title: MO_DH3c_SON_NCBI

status: Public on Aug 15 2006

type: RNA

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: SON - 3d Dehydrated

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Microarray Suite version 5.0

molecule: total RNA

organism: Rattus norvegicus

source_name: Supraoptic nucleus_3d Dehydration

label_protocol: In vitro transcription of template was carried out in the presence of biotinylated UTP and CTP using the Enzo BioArray High Yield RNA Transcript Labelling Kit (Affymetrix, Santa Clara, CA, USA and Enzo Diagnostics).

tag: Strain

value: Sprague Dawley

tag: Gender

value: Male

tag: Age

value: 10-12 weeks

tag: Tissue

value: Supraoptic nucleus


title: MO_DH3a_SON_NCBI

description: SON - 3d Dehydrated

label: Enzo BioArray High Yield RNA Transcript Labelling Kit (Affymetrix, Santa Clara, CA, USA and Enzo Diagnostics).


title: MO_CTb_SON_NCBI

description: SON - Control

source_name: Supraoptic nucleus_control


title: MO_DH1a_SON_NCBI

description: SON - 1d Dehydrated

source_name: Supraoptic nucleus_1d Dehydrated


title: MO_CTa_SON_NCBI

description: SON - Control


title: MO_CTC_SON_NCBI

description: SON - Control


title: Plus_spleen_Mu11KsubB_rep1

status: Public on Aug 08 2006

city: Muenster

first: Martin

last: Eisenacher

state: NRW

address: von-Esmarch-Str. 56

department: Integrierte Funktionelle Genomik (IFG)

country: Germany

description: original experiment name: V9PM1-040401B_TGT1000

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0, statistical algorithm, scaling target value 1000

label: biotin

organism: Mus musculus

source_name: MRP14(S100A9)-positive-mouse bone-marrow granulocytes (without erythrocytes)

label_protocol: during in-vitro transcription; standard Affymetrix procedures

extract_protocol: lysis in RLT buffer (Qiagen); total-RNA extracted with RNeasy kit (Qiagen)

tag: not stimulated


title: blood_probandEB_male_rep1

status: Public on Aug 12 2006

description: HG_U95A, original experiment name: S29-116-280601_TGT1000

organism: Homo sapiens

source_name: venous blood of adult human proband

tag: total RNA of approx. 50 ml human venous blood, probands have no known diseases


title: Plus_LPS4h_Mu11KsubB_rep3

description: original experiment name: V7PL4-200401B_TGT1000

tag: stimulated for 4h with LPS


title: blood_probandEL_female_rep3

description: HG_U95A, original experiment name: S30-121-050701_TGT1000


title: blood_probandS_female_rep1

description: HG_U95A, original experiment name: S29-113-280601_TGT1000


title: blood_probandEL_female_rep1

description: HG_U95A, original experiment name: 26-103-150301_TGT1000


title: blood_probandB_female_rep1

description: HG_U95A, original experiment name: 26-102-150301_TGT1000


title: blood_probandR_male_rep1

description: HG_U95A, original experiment name: RV-280201_TGT1000


title: Minus_LPS4h_Mu11KsubB_rep3

description: original experiment name: V7ML4-200401B_TGT1000

source_name: MRP14(S100A9)-negative-mouse bone-marrow granulocytes (without erythrocytes)


title: Plus_Kontrolle4h_Mu11KsubB_rep5

description: original experiment name: V7PK4-270301B_TGT1000

tag: not stimulated 4h


title: MO_DH1c_SON_NCBI

description: SON - 1d Dehydrated


title: MO_DH3b_SON_NCBI

description: SON - 3d Dehydrated


title: blood_probandEL_female_rep2

description: HG_U95A, original experiment name: S29-118-280601_TGT1000


title: blood_probandR_male_rep4

description: HG_U95A, original experiment name: S30-122-050701_TGT1000


title: blood_probandB_female_rep2

description: HG_U95A, original experiment name: S29-117-280601_TGT1000


title: Plus_A23187.4h_Mu11KsubB_rep4

description: original experiment name: V8PA4-040401B_TGT1000

tag: stimulated for 4h with A23187


title: blood_probandR_male_rep2


title: Minus_A23187.4h_Mu11KsubB_rep4

description: original experiment name: V8MA4-040401B_TGT1000


title: blood_probandR_male_rep3

description: HG_U95A, original experiment name: S29-115-280601_TGT1000


title: blood_probandB_female_rep3

description: HG_U95A, original experiment name: S30-120-050701_TGT1000


title: MO_DH1b_SON_NCBI

description: SON - 1d Dehydrated

source_name: Supraoptic nucleus_1d dehydrated


title: Minus_spleen_Mu11KsubB_rep1

description: original experiment name: V9MM1-040401B_TGT1000


title: blood_probandH_male_rep1


title: Minus_Kontrolle4h_Mu11KsubB_rep5

description: original experiment name: V7MK4-200401B_TGT1000


title: Minus_Kontrolle4h_Mu11KsubB_rep3

description: original experiment name: V3MK4-260301B_TGT1000


title: Plus_Kontrolle4h_Mu11KsubB_rep4

description: original experiment name: V4PK4-260301B_TGT1000


title: Minus_Kontrolle4h_Mu11KsubB_rep4

description: original experiment name: V4MK4-260301B_TGT1000


title: Plus_PMA4h_Mu11KsubB_rep1

description: original experiment name: V6PP4-270301B_TGT1000

tag: stimulated for 4h with PMA (a phorbolester)


title: Plus_Kontrolle4h_Mu11KsubB_rep3

description: original experiment name: V3PK4-260301B_TGT1000


title: Plus_Kontrolle0h_Mu11KsubB_rep2

description: original experiment name: V20PK1-200701B_TGT1000

tag: not stimulated 0h


title: Minus_PMA4h_Mu11KsubB_rep1

description: original experiment name: V6MP4-270301B_TGT1000


title: Minus_Kontrolle0h_Mu11KsubB_rep1

description: original experiment name: V1MK1-260301B_TGT1000


title: Minus_Kontrolle0h_Mu11KsubB_rep2

description: original experiment name: V20MK1-200701B_TGT1000


title: Minus_Kontrolle4h_Mu11KsubB_rep1

description: original experiment name: V14MK4-270601B_TGT1000


title: Plus_Kontrolle0h_Mu11KsubB_rep1

description: original experiment name: V1PK1-260301B_TGT1000


title: Plus_LPS4h_Mu11KsubB_rep1

description: original experiment name: V17PL4-130701B_TGT1000


title: Plus_A23187.4h_Mu11KsubB_rep3

description: original experiment name: V19PA4-200701B_TGT1000


title: Minus_LPS4h_Mu11KsubB_rep2

description: original experiment name: V18ML4-130701B_TGT1000


title: Plus_Kontrolle4h_Mu11KsubB_rep2

description: original experiment name: V15PK4-270601B_TGT1000


title: Plus_LPS4h_Mu11KsubB_rep2

description: original experiment name: V18PL4-130701B_TGT1000


title: Minus_A23187.4h_Mu11KsubB_rep2

description: original experiment name: V16MA4B-260601B_TGT1000


title: Plus_Kontrolle4h_Mu11KsubB_rep1

description: original experiment name: V14PK4-270601B_TGT1000


title: Minus_A23187.4h_Mu11KsubB_rep3

description: original experiment name: V19MA4-200701B_TGT1000


title: Minus_A23187.4h_Mu11KsubB_rep1

description: original experiment name: V16MA4A-260601B_TGT1000


title: Plus_A23187.4h_Mu11KsubB_rep1

description: original experiment name: V16PA4A-260601B_TGT1000


title: Plus_spleen_Mu11KsubA_rep1

description: original experiment name: V9PM1-040401A_TGT1000


title: Minus_LTB-4_Mu11KsubB_rep1

description: original experiment name: V13MLT4-280601B_TGT1000

tag: stimulated for 4h with LTB-4 (leukotrien B4)


title: Plus_LTB-4_Mu11KsubB_rep1

description: original experiment name: V13PLT4-280601B_TGT1000


title: Minus_Kontrolle4h_Mu11KsubB_rep2

description: original experiment name: V15MK4-270601B_TGT1000


title: Plus_A23187.4h_Mu11KsubB_rep2

description: original experiment name: V16PA4B-260601B_TGT1000


title: Minus_LPS4h_Mu11KsubB_rep1

description: original experiment name: V17ML4-130701B_TGT1000


title: Minus_spleen_Mu11KsubA_rep1

description: original experiment name: V9MM1-040401A_TGT1000


title: Plus_A23187.4h_Mu11KsubA_rep4

description: original experiment name: V8PA4-040401A_TGT1000


title: Minus_A23187.4h_Mu11KsubA_rep4

description: original experiment name: V8MA4-040401A_TGT1000


title: Minus_LPS4h_Mu11KsubA_rep3

description: original experiment name: V7ML4-200401A_TGT1000


title: Plus_Kontrolle4h_Mu11KsubA_rep4

description: original experiment name: V4PK4-260301A_TGT1000


title: Minus_Kontrolle4h_Mu11KsubA_rep4

description: original experiment name: V4MK4-260301A_TGT1000


title: Minus_Kontrolle4h_Mu11KsubA_rep3

description: original experiment name: V3MK4-260301A_TGT1000


title: Plus_Kontrolle4h_Mu11KsubA_rep5

description: original experiment name: V7PK4-270301A_TGT1000


title: Plus_LPS4h_Mu11KsubA_rep3

description: original experiment name: V7PL4-200401A_TGT1000


title: Plus_Kontrolle4h_Mu11KsubA_rep2

description: original experiment name: V15PK4-270601A_TGT1000


title: Minus_A23187.4h_Mu11KsubA_rep3

description: original experiment name: V19MA4-200701A_TGT1000


title: Minus_A23187.4h_Mu11KsubA_rep2

description: original experiment name: V16MA4B-260601A_TGT1000


title: Plus_Kontrolle4h_Mu11KsubA_rep3

description: original experiment name: V3PK4-260301A_TGT1000


title: Plus_A23187.4h_Mu11KsubA_rep3

description: original experiment name: V19PA4-200701A_TGT1000


title: Minus_Kontrolle4h_Mu11KsubA_rep5

description: original experiment name: V7MK4-200401A_TGT1000


title: Plus_Kontrolle0h_Mu11KsubA_rep1

description: original experiment name: V1PK1-260301A_TGT1000


title: Plus_Kontrolle0h_Mu11KsubA_rep2

description: original experiment name: V20PK1-200701A_TGT1000


title: Plus_PMA4h_Mu11KsubA_rep1

description: original experiment name: V6PP4-270301A_TGT1000


title: Minus_PMA4h_Mu11KsubA_rep1

description: original experiment name: V6MP4-270301A_TGT1000


title: Minus_Kontrolle0h_Mu11KsubA_rep2

description: original experiment name: V20MK1-200701A_TGT1000


title: Plus_A23187.4h_Mu11KsubA_rep1

description: original experiment name: V16PA4A-260601A_TGT1000


title: Plus_LPS4h_Mu11KsubA_rep1

description: original experiment name: V17PL4-130701A_TGT1000


title: Plus_LPS4h_Mu11KsubA_rep2

description: original experiment name: V18PL4-130701A_TGT1000


title: Minus_A23187.4h_Mu11KsubA_rep1

description: original experiment name: V16MA4A-260601A_TGT1000


title: Minus_Kontrolle4h_Mu11KsubA_rep2

description: original experiment name: V15MK4-270601A_TGT1000


title: Minus_LPS4h_Mu11KsubA_rep1

description: original experiment name: V17ML4-130701A_TGT1000


title: Plus_A23187.4h_Mu11KsubA_rep2

description: original experiment name: V16PA4B-260601A_TGT1000


title: Minus_Kontrolle0h_Mu11KsubA_rep1

description: original experiment name: V1MK1-260301A_TGT1000


title: Minus_LPS4h_Mu11KsubA_rep2

description: original experiment name: V18ML4-130701A_TGT1000


title: Plus_Kontrolle4h_Mu11KsubA_rep1

description: original experiment name: V14PK4-270601A_TGT1000


title: Minus_Kontrolle4h_Mu11KsubA_rep1

description: original experiment name: V14MK4-270601A_TGT1000


title: Plus_LTB-4_Mu11KsubA_rep1

description: original experiment name: V13PLT4-280601A_TGT1000


title: Minus_LTB-4_Mu11KsubA_rep1

description: original experiment name: V13MLT4-280601A_TGT1000


title: blood_probandEB_male_rep2

description: HG_U95A, original experiment name: S30-123-050701_TGT1000


title: KC ecdysone

status: Public on Aug 05 2006

city: Dallas

first: John

middle: M

last: Abrams

state: TX

address: 5323 Harry Hines Blvd

department: Cell Biology

country: USA

institute: University of Texas Southwestern Medical Center

description: Kc167 cells, ecdysone

data_processing: Affymetrix Microarray Suite version 5.0

organism: Drosophila melanogaster

source_name: tissue culture, embryo-derived cells, female, ecdysone

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

growth_protocol: Kc167 cells were maintained in serum-free CCM3 media supplemented with 1:200 dilution of Penicilin-Streptomycin (Gibco) at 25 degrees C.

