title: Kidney - 256888

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Pathological T: 1b
Pathological N: X
Pathological M: 1
Pathological Metastatic Sites: Brain
Pathological Stage: 4
Pathological Grade: 4
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Breast - 256870

status: Public on Apr 06 2007

type: RNA

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

country: USA

institute: IGC

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

molecule: total RNA

organism: Homo sapiens

source_name: Breast


title: Omentum - 256946

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 150
Prior Therapy: Chemotherapy
Pathological T: 3a
Pathological N: X
Pathological M: 1
Pathological Metastatic Sites: Peritoneum
Pathological Stage: 4B
Pathological Grade: X
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Endometrium
Histology: Metastatic Malignant mixed Mullerian tumor

source_name: Omentum


title: Kidney - 256885

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma

source_name: Kidney


title: Colon - 256875

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 12
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Kidney - 256871

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 3
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 4
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Liver - 254443

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Retreatment T: 1
Retreatment N: 1
Retreatment M: 1
Retreatment Metastatic Sites: Hepatic
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Colon
Histology: Metastatic Adenocarcinoma

source_name: Liver


title: Colon - 254440

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Breast - 254393

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 150
Prior Therapy: Chemotherapy
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 6-10
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Breast - 254378

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-50
Gender: Female
Ethnic Background: Asian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 40
Mammogram: Yes
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 1a
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Primary Site: Breast
Histology: Ductal Carcinoma


title: Colon - 254435

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 10
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma


title: Rectum - 254351

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 56-60
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Diarrhea
Screening studies performed?: No
Diagnosis made by: Sigmoidoscopy
Retreatment T: X
Retreatment N: 2
Retreatment M: 1
Retreatment Metastatic Sites: Pulmonary
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: Ovary - 254387

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological Question: Stage
Pathological Value: 3C
Pathological Question: Grade
Pathological Value: 3
Primary Site: Peritoneum
Pathological Question: Histology
Pathological Value: Papillary serous adenocarcinoma

source_name: Ovary


title: Kidney - 254355

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 8
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Colon - 251039

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Cigars
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 18
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Ovary - 242929

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 13
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Endometrioid adenocarcinoma


title: Kidney - 251041

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Breast - 242928

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 120
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: Yes
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Ovary - 241196

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 16
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma


title: Kidney - 242925

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 90
Clinical T: 3b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Lung - 242924

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 35
Presenting Symptoms: SOB
Workplace or household smokers?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS

source_name: Lung


title: Ovary - 241199

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 13
Presenting Symptoms: Abdominal mass
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Papillary serous cystadenocarcinoma


title: Pelvic lymph node - 241186

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Clinical Question: T
Clinical Value: X
Clinical Question: N
Clinical Value: X
Clinical Question: M
Clinical Value: X
Clinical Question: Stage
Clinical Value: Unknown
Clinical Question: Grade
Clinical Value: X
Primary Site: Skin of scrotum
Clinical Question: Histology
Clinical Value: Metastatic Squamous cell carcinoma

source_name: Pelvic lymph node


title: Uterus - 242918

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1B
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Uterus


title: Uterus - 241200

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 85
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Colon - 241194

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Black tarry stools
Presenting Symptoms: Constipation
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma


title: Kidney - 241189

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 51-55
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Pipe
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 45
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Acetabulum - 234331

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigars
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 56
Prior Therapy: Chemotherapy
Pathological Question: T
Pathological Value: 1
Pathological Question: N
Pathological Value: 0
Pathological Question: M
Pathological Value: 0
Pathological Question: Stage
Pathological Value: 2A
Pathological Question: Grade
Pathological Value: High
Pathological Question: Stage During or Following Multimodality Therapy
Pathological Value: Yes
Primary Site: Pelvis
Pathological Question: Histology
Pathological Value: Dedifferentiated chondrosarcoma

source_name: Acetabulum


title: Kidney - 241195

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 51-55
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Omentum - 234327

description:
Quality metric = 28S to 18S: 1.1
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 11-15
Retreatment T: 3c
Retreatment N: X
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Grade: X
Primary Site: Ovary
Histology: Metastatic Malignant granulosa cell tumor


title: Uterus - 242921

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 5
Clinical Question: Stage
Clinical Value: No AJCC Scheme for this site and histology
Clinical Question: Grade
Clinical Value: 3
Clinical Question: Metastatic Sites
Clinical Value: Lung
Primary Site: Myometrium
Clinical Question: Histology
Clinical Value: Leiomyosarcoma


title: Ileum - 235698

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Pathological Question: Stage
Pathological Value: 2
Pathological Question: Symptoms
Pathological Value: A
Primary Site: Ileum
Pathological Question: Histology
Pathological Value: Anaplastic large cell lymphoma

source_name: Ileum


title: Colon - 241175

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Relapse Since Primary Treatment: No
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Clear cell adenocarcinoma


title: Ovary - 234329

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 20
Clinical T: 3c
Clinical N: 0
Clinical M: 0
Clinical Stage: 3C
Clinical Grade: 3
Primary Site: Ovary
Histology: Papillary Serous Carcinoma


title: Pelvic mass - 234316

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Retreatment T: 2b
Retreatment N: X
Retreatment M: X
Retreatment Stage: Unknown
Retreatment Grade: X
Primary Site: Ovary
Histology: Metastatic Carcinoma, NOS

source_name: Pelvic mass


title: Ovary - 211372

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 1
Pathological M: X
Pathological Stage: 3C
Pathological Grade: 2
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Adenocarcinoma, endometrioid and papillary serous


title: Uterus - 226427

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 51-55
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Ovary - 211371

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Bloating
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Primary Site: Ovary
Histology: Papillary Serous Carcinoma


title: Breast - 209694

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: No
Oophorectomy?: Yes
Hormonal therapy (# of Years)?: 11-15
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 1
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Kidney - 231861

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Omentum - 241183

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 3c
Retreatment N: X
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Grade: X
Primary Site: Ovary
Histology: Metastatic Papillary Serous Adenocarcinoma


title: Colon - 209691

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 3
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Corpus Uteri - 202039

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Corpus Uteri


title: Lung - 199405

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Pipe
Alcohol Consumption?: No
Family History of Cancer?: Yes
Workplace or household smokers?: No
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous Cell Carcinoma, Non-Keratinizing


title: Colon - 209690

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 30-40
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 11
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Colon - 209692

