title: Colon - 8246

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 56-60
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Black tarry stools
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Presenting Symptoms: Nausea
Screening studies performed?: Yes
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: Mucinous Carcinoma

source_name: Rectosigmoid Junction


title: Rectum - 8242

status: Public on Jan 15 2005

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: 1.6
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 119
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Constipation
Screening studies performed?: No
Diagnosis made by: Barium enema
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological Dukes Stage: B
Primary Site: Rectum
Histology: Adenocarcinoma

molecule: total RNA

organism: Homo sapiens

source_name: Rectum


title: Fallopian tube - 8224

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
Pathological T: 3c
Pathological Grade: 3
Primary Site: Fallopian tube
Histology: Papillary serous carcinoma

source_name: Fallopian Tube


title: Breast - 8232

description:
Quality metric = 28S to 18S: 1.6
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?: Yes
Days from Patient Diagnosis to Excision: 9
Mammogram: Yes
Number of years in which a mammogram was obtained?: 26-30
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 6-10
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Omentum - 8236

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Primary Site: Unknown
Histology: Metastatic Carcinoma, NOS

source_name: Omentum


title: Omentum - 8240

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
Prior Therapy: Chemotherapy
Prior Therapy: Hormonal Treatment
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 11-15
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Peritoneum
Retreatment Stage: 4
Retreatment Grade: 3
Retreatment ER: Positive
Retreatment PR: Positive
Primary Site: Breast
Histology: Metastatic Lobular Carcinoma

source_name: Ovary


title: Uterus - 8216

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
Days from Patient Diagnosis to Excision: 14
Pathological T: 4
Pathological N: X
Pathological M: 0
Pathological Stage: 4A
Pathological Grade: 3
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Endometrium


title: Breast - 8212

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 70
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: Yes
Mammogram calcifications?: Yes
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 2
Pathological Multiple Tumors: No
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: Breast - 8234

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 24
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 26-30
Oophorectomy?: No
Fibrocystic disease?: Yes
Mammogram calcifications?: No
Pathological T: 3
Pathological N: 3a
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: Ovary - 8226

description:
Quality metric = 28S to 18S: 1.7
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?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 34
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Papillary Serous Carcinoma


title: Axillary Lymph Nodes - 8218

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Chewing Tobacco
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 3b
Retreatment N: 0
Retreatment M: 1a
Retreatment Metastatic Sites: Lymph Nodes
Retreatment Stage: 4
Primary Site: Skin of Left Flank
Histology: Metastatic Malignant melanoma, NOS

source_name: Axillary Lymph Nodes


title: Breast - 8208

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?: No
Days from Patient Diagnosis to Excision: 59
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
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 16-20
Pathological T: 1c
Pathological N: 0(i-)
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 1
Pathological Multiple Tumors: No
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: Prostate - 8206

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Male
Ethnic Background: African-American
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: 21
PSA: Elevated
# of years PSA Tested?: 11-15
Cancer discovered by digital exam?: Yes
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Colon - 8228

description:
Quality metric = 28S to 18S: 1.3
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: 21
Presenting Symptoms: Abdominal Pain
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 3
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Colon - 8200

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Screening studies performed?: Yes
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

source_name: Rectosigmoid


title: Colon - 8202

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?: Yes
Days from Patient Diagnosis to Excision: 10
Presenting Symptoms: Abdominal Pain
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 3
Primary Site: Colon
Histology: Metastatic Adenocarcinoma

source_name: Liver


title: Lymph Nodes - 8198

description:
Quality metric = 28S to 18S: 1.4
Primary Site: Lymph Nodes
Histology: Mature (peripheral) B-cell lymphoma
Patient Age: 50-60
Ethnic Background: Caucasian
Sex: Male
Years of Tobacco Use: 6-10
Type of Tobacco Use: Pipe
Alcohol Consumption?: Yes
Tobacco Use : Yes
Presenting Symptoms: Lymphadenopathy
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Have you ever had mononucleousis?: No

source_name: Lymph Nodes


title: Colon - 8196

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 36
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma


title: Peritoneum - 8188

description:
Quality metric = 28S to 18S: 1.7
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?: Yes
Days from Patient Diagnosis to Excision: 11
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Metastatic Papillary Serous Carcinoma


title: Small Bowel - 8182

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Hormonal Treatment
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 3c
Retreatment N: X
Retreatment M: 1
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Fallopian Tube
Histology: Metastatic Papillary serous carcinoma

source_name: Small bowel


title: Colon - 8194

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 22
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Kidney - 8192