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco/BRL).

treatment_protocol: Kc167 cells were diluted to 1x10^6 cells/ml in CCM3 media and plated in a 150mm culture dish.  10uM Ecdysone analog, Muristerone A (Invitrogen) was added.  All samples were incubated for 72 hours, mock-treated, allowed to rest for 90 minutes, and then prepped for total RNA.

tag: Wild type, Cell Type Kc167, ecdysone


title: KC gamma-irradiated

description: Kc167 cells, gamma-irradiated

source_name: tissue culture, embryo-derived cells, female, gamma-irradiated

treatment_protocol: Kc167 cells were diluted to 1x10^6 cells/ml in CCM3 media and plated in a 150mm culture dish.  All samples were incubated for 72 hours, gamma-irradiated at 280 Gy, allowed to rest for 90 minutes, and then prepped for total RNA.

tag: Wild type, Cell Type Kc167, gamma-irradiated


title: MC381

status: Public on Aug 04 2006

city: Richmond Hill

first: Jun

last: Ma

state: Ontario

address: 2 East Beaver Creek Road, Building 2

country: Canada

institute: GeneNews Limited

data_processing: GC-RMA in Genespring

source_name: Human peripheral blood cells

tag: Sex	M

tag: Age (y)	39

tag: Glucose (mmol/L)	4.4

tag: Cholesterol (mmol/L)	4.67

tag: Triglyceride (mmol/L)	0.85

tag: HDL (mmol/L)	1.43

tag: LDL (mmol/L)	2.85

tag: Platelets (E9/L)	241

tag: Neutrophil (E9/L)	3.47

tag: Lymphocytes (E9/L)	1.17

tag: Monocytes (E9/L)	0.31

tag: Eosinophil (E9/L)	0.1

tag: Basophil (E9/L)	0.05


title: MC349

tag: Sex	F

tag: Age (y)	50

tag: Glucose (mmol/L)	4.6

tag: Cholesterol (mmol/L)	4.75

tag: Triglyceride (mmol/L)	0.57

tag: HDL (mmol/L)	2.55

tag: LDL (mmol/L)	1.94

tag: Platelets (E9/L)	161

tag: Neutrophil (E9/L)	3.37

tag: Lymphocytes (E9/L)	1.12

tag: Monocytes (E9/L)	0.51

tag: Eosinophil (E9/L)	0.05


title: KC ecdysone + gamma-irradiated

description: Kc167 cells, ecdysone & gamma-irradiated

source_name: tissue culture, embryo-derived cells, female, ecdysone, gamma-irradiated

treatment_protocol: Kc167 cells were diluted to 1x10^6 cells/ml in CCM3 media and plated in a 150mm culture dish.  10uM Ecdysone analog, Muristerone A (Invitrogen) was added.  All samples were incubated for 72 hours, gamma-irradiated at 280 Gy, allowed to rest for 90 minutes, and then prepped for total RNA.

tag: Wild type, Cell Type Kc167, ecdysone, gamma-irradiated


title: MC240

tag: Age (y)	31

tag: Glucose (mmol/L)	3.2

tag: Cholesterol (mmol/L)	3.14

tag: Triglyceride (mmol/L)	0.5

tag: HDL (mmol/L)	1.59

tag: LDL (mmol/L)	Missing

tag: Platelets (E9/L)	160

tag: Neutrophil (E9/L)	2.3

tag: Lymphocytes (E9/L)	1.67

tag: Monocytes (E9/L)	0.41

tag: Basophil (E9/L)	0.09


title: KC control

description: Kc167 cells, control

source_name: tissue culture, embryo-derived cells, female, control

treatment_protocol: Kc167 cells were diluted to 1x10^6 cells/ml in CCM3 media and plated in a 150mm culture dish.  All samples were incubated for 72 hours, mock-treated, allowed to rest for 90 minutes, and then prepped for total RNA.