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 3
Primary Site: Colon
Histology: Adenocarcinoma


title: Gallbladder - 199404

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-90
Gender: Male
Ethnic Background: Asian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Pathological Question: T
Pathological Value: 2
Pathological Question: N
Pathological Value: 0
Pathological Question: M
Pathological Value: 0
Pathological Question: Stage
Pathological Value: 1B
Pathological Question: Grade
Pathological Value: 2
Primary Site: Gallbladder
Pathological Question: Histology
Pathological Value: Adenocarcinoma

source_name: Gallbladder


title: Ovary - 199399

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Prior Therapy: Chemotherapy
Clinical T: 3b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3B
Clinical Grade: 3
Primary Site: Ovary
Histology: Carcinoma, NOS


title: Connective tissue of abdomen - 199376

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Clinical Question: Stage
Clinical Value: No AJCC Scheme for this site and histology
Clinical Question: Metastatic Sites
Clinical Value: None
Clinical Question: Multiple Tumors
Clinical Value: No
Primary Site: Connective tissue of abdomen
Clinical Question: Histology
Clinical Value: Gastrointestinal stromal tumor, uncertain malignant potential

source_name: Connective tissue of abdomen


title: Uterus - 195194

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 62
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1A
Clinical Grade: 1
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Kidney - 199394

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 28
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Ovary - 199400

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 13
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Adenocarcinoma with mixed subtypes


title: Lung - 170813

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 120
Prior Therapy: Chemotherapy
Workplace or household smokers?: No
Pathological T: 1
Pathological N: 2
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 2
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Lung
Histology: Adenosquamous Carcinoma


title: Prostate - 193028

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Nocturia
PSA: Elevated
Current status of disease: Under Therapy
Pathological T: 2c
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Prostate - 193004

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
PSA: Elevated
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Clinical T: 2c
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 2
Clinical Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Colon - 199354

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 34
Presenting Symptoms: Black tarry stools
Presenting Symptoms: Diarrhea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Abdominal mass - 187248

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-70
Gender: Female
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment Question: Stage
Retreatment Value: No AJCC Staging scheme for this site and histology
Retreatment Question: Metastatic Sites
Retreatment Value: Small bowel mesentery
Primary Site: Corpus Uteri
Retreatment Question: Histology
Retreatment Value: Metastatic Myxoid leiomyosarcoma

source_name: Abdominal mass


title: Lung - 187252

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Colon - 195191

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 2
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Breast - 193026

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Mammogram: Yes
Number of years in which a mammogram was obtained?: 21-25
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma

source_name: Breast


title: Uterus - 187254

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Kidney - 193000

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 50
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma

source_name: Kidney


title: Ovary - 187253

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 40-50
Gender: Female
Ethnic Background: Asian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Vaginal bleeding
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Clear cell adenocarcinoma


title: Breast - 6630

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Mammogram: Yes
Number of years in which a mammogram was obtained?: 26-30
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 6-10
Oophorectomy?: No
Fibrocystic disease?: Yes
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 21-25
Pathological T: 2
Pathological N: 0(i-)
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Cervix - 129657

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 8
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma, non-keratinizing

source_name: Cervix


title: Pancreas - 78393

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Primary Site: Exocrine Pancreas
Histology: Ductal adenocarcinoma

source_name: Pancreas


title: Rectum - 127824

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: U-2OS (decitabine treated) expression profile (AffyChip U133 Plus 2.0 platform)

status: Public on Apr 05 2007

city: Toronot

first: Khaldoun

last: Al-Romaih

address: 610 University Ave

department: AMO

country: Canada

institute: Ontario Cancer Institute

description: non

hyb_protocol: For each case, 10 µg of RNA was labeled and hybridized to the Affymetrix HG-U133A GeneChips using the manufacturer’s protocol (Affymetrix, Santa Clara, CA) by the Center of Applied Genomics at the Hospital for Sick Children (Toronto, Canada).

scan_protocol: Data were extracted using the Microarray Suite (MAS) version 5.0 (Affymetrix) and linearly scaled to achieve an average intensity of 150 across each chip.

label: Biotin

source_name: U-2OS cell line from ATCC

label_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Germany) from U-2OS cells at Day3 after treatment with 1 µM decitabine or medium alone (control).  In each experiment RNA yields were pooled from two independent cultures per treatment arm to minimize experimental noise.  For each case, 10 µg of RNA was labeled using the two cycle target labeling assays as described by Affymetrix manual.

extract_protocol: RNAeasy kit from Qiagen

tag: human bone tumor cell line treated with 1 uM decitabine for 3 days


title: 16.5_KO_591C

status: Public on Apr 04 2007

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description: Wild type [WT] pancreata were dissected from day 14 and 16 mouse embryos. A Pdx1-cre transgenic line was crossed with a floxed allel of beta-catenin to generate beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points.

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer.  Heat hybridization cocktail to 99oC for 5 minutes, to 45oC for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45oC for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45oC for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine MOE 430 2.0  gene chips were used.GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using David 2.0(http://david.abcc.ncifcrf.gov/summary.jsp).

label: biotin

organism: Mus musculus

source_name: Embryonic day 16.5 pancreas

label_protocol: 120 ng of total RNA from 2 wild type [WT] and 4 beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

extract_protocol:
Pancreata were dissected from 12.5, 14.5 and 16.5 day mouse embryos taken from timed matings of Pdx1Cre/+ ; beta-cateninflox/+ mice and immediately submerged in RNAlater [Ambion, Inc., Austin, TX].
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

tag: Embryonic day 14.5 and 16.5 pancreas


title: 14.5_WT_522B

source_name: Embryonic day 14.5 pancreas


title: Kidney - 2489

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1b
Clinical N: X
Clinical M: X
Clinical Stage: Unknown
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: 16.5_KO_541J


title: 16.5_WT_622A


title: 14.5_KO_615B


title: 16.5_KO_541L


title: U-2OS (no-treatment) expression profile (AffyChip U133 Plus 2.0 platform)

description: non

data_processing: Data were extracted using the Microarray Suite (MAS) version 5.0 (Affymetrix) and linearly scaled to achieve an average intensity of 150 across each chip.

source_name: Human osteosarcoma cell line

tag: Bone tumor cell line purchased from ATCC


title: 14.5_KO_615A


title: 16.5_KO_591D


title: Colon - 1001

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 80-90
Gender: Male
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 16
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma arising in a villous adenoma

source_name: Colon


title: 14.5_WT_522C


title: 14.5_KO_540G


title: Skinbiopsy_7hoursnickel_nickel_allergic_subject_P6

status: Public on Apr 03 2007

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: The sample is a part of an analysis of gene expression time-course in the human skin during elicitation of allergic contact dermatitis

hyb_protocol: The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used according to the protocol supplied with the kit.

scan_protocol: The Affymetrix system was used and the protocols supplied by Affymetrix followed.

