was milled in a Micro-Dismembrator S (B. Braun, Melsungen, Germany). Total RNA derived from human cerebellums from a pool of 24 donors (Clontech, LOT No.6060073) was used as reference.

extract_protocol: RNA was extracted from biopsy samples using Trizol and RNeasy mini columns following the manufacturer’s instructions.

value: medulloblastoma

tag: gender

value: female

tag: age (years)

tag: subtype

value: WNT

tag: histology

value: classic

tag: ctnnb1 mutation

value: mutated

source_name: normal cerebellum

value: cerebellum

tag: disease status

value: normal

value: reference