tag: Wild type, Cell Type Kc167, control


title: MC242

tag: Sex	F

tag: Age (y)	36

tag: Glucose (mmol/L)	4.7

tag: Cholesterol (mmol/L)	4.06

tag: Triglyceride (mmol/L)	1.05

tag: HDL (mmol/L)	1.84

tag: LDL (mmol/L)	1.74

tag: WBC (E9/L)	7

tag: Platelets (E9/L)	196

tag: Neutrophil (E9/L)	5.11

tag: Lymphocytes (E9/L)	1.33

tag: Monocytes (E9/L)	0.42

tag: Eosinophil (E9/L)	0.07

tag: Basophil (E9/L)	0.07


title: MC249

tag: Sex	M

tag: Age (y)	31

tag: Glucose (mmol/L)	4.1

tag: Cholesterol (mmol/L)	3.99

tag: Triglyceride (mmol/L)	0.85

tag: HDL (mmol/L)	1.1

tag: LDL (mmol/L)	2.5

tag: Platelets (E9/L)	222

tag: Neutrophil (E9/L)	2.2

tag: Lymphocytes (E9/L)	2.53

tag: Monocytes (E9/L)	0.44

tag: Eosinophil (E9/L)	0.11

tag: Basophil (E9/L)	0.17


title: MC247

tag: Age (y)	53

tag: Glucose (mmol/L)	5.5

tag: Cholesterol (mmol/L)	5.86

tag: Triglyceride (mmol/L)	2.25

tag: HDL (mmol/L)	1.73

tag: LDL (mmol/L)	3.1

tag: Platelets (E9/L)	277

tag: Neutrophil (E9/L)	2.41

tag: Lymphocytes (E9/L)	2.58

tag: Monocytes (E9/L)	0.39

tag: Eosinophil (E9/L)	0.06

tag: Basophil (E9/L)	0.11


title: MC317

tag: Sex	F

tag: Age (y)	66

tag: Glucose (mmol/L)	5.2

tag: Cholesterol (mmol/L)	5.11

tag: Triglyceride (mmol/L)	0.95

tag: HDL (mmol/L)	1.93

tag: LDL (mmol/L)	2.74

tag: Platelets (E9/L)	310

tag: Neutrophil (E9/L)	10.69

tag: Lymphocytes (E9/L)	1.72

tag: Monocytes (E9/L)	0.66

tag: Eosinophil (E9/L)	0.13

tag: Basophil (E9/L)	0


title: MC239

tag: Age (y)	32

tag: Glucose (mmol/L)	4.4

tag: Cholesterol (mmol/L)	4.04

tag: Triglyceride (mmol/L)	0.76

tag: HDL (mmol/L)	1.85

tag: LDL (mmol/L)	1.84

tag: Platelets (E9/L)	207

tag: Neutrophil (E9/L)	3.93

tag: Lymphocytes (E9/L)	2.93

tag: Monocytes (E9/L)	0.54

tag: Eosinophil (E9/L)	0.15

tag: Basophil (E9/L)	0.15


title: MC202

tag: Sex	M

tag: Age (y)	63

tag: Glucose (mmol/L)	5.2

tag: Cholesterol (mmol/L)	3.87

tag: Triglyceride (mmol/L)	0.61

tag: HDL (mmol/L)	1.62

tag: LDL (mmol/L)	1.97

tag: Platelets (E9/L)	175

tag: Neutrophil (E9/L)	3.46

tag: Lymphocytes (E9/L)	1.4

tag: Monocytes (E9/L)	0.32

tag: Eosinophil (E9/L)	0.16

tag: Basophil (E9/L)	0.05


title: MC225

tag: Age (y)	45

tag: Cholesterol (mmol/L)	5.18

tag: Triglyceride (mmol/L)	1.46

tag: HDL (mmol/L)	1.29

tag: LDL (mmol/L)	3.22

tag: Platelets (E9/L)	154

tag: Neutrophil (E9/L)	3.78

tag: Lymphocytes (E9/L)	1.76

tag: Monocytes (E9/L)	0.5

tag: Eosinophil (E9/L)	0.13

tag: Basophil (E9/L)	0.13


title: MC332

tag: Sex	F

tag: Age (y)	55

tag: Glucose (mmol/L)	5

tag: Cholesterol (mmol/L)	6.10

tag: Triglyceride (mmol/L)	1.03

tag: HDL (mmol/L)	2.42

tag: LDL (mmol/L)	3.21

tag: Platelets (E9/L)	224

tag: Neutrophil (E9/L)	3.42

tag: Lymphocytes (E9/L)	2.14

tag: Monocytes (E9/L)	0.43

tag: Eosinophil (E9/L)	0.06

tag: Basophil (E9/L)	0.06


title: MC369

tag: Sex	M

tag: Age (y)	70

tag: Glucose (mmol/L)	5.2

tag: Cholesterol (mmol/L)	5.01

tag: Triglyceride (mmol/L)	0.78

tag: HDL (mmol/L)	1.95

tag: LDL (mmol/L)	2.7

tag: Platelets (E9/L)	152

tag: Neutrophil (E9/L)	1.85

tag: Lymphocytes (E9/L)	1.26

tag: Monocytes (E9/L)	0.44

tag: Eosinophil (E9/L)	0.07

tag: Basophil (E9/L)	0.04


title: MC345

tag: Age (y)	30

tag: Cholesterol (mmol/L)	5.65

tag: Triglyceride (mmol/L)	1.02

tag: HDL (mmol/L)	1.41

tag: LDL (mmol/L)	3.77

tag: Platelets (E9/L)	158

tag: Neutrophil (E9/L)	2.31

tag: Lymphocytes (E9/L)	2.59

tag: Monocytes (E9/L)	0.5


title: MC245

tag: Sex	M

tag: Age (y)	33

tag: Glucose (mmol/L)	5.3

tag: Cholesterol (mmol/L)	5.66

tag: Triglyceride (mmol/L)	1.01

tag: HDL (mmol/L)	1.37

tag: LDL (mmol/L)	3.83

tag: WBC (E9/L)	5

tag: Platelets (E9/L)	249

tag: Neutrophil (E9/L)	2.1

tag: Lymphocytes (E9/L)	2.2

tag: Monocytes (E9/L)	0.45

tag: Eosinophil (E9/L)	0.2

tag: Basophil (E9/L)	0.1


title: MC251

tag: BMI (kg/m2)	25

tag: Glucose (mmol/L)	4.9

tag: Cholesterol (mmol/L)	4.01

tag: Triglyceride (mmol/L)	1.2

tag: HDL (mmol/L)	1.16

tag: LDL (mmol/L)	2.3

tag: Platelets (E9/L)	190

tag: Neutrophil (E9/L)	2.05

tag: Lymphocytes (E9/L)	1.6

tag: Monocytes (E9/L)	0.25

tag: Eosinophil (E9/L)	0.16

tag: Basophil (E9/L)	0.04


title: MC115

tag: Sex	M

tag: Age (y)	55

tag: Glucose (mmol/L)	4.5

tag: Cholesterol (mmol/L)	6.33

tag: Triglyceride (mmol/L)	1.24

tag: HDL (mmol/L)	2.72

tag: LDL (mmol/L)	3.04

tag: Platelets (E9/L)	256

tag: Neutrophil (E9/L)	3.55

tag: Lymphocytes (E9/L)	2.56

tag: Monocytes (E9/L)	0.64

tag: Eosinophil (E9/L)	0.21

tag: Basophil (E9/L)	0.14


title: MC133

tag: Age (y)	36

tag: Glucose (mmol/L)	4.3

tag: Cholesterol (mmol/L)	5.38

tag: Triglyceride (mmol/L)	0.69

tag: HDL (mmol/L)	1.38

tag: LDL (mmol/L)	3.68

tag: Platelets (E9/L)	243

tag: Neutrophil (E9/L)	2.85

tag: Lymphocytes (E9/L)	2.99

tag: Monocytes (E9/L)	0.73

tag: Eosinophil (E9/L)	0.73

tag: Basophil (E9/L)	0


title: MC091

tag: Sex	M

tag: Age (y)	39

tag: BMI (kg/m2)	19

tag: Glucose (mmol/L)	4.8

tag: Cholesterol (mmol/L)	5.68

tag: Triglyceride (mmol/L)	1.02

tag: HDL (mmol/L)	1.64

tag: LDL (mmol/L)	3.57

tag: Platelets (E9/L)	244

tag: Neutrophil (E9/L)	1.89

tag: Lymphocytes (E9/L)	2.6

tag: Monocytes (E9/L)	0.31

tag: Eosinophil (E9/L)	0.15

tag: Basophil (E9/L)	0.15


title: MC117

tag: Age (y)	47

tag: Glucose (mmol/L)	5.1

tag: Cholesterol (mmol/L)	5.16

tag: Triglyceride (mmol/L)	1.62

tag: HDL (mmol/L)	1.59

tag: LDL (mmol/L)	2.83

tag: Neutrophil (E9/L)	2.61

tag: Lymphocytes (E9/L)	2.32

tag: Monocytes (E9/L)	0.52

tag: Eosinophil (E9/L)	0.12

tag: Basophil (E9/L)	0.23


title: MC119

tag: Sex	M

tag: Age (y)	30

tag: BMI (kg/m2)	26

tag: Glucose (mmol/L)	4.2

tag: Cholesterol (mmol/L)	4.82

tag: Triglyceride (mmol/L)	1.02

tag: HDL (mmol/L)	1.25

tag: LDL (mmol/L)	3.1

tag: Platelets (E9/L)	257

tag: Neutrophil (E9/L)	2.35

tag: Lymphocytes (E9/L)	1.46

tag: Monocytes (E9/L)	0.75

tag: Eosinophil (E9/L)	0.09

tag: Basophil (E9/L)	0.05


title: MC189

tag: Sex	F

tag: Age (y)	54

tag: Glucose (mmol/L)	4.8

tag: Cholesterol (mmol/L)	6.41

tag: Triglyceride (mmol/L)	1.67

tag: HDL (mmol/L)	1.65

tag: LDL (mmol/L)	3.99

tag: Platelets (E9/L)	191

tag: Neutrophil (E9/L)	2.92

tag: Lymphocytes (E9/L)	1.84

tag: Monocytes (E9/L)	0.38

tag: Eosinophil (E9/L)	0.16


title: MC092

tag: Sex	M

tag: Age (y)	48

tag: Glucose (mmol/L)	5.3

tag: Cholesterol (mmol/L)	4.56

tag: Triglyceride (mmol/L)	0.69

tag: HDL (mmol/L)	2.2

tag: LDL (mmol/L)	2.04

tag: Platelets (E9/L)	192

tag: Neutrophil (E9/L)	2.06

tag: Lymphocytes (E9/L)	1.51

tag: Monocytes (E9/L)	0.46

tag: Eosinophil (E9/L)	0.13

tag: Basophil (E9/L)	0.04


title: MC252

tag: Sex	F

tag: Age (y)	54

tag: Glucose (mmol/L)	4.6

tag: Cholesterol (mmol/L)	4.72

tag: HDL (mmol/L)	2.24

tag: LDL (mmol/L)	2.16

tag: Platelets (E9/L)	199

tag: Neutrophil (E9/L)	1.37

tag: Lymphocytes (E9/L)	2.03

tag: Monocytes (E9/L)	0.39

tag: Eosinophil (E9/L)	0.08


title: MC190

tag: Age (y)	60

tag: Glucose (mmol/L)	6.1

tag: Cholesterol (mmol/L)	5.18

tag: Triglyceride (mmol/L)	0.75

tag: HDL (mmol/L)	2.14

tag: LDL (mmol/L)	2.7

tag: Platelets (E9/L)	236

tag: Neutrophil (E9/L)	2.09

tag: Lymphocytes (E9/L)	1.22

tag: Monocytes (E9/L)	0.3

tag: Basophil (E9/L)	0.08


title: MC070

tag: Sex	F

tag: Age (y)	42

tag: Glucose (mmol/L)	3.2

tag: Cholesterol (mmol/L)	4.50

tag: Triglyceride (mmol/L)	0.63

tag: HDL (mmol/L)	2.17

tag: LDL (mmol/L)	2.04

tag: Platelets (E9/L)	251

tag: Neutrophil (E9/L)	2.87

tag: Lymphocytes (E9/L)	1.32

tag: Monocytes (E9/L)	0.38

tag: Eosinophil (E9/L)	0.09

tag: Basophil (E9/L)	0.05


title: MC278

tag: Age (y)	57

tag: Glucose (mmol/L)	4.4

tag: Cholesterol (mmol/L)	7.34

tag: Triglyceride (mmol/L)	0.61

tag: HDL (mmol/L)	2.67

tag: LDL (mmol/L)	4.39

tag: Platelets (E9/L)	260

tag: Neutrophil (E9/L)	1.56

tag: Lymphocytes (E9/L)	1.76

tag: Monocytes (E9/L)	0.41

tag: Eosinophil (E9/L)	0.29


title: MC066

tag: Sex	F

tag: Age (y)	69

tag: Glucose (mmol/L)	4.5

tag: Cholesterol (mmol/L)	5.37

tag: Triglyceride (mmol/L)	0.6

tag: HDL (mmol/L)	2.6

tag: LDL (mmol/L)	2.49

tag: Platelets (E9/L)	265

tag: Neutrophil (E9/L)	2.7

tag: Lymphocytes (E9/L)	2.04

tag: Monocytes (E9/L)	0.44

tag: Eosinophil (E9/L)	0.22

tag: Basophil (E9/L)	0.11


title: MC158

tag: Age (y)	66

tag: Glucose (mmol/L)	4.6

tag: Cholesterol (mmol/L)	7.37

tag: Triglyceride (mmol/L)	1.84

tag: HDL (mmol/L)	1.9

tag: LDL (mmol/L)	4.63

tag: Platelets (E9/L)	204

tag: Neutrophil (E9/L)	2.07

tag: Lymphocytes (E9/L)	1.3

tag: Monocytes (E9/L)	0.26

tag: Eosinophil (E9/L)	0

tag: Basophil (E9/L)	0.04


title: MC0024

tag: Sex	M

tag: Age (y)	26

tag: Glucose (mmol/L)	4.4

tag: Cholesterol (mmol/L)	4.79

tag: Triglyceride (mmol/L)	1.38

tag: HDL (mmol/L)	1.25

tag: LDL (mmol/L)	2.91

tag: Platelets (E9/L)	197

tag: Neutrophil (E9/L)	1.64

tag: Lymphocytes (E9/L)	2.54

tag: Monocytes (E9/L)	0.42

tag: Eosinophil (E9/L)	0.53

tag: Basophil (E9/L)	0.16


title: MC036

tag: Sex	F

tag: Glucose (mmol/L)	3.7

tag: Cholesterol (mmol/L)	4.15

tag: Triglyceride (mmol/L)	0.5

tag: HDL (mmol/L)	1.36

tag: LDL (mmol/L)	2.56

tag: Platelets (E9/L)	247

tag: Neutrophil (E9/L)	2.88

tag: Lymphocytes (E9/L)	3.08

tag: Monocytes (E9/L)	0.47

tag: Eosinophil (E9/L)	0.07

tag: Basophil (E9/L)	0.2


title: MC062

tag: Age (y)	27

tag: Glucose (mmol/L)	3.3

tag: Cholesterol (mmol/L)	3.78

tag: Triglyceride (mmol/L)	1.4

tag: HDL (mmol/L)	2.02

tag: LDL (mmol/L)	1.12

tag: Platelets (E9/L)	264

tag: Neutrophil (E9/L)	3.89

tag: Lymphocytes (E9/L)	2.38

tag: Monocytes (E9/L)	0.72

tag: Eosinophil (E9/L)	0.14

tag: Basophil (E9/L)	0.07


title: MC008

tag: Sex	F

tag: Age (y)	32

tag: Glucose (mmol/L)	4.4

tag: Cholesterol (mmol/L)	4.71

tag: Triglyceride (mmol/L)	0.74

tag: HDL (mmol/L)	1.72

tag: LDL (mmol/L)	2.65

tag: Platelets (E9/L)	244

tag: Neutrophil (E9/L)	4.82

tag: Lymphocytes (E9/L)	1.68

tag: Monocytes (E9/L)	0.66


title: Caco-2-cells_filter-grown_not-induced_rep2

description: original experiment name: Coculture-Caco_08_01_Kontr_TGT1000

source_name: filter-grown not-induced Caco-2-cells

tag: colon adeno carcinoma cell line (Caco-2) on a Transwell filter


title: Caco-2-cells_filter-grown_lymphocyte-induced_rep1

description: original experiment name: Coculture-Caco1_08_01_TGT1000

source_name: filter-grown lymphocyte-induced Caco-2-cells and lymphocytes from human venous blood

tag: colon adeno carcinoma cell line (Caco-2) on a Transwell filter, induced by human venous lymphocytes


title: Caco-2-cells_filter-grown_lymphocyte-induced_rep3

description: original experiment name: Coculture-Cacos-Lym-16-10_TGT1000


title: Caco-2-cells_filter-grown_lymphocyte-induced_rep2

description: original experiment name: Coculture-Caco2_08_01_TGT1000


title: Lymphocytes_bottle-grown_rep1

description: original experiment name: Coculture-Lymphos-16-10_TGT1000

source_name: bottle-grown lymphocytes

tag: human venous lymphocytes


title: CtrXM_8hr.2_m

status: Public on Aug 02 2006

city: Singapore

first: Siew Hong

last: Lam

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description:
Fish were treated with arsenic [As(V)] acid (Na2HAsO4.7H2O; Sigma, USA) at 60 mg/L in a static condition for 96 hours (h) whereby less than 10% mortality occurred in arsenic-treated group within the experiment duration. No mortality was observed in the control group. The concentration was chosen based on an initial survival versus concentration experiment.  Fish livers were sampled at 8 h, 24 h, 48 h and 96 h, and 12 fish livers were separated into 3 pooled-samples (each pooled samples consist of 4 livers) at each time point.
Three biological replicates are performed for each time point (8,24,48,96 hrs).  Test and control samples are hybridized against a reference.  No dye swap experiment has been performed.

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized.Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: Zebrafish liver tissue

label_protocol:
For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were
reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and
resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were reared at room temperature (27 ± 2°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

tag: Zebrafish liver tissue exposed to arsenic

tag: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues

tag: of wild-type zebrafish.


title: CtrXM_24hr.1_m

label_protocol:
For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse
transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and resuspended in
DIG EasyHyb (Roche Applied Science) buffer for hybridization.


title: CtrXM_24hr.3_m


title: Caco-2-cells_bottle-grown_not-induced_rep1

description: original experiment name: Coculture-Cacos-pur-16-10_TGT1000

source_name: bottle-grown not-induced Caco-2-cells

tag: colon adeno carcinoma cell line (Caco-2)


title: Caco-2-cells_filter-grown_not-induced_rep1

description: original experiment name: Coculture-Caco-Co-16-10_TGT1000


title: CtrXM_96hr.3_m


title: As_8hr.3_M


title: CtrXM_24hr.2_m


title: CtrXM_48hr.2_m


title: As_8hr.2_M


title: As_96h.2_M


title: CtrXM_8hr.1_m


title: As_96h.3_M


title: CtrXM_8hr.3_m


title: CtrXM_96hr.2_m


title: As_96h.1_M


title: CtrXM_48hr.3_m


title: As_48h.1_M


title: CtrXM_48hr.1_m


title: As_48h.3_M


title: As_8hr.1_M


title: As_24hr.1_M


title: CtrXM_96hr.1_m


title: As_48h.2_M


title: Patient 19 LPS treated

status: Public on Aug 01 2006

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

description: Patient 19 LPS treated

data_processing: GCRMA

source_name: Neutrophil

label_protocol: Approximately 3 µg of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol

extract_protocol: Approximately 20 million peripheral blood neutrophils, previously stabilized in RNAlater (Ambion), were lysed in Trizol (Life Technologies) and total RNA isolated with Rneasy MinElute columns (Qiagen).