data_processing: Log(2) transformed expression measures were calculated with the RMA procedure using the software from www.Bioconductor.org

label: Phycoerythrin

source_name: Skin biopsy from upper nates taken 7 hours after exposure to 5% nickel sulfate

label_protocol: First strand cDNA was synthesized from 1 ug total RNA by incubation (42C, 1 hr) in a 20 ul reaction volume containing 2.5 mM T7-(dT)24 primer, 50 mM Tris-HCl pH 8.3, 75 mM KCL, 3 mM MgCl2, 10 mM DTT and 500 mM dNTP, 10 U/ml Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA).Second strand cDNA was synthesized directly by adding 91 ul RNase free water, 30 ul 5 times second strand reaction buffer (Invitrogen), 3 ul 10 mM dNTP, 1 ul Escherichia coli DNA ligase (10 U/ml), 4 ul E. coli DNA polymerase I (10 U/ml), 1 ul E. coli RNase H (2 U/ml) followed by incubation (2 hr, 16C). The ends of the double-stranded cDNA were polished using T4 DNA polymerase (20 U, 5 min, 16C). The cDNA was purified and concentrated by phenol/ chloroform extraction and ethanol precipitation.

extract_protocol: For RNA extraction, the skin biopses were placed in a morter filled with liquid nitrogen and ground mechanically using a pistil. The tissue was transferred to a lysis buffer and RNA was extracted using the RNase Lipid Tissue Kit (Qiagen, Valencia; CA). The amount and quality of the extracted RNA was evaluated using a lab-on-a-chip Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: A total of 3 patch tests with 5% nickel sulfate was taken from each subject: i) the first patch test was exposed for 7h and a skin biopsy was taken immediately after removing the patch test ii) the second patch test was exposed for 48h immediately followed by a skin biopsy and iii) the third patch test was exposed for 48h and the skin biopsy was taken 48h after removing the patch test (the 96h biopsy). In addition, all participants were exposed to an empty patch test exposed for 48h followed by a skin biopsy.

tag: Nickel allergic female (age range 33-49), skin biopsy from upper nates taken 7 hours after nickel exposure


title: Skinbiopsy_96hoursnickel_nickel_allergic_subject_P4

source_name: Skin biopsy from upper nates taken 96 hours after exposure to 5% nickel sulfate

tag: Nickel allergic female (age range 33-49), skin biopsy from upper nates taken 96 hours after nickel exposure


title: 16.5_WT_628G


title: 14.5_KO_540C


title: Skinbiopsy_7hoursnickel_nickel_allergic_subject_P7


title: Skinbiopsy_48hoursnickel_nickel_allergic_subject_P4

source_name: Skin biopsy from upper nates taken 48 hours after exposure to 5% nickel sulfate

tag: Nickel allergic female (age range 33-49), skin biopsy from upper nates taken 48 hours after nickel exposure


title: Skinbiopsy_96hoursnickel_nickel_allergic_subject_P3


title: Skinbiopsy_96hoursnickel_nickel_allergic_subject_P6


title: Skinbiopsy_7hoursnickel_nickel_allergic_subject_P5


title: Skinbiopsy_0hoursnickel_nickel_allergic_subject_P6

source_name: Skin biopsy from upper nates no nickel exposure

tag: Nickel allergic female (age range 33-49), skin biopsy from upper nates. No nickel exposure.


title: Skinbiopsy_48hoursnickel_nickel_allergic_subject_P7


title: Skinbiopsy_0hoursnickel_nickel_allergic_subject_P4

tag: Nickel allergic female (age range 33-49), skin biopsy from upper nates. No nickel exposure


title: Skinbiopsy_96hoursnickel_nickel_allergic_subject_P7


title: Skinbiopsy_96hoursnickel_nickel_allergic_subject_P5


title: Skinbiopsy_0hoursnickel_nickel_allergic_subject_P5


title: Skinbiopsy_7hoursnickel_controlsubject_k5

tag: Female (age range 33-49), skin biopsy taken from upper nates 7 hours after nickel exposure


title: Skinbiopsy_7hoursnickel_nickel_allergic_subject_P4


title: Skinbiopsy_0hoursnickel_nickel_allergic_subject_P2


title: Skinbiopsy_48hoursnickel_controlsubject_k5

tag: Female (age range 33-49), skin biopsy from upper nates taken 48 hours after nickel exposure


title: Skinbiopsy_0h_controlsubject_k5

label_protocol: First strand cDNA was synthesized from 1 ug total RNA by incubation (42C, 1 hr) in a 20 ml reaction volume containing 2.5 mM T7-(dT)24 primer, 50 mM Tris-HCl pH 8.3, 75 mM KCL, 3 mM MgCl2, 10 mM DTT and 500 mM dNTP, 10 U/ml Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA).Second strand cDNA was synthesized directly by adding 91 ml RNase free water, 30 ml 5 times second strand reaction buffer (Invitrogen), 3 ml 10 mM dNTP, 1 ml Escherichia coli DNA ligase (10 U/ml), 4 ml E. coli DNA polymerase I (10 U/ml), 1 ml E. coli RNase H (2 U/ml) followed by incubation (2 hr, 16C). The ends of the double-stranded cDNA were polished using T4 DNA polymerase (20 U, 5 min, 16C). The cDNA was purified and concentrated by phenol/ chloroform extraction and ethanol precipitation.

tag: Female (age range 33-49), skin biopsy from upper nates. No nickel exposure


title: heartgraft_Syngeneic_early_rep4.

city: Los Angeles

first: Tomoko

last: Doki

state: CA

address: 4661 Sunset Blvd.

department: Cardiothoracic Surgery Research

institute: Childrens Hospital Los Angeles

description: Gene expression data from heart graft transplanted in syngeneic recipient

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Mouse 430_2.0 Array. GeneChips were washed and stained using Affymetrix Hyb/Wash/Stain Kit.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing:
The probe set level data was analyzed with the dCHIP software (dCHIP 2006, Build date: Jul 18 2006) and only the values as determined by the model-based expression level deemed ”present” using the perfect/mis match difference correction model with single probe rejection were considered further.
[dChip Expression Data File]
FileName=C:\Dennis\data\tomoko\MaryK-new2expression.xls
dChipVersion=dChip 2006 (DNA-Chip Analyzer), Build date: Jul 18 2006
BaselineArray=C:\Dennis\data\tomoko\J888-A-Mouse430_2-01-1 (102206).CEL
ModelMethod=PM/MM difference model
CheckOutlier=Single,Probe,
ImageSpikeAsSingleOutlier=Yes
ArrayListFile=
ReplicateNotAllOutlier=No
LogTransformed=No (with base 2)
TruncateLowValue=Yes (to value 0)
TruncateToAbsentPercent=Yes (to percent 10)
PSIFileUsage=Do not use (C:\Dennis\specsU133a.psi)
OutputArrayOutlierAsBlank=No
OutputBothSignalAndCall=Yes
OutputStandardError=Yes

source_name: heart graft, Syngeneic, day 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Intra-abdominal heterotopic heart transplantation was performed at 2 to 4 weeks after BMT. Heart grafts from C57BL/6 mice were transplanted into GalT BMT mice and C57BL/6 syngeneic control mice.