tag: none provided


title: Patient 08 LPS treated

description: Patient 08 LPS treated


title: Patient 12 LPS treated

description: Patient 12 LPS treated


title: Patient 15 LPS treated

description: Patient 15 LPS treated


title: As_24hr.3_M


title: AS_24hr.2_M


title: Patient 09 LPS treated

description: Patient 09 LPS treated


title: Patient 15 HMGB1 treated

description: Patient 15 HMGB1 treated


title: Patient 07 LPS treated

description: Patient 07 LPS treated


title: Patient 06 HMGB1 treated

description: Patient 06 HMGB1 treated


title: Patient 12 HMGB1 treated

description: Patient 12 HMGB1 treated


title: Patient 06 LPS treated

description: Patient 06 LPS treated


title: Patient 19 HMGB1 treated

description: Patient 19 HMGB1 treated


title: Patient 05 LPS treated

description: Patient 05 LPS treated


title: Patient 09 HMGB1 treated

description: Patient 09 HMGB1 treated


title: Patient 19 control

description: Patient 19 control


title: Patient 05 HMGB1 treated

description: Patient 05 HMGB1 treated


title: Patient 15 control

description: Patient 15 control


title: Patient 07 control

description: Patient 07 control


title: Patient 06 control

description: Patient 06 control


title: Patient 08 control

description: Patient 08 control


title: Patient 07 HMGB1 treated

description: Patient 07 HMGB1 treated


title: Patient 08 HMGB1 treated

description: Patient 08 HMGB1 treated


title: Patient 09 control

description: Patient 09 control


title: Patient 12 control

description: Patient 12 control


title: WT vs aflR mutant timecourse slide 11

status: Public on Jun 01 2006

city: Lynchburg

first: Michael

middle: S

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

description:
RNA was isolated from lyophilized cultures of a wild type and an aflR- strain of Aspergillus parasiticus SU1 using Trizol (Life Technologies, Rockville, MD) according to the manufacturers instructions. cDNA synthesis, labeling, and hybridization were performed using a protocol modified from Chhabra, et al., 2003. J Biol Chem 278:7540.
Keywords = aspergillus
Keywords = aflatoxin
Keywords = secondary metabolism

organism: Aspergillus parasiticus

source_name: A. parasiticus aflR- at 24hr

source_name: A. parasiticus SU1 at 24hr


title: WT vs aflR mutant timecourse slide 7

source_name: A. parasiticus aflR- at 8hr

source_name: A. parasiticus SU1 at 8hr


title: Patient 05 control

description: Patient 05 control


title: WT vs aflR mutant timecourse slide 10

source_name: A. parasiticus SU1 at 16hr


title: WT vs aflR mutant timecourse slide 5


title: Control accumbens

status: Public on Feb 03 2006

city: Tokushima

first: Gen

last: Tamiya

state: Tokushima

address: Kuramoto

department: Department of Neurology, Graduate School of Medicine

country: Japan

institute: Tokushima University

hyb_protocol: Standard Affymetrix procedures for hybridization, blocking and washing, including any post-processing steps

scan_protocol: Affymetrix GeneChip scanner 3000 (00-0074)

data_processing: Standard Affymetrix procedures.

label: Biotin

source_name: nucleus accumbens

label_protocol: Standard Affymetrix procedure for biotin labeling. Approximately 2 micro-g of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Standard QIAGEN procedure for total RNA extraction using RNeasy Lipid Tissue Midi kit (QIAGEN)

treatment_protocol: The specimen was frozen in liquid nitrogen at autopsy.

tag: The nucleus accumbens from a neurologically normal Jpanese male (aged 60 yr).


title: WT vs aflR mutant timecourse slide 9

source_name: A. parasiticus aflR- at 16hr


title: WT vs aflR mutant timecourse slide 3


title: WT vs aflR mutant timecourse slide 8


title: WT vs aflR mutant timecourse slide 6


title: WT vs aflR mutant timecourse slide 1


title: B2 replicate 2

status: Public on Jan 31 2006

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Wild type, C57BL/6, spleen B2-B cells, IgM(int)IgD(hi)CD11b-

data_processing: RMA

source_name: Splenic B2-B cells

label_protocol: Approximately 2 µg of amplified RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 100,000 B2-B cells were sorted. Total RNA was extracted from the sorted cells using TRIZOL.


title: XDP caudate nucleus

source_name: caudate nucleus

treatment_protocol: The specimen was frozen in a deep freezer at autopsy immediately after his death from pneumonia.

tag: The caudate nucleus from an XDP Filipino (aged 52 yr) .


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (12%-3)

status: Public on Feb 17 2006

city: La Jolla

first: Dan

last: Zhou

state: CA

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

data_processing: D Zhou, J Xue, O Gavrialov and GG Haddad. Physiol Genomics 18(3):331-339, 2004

source_name: Lung from 2-week chronic 12% CO2 treated mouse

tag: Strain

tag: Age

value: 16 days

tag: Tissue

value: Lung

tag: Treatment

value: 2-week chronic 12% CO2

source_name: Lung, from 16 days old control mouse

value: Control


title: XDP nucleus accumbens

tag: An XDP Filipino (aged 52 yr)


title: B2 replicate 1

tag: Wild type, C57BL/6, spleen B2-B cells, IgM(int)IgD(hi)CD11b-


title: WT vs aflR mutant timecourse slide 12


title: B1 replicate 2

description: Wild type, C57BL/6, Peritoneal B1-B cells, IgM(hi)IgD(int)CD11b+

source_name: Peritoneal B1-B cells

extract_protocol: Approximately 100,000 B1-B cells were sorted. Total RNA was extracted from the sorted cells using TRIZOL.


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (8%-4)

source_name: Lung from 2-week chronic 8% CO2 treated mouse

value: 2-week chronic CO2


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (12%-4)

source_name: Lung from 16 days old control mouse

source_name: Lung, from 2-week chronic 12% CO2 treated mouse


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (8%-5)

value: 2-week chronic 8% CO2


title: CD8aaT replicate 2

description: CD8 alpha alpha RTOC cells selected by high-dose agonist (10 mM Smcy). TCRb+CD8a+CD8b-

source_name: RTOC CD8aaT cells

extract_protocol: Approximately 50,000 CD8aa T cells were sorted. Total RNA was extracted from the sorted cells using TRIZOL.


title: Control caudate

scan_protocol: Affymetrix GeneChip scanner 3000 (00-0074) Affymetrix GeneChip Operating Software (GCOS) ver. 1.1 (690036) Standard Affymetrix parameters

tag: The caudate nucleus from a neurologically normal Jpanese male (aged 60 yr).


title: CD8abT replicate 3

description: CD8 alpha beta RTOC cells selected by low-dose agonist (100 nM Smcy). TCRb+CD8a+CD8b+

source_name: RTOC CD8abT cells

extract_protocol: Approximately 50,000 CD8ab T cells were sorted. Total RNA was extracted from the sorted cells using TRIZOL.


title: CD8aaT replicate 1

tag: CD8 alpha alpha RTOC cells selected by high-dose agonist (10 mM Smcy). TCRb+CD8a+CD8b-


title: WT vs aflR mutant timecourse slide 2


title: B1 replicate 1

tag: Wild type, C57BL/6, Peritoneal B1-B cells, IgM(hi)IgD(int)CD11b+


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (12%-2)


title: WT vs aflR mutant timecourse slide 4

source_name: A. parasiticus aflR- at 24hr


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (8%-3)

source_name: Lung, from 2-week chronic 8% CO2 treated mouse


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (8%-2)


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach (12%-1)


title: Effect of Carbon Dioxide on Neonatal Mouse Lung: A Genomic Approach

value: 2-week Chronic 8% CO2

source_name: Lung, from 16 days old mouse

value: control


title: CD8abT replicate 1

tag: CD8 alpha beta RTOC cells selected by low-dose agonist (100 nM Smcy). TCRb+CD8a+CD8b+


title: NKT replicate 3

description: Wild type, C57BL/6, spleen NKT cells, CD3+CD4+NK1.1+

source_name: Splenic NKT cells

extract_protocol: Approximately 100,000 wild-type splenic NKT cells were sorted. Total RNA was extracted from the sorted cells using TRIZOL.


title: CD4T replicate 2

description: Wild type, C57BL/6, spleen CD4 T cells, CD3+CD4+NK1.1-

source_name: Splenic CD4 T cells

extract_protocol: Approximately 100,000 wild-type CD4 splenic T cells were sorted. Total RNA was extracted from the sorted cells using TRIZOL.


title: CD8abT replicate 2


title: NKT replicate 1

tag: Wild type, C57BL/6, spleen NKT cells, CD3+CD4+NK1.1+


title: CD4T replicate 1

tag: Wild type, C57BL/6, spleen CD4 T cells, CD3+CD4+NK1.1-


title: NKT replicate 2


title: CD4T replicate 3


title: GM09582 gamma vs. GM09582 mock (ExpID 137) Rep 1

status: Public on Jan 15 2006

city: DURHAM

first: Cynthia

last: Innes

state: NC

address: 111 ALEXANDER DR

department: NCT

institute: NIEHS

description: Human Ataxia telangiectasia non-fetal B-lymphocytes, EBV-immortalized, Coriell Institute for Medical Research, 12 yr old, Caucasian, female

data_processing: See Heinloth et al, 2003, Molecular Carcinogenesis 37:65-82

source_name: SR: GM09582 gamma (Cy3)

tag: GM09582 gamma

source_name: SG: GM09582 mock (Cy5)

tag: GM09582 mock


title: GM03714 5G + 6hr vs. GM03714 mock for 5G+6hr (ExpID 543) Rep 4

description: Human apparently healthy non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 10 yr old, Caucasian, European, female

source_name: GM03714 mock for 5G+6hr (Cy3)

tag: GM03714 mock for 5G+6hr


title: GM09582 gamma vs. GM09582 mock (ExpID 137) Rep 3

source_name: GM09582 gamma (Cy5)

source_name: GM09582 mock (Cy3)


title: GM03714 5G + 6hr vs. GM03714 mock for 5G+6hr (ExpID 543) Rep 1

source_name: SG: GM03714 mock for 5G+6hr (Cy5)


title: GM03714 5G + 6hr vs. GM03714 mock for 5G+6hr (ExpID 543) Rep 2


title: GM09582 gamma vs. GM09582 mock (ExpID 137) Rep 2


title: GM09582 gamma vs. GM09582 mock (ExpID 137) Rep 4


title: GM03657 gamma vs. GM03657 mock (ExpID 135) Rep 2

description: Human apparently healthy non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 68 yr old, Caucasian, male

source_name: SR: GM03657 gamma (Cy3)

tag: GM03657 gamma

source_name: SG: GM03657 mock (Cy5)

tag: GM03657 mock


title: GM03714_AT+/+_1GyIR_ vs. GM03714_AT+/+_mock_6 (ExpID 91) Rep 1


title: GM03714_AT+/+_1GyIR_ vs. GM03714_AT+/+_mock_6 (ExpID 91) Rep 3


title: GM03332 5G Irr (5/4) vs. GM03332 mock for 5G (5/4) (ExpID 541) Rep 4

description: Human Ataxia telangiectasia non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 13 yr old, Black male


title: GM03657 gamma vs. GM03657 mock (ExpID 135) Rep 4

source_name: GM03657 gamma (Cy5)

source_name: GM03657 mock (Cy3)


title: GM03657 gamma vs. GM03657 mock (ExpID 135) Rep 1


title: GM03714_AT+/+_1GyIR_ vs. GM03714_AT+/+_mock_6 (ExpID 91) Rep 4


title: GM03332 5G Irr (5/4) vs. GM03332 mock for 5G (5/4) (ExpID 541) Rep 1


title: GM03714_AT+/+_1GyIR_ vs. GM03714_AT+/+_mock_6 (ExpID 91) Rep 2


title: GM03332_AT-/-_1GyIR_ vs. GM03332_AT-/-_mock_6 (ExpID 89) Rep 2

description: Human Ataxia telangiectasia non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 13 yr old, Black, male


title: GM03657 gamma vs. GM03657 mock (ExpID 135) Rep 3


title: GM03332_AT-/-_1GyIR_ vs. GM03332_AT-/-_mock_6 (ExpID 89) Rep 4


title: GM03332_AT-/-_1GyIR_ vs. GM03332_AT-/-_mock_6 (ExpID 89) Rep 3


title: GM03332 5G Irr (5/4) vs. GM03332 mock for 5G (5/4) (ExpID 541) Rep 3


title: GM03714 5G + 6hr vs. GM03714 mock for 5G+6hr (ExpID 543) Rep 3


title: GM03332_AT-/-_1GyIR_ vs. GM03332_AT-/-_mock_6 (ExpID 89) Rep 1


title: GM03332 mock for 5G, 5/14/01 vs. GM03332 5G, 5/14/01 (ExpID 541) Rep 2


title: GM03189 gamma vs. GM03189 mock (ExpID 138) Rep 4

description: Human Ataxia telangiectasia non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 7 yr old, Caucasian, male

source_name: GM03189 gamma (Cy5)

tag: GM03189 gamma

source_name: GM03189 mock (Cy3)

tag: GM03189 mock


title: GM03189(AT) 5G Irr+6hr vs. GM03189 mock + 6hr, 10/15/01 (ExpID 548) Rep 4

tag: GM03189(AT) 5G Irr+6hr


title: GM03189(AT) 5G Irr+6hr vs. GM03189 mock + 6hr, 10/15/01 (ExpID 548) Rep 2

source_name: SR: GM03189(AT) 5G Irr+6hr (Cy3)


title: GM03189 5G Irr (5/24) vs. GM03189 mock (5G) Irr (5/24) (ExpID 548) Rep 1


title: CD8aaT replicate 3

source_name: RTOC CD8aaT cells


title: GM03189 gamma vs. GM03189 mock (ExpID 138) Rep 3


title: GM03189 gamma vs. GM03189 mock (ExpID 138) Rep 1

source_name: SR: GM03189 gamma (Cy3)

source_name: SG: GM03189 mock (Cy5)


title: GM03189(AT) 5G Irr+6hr vs. GM03189(AT) mock+6hr (ExpID 548) Rep 3

source_name: GM03189(AT) mock+6hr (Cy3)

tag: GM03189(AT) mock+6hr


title: GM02782 gamma 5G+6hr, 12/5/01 vs. GM02782 mock + 6hr, 12/5/01 (ExpID 542) Rep 2

description: Human Ataxia telangiectasia non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 5 yr old, Caucasian, Iranian, male


title: GM02782 gamma 5G+6hr, 12/5/01 vs. GM02782 mock + 6hr, 12/5/01 (ExpID 542) Rep 4


title: GM02254_AT+/+_1GyIR_ vs. GM02254_AT+/+_mock_6 (ExpID 92) Rep 4

description: Human apparently healthy non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 22 yr old, Caucasian, female


title: GM02782 gamma 5G+6hr, 12/5/01 vs. GM02782 mock + 6hr, 12/5/01 (ExpID 542) Rep 3


title: GM02782_AT-/-_1GyIR_ vs. GM02782_AT-/-_mock_6 (ExpID 90) Rep 3


title: GM02782 gamma 5G+6hr, 12/5/01 vs. GM02782 mock + 6hr, 12/5/01 (ExpID 542) Rep 1


title: GM02254 gamma 5G+6hr, 8/29/01 vs. GM02254 mock+6hr, 8/29/01 (ExpID 544) Rep 1


title: GM02782_AT-/-_1GyIR_ vs. GM02782_AT-/-_mock_6 (ExpID 90) Rep 4


title: GM02254 gamma 5G+6hr, 8/29/01 vs. GM02254 mock+6hr, 8/29/01 (ExpID 544) Rep 4


title: GM02254 gamma 5G+6hr, 8/29/01 vs. GM02254 mock+6hr, 8/29/01 (ExpID 544) Rep 3


title: GM02782_AT-/-_1GyIR_ vs. GM02782_AT-/-_mock_6 (ExpID 90) Rep 1


title: GM02254_AT+/+_1GyIR_ vs. GM02254_AT+/+_mock_6 (ExpID 92) Rep 1


title: GM01815 5G Irr vs. GM01815 mock for 5G (ExpID 546) Rep 2

description: Human apparently healthy non-fetal B-lymphocytes, EBV-immortalized, from Coriell Institute for Medical Research, 42 yr old, Caucasian, male

source_name: SR: GM01815 5G Irr (Cy3)

tag: GM01815 5G Irr

source_name: SG: GM01815 mock for 5G (Cy5)

tag: GM01815 mock for 5G


title: GM02254_AT+/+_1GyIR_ vs. GM02254_AT+/+_mock_6 (ExpID 92) Rep 2


title: GM01815, WT 1G Ir vs. GM01815, WT mock (ExpID 136) Rep 2

source_name: SR: GM01815, WT 1G Ir (Cy3)

tag: GM01815, WT 1G Ir

source_name: SG: GM01815, WT mock (Cy5)

tag: GM01815, WT mock


title: GM01815 5G Irr vs. GM01815 mock for 5G (ExpID 546) Rep 3

source_name: GM01815 mock for 5G (Cy3)


title: GM01815 gamma vs. GM01815 mock (ExpID 136) Rep 1

source_name: SR: GM01815 gamma (Cy3)

tag: GM01815 gamma

source_name: SG: GM01815 mock (Cy5)

tag: GM01815 mock


title: GM01815 gamma vs. GM01815 mock (ExpID 136) Rep 3

source_name: GM01815 gamma (Cy5)

source_name: GM01815 mock (Cy3)


title: GM01815 5G Irr vs. GM01815 mock for 5G (ExpID 546) Rep 1


title: E18.5 wt skin 2 B-chip

status: Public on Dec 10 2005

city: Houston

first: Maranke

last: Koster

address: One Baylor Plaza, Room T707

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Whole skin isolated from E18.5 wt embryo

source_name: E18.5 whole skin

extract_protocol: Trizol followed by RNeasy clean-up

tag: Whole skin isolated from E18.5 embryo


title: E18.5 p63 wt skin 1 A-chip

description: Whole skin isolated from E18.5 wt embryo.

extract_protocol: TriZol followed by RNeasy clean-up


title: E18.5 p63 wt skin 2 A-chip


title: E18.5 p63 null skin 2 A-chip

description: Whole skin isolated from E18.5 p63 null embryo.


title: E18.5 p63 null skin 1 B-chip

description: Whole skin isolated from E18.5 p63 null embryo


title: E18.5 wt skin 1 B-chip


title: E18.5 p63 null skin 2 B-chip


title: GM02782_AT-/-_1GyIR_ vs. GM02782_AT-/-_mock_6 (ExpID 90) Rep 2


title: GM02254 gamma 5G+6hr, 8/29/01 vs. GM02254 mock+6hr, 8/29/01 (ExpID 544) Rep 2


title: GM02254_AT+/+_1GyIR_ vs. GM02254_AT+/+_mock_6 (ExpID 92) Rep 3


title: GM01815 5G Irr vs. GM01815 mock for 5G (ExpID 546) Rep 4


title: GM01815, WT 1G Ir vs. GM01815, WT mock (ExpID 136) Rep 4

source_name: GM01815, WT mock (Cy3)


title: E18.5 p63 null skin 1 A-chip

tag: E18.5 whole skin


title: day15 slide7

status: Public on Dec 05 2005

city: Lelystad

first: Saskia

middle: van

last: Hemert

address: PO box 65

country: Netherlands

institute: Animal Sciences Group

description: comparison 2 chicken lines

data_processing: genepix pro

organism: Gallus gallus

source_name: jejunum fast salmonella d15

tag: tissue

value: jejunum

tag: infection

value: salmonella

source_name: jejunum slow salmonella d15


title: day11 slide 5

description: comparison 2 chicken lines

source_name: jejunum fast control d11

source_name: jejunum slow control d11


title: day15 slide6

description: comparison 2 chicken lines

source_name: jejunum slow control d15

source_name: jejunum fast control d15


title: day15 slide5

description: comparison 2 chicken lines


title: day15 slide8

description: comparison 2 chicken lines


title: GM03189 gamma vs. GM03189 mock (ExpID 138) Rep 2

source_name: SR: GM03189 gamma (Cy3)

source_name: SG: GM03189 mock (Cy5)


title: day15 slide4

description: comparison 2 chicken lines


title: day15 slide1

description: comparison 2 chicken lines


title: day11 slide 1

description: comparison 2 chicken lines

source_name: jejunum fast salmonella d11


title: day11 slide2

description: comparison 2 chicken lines


title: day11 slide3

description: comparison 2 chicken lines

source_name: jejunum slow salmonella d11


title: day11 slide7

description: comparison 2 chicken lines

source_name: jejuum slow salmonella d11


title: day11 slide4

description: comparison 2 chicken lines


title: day9 slide 7

description: comparison 2 chicken lines

source_name: jejunum fast salmonella d9

source_name: jejunum slow salmonella d9


title: day11 slide6

description: comparison 2 chicken lines


title: day9 slide5

description: comparison 2 chicken lines

source_name: jejunum fast control d9

source_name: jejunum slow control d9


title: day9 slide3

description: comparison 2 chicken lines


title: day15 slide2

description: comparison 2 chicken lines


title: day9 slide4

description: comparison 2 chicken lines


title: day15 slide3

description: comparison 2 chicken lines


title: day7 slide8

description: comparison 2 chicken lines

source_name: jejunum slow salmonella d7

source_name: jejunum fast salmonella d7


title: day9 slide 6

description: comparison 2 chicken lines


title: day9 slide8

description: comparison 2 chicken lines


title: day7 slide7

description: comparison 2 chicken lines


title: day7 slide3

description: comparison 2 chicken lines

source_name: jejunum slow control d7

source_name: jjeunum slow salmonella d7


title: day7 slide4

description: comparison 2 chicken lines


title: day7 slide 6

description: comparison 2 chicken lines

source_name: jejunum fast control


title: day9 slide2

description: comparison 2 chicken lines


title: day 5 slide8

description: comparison 2 chicken lines

source_name: jejunum slow salmonella d5

source_name: jejunum fast salmonella d5


title: day7 slide2

description: comparison 2 chicken lines

source_name: jejunum fast control d7


title: day5 slide 6

description: comparison 2 chicken lines

source_name: jejunum slow control d5

source_name: jejunum fast control d5


title: day5 slide 5

description: comparison 2 chicken lines


title: day5 slide 2

description: comparison 2 chicken lines

source_name: jejunum fast control day5


title: day5 slide4

description: comparison 2 chicken lines


title: day3 slide7

description: comparison 2 chicken lines

source_name: jejunum fast salmonella d3

source_name: jejunum slow salmonella d3


title: day 5 slide 7

description: comparison 2 chicken lines


title: day7 slide 1

description: comparison 2 chicken lines


title: day3 slide5

description: comparison 2 chicken lines

source_name: jejunum fast control d3

source_name: jejunum slow control d3


title: day7 slide 5

description: comparison 2 chicken lines

source_name: jejunum fast cntrol d7


title: day3 slide3

description: comparison 2 chicken lines


title: day3 slide 4

description: comparison 2 chicken lines

source_name: jejunumslow control d3


title: day3 slide 8

description: comparison 2 chicken lines


title: day3 slide 2

description: comparison 2 chicken lines


title: day3 slide 6

description: comparison 2 chicken lines


title: day 1 slide 7

description: comparison 2 chicken lines

source_name: jejunum fast salmonella d1

source_name: jejunum slow salmonella d1


title: day 1 slide 6

description: comparison 2 chicken lines

source_name: jejunumslow control d1

source_name: jejunum fast control d21


title: day 1 slide 4

description: comparison 2 chicken lines

source_name: jejunum slow control d1


title: day3 slide1

description: comparison 2 chicken lines


title: day 1 slide 3

description: comparison 2 chicken lines


title: day 1 slide 1

description: comparison 2 chicken lines

source_name: jejunum fast control d1


title: day 1 slide 8

description: comparison 2 chicken lines

source_name: jejunum fast salmonella


title: day 1 slide 2

description: comparison 2 chicken lines


title: d21 slide7

description: comparison 2 chicken lines

source_name: jejunum fast salmonella d21

source_name: jejunum slow salmonella d21

tag: infection salmonella


title: day 21 slide 8

description: comparison 2 chicken lines

source_name: jejunum slow salmonella


title: day 1 slide 5

description: comparison 2 chicken lines


title: day21 slide 6

description: comparison 2 chicken lines

source_name: jejunum slow control d21


title: day21 slide 5

description: comparison 2 chicken lines

tag: Tissue

tag: Infection

source_name: jejunum S control d21


title: MZZ_Fe_He_01

status: Public on Dec 04 2005

city: Ibaraki

first: Naoki

last: Osada

state: Osaka

address: 7-6-8 Saito-Asagi

department: Division of Biomedical Research Resources

institute: National Institute of Biomedical Innovation

description:
Analysis of ZM behavioral differentiation.
3-5 days 100-200 nonvirgin fly heads.
Each character denotes where first, second, and third chromosomes are derived (Z:Z30, M:Fr).

source_name: MZZ nonvirgin female heads


title: ZMZ_Fe_He_01

source_name: ZMZ nonvirgin female heads


title: MMZ_Fe_He_01

source_name: MMZ nonvirgin female heads


title: Z30_Fe_He_01

description:
Analysis of ZM behavioral differentiation.
3-5 days 100-200 nonvirgin fly heads.