extract_protocol: Total RNA was extracted from graft heart tissue using RNeasy Fibrous Tissue Mini (QIAGEN) according to manufacturer's protocol.

treatment_protocol: At Day 10 post heart transplantation, recipient mice were euthanized for examination. The graft heart tissues for RNA extraction were immediately frozen and kept at -80°C.

tag: Strain

value: C57BL/6, Gender:male, Age:16 weeks, Tissue:heart (transplanted graft)


title: Skinbiopsy_7hoursnickel_nickel_allergic_subject_P2


title: Skinbiopsy_96hoursnickel_controlsubject_k4

tag: Female (age range 33-49), skin biopsy taken from upper nates 96 hours after nickel exposure


title: Skinbiopsy_7hoursnickel_controlsubject_k4


title: Skinbiopsy_48hoursnickel_controlsubject_k4

tag: Female (age range 33-49), skin biopsy taken from upper nates 48 hours after nickel exposure


title: Skinbiopsy_48hoursnickel_nickel_allergic_subject_P1


title: heartgraft_GalTBMT_early_rep4.

description: Gene expression data from heart graft transplanted in GalT BMT recipient

source_name: heart graft, GalT BMT, day 10

value: C57BL/6, Gender:male, Age:12 weeks, Tissue:heart (transplanted graft)


title: heartgraft_GalTBMT_early_rep2.

value: C57BL/6, Gender:male, Age:14 weeks, Tissue:heart (transplanted graft)


title: Skinbiopsy_48hoursnickel_controlsubject_k3


title: heartgraft_Syngeneic_early_rep3.


title: Skinbiopsy_7hoursnickel_controlsubject_k3


title: Skinbiopsy_96hoursnickel_controlsubject_k3


title: Skinbiopsy_96hoursnickel_controlsubject_k2


title: heartgraft_Syngeneic_early_rep2.

value: C57BL/6, Gender:male, Age:15 weeks, Tissue:heart (transplanted graft)


title: Skinbiopsy_96hoursnickel_nickel_allergic_subject_P1


title: Skinbiopsy_96hoursnickel_controlsubject_k1


title: Skinbiopsy_0h_controlsubject_k4

tag: Female (age range 33-49), skin biopsy taken from upper nates no nickel exposure


title: heartgraft_Syngeneic_early_rep1.


title: heartgraft_GalTBMT_early_rep3.

value: C57BL/6, Gender:male, Age:13 weeks, Tissue:heart (transplanted graft)


title: Skinbiopsy_0h_controlsubject_k2

tag: Female (age range 33-49), skin biopsy upper nates. No nickel exposure


title: Skinbiopsy_7hoursnickel_controlsubject_k2


title: heartgraft_GalTBMT_early_rep1.


title: Skinbiopsy_48hoursnickel_controlsubject_k1


title: Skinbiopsy_7hoursnickel_controlsubject_k1

tag: Female (age range 33-49), skin biopsy from upper nates taken 7 hours after nickel exposure


title: MCF7  DN-CLIM high Replicate3

status: Public on Apr 01 2007

city: Irvine

first: Kevin

middle: K

last: Lin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: LMO4 - LIM-only protein 4

hyb_protocol: Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133A array.

scan_protocol: The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: MAS 5.0

source_name: MCF7-DN-CLIM-TetOff cells

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY).  15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: Without doxycycline treatment results in high DN-CLIM level.


title: MCF7 DN-CLIM low Replicate3

description: LMO4 - LIM-only protein 4

tag: Treatment with doxycycline results in low DN-CLIM level.


title: NTg-1

status: Public on Mar 31 2007

city: Newark

first: Bin

last: Tian

state: NJ

address: 185 South Orange Ave.

department: Biochemistry and Molecular Biology

institute: UMDNJ-New Jersey Medical School

hyb_protocol: Hybridization, and processing of Affymetrix arrays were performed according to Affymetrix’s standard protocol.

scan_protocol: Affymetrix’s standard protocol.

data_processing: Intensity values of all probe sets (45,101 total), from each array, were normalized by the Robust Multichip Analysis (RMA) method using the Affymetrix® Expression Console™ Software.

source_name: wild type

label_protocol: Affymetrix’s standard protocol.

extract_protocol: Mice were bred and maintained using standard conditions. Mice were euthanized using pentobarbital 120 mg/kg. The hearts were removed and snap frozen by liquid nitrogen.

tag: Wild type mouse


title: MCF7  DN-CLIM high Replicate1

description: LMO4 - LIM-only protein 4


title: MCF7 DN-CLIM low Replicate2

description: LMO4 - LIM-only protein 4


title: MCF7 DN-CLIM low Replicate1

description: LMO4 - LIM-only protein 4


title: Trauma Hemorrhage Sham Spleen 7 day rep 3

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description: trauma hemorrage injury model

hyb_protocol: Labeled targets were hybridized to Affymetrix (Santa Clara, CA) Mouse Genome 430 2.0 Array GeneChip™ microarrays for 16 hours at 45° C. The arrays were washed and scanned according to Affymetrix standard protocols

scan_protocol: Scanned according to Affymetrix standard protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0/GCOS 1.4 ) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: mouse splenocytes

label_protocol: 1-2 μg of total RNA was used to make single-stranded antisense cDNA using the NuGEN Technologies (San Carlo, CA) Ovation™ Biotin System in accordance with the manufacturer’s directions.

extract_protocol: Total RNA was isolated using the manufacturer’s recommended protocol for RNeasy (Qiagen, Valencia, CA).

treatment_protocol: Leukocyte isolation from cardiac puncture followed by RBC lysis with proprietary buffer, followed by suspension in RLT buffer ;  Splenocytes in Dulbeco's PBS followed by the same RBC lysis RLT suspension process.

tag: Male C57BL/6J


title: NTg-2

source_name: Wild type mouse


title: Tg-Sirt1-1

source_name: transgenic mouse

tag: transgenic mouse


title: Tg-Sirt1-2


title: Trauma Hemorrhage Sham Spleen 3 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 3 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 1 day rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 7 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 7 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 1 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 1 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 3 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 2 hr rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 7 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 2 hr rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 2 hr rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 2 hr rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 7 day rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 7 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 7 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 1 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 3 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 3 day rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 3 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 1 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 2 hr rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 2 hr rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 1 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 1 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 1 day rep 3

description: trauma hemorrage injury model


title: Burn Sham Spleen 7 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 3 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 2 hr rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Spleen 2 hr rep 4

description: trauma hemorrage injury model


title: Burn Sham Spleen 7 day rep 4

description: trauma hemorrage injury model


title: Burn Sham Spleen 7 day rep 3

description: trauma hemorrage injury model


title: Burn Sham Spleen 7 day rep 2

description: trauma hemorrage injury model


title: Burn Sham Spleen 3 day rep 4

description: trauma hemorrage injury model


title: Burn Sham Spleen 3 day rep 3

description: trauma hemorrage injury model


title: Burn Sham Spleen 1 day rep 2

description: trauma hemorrage injury model


title: Burn Sham Spleen 3 day rep 2

description: trauma hemorrage injury model


title: Burn Sham Spleen 1 day rep 4

description: trauma hemorrage injury model


title: Burn Sham Spleen 2 hr rep 3

description: trauma hemorrage injury model


title: Burn Sham Spleen 2 hr rep 2

description: trauma hemorrage injury model


title: Burn Spleen 7 day rep 4

description: trauma hemorrage injury model


title: Burn Sham Spleen 1 day rep 1

description: trauma hemorrage injury model


title: Burn Sham Spleen 1 day rep 3

description: trauma hemorrage injury model


title: Burn Sham Spleen 2 hr rep 4

description: trauma hemorrage injury model


title: Burn Sham Spleen 2 hr rep 1

description: trauma hemorrage injury model


title: Burn Spleen 7 day rep 3

description: trauma hemorrage injury model


title: Burn Spleen 7 day rep 2

description: trauma hemorrage injury model


title: MCF7  DN-CLIM high Replicate2

description: LMO4 - LIM-only protein 4


title: Burn Spleen 7 day rep 1

description: trauma hemorrage injury model


title: Burn Spleen 3 day rep 1

description: trauma hemorrage injury model


title: Melanoma cell line SKMEL28

city: Herston

first: Leisl

last: Packer

state: QLD

address: 300 Herston Rd

department: Cancer and Cell Biology

country: Australia

institute: Queensland Institute of Medical Research

description: For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.

source_name: Melanoma cell line SKMEL28

growth_protocol: Melanoma cell lines were cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

extract_protocol: RNA extractions were performed using Qiagen RNeasy Midi-kits as per the manufacturer’s instructions. RNA quality and concentration were assessed using a 2100 BioAnalyser (Agilent Technologies).

tag: Melanoma cell line


title: Burn Spleen 1 day rep 2

description: trauma hemorrage injury model


title: Melanoma cell line SKMEL13

hyb_protocol: This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2).

data_processing: Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.

source_name: Melanoma cell line SKMEL13

label_protocol: For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA).

tag: Melanoma cell line established from metastatic melanoma


title: Burn Spleen 3 day rep 3

description: trauma hemorrage injury model


title: Burn Spleen 1 day rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Spleen 3 day rep 3

description: trauma hemorrage injury model


title: Burn Spleen 3 day rep 4

description: trauma hemorrage injury model


title: Burn Spleen 3 day rep 2

description: trauma hemorrage injury model


title: Melanoma cell line A04

source_name: Melanoma cell line A04


title: Trauma Hemorrhage Sham Spleen 7 day rep 1

description: trauma hemorrage injury model


title: Burn Spleen 1 day rep 4

description: trauma hemorrage injury model


title: Burn Spleen 1 day rep 1

description: trauma hemorrage injury model


title: Melanoma cell line MM548

source_name: Melanoma cell line MM548


title: Melanoma cell line D32

description: No other data to add

source_name: Melanoma cell line D32


title: Melanoma cell line MM229

source_name: Melanoma cell line MM229


title: Burn Spleen 2 hr rep 3

description: trauma hemorrage injury model


title: Melanoma cell line CJM

source_name: Melanoma cell line CJM


title: Burn Spleen 2 hr rep 1

description: trauma hemorrage injury model


title: Melanoma cell line MM608

source_name: Melanoma cell line MM608


title: Melanoma cell line A15

source_name: Melanoma cell line A15


title: Burn Spleen 2 hr rep 4

description: trauma hemorrage injury model


title: Burn Spleen 2 hr rep 2

description: trauma hemorrage injury model


title: Melanoma cell line MM540

source_name: Melanoma cell line MM540

tag: Melanoma cell line established from primary melanoma


title: Melanoma cell line MM622

source_name: Melanoma cell line MM622


title: Melanoma cell line WSB

source_name: Melanoma cell line WSB


title: Trauma Hemorrhage Sham Burn 7 day rep 4

description: trauma hemorrage injury model

source_name: mouse leukocytes


title: Trauma Hemorrhage Sham Burn 7 day rep 3

description: trauma hemorrage injury model


title: Melanoma cell line D01

source_name: Melanoma cell line D01


title: Trauma Hemorrhage Sham Burn 7 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Burn 3 day rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Burn 7 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Burn 3 day rep 2

description: trauma hemorrage injury model


title: Melanoma cell line MM426

source_name: Melanoma cell line MM426


title: Melanoma cell line MM576

source_name: Melanoma cell line MM576


title: Trauma Hemorrhage Sham Burn 1 day rep 4

description: trauma hemorrage injury model


title: Melanoma cell line A13

source_name: Melanoma cell line A13


title: Melanoma cell line MM595

source_name: Melanoma cell line MM595


title: Melanoma cell line A02

source_name: Melanoma cell line A02


title: Trauma Hemorrhage Sham Burn 3 day rep 1

description: trauma hemorrage injury model


title: Melanoma cell line A06

source_name: Melanoma cell line A06


title: Melanoma cell line MM485

source_name: Melanoma cell line MM485

tag: Melanoma cell line established in metastatic melanoma


title: Trauma Hemorrhage Sham Burn 3 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Burn 1 day rep 3

description: trauma hemorrage injury model


title: Melanoma cell line BL

source_name: Melanoma cell line BL


title: Melanoma cell line D40

source_name: Melanoma cell line D40


title: Melanoma cell line D41

source_name: Melanoma cell line D41


title: Trauma Hemorrhage Sham Burn 1 day rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  7 day rep 3

description: trauma hemorrage injury model


title: Melanoma cell line D36

source_name: Melanoma cell line D36


title: Trauma Hemorrhage Sham Burn 2 hr rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Sham Burn 2 hr rep 3

description: trauma hemorrage injury model


title: Melanoma cell line D10

source_name: Melanoma cell line D10


title: Melanoma cell line D25

source_name: Melanoma cell line D25


title: Trauma Hemorrhage Sham Burn 2 hr rep 1

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  7 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  7 day rep 4

description: trauma hemorrage injury model


title: melanoma cell line D20

source_name: Melanoma cell line D20


title: melanoma cell line D14

source_name: melanoma cell line D14

tag: melanoma cell line D14 established from metastatic melanoma


title: Melanoma cell line D29

source_name: Melanoma cell line D29


title: Trauma Hemorrhage Burn  3 day rep 3

description: trauma hemorrage injury model

source_name: mouse leukocytes


title: Trauma Hemorrhage Burn  3 day rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  3 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  1 day rep 4

description: trauma hemorrage injury model


title: Melanoma cell line MM455

source_name: Melanoma cell line MM455

treatment_protocol: Melanoma cell lines were cultured in RPMI 1640 in the presence of 10% fetal bovine serum.