source_name: Z30 nonvirgin female heads


title: MZM_Fe_He_01

source_name: MZM nonvirgin female heads


title: d21slide4

description: compare salmonella and control

data_processing: Genepix pro

source_name: jejunum d21 slowgrowing salmonella

source_name: jejunum d21 slowgrowing control


title: ZZM_Fe_He_01

source_name: ZZM nonvirgin female heads


title: Z30_Fe_He_02

description: Analysis of ZM behavioral differentiation.3-5 days 100-200 nonvirgin fly heads.


title: ZMM_Fe_He_01

source_name: ZMM nonvirgin female heads


title: Fr_Fe_He_02

source_name: Fr nonvirgin female heads


title: d21slide3

description: control vs salmonella

source_name: jejunum 21 days P.I. slowgrowing control

source_name: jejunum 21 days P.I. slowgrowing infected


title: day21 slide1

description: compare salmonella and control conditions

source_name: jejunum d21 fastgrowing control

source_name: jejunum d21 fastgrowing salmonella


title: d21slide2

description: compare control and salmonella

source_name: jejunum day21 fastgrowing salmonella

source_name: jejunum day21 fastgrowing control


title: Fr_Fe_He_01


title: MCF7_OF_6_Illumina

status: Public on Dec 01 2005

city: Oxford

first: Ioannis

last: Ragoussis

address: Roosevelt Drive

department: The Wellcome Trust Centre for Human Genetics

institute: University of Oxford

description: MCF7 cells exposed to oligofectamine and grown in Hypoxia

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Background was subtracted using the Illumina Studio, intensities were shifted to a minimum value of 20 and quantile normalization was performed using functions within R

label: Biotin-Labeled cRNA

source_name: MCF7, oligofectamine, Hypoxia 1% Oxygen, 16 hours

growth_protocol: Media: DMEM, 2mM L-Glutamine and 10% Fetal Bovine Serum

extract_protocol: Absolutely RNA RT-PCR Miniprep Kit (Stratagene)

treatment_protocol: Cells were exposed to oligofectamine transfection reagent and grown in Hypoxia (1% Oxygen) for 16 hours

tag: human breast carcinoma MCF7 cells


title: MCF7_HIF2_4_Illumina

description: MCF7 cells transfected with HIF-2alpha siRNA and grown in Hypoxia

scan_protocol: Refer to the Illumina Gene Expression System Manual

source_name: MCF7, HIF-2alpha siRNA, Hypoxia 1% Oxygen, 16 hours

treatment_protocol: Cells were transfected with HIF-2alpha siRNA and grown in Hypoxia (1% Oxygen) for 16 hours


title: MCF7_HIF1_5_Illumina

description: MCF7 cells transfected with HIF-1alpha siRNA and grown in Hypoxia

source_name: MCF7, HIF-1alpha siRNA, Hypoxia 1% Oxygen, 16 hours

label_protocol: Refer to the Illumina Gene Expression System Manual

treatment_protocol: Cells were transfected with HIF-1alpha siRNA and grown in Hypoxia (1% Oxygen) for 16 hours


title: MCF7_OF_5_Illumina


title: MCF7_HIF12_4_Illumina

description: MCF7 cells transfected with HIF-1alpha and HIF-2alpha siRNA and grown in Hypoxia

source_name: MCF7, HIF-1alpha and HIF-2alpha siRNA, Hypoxia 1% Oxygen, 16 hours

treatment_protocol: Cells were transfected with HIF-1alpha and HIF-2alpha siRNA and grown in Hypoxia (1% Oxygen) for 16 hours


title: MCF7_HIF2_6_Illumina


title: MCF7_HIF12_6_Illumina


title: MCF7_HIF2_5_Illumina


title: MCF7_HIF1_6_Illumina


title: MCF7_DMOG_2_Illumina

description: MCF7 cells grown in Normoxia and exposed to DMOG (dimethyloxalylglycine)

data_processing: Background was subtracted using the Illumina Studio, intensities were shifted to a minimum value of 20 and quantile normalization was performed using functions within R.

source_name: MCF7, Normoxia 21% Oxygen, DMOG

extract_protocol: Absolutely RNA RT-PCR Miniprep Kit(Stratagene)

treatment_protocol: Cells grown in Normoxia (21% Oxygen) and exposed to DMOG (2 mM) for 16 hours


title: MCF7_HIF12_5_Illumina


title: day5 slide1

description: comparison 2 chicken lines

source_name: jejunum fast control d5

source_name: jejunum fast salmonella d5


title: MCF7_DMOG_1

hyb_protocol: Refer to the Affymetrix Expression Analysis Technical Manual

data_processing: Normalized using the GCRMA algorithm


title: MCF7_Normoxia_3_Illumina

description: MCF7 cells grown in Normoxia

source_name: MCF7, Normoxia 21% Oxygen

treatment_protocol: Normoxia (21% oxygen)


title: MCF7_DMOG_3_Illumina


title: MCF7_Hypoxia_3

description: MCF7 cells grown in Hypoxia

scan_protocol: Refer to the Affymetrix Expression Analysis Technical Manual

source_name: MCF7, Hypoxia 1% Oxygen, 16 hours

treatment_protocol: Hypoxia 1% Oxygen, 16 hours in an Invivo2 Hypoxia Workstation


title: MCF7_DMOG_3

label_protocol: Refer to the Affymetrix Expression Analysis Technical Manual


title: MCF7_Normoxia_2_Illumina

description: MCF7 cells grown in Normoxia


title: MCF7_Hypoxia_2

description: MCF7 cells grown in Hypoxia


title: MCF7_DMOG_2


title: MCF7_Hypoxia_2_Illumina

description: MCF7 cells grown in Hypoxia


title: MCF7_Hypoxia_1

description: MCF7 cells grown in Hypoxia


title: MCF7_Normoxia_3

description: MCF7 cells grown in Normoxia


title: MCF7_OF_4_Illumina


title: MCF7_Normoxia_2

description: MCF7 cells grown in Normoxia


title: MCF7_Hypoxia_3_Illumina

description: MCF7 cells grown in Hypoxia


title: day5 slide 3

description: comparison 2 chicken lines

source_name: jejunum slow control d5

source_name: jejunum slow salmonella d5


title: MCF7_Normoxia_1

description: MCF7 cells grown in Normoxia


title: MCF7_HIF1_2


title: MCF7_HIF2_3


title: MCF7_HIF1_1


title: MCF7_HIF2_2


title: MCF7_HIF2_1


title: MCF7_OF_1


title: siWTAP 1

status: Public on Nov 30 2005

city: Kawasaki

first: Horiuchi

last: Keiko

state: Kanagawa

address: 1-396 Kosugi-cho, Nakahara-ku,

department: Protein-Protein Interaction

institute: Institute for Advanced Medical Sciences, Nippon Medical School

description: one of four samples (two control, two WTAP knockdown). The experiment studied the effect of knockdown WTAP in HUVEC.

source_name: Human umbilical vein endothelial cells (HUVEC)


title: siRNA mediated WTAP knockdown in HUVEC


title: control 2


title: MCF7_HIF1_4_Illumina


title: MCF7_OF_2


title: MCF7_HIF12_1


title: MCF7_HIF1_3


title: MCF7_HIF12_3


title: siWTAP 2


title: MCF7_HIF12_2


title: MCF7_OF_3


title: 8 h salt stressed replicate 1

status: Public on Nov 18 2005

city: Riverside

first: HARKAMAL

last: WALIA

address: Department of Botany & Plant Sciecnes

institute: University of California

description: salt stressed

data_processing: GCOS 1.2

organism: Hordeum vulgare

source_name: shoot tissue

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 12 plants were used for RNA extraction

tag: cv. Morex


title: 27 h salt stressed replicate 2

description: salt stressed


title: 27 h salt stressed replicate 3

description: salt stressed


title: 27 h control replicate 1

description: control


title: 27 h control replicate 2

description: control


title: 8 h salt stressed replicate 3

description: salt stressed


title: 8 h salt stressed replicate 2

description: salt stressed


title: 8 h control replicate 2

description: control


title: 27 h salt stressed replicate 1

description: salt stressed


title: 8 h control replicate 3

description: control


title: 8 h control replicate 1

description: control


title: 3 h salt stressed replicate 2

description: salt stressed


title: 3 h control replicate 1

description: control


title: 27 h control replicate3

description: control


title: 3 h salt stressed replicate 3

description: salt stressed


title: 50US_50P_B_Illumina

status: Public on Nov 08 2005

city: Cincinnati

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

description: Technical labeling replicate of 50US_50P_A_Illumina (GSM67541).

data_processing: Quantile Normalized

label: Illumina Standard

source_name: PBMC and Placenta

tag: Approximately 50 mL whole blood was collected from 30 adult, apparently healthy, volunteers using Acid Citrate Dextrose (ACD) as an anti-coagulant. Samples were processed immediately following blood draw. Cells were isolated by Ficoll gradient centrifugation and total RNA was isolated using Trizol (Invitrogen Life Technologies; Carlsbad, CA) according to manufacturer’s protocol, aliquoted and stored at -80°C until use. Whole placenta was collected and immediately frozen in liquid nitrogen. RNA was extracted using TRI reagent, purified using RNeasy columns (Qiagen; Valencia, CA), aliquoted and stored at -80°C until use. RNA mixtures (100:0, 95:5, 75:25, 50:50, 25:75, 0:100; PBMC

value: placenta) were prepared in single aliquots.


title: 3 h salt stressed replicate 1

description: salt stressed


title: 3 h control replicate 3

description: control


title: 100P_B_Illumina

description: Technical labeling replicate of 100_P_Illumina (GSM67642).

source_name: Placenta


title: 3 h control replicate 2

description: control


title: 50US_50P_A_Illumina

description: Technical labeling replicate of 50US_50P_B_Illumina (GSM67542).


title: 75US_25P_B_Illumina

description: Technical labeling replicate of 75US_25P_A_Illumina (GSM67538).


title: 25US_75P_B_Illumina

description: Technical labeling replicate of 24US_75P_A_Illumina (GSM67543).


title: 25US_75P_A_Illumina

description: Technical labeling replicate of 25US_75P_B_Illumina (GSM67544).


title: 95US_5P_B_Illumina

description: Technical labeling replicate of 95US_5P_A_Illumina (GSM67536).


title: 95US_5P_A_Illumina

description: Technical labeling replicate of 95US_5P_B_Illumina (GSM67537).


title: 100P_A_Illumina

description: Technical labeling replicate of 100P_B_Illumina (GSM67642).


title: 100US_B_Illumina

description: Technical labeling replicate of 100US_A_Illumina (GSM6734).

source_name: PBMC


title: 100US_A_Illumina

description: Technical labelig replicate of 100US_B_Illumina (GSM67535)


title: 75US_25P_A_Illumina

description: Technical labeling replicate of 75US_25P_B_Illumina (GSM67540).


title: ST01-393

status: Public on Oct 01 2005

first: Bradley

middle: J

last: Quade

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: Atypical (aka symplastic, bizarre, pleomorphic ) uterine leiomyomata having karyotype = 45,XX,-1,+8,der(9)ins(9;1)(q11;q11q32-q41),-18. Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.

hyb_protocol: by standard Affymetrix protocol

scan_protocol: by standard Affymetrix protocol

source_name: atypical uterine leiomyoma

label_protocol: by standard Affymetrix protocol

extract_protocol: Trizol

tag: Histological type

value: Atypical

tag: Karyotype


title: GEIM128-NORM

first: Steven

middle: Alan

last: Greenberg

department: Neurology

description: Patient #128 with NORM

label: streptavidin phycoerythrin

source_name: muscle

tag: Human skeletal muscle biopsy sample

tag: Patient #128 with NORM


title: GEIM57-NORM

description: Patient #57 with NORM

tag: Patient #57 with NORM


title: GEIM133-NORM

description: Patient #133 with NORM

tag: Patient #133 with NORM


title: GEIM193-NORM

description: Patient #193 with NORM

tag: Patient #193 with NORM


title: GEIM175-PM

description: Patient #175 with PM

tag: Patient #175 with PM


title: GEIM63-NORM

description: Patient #63 with NORM

tag: Patient #63 with NORM


title: GEIM16-PM

description: Patient #16 with PM

tag: Patient #16 with PM


title: GEIM17-PM

description: Patient #17 with PM

tag: Patient #17 with PM


title: GEIM110-NORM

description: Patient #110 with NORM

tag: Patient #110 with NORM


title: GEIM50-NORM

description: Patient #50 with NORM

tag: Patient #50 with NORM


title: GEIM45-NORM

description: Patient #45 with NORM

tag: Patient #45 with NORM


title: ST01-298

description: Cellular uterine leiomyoma with karyotype = 44,XX,del(1)(p11-12),-19,-21/44,idem,del(13)(q14q22). Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.