title: Melanoma cell line D24

source_name: Melanoma cell line D24


title: Trauma Hemorrhage Burn  1 day rep 3

description: trauma hemorrage injury model


title: Melanoma cell line D04

source_name: Melanoma cell line D04

tag: Melanoma cell line D04 established from metastatic melanoma


title: Melanoma cell line MM648

source_name: Melanoma cell line MM648


title: Trauma Hemorrhage Burn  3 day rep 1

description: trauma hemorrage injury model


title: Melanoma cell line D22

source_name: Melanoma cell line D22


title: Melanoma cell line MM253

source_name: Melanoma cell line MM253

tag: Melanoma cell line MM253 established from metastatic melanoma


title: Melanoma cell line MM537

source_name: Melanoma cell line MM537

tag: Melanoma cell line MM537 established from metastatic melanoma


title: Melanoma cell line MM466

source_name: Melanoma cell line MM466


title: Melanoma cell line MM473

source_name: Melanoma cell line MM473


title: Trauma Hemorrhage Burn  1 day rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  2 hr rep 4

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  2 hr rep 2

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  2 hr rep 3

description: trauma hemorrage injury model


title: Trauma Hemorrhage Burn  1 day rep 1

description: trauma hemorrage injury model


title: Burn Sham Blood 7 day rep 4

description: burn injury model


title: Trauma Hemorrhage Burn  2 hr rep 1

description: trauma hemorrage injury model


title: Melanoma cell line MM127

source_name: Melanoma cell line MM127

growth_protocol: Melanoma cell line was cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

tag: Melanoma cell line established from a metastatic melanoma.


title: Melanoma cell line COLOF

source_name: Melanoma cell line COLOF


title: Burn Sham Blood 7 day rep 3

description: burn injury model


title: Melanoma cell line MM170

source_name: Melanoma cell line MM170

tag: Melanoma cell line MM170 established from a metastatic melanoma


title: Melanoma cell line C-32

source_name: Melanoma cell line C-32


title: Melanoma cell line A11

source_name: Melanoma cell line A11

tag: Melanoma cell line established from a metastatic melanoma


title: Melanoma cell line AF6

source_name: Melanoma cell line AF6


title: Burn Sham Blood 7 day rep 2

description: burn injury model


title: Burn Sham Blood 7 day rep 1

description: burn injury model


title: Burn Sham Blood 3 day rep 4

description: burn injury model


title: Burn Sham Blood 3 day rep 3

description: burn injury model


title: Trasnsformed Lymphocytes Unaffected Twin Pair 3 (DCBD3.2)(TP10)

city: Brisbane

first: Nicholas

last: Matigian

state: Queensland

address: 170 Kessels Rd, Nathan

institute: National Adult Stem Cell Centre

hyb_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

data_processing: Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared

label: botin

source_name: Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 3)

extract_protocol: LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software

tag: Sample ID:TP10

tag: Twin Pair ID:DCBD3.2

tag: Clinical Status:Control

tag: Age of Onset:-

tag: Age at interview & blood sampling:35

tag: Current Age (2007):38

tag: Sex

value: Female

tag: Medication at interview (duration) :None


title: Melanoma cell line HT144

source_name: Melanoma cell line HT144

tag: Melanoma cell line HT144 established from a metastatic melanoma.


title: Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 2 (DCBD2.1)(TP7)

scan_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

source_name: Trasnsformed Lymphocytes Bipolar Disorder Affected (Affected pateint of MZ twin pair 2)

tag: Sample ID:DCBD2.1

tag: Twin Pair ID:TP7

tag: Clinical Status:BD1 with psychotic features

tag: Age of Onset:19

tag: Age at interview & blood sampling:20

tag: Current Age (2007):24

value: Male

tag: Medication at interview (duration) :lithium & olanzapine (64 weeks)


title: Trasnsformed Lymphocytes Unaffected Twin Pair 2 (DCBD2.2)(TP8)

source_name: Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 2)

label_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

tag: Twin Pair ID:TP8

tag: Medication at interview (duration) :none


title: Burn Sham Blood 3 day rep 2

description: burn injury model

source_name: mouse leukocytes

tag: Male C57BL/6J


title: Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 1 (DCBD1.1)(TP5)

source_name: Trasnsformed Lymphocytes Bipolar Disorder Affected (Affected pateint of MZ twin pair 1)

tag: Sample ID:TP5

tag: Twin Pair ID:DCBD1.1

tag: Age at interview & blood sampling:55

tag: Current Age (2007):58

tag: Medication at interview (duration) :lithium & citalopram (22.5 years)


title: Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 3 (DCBD3.1)(TP9)

source_name: Trasnsformed Lymphocytes Bipolar Disorder Affected (Affected pateint of MZ twin pair 3)

tag: Sample ID:TP9

tag: Twin Pair ID:DCBD3.1

tag: Age of Onset:18

tag: Age at interview & blood sampling:35

tag: Current Age (2007):38

tag: Sex

tag: Medication at interview (duration) :sodium valproate (5 years)


title: Trasnsformed Lymphocytes Unaffected Twin Pair 1(DCBD1.2)(TP6)

source_name: Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 1)

tag: Sample ID:TP6

tag: Twin Pair ID:DCBD1.2

tag: Clinical Status:Control

tag: Age of Onset:-

tag: Medication at interview (duration) :None


title: Burn Sham Blood 1 day rep 4

description: burn injury model

tag: Male C57BL/6J


title: Burn Sham Blood 1 day rep 3

description: burn injury model


title: Burn Sham Blood 2 hr rep 2

description: burn injury model


title: Burn Sham Blood 3 day rep 1

description: burn injury model


title: Burn Blood 3 day rep 2

description: burn injury model


title: Burn Sham Blood 2 hr rep 1

description: burn injury model


title: Burn Blood 7 day rep 2

description: burn injury model


title: Burn Blood 7 day rep 3

description: burn injury model


title: Burn Sham Blood 1 day rep 1

description: burn injury model


title: Burn Blood 3 day rep 3

description: burn injury model


title: Burn Sham Blood 1 day rep 2

description: burn injury model


title: Burn Blood 7 day rep 1

description: burn injury model


title: Burn Sham Blood 2 hr rep 4

description: burn injury model


title: Burn Blood 3 day rep 4

description: burn injury model


title: Burn Blood 3 day rep 1

description: burn injury model


title: Trauma Hemorrhage Sham Burn 1 day rep 2

description: trauma hemorrage injury model


title: Burn Sham Blood 2 hr rep 3

description: burn injury model


title: Burn Blood 1 day rep 4

description: burn injury model


title: Burn Blood 7 day rep 4

description: burn injury model


title: Burn Blood 2 hr rep 3

description: burn injury model


title: IRAK4-KD-MEFs_IL1b-stimulated_4hours_rep2

status: Public on Mar 30 2007

city: Basel

first: Anton

last: Glück

country: Switzerland

institute: Novartis Institutes for BioMedical Research

description: no additional description

scan_protocol: see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001 Affymetrix 11 µm feature parameter settings: alpha 1 = 0.05, alpha 2 = 0.065, tau = 0.15

data_processing: Affymetrix MAS 5.0, trimmed mean (trimming off the top and bottom 2%) set to 150

label: biotin/SAPE

label_protocol: NuGEN Ovation protocol following the manufacturer's recommendations

growth_protocol: cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% (v/v) foetal calf serum at 37°C in a humidified CO2 (5%) incubator

extract_protocol: Qiagen RNeasy protocol following the manufacturer's recommendations

treatment_protocol: stimulation with 1 ng/ml mouse IL-1b for 4 hours

tag: embryonic fibroblasts from male IRAK4 kinase dead Balb/c mice


title: Burn Blood 2 hr rep 2

description: burn injury model


title: Burn Blood 2 hr rep 1

description: burn injury model


title: Burn Blood 1 day rep 1

description: burn injury model


title: Trauma Hemorrhage Sham Burn 2 hr rep 4

description: trauma hemorrage injury model


title: Burn Blood 1 day rep 2

description: burn injury model


title: Burn Blood 2 hr rep 4

description: burn injury model


title: Burn Blood 1 day rep 3

description: burn injury model


title: IRAK4-KD-MEFs_IL1b-stimulated_4hours_rep1

description: no additional description

hyb_protocol: see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001


title: IRAK4-KD-MEFs_IL1b-stimulated_1hour_rep2

description: no additional description

treatment_protocol: stimulation with 1 ng/ml mouse IL-1b for 1 hour


title: IRAK4-KD-MEFs_unstimulated_4hours_rep2

description: no additional description

treatment_protocol: no treatment


title: WT-MEFs_IL1b-stimulated_4hours_rep2

description: no additional description

source_name: WT mouse embryonic fibroblasts, IL-1b stimulated, 4 hours

tag: embryonic fibroblasts from female wild type Balb/c mice


title: WT-MEFs_unstimulated_4hours_rep2

description: no additional description

source_name: WT mouse embryonic fibroblasts, unstimulated, 4 hours


title: WT-MEFs_IL1b-stimulated_1hour_rep1

description: no additional description

source_name: WT mouse embryonic fibroblasts, IL-1b stimulated, 1 hour


title: IRAK4-KD-MEFs_IL1b-stimulated_1hour_rep1

description: no additional description


title: WT-MEFs_IL1b-stimulated_1hour_rep2

description: no additional description


title: IRAK4-KD-MEFs_unstimulated_4hours_rep1

description: no additional description


title: WT-MEFs_IL1b-stimulated_4hours_rep1

description: no additional description


title: Neuroblastoma cell line SK-N-SH (SKNSH_G_graCNV)

status: Public on Mar 29 2007

type: genomic

city: Columbus

first: David

middle: Lawrence

last: Newsom

address: 700 Children's Drive

department: Microbial Pathogenesis

institute: Nationwide Children's Hospital

description: Peripheral Blood Mononuclear cells

hyb_protocol: see the Functional Genomics Core website (dnaarrays.org) of Ohio State University. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: The data was analyzed with WPP as described in the associated publication.

molecule: genomic DNA

source_name: Neuroblastoma cell line SK-N-SH from (ATCC)

extract_protocol: Spin Doctor Genomic DNA Isolation kit (Gerard Biotech, Oxford, OH).

tag: Female


title: Peripheral Blood Mononuclear cells (C4_graCNV)

description: Peripheral Blood Mononuclear cells

source_name: Peripheral Blood Mononuclear cells

label_protocol: see the Functional Genomics Core website (dnaarrays.org) of Ohio State University

tag: Female, Caucasian


title: Wild-type postnatal day 10 rep 1

city: San Francisco

first: Yong

last: Zhao

address: 1650 owens street

department: Gladstone Institute of Cardiovascular Disease

institute: The J. David Gladstone Institutes

description: Wild-type, postnatal day 10

hyb_protocol: see GeneChip Expression Analysis Technical Manual 701021 Rev. 3

data_processing: GCOS 1.4, RMA

source_name: Wild-type postnatal day 10

label_protocol: Ambion MessageAmp II Biotin Enhanced single round aRNA amplification protocol

extract_protocol: total RNA was extracted by Trizol

tag: heart tissue


title: Neuroblastoma cell line SK-N-SH (SKNSH_L_graCNV)

description: Peripheral Blood Mononuclear cells

data_processing: The data was analyzed with WPP as described in the associated publication


title: Neuroblastoma cell line SK-N-AS (SKNAS_graCNV)

description: Peripheral Blood Mononuclear cells

source_name: Neuroblastoma cell line SK-N-AS from ATCC


title: Knock-out postnatal day 10 rep 2

description: Knock-out, postnatal day 10

source_name: Knock-out postnatal day 10


title: Knock-out postnatal day 10 rep 1

description: Knock-out, postnatal day 10


title: Peripheral Blood Mononuclear cells (C6_graCNV)

description: Peripheral Blood Mononuclear cells


title: Knock-out postnatal day 10 rep 3

description: Knock-out, postnatal day 10


title: Wild-type postnatal day 10 rep 3

description: Wild-type, postnatal day 10


title: Peripheral Blood Mononuclear cells (C5_graCNV)

description: Peripheral Blood Mononuclear cells


title: Wild-type postnatal day 10 rep 2

description: Wild-type, postnatal day 10


title: Neuroblastoma cell line IMR32_graCNV

description: neuroblastoma cell line IMR32 (ATCC)

source_name: IMR32 neuroblastoma cells (ATCC)

tag: Male, Caucasian. The tumor was diagnosed as a neuroblastoma with rare areas of organoid differentiation.