source_name: cellular uterine leiomyoma

value: Cellular


title: GEIM186-NORM

description: Patient #186 with NORM

tag: Patient #186 with NORM


title: GEIM218-NORM

description: Patient #218 with NORM

tag: Patient #218 with NORM


title: GEIM197-PM

description: Patient #197 with PM

tag: Patient #197 with PM


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-49, patient 1

status: Public on Nov 01 2005

city: Trondheim

first: Kristin

last: Nørsett

department: Dept of Cancer Research and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

description: This represents hybridization of gastric mucosa total RNA from one of eight patients given omeprazole (40 mg omeprazole once daily for 90 days) vs. gastric mucosa total RNA from the same patient before treatment.

hyb_protocol: The Cy3 and Cy5 labeled samples (combined volume 5 microliter) were mixed with 31 microliter of the hybridization solution containing 0.25 M NaPO4, 1 mM EDTA, 4.5% SDS, 1 x SSC, 2 x Denhardt's solution, 1 microliter High-End Differential Enhancer (Genisphere) and 0.2 microgram human COT-1 DNA (GIBCO BRL Life Technologies), added onto the array and covered with 22 x 50mm cover slip. The array was assembled into humidified hybridization chamber (Corning) and hybridized at 65 degree C for 18 h by submerging in a water bath. Post-hybridization washes were done once in 2 x SSC, 0.2% SDS at 55 degree C for 15 min, then in 2 x SSC at room temperature for 15 min, and finally with 0.2 x SSC at room temperature for 15 min.

scan_protocol: Arrays were scanned at 10 micrometer resolution with a ScanArray Express HT scanner (Packard BioSciences, Billerica, MA).

data_processing: Microarray image analysis was done with MicroArray Suite software version 2.1 (Scanalytics, Inc., Fairfax VA) with default settings. A signal to noise ratio based criterion was applied to remove the spots with spot intensity vs. background intensity ratio less than 1 in either channel. A spot area based criterion was applied to remove the spots with the area less than 10 pixels in either channel. Print tip-dependent normalization was applied to the data in order to compensate for systematic errors. The data was normalized by subtraction of the smooth curve found by the LOWESS (LOcally Weighted Scatter plot Smoothing) algorithm. The normalized ratio of the duplicates were averaged.

source_name: Gastric mucosa from omeprazole treated patient

label_protocol: Total RNA from patients before treatment (2 microgram each) and patients after treatment (2 microgram each) were reverse transcribed and labeled with Cy3- and Cy5-attached dendrimer, respectively, using 3DNA Array Detection Submicro kit as described in the manufacturer's protocols (Genisphere, Montvale, NJ). The labeling reactions were also spiked with exogenous control RNAs (Stratagene) at expected Cy5/Cy3 ratios of 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 0.5, 0.33, 0.25 and 0.125 for control spike 1, 2, 3, 4, 5, 6, 8, 9, 10 and 7, respectively.

extract_protocol: Total RNA extraction was performed first by Rneasy kit of Qiagen (Basel, Switzerland) and then using TRIZOL Reagent (GIBCO BRL Life Technologies, New York, NY).

treatment_protocol: Patient was treated with 40 mg omeprazole (Losec, Astra AB, Gothenburg, Sweden) once daily for 90 days. Biopsy speciments were taken form the oxyntic mucosa during the last week of treatment.

source_name: Gastric mucosa from same patient before treatment

treatment_protocol: Patient was treated with 40 mg omeprazole (Losec, Astra AB, Gothenburg, Sweden) once daily for 90 days. Biopsy speciments were taken form the oxyntic mucosa before treatment.


title: GEIM176-NORM

description: Patient #176 with NORM

tag: Patient #176 with NORM


title: GEIM80-PM

description: Patient #80 with PM

tag: Patient #80 with PM


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-64, patient 13

scan_protocol: Arrays were scanned at 10 micrometer resolution with a ScanArray Express HT scanner (Packard BioSciences, Billerica, MA). Microarray image analysis was done with MicroArray Suite software version 2.1 (Scanalytics, Inc., Fairfax VA) with default settings.

data_processing: A signal to noise ratio based criterion was applied to remove the spots with spot intensity vs. background intensity ratio less than 1 in either channel. A spot area based criterion was applied to remove the spots with the area less than 10 pixels in either channel. Print tip-dependent normalization was applied to the data in order to compensate for systematic errors. The data was normalized by subtraction of the smooth curve found by the LOWESS (LOcally Weighted Scatter plot Smoothing) algorithm. The normalized ratio of the duplicates were averaged.

tag: Gastric mucosa from omeprazole treated patient

tag: Gastric mucosa from same patient before treatment


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-63, patient 11


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-61, patient 6


title: GEIM251-IBM

description: Patient #251 with IBM

data_processing: Affymetrix Microarray Suite version 5.0

tag: Human skeletal muscle biopsy sample

tag: Patient #251 with IBM


title: GEIM164-PM

description: Patient #164 with PM

tag: Patient #164 with PM


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-48, patient 5


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-47, patient 3

data_processing: Microarray image analysis was done with MicroArray Suite software version 2.1 (Scanalytics, Inc., Fairfax VA) with default settings. A signal to noise ratio based criterion was applied to remove the spots with spot intensity vs. background intensity ratio less than 1 in either channel. A spot area based criterion was applied to remove the spots with the area less than 10 pixels in either channel. Print tip-dependent normalization was applied to the data in order to compensate for systematic errors. The data was normalized by subtraction of the smooth curve found by the LOWESS (LOcally Weighted Scatter plot Smoothing) algorithm. The normalized ratio of the duplicates were averaged. Further analysis was done on the log2 transformed ratios. A gene was considered undetected and not tested, if the average ratio were missing on more than 50% of the microarrays. In order to assess the significance of up- or downregulation of the genes, a one sample t-Student test was performed. The p-value for rejecting the null hypothesis that the gene did not vary, was calculated for each gene. Setting a threshold on the p-value, significantly expressed genes were selected. The False Discovery Rate was calculated using the Benjamini-Hochberg procedure.


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-59, patient 4


title: NMC 7.7k duplicate human cDNA arrays, Ser 020617-62, patient 10


title: GEIM169-IBM

description: Patient #169 with IBM

tag: Patient #169 with IBM


title: GEIM223-IBM

description: Patient #223 with IBM

tag: Patient #223 with IBM


title: GEIM27-IBM

description: Patient #27 with IBM

tag: Patient #27 with IBM


title: GEIM91-IBM

description: Patient #91 with IBM

tag: Patient #91 with IBM


title: GEIM112-IBM

description: Patient #112 with IBM

tag: Patient #112 with IBM


title: GEIM170-IBM

description: Patient #170 with IBM

tag: Patient #170 with IBM


title: GEIM167-IBM

description: Patient #167 with IBM

tag: Patient #167 with IBM


title: GEIM180-IBM

description: Patient #180 with IBM

tag: Patient #180 with IBM


title: GEIM83-IBM

description: Patient #83 with IBM

tag: Patient #83 with IBM


title: GEIM127-IBM

description: Patient #127 with IBM

tag: Patient #127 with IBM


title: GEIM7-IBM

description: Patient #7 with IBM

tag: Patient #7 with IBM


title: GEIM67-IBM

description: Patient #67 with IBM

tag: Patient #67 with IBM


title: GEIM79-IBM

description: Patient #79 with IBM

tag: Patient #79 with IBM


title: GEIM54-IBM

description: Patient #54 with IBM

tag: Patient #54 with IBM


title: GEIM61-IBM

description: Patient #61 with IBM

tag: Human skeletal muscle biopsy sample

tag: Patient #61 with IBM


title: GEIM38-IBM

description: Patient #38 with IBM

tag: Patient #38 with IBM


title: AI-06

city: Bethesda

first: Carolyn

middle: J. M.

last: Best

state: MD

address: 37 Convent Drive

institute: NCI, NIH

description: androgen-independent primary prostate cancer; frozen; Gleason at initial Dx = 7; tumor cells microdissected from biopsy

source_name: androgen-independent primary human prostate cancer


title: AI-04

description: androgen-independent primary prostate cancer; frozen; Gleason at initial Dx = 8; tumor cells microdissected from biopsy


title: AI-09


title: AI-10

description: androgen-independent primary prostate cancer; frozen; Gleason at initial Dx = 9; tumor cells microdissected from biopsy


title: GEIM20-IBM

description: Patient #20 with IBM

tag: Patient #20 with IBM


title: AI-08


title: AD-08

description: untreated primary prostate cancer; frozen; Gleason = 5; tumor cells microdissected from whole mount

source_name: untreated human prostate cancer


title: GEIM36-IBM

description: Patient #36 with IBM

tag: Patient #36 with IBM


title: AD-09


title: AI-03


title: AD-03

description: untreated primary prostate cancer; frozen; Gleason = 6; tumor cells microdissected from whole mount


title: AD-04

description: untreated primary prostate cancer; frozen; Gleason = 7; tumor cells microdissected from whole mount


title: AD-06


title: AI-01


title: AI-02


title: GEIM183-IBM

description: Patient #183 with IBM

tag: Patient #183 with IBM


title: AI-07


title: AD-10

description: untreated primary prostate cancer; frozen; Gleason = 9; tumor cells microdissected from whole mount


title: AD-07

description: untreated primary prostate cancer; frozen; Gleason = 8; tumor cells microdissected from whole mount


title: AD-05


title: S5_S5010928

status: Public on Sep 26 2005

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: normal smoker, 10 pack-yr

data_processing: MAS 5.0

source_name: alveolar macrophages from bronchoalveolar lavage

tag: Gender

tag: Age

tag: Ethnicity

value: White


title: AD-02


title: S3_S010809

description: normal smoker, 14 pack-yr

value: Male

value: Black


title: AD-01

description: sample: untreated primary prostate cancer; frozen; Gleason= 6; tumor cells microdissected from whole mount


title: S4_S010926

description: normal smoker, 20 pack-yr

source_name: alveolar macrophage from bronchoalveolar lavage


title: NS5_NS010926

description: normal non-smoker

value: male


title: S1_S010228

description: normal smoker, 30 pack-yr

value: Hispanic


title: S2_S010403

description: normal smoker, 14 pack-yr


title: GEIM1-IBM

description: Patient #1 with IBM

tag: Patient #1 with IBM


title: GEIM62-IBM

description: Patient #62 with IBM

tag: Patient #62 with IBM


title: NS4_NS010827

description: normal non-smoker


title: NS3_NS010823

description: normal non-smoker


title: dF508-CFTR Rep1 of 4, Slide 1B

status: Public on Sep 20 2005

first: Nina

last: Reiniger

address: 181 Longwood Ave

institute: Brigham & Women's Hospital, Channing Laboratory

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.

source_name: Uninfected

source_name: P.aeruginosa infected


title: dF508-CFTR Rep1 of 4, Slide 1A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: dF508-CFTR Rep1 of 4, Slide 2A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 2 for this set.


title: dF508-CFTR Rep2 of 4, Slide 2B

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: dF508-CFTR Rep2 of 4, Slide 2A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 2 for this set.


title: dF508-CFTR Rep3 of 4, Slide 1A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: dF508-CFTR Rep2 of 4, Slide 1B

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.


title: dF508-CFTR Rep1 of 4, Slide 2B

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: NS2_NS010119

description: normal nonsmoker

value: white


title: dF508-CFTR Rep2 of 4, Slide 1A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: NS1_NS010112

description: normal non-smoker

value: black


title: dF508-CFTR Rep3 of 4, Slide 1B

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.


title: dF508-CFTR Rep3 of 4, Slide 2B

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: dF508-CFTR Rep4 of 4, Slide 2B

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 4th of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: WT-CFTR Rep1 of 4, Slide 1A

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the wild-type CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: dF508-CFTR Rep4 of 4, Slide 1A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 4th of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: dF508-CFTR Rep4 of 4, Slide 2A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 4th of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 2 for this set.


title: dF508-CFTR Rep4 of 4, Slide 1B

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 4th of 4 replicates of the dF508 CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep1 of 4, Slide 2B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: GEIM237-IBM

description: Patient #237 with IBM

tag: Patient #237 with IBM


title: WT-CFTR Rep1 of 4, Slide 1B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep2 of 4, Slide 1A

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the wild-type CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep2 of 4, Slide 1B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep2 of 4, Slide 2B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: WT-CFTR Rep2 of 4, Slide 2A

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 2nd of 4 replicates of the wild-type CFTR cell line. This is the 1st set of duplicate spots on slide 2 for this set.


title: WT-CFTR Rep3 of 4, Slide 1A

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the wild-type CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep3 of 4, Slide 1B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep4 of 4, Slide 1A

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 4th of 4 replicates of the wild-type CFTR cell line. This is the 1st set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep3 of 4, Slide 2B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: WT-CFTR Rep4 of 4, Slide 1B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 4th of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 1 for this set.


title: WT-CFTR Rep4 of 4, Slide 2A

description:
Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1.

This data set is the 4th of 4 replicates of the wild-type CFTR cell line.  This is the 1st set of duplicate spots on slide 2 for this set.


title: WT-CFTR Rep4 of 4, Slide2B

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 4th of 4 replicates of the wild-type CFTR cell line. This is the 2nd set of duplicate spots on slide 2 for this set.


title: dF508-CFTR Rep3 of 4, Slide 2A

description: Human bronchial epithelial cells with dF508 CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the dF508 CFTR cell line. This is the 1st set of duplicate spots on slide 2 for this set.


title: C18-2

status: Public on Sep 19 2005

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Standard affymetrix protocol

label: Streptavidin-phycoerythrin

source_name: Biopsy 2 form cystectomy 18

tag: Normal bladder mucosa


title: AI-05

description: androgen-independent primary prostate cancer; frozen; Gleason at initial Dx = 9; tumor cells microdissected from biopsy


title: C18-1

description: Standard affymetrix protocol

source_name: Biopsy 1 from cystectomy 18

tag: CIS


title: WT-CFTR Rep1 of 4, Slide 2A

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 1st of 4 replicates of the wild-type CFTR cell line. This is the 1st set of duplicate spots on slide 2 for this set.


title: C15-7

description: Standard affymetrix protocol

source_name: Biopsy 7 from cystectomy 15


title: C15-2

description: Standard affymetrix protocol

source_name: Biopsy 2 from cystectomy 15


title: WT-CFTR Rep3 of 4, Slide 2A

description: Human bronchial epithelial cells with wild-type CFTR were uninfected or infected for 3 hours by P.aeruginosa strain PAO1. This data set is the 3rd of 4 replicates of the wild-type CFTR cell line. This is the 1st set of duplicate spots on slide 2 for this set.


title: C5-7

description: Standard affymetrix protocol

source_name: Biopsy 7 from cystectomy 5


title: 1354-1

description: Standard affymetrix protocol

source_name: Bladder tumor tissue

tag: Ta gr3


title: C5-1

description: Standard affymetrix protocol

source_name: Biopsy 1 from cystectomy 5


title: C16-1

description: Standard affymetrix protocol

source_name: Biopsy 1 from cystectomy 16


title: 1482-1

description: Standard affymetrix protocol


title: 1385-1

description: Standard affymetrix protocol

tag: T4a gr3


title: 1345-2

description: Standard affymetrix protocol

tag: Ta gr3, surrounding CIS


title: C16-4

description: Standard affymetrix protocol

source_name: Biopsy 4 from cystectomy 16


title: 1337-1

description: Standard affymetrix protocol

tag: T1 gr3, surrounding CIS


title: C10-3

description: Standard affymetrix protocol

source_name: Biopsy 3 from cystectomy 10


title: C10-4

description: Standard affymetrix protocol

source_name: Biopsy 4 from cystectomy 10


title: 1321-1

description: Standard affymetrix protocol

tag: T3b gr?


title: 1330-1

description: Standard affymetrix protocol


title: 1350-1

description: Standard affymetrix protocol


title: 1303-1

description: Standard affymetrix protocol

tag: Ta gr2


title: 1625-1

description: Standard affymetrix protocol

tag: Ta gr2, surrounding CIS


title: 1215-1

description: Standard affymetrix protocol

tag: T4b gr3


title: 1154-1

description: Standard affymetrix protocol

tag: T3a gr3


title: 1276-1

description: Standard affymetrix protocol


title: 1124-1

description: Standard affymetrix protocol


title: 1167-1

description: Standard affymetrix protocol

tag: T3b gr4


title: 1178-1

description: Standard affymetrix protocol


title: 1182-1

description: Standard affymetrix protocol

tag: Ta gr3, CIS in subsequent visits


title: 1264-1

description: Standard affymetrix protocol


title: 1271-1

description: Standard affymetrix protocol


title: 1109-1

description: Standard affymetrix protocol

tag: T2 gr3


title: 1146-1

description: Standard affymetrix protocol


title: 1216-1

description: Standard affymetrix protocol


title: 1093-1

description: Standard affymetrix protocol


title: 763-1

description: Standard affymetrix protocol


title: 797-1

description: Standard affymetrix protocol


title: 1070-1

description: Standard affymetrix protocol


title: 1055-1

description: Standard affymetrix protocol


title: 692-1

description: Standard affymetrix protocol


title: 1024-1

description: Standard affymetrix protocol


title: Normal bladder 272-99

description: Standard affymetrix protocol

source_name: Normal bladder biopsy

tag: Normal bladder


title: 1041-1

description: Standard affymetrix protocol

source_name: Bladder timor tissue


title: Normal bladder 81-99

description: Standard affymetrix protocol


title: 602-8

description: Standard affymetrix protocol


title: 1062-2

description: Standard affymetrix protocol


title: Normal bladder 18-99

description: Standard affymetrix protocol


title: 1066-1

description: Standard affymetrix protocol


title: 989-1

description: Standard affymetrix protocol


title: Normal bladder 61-99

description: Standard affymetrix protocol


title: 1015-1

description: Standard affymetrix protocol


title: 524-1

description: Standard affymetrix protocol


title: 1044-1

description: Standard affymetrix protocol


title: Human Oral SCC cell line UM1 II, 5-Aza-CdR

status: Public on Sep 16 2005

first: Takanori

last: Tsuji

address: 77 AVenue Louis Pasteur

description: Reference; Nakayama, S. et al. Invasion Metastasis. 18:219-228, 1998/1999.

hyb_protocol: BD Biosciences protocol

scan_protocol: The hybridized membrane was exposed to a BIO-RAD Imaging Screen-K phosphor screen for 3 days at room temperature. The screen image was scanned a Molecular Dynamics STORM phosphorimager.

data_processing: The data analysis was performed using BD Biosciences BD AtlasImage 2.7 software. The Global Normalization method (Sum method) was utilized to normalize the signals. The VALUE column was created by subtracting background value from each signal value.

source_name: Tongue squamous cell carcinoma, metastatic

label_protocol: BD Biosciences protocol

growth_protocol: Cells were cultured with DMEM/F12 medium supplemented with 10 % FBS at 37°C in humidified 5 % CO2.

extract_protocol: Total RNA was extracted using guanidium thiocyanate and cesium chloride (Chirgwin, J.M. et al. Biochemistry 18:5294-5299, 1979).

treatment_protocol: Cells were treated with 10 μM 5-Aza-2’-deoxycytidine for 7 days.

tag: Human

tag: Male

tag: Tongue


title: Normal bladder 277-99

description: Standard affymetrix protocol


title: 1060-1

description: Standard affymetrix protocol


title: 775-1

description: Standard affymetrix protocol


title: Normal bladder 283-99

description: Standard affymetrix protocol


title: 956-2

description: Standard affymetrix protocol


title: Normal bladder 9-99

description: Standard affymetrix protocol


title: Normal bladder 7-99

description: Standard affymetrix protocol


title: 320-7

description: Standard affymetrix protocol


title: Human Oral SCC cell line UM1 III, 5-Aza-CdR


title: Human Oral SCC cell line UM1 II, ODC-Az

data_processing: The data analysis was performed using BD Biosciences BD AtlasImage 2.7 software. The Global Normalization method (Sum method) was utilized to normalize the signals. The VALUE column was created by subtracting background value from each signal value. Note that the signal intensities of H365, H366, H367, H160, SK029, N353, N447, N132, N382 are affected by bleeding of CA410 signal. Please exclude the outcome of these genes.

treatment_protocol: Zinc inducible gene expression plasmid (MTCB6+HuFSAz-wt) was employed. Expression of the human ODC-Az gene was induced with 100 μM ZnSO4 for 7 days.


title: Human Oral SCC cell line UM1 II

description: Reference; Nakayama, S. et al. Invasion Metastasis. 18:219-228, 1998/99.

scan_protocol: The hyridized membrane was exposed to a BIO-RAD Imaging Screen-K phosphor screen for 3 days at room temperature. The screen image was scanned by a Molecular Dynamics STORM phosphorimager.

data_processing: The data analysis was performed using BD Biosciences BD AtlasImage 2.7 software. The Global Normalization method (Sum method) was utilized to normalize the signals. The VALUE column was calculated by subtracting background value from each signal intensity.

growth_protocol: Cells were cultured with DMEM/F12 medium supplemented with 10% FBS at 37C in humidified 5% CO2

extract_protocol: Total RNA was extracted using guanidinium thiocyanate and cesium chloride (Chirgwin, J.M. et al. Biochemistry 18:5294-5299, 1979.)

treatment_protocol: No special treatment

tag: 47-year-old Japanese


title: Human Oral SCC cell line UM1 III

description:
Reference;
Nakayama, S. et al. Invasion Metastasis. 18: 219-228, 1998/1999.

scan_protocol: The hybridized membrane was exposed to a BIO-RAD Imaging Screen-K phosphor screen for 3 days at room temperature. The screen image was scanned by a Molecular Dynamics STORM phosphorimager.

growth_protocol: Cells were cultured with DMEM/F12 medium supplemented with 10% FBS at 37C in humidified 5% CO2.

treatment_protocol: No special treatment.


title: Human Oral SCC cell line UM1, ODC-Az

scan_protocol: The hybridized membrane was exposed to a BIO-RAD Image Screen-K phosphor screen for 3 days at room temperature. The screen image was scanned by a Molecular Dynamics STORM phosphorimager.

data_processing: The data analysis was performed using BD Biosciences BD AtlasImage 2.7 software. The Global Normalization method (Sum method) was utilized to normalize the signals. The VALUE column was created by subtracting background value from each value.

treatment_protocol: Zinc inducible gene expression plasmid (pMT/CB6+HuFSAZ-wt) was employed. Expression of the human ODC-Az gene was induced with 100 uM ZnSO4 for 7 days.


title: Normal bladder 16-99

description: Standard affymetrix protocol

data_processing: RMA


title: Human Oral SCC cell line UM1, 5-Aza-CdR


title: Human Oral SCC cell line UM1 III, ODC-Az


title: Human Oral SCC cell line UM1

description:
Reference;
Nakayama, S. et al. Invasion Metastasis. 18:219-228, 1998/1999.


title: H33dN_3/TOTAL_4 cDNA

status: Public on Sep 11 2005

type: genomic

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.

data_processing: Medians of Cy5 and Cy3 signals and backgrounds were computed, the median background was subtracted from the median signal, and the log base 2 of the ratio was computed

molecule: genomic DNA

source_name: Chromatin affinity-purified DNA with tagged histone H3.3 core region from Drosophila S2 cells

source_name: Input DNA

tag: Input DNA


title: H33dN_2/TOTAL_3 cDNA

tag: Chromatin affinity-purified DNA with tagged histone H3.3 core region from Drosophila S2 cells


title: H3_#1/Total_2 cDNA

source_name: Chromatin affinity-purified DNA with tagged histone H3 from Drosophila S2 cells


title: H3_#2/Total_2 cDNA

tag: Chromatin affinity-purified DNA with tagged histone H3 from Drosophila S2 cells


title: Muvar_67w18w

status: Public on Sep 04 2005

city: Cambridge

first: Scott

middle: A

last: Rifkin

address: 16 Divinity Ave

department: OEB

institute: Harvard University

description:
Comparison between mutation accumulation lines 67 at the start of pupariation (white prepupae) and 18 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 67, start of pupariation (white prepupae)

source_name: Mutation accumulation line 18, start of pupariation (white prepupae)


title: Muvar_59b59w

description:
Comparison between mutation accumulation lines 59 at the late 3rd instar larvae (blue gut) and 59 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0.  http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster

source_name: Mutation accumulation line 59, late 3rd instar larvae (blue gut)

source_name: Mutation accumulation line 59, start of pupariation (white prepupae)