title: MEFs_unstimulated_4hours_rep1

description: no additional description

scan_protocol: see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001. Affymetrix 11 µm feature parameters settings: alpha 1 = 0.05, alpha 2 = 0.065, tau = 0.15

source_name: mouse embryonic fibroblasts, unstimulated, 4 hours

growth_protocol: cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% (v/v) foetal calf serum at 37°C in a humidified CO2 (5%) incubator


title: gid1a-1 gid1b-1 gid1c-2 mock treated for 1 hr, replicate 3

status: Public on Mar 24 2007

city: Freising

first: Claus

last: Schwechheimer

address: Emil-Ramann-Str. 4

department: Plant Systems Biology

country: Germany

institute: TUM

description: Gene expression data from 7 day old gid1a-1 gid1b-1 gid1c-2 mutant seedlings treated with 100µM GA3 for 1h

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

organism: Arabidopsis thaliana

source_name: 7 day old gid1a-1 gid1b-1 gid1c-2 mutant seedlings mock-treated for 1h

label_protocol: Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) according to the manufacturer's instructions.

extract_protocol: Approximately 80 mg from 7 day old, light grown gid1a-1 gid1b-1 gid1c-2  mutant seedlings were mock-treated for 1h, collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: gid1a-1 gid1b-1 gid1c-2 mutant, 7 day old seedlings, light grown, mock-treated for 1h


title: gid1a-1 gid1b-1 gid1c-2 treated for 1 hr with 100 uM GA3, replicate 1

source_name: 7 day old gid1a-1 gid1b-1 gid1c-2 seedlings treated for 1h with 100µM GA3

extract_protocol: Approximately 80 mg from 7 day old light grown gid1a-1 gid1b-1 gid1c-2  mutant seedlings were treated with 100µM GA3 for 1h, collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: gid1a-1 gid1b-1 gid1c-2 mutant, 7 day old seedlings, light grown, treated for 1h with 100µM GA3


title: gid1a-1 gid1b-1 gid1c-2 treated for 1 hr with 100 uM GA3, replicate 3


title: ga-1 (SALK_109115) treated for 1 hr with 100 uM GA3, replicate 2

description: Gene expression data from 7 day old ga-1 (SALK_109115) mutant seedlings treated with 100µM GA3 for 1h

source_name: 7 day old ga-1 (SALK_109115) seedlings treated for 1h with 100µM GA3

extract_protocol: Approximately 80 mg from 7 day old light grown ga-1 (SALK_109115)  mutant seedlings were treated with 100µM GA3 for 1h, collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: ga-1 (SALK_109115) mutant, 7 day old seedlings, light grown, treated for 1h with 100µM GA3


title: ga-1 (SALK_109115) treated for 1 hr with 100 uM GA3, replicate 1


title: gid1a-1 gid1b-1 gid1c-2 mock treated for 1 hr, replicate 2


title: gid1a-1 gid1b-1 gid1c-2 mock treated for 1 hr, replicate 1

description: Gene expression data from 7 day old gid1a-1 gid1b-1 gid1c-2  mutant seedlings treated with 100µM GA3 for 1h


title: gid1a-1 gid1b-1 gid1c-2 treated for 1 hr with 100 uM GA3, replicate 2


title: ga-1 (SALK_109115) mock treated for 1 hr, replicate 2

description: Gene expression data from 7 day old ga-1(SALK_109115)  mutant seedlings treated with 100µM GA3 for 1h

source_name: 7 day old ga-1 (SALK_109115) mutant seedlings mock-treated for 1h

extract_protocol: Approximately 80 mg from 7 day old, light grown ga-1 (SALK_109115)  mutant seedlings were mock-treated for 1h, collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: ga-1 (SALK_109115) mutant, 7 day old seedlings, light grown, mock-treated for 1h


title: ga-1 (SALK_109115) mock treated for 1 hr, replicate 3


title: ga-1 (SALK_109115) treated for 1 hr with 100 uM GA3, replicate 3


title: p38alpha wild type fetal liver E15.5, biological rep3

status: Public on Mar 23 2007

city: Vienna

first: Norbert

last: Schweifer

address: Dr. Boehringer Gasse 5-11

country: Austria

institute: Boehringer Ingelheim Austria

description: Gene expression data from fetal liver wild type in respect to p38alpha

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Murine Genome U74 Version 2 Set MG-U74A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was normalized with RMA (default settings) as implemented in Bioconductor. RMA gives log2 transformed data

source_name: fetal liver, wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: No in vitro culture

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

treatment_protocol: No treatment

tag: Genotype

value: p38alpha wt

tag: Age


title: p38alpha wild type fetal liver E15.5, biological rep2


title: p38alpha wild type fetal liver E15.5, biological rep1


title: ga-1 (SALK_109115) mock treated for 1 hr, replicate 1

description: Gene expression data from 7 day old ga-1 (SALK_109115)  mutant seedlings treated with 100µM GA3 for 1h


title: p38alpha knock out fetal liver E15.5, biological rep3

description: Gene expression data from fetal liver deficient in p38alpha

source_name: fetal liver with p38alpha knock out

value: p38alpha KO


title: p38alpha knock out fetal liver E13.5, biological rep3


title: p38alpha knock out fetal liver E13.5, biological rep1


title: p38alpha wild type fetal liver E13.5, biological rep1


title: p38alpha knock out fetal liver E15.5, biological rep1


title: p38alpha wild type fetal liver E13.5, biological rep3


title: p38alpha knock out fetal liver E13.5, biological rep2


title: p38alpha wild type fetal liver E13.5, biological rep2


title: Pof Mutant 1stInstar larvae rep1

status: Public on Mar 22 2007

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

description: Gene expression data from whole 1st instar larvae (Wt and pof mutant).

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Raw data was normalized using RMA (R and Bioconductor)

organism: Drosophila melanogaster

source_name: pof mutant 1st instar larvae

label_protocol: Standard Affymetrix

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) followed by a purification using RNeasy kit (Qiagen) according to the instruction by the suppliers.

tag: Gender

value: mixed

tag: Tissue


title: Pof Mutant 1stInstar larvae rep3


title: Wt 1stInstar larvae rep2

source_name: Wt 1st instar larvae


title: Pof Mutant 1stInstar larvae rep2


title: p38alpha knock out fetal liver E15.5, biological rep2


title: Wt 1stInstar larvae rep3


title: Wt 1stInstar larvae rep1