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: American Indian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 24
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Breast - 8170

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 16
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 16-20
Oophorectomy?: No
Fibrocystic disease?: No
Pathological T: 4b
Pathological N: 1a
Pathological Grade: 2
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Lung - 2483

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
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?: Yes
Days from Patient Diagnosis to Excision: 68
Presenting Symptoms: SOB
Workplace or household smokers?: No
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 3
Primary Site: Lung
Histology: Adenocarcinoma, NOS

source_name: Bronchus & Lung


title: Omentum - 8174

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 80-90
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: 142
Prior Therapy: Chemotherapy
Primary Site: Ovary
Histology: Metastatic Papillary Serous Carcinoma


title: Myometrium - 8184

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Days from Patient Diagnosis to Excision: 14
Clinical Question: Grade
Clinical Value: High
Clinical Question: Stage
Clinical Value: No AJCC scheme for this site and histology
Primary Site: Myometrium
Clinical Question: Histology
Clinical Value: Epithelioid leiomyosarcoma

source_name: Uterus, NOS


title: Uterus - 8180

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Adrenal gland - 8190

description:
Quality metric = 28S to 18S: 1.4
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
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: No
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Adrenals
Retreatment Stage: 4
Retreatment Grade: 3
Primary Site: Lung
Histology: Metastatic Non-small cell carcinoma

source_name: Adrenal gland


title: Lung - 2479

description:
Quality metric = 28S to 18S: 1.4
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?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 39
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Ovary - 8172

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Female
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: 25
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Papillary Serous Carcinoma


title: Omentum - 8186

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
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: 105
Prior Therapy: Chemotherapy
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: X
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 4
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary vs Peritoneum
Histology: Metastatic Papillary Serous Carcinoma


title: Colon - 2485

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Male
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
Days from Patient Diagnosis to Excision: 12
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 2
Primary Site: Colon
Histology: Adenocarcinoma


title: Breast - 3377

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 36
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 16-20
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Abdominal wall mass - 8176

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Bloating
Retreatment T: 3c
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Other
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Ovary
Histology: Metastatic Papillary Serous Carcinoma


title: Breast - 2481

description:
Quality metric = 28S to 18S: 1.0
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: 22
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?: Yes
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 16-20
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Primary Site: Breast
Histology: Ductal Carcinoma


title: Breast - 2477

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Hispanic
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 43
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
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 0-5
Pathological T: 2
Pathological N: 0(i-)
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Spleen - 2475

description:
Quality metric = 28S to 18S: 1.6
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
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Abdominal mass
Retreatment T: 3c
Retreatment N: X
Retreatment M: X
Retreatment Stage: Unknown
Retreatment Grade: X
Primary Site: Ovary
Histology: Carcinoma, NOS

source_name: Spleen


title: Corpus Uteri - 2045

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Years of Tobacco Use: 0-5
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 16
Hormonal therapy (# of Years)?: 0-5
Pathological T: 4
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Pulmonary
Pathological Stage: 4B
Pathological Grade: X
Primary Site: Corpus Uteri
Histology: Serous adenocarcinoma (papillary serous)

source_name: Corpus Uteri


title: Colon - 2471

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 13
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: X
Pathological Multiple Tumors: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Breast - 13491

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Chewing Tobacco
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 8
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Pathological T: 4b
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Breast - 2051

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Female
Ethnic Background: Other
Ethnic Background: Hawaiian
Tobacco Use : No
Family History of Cancer?: No
Mammogram: Yes
Oral contraceptives?: Yes
Pathological T: 2
Pathological N: 1a
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: ANOXIA EXPERIMENT 1

status: Public on Jan 10 2005

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

description:
Arabidopsis thaliana ecotype Columbia glabra were grown for 4 days in the dark at 23°C in multiwell plates containing half-strenght murashige skoog medium without added sucrose. Sample was subsequently kept for 6h under anoxia.  RNA was extracted using a Ambion RNaqueous kit. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  Each independent experiment consisted of four replicated seedlings cultures, pooled after RNA extraction.
Keywords = Arabidopsis, anoxic, seedling, dark grown

organism: Arabidopsis thaliana

source_name: 4 days old, dark grown seedlings


title: ANOXIA+SUCROSE EXPERIMENT 2

description:
Arabidopsis thaliana ecotype Columbia glabra were grown for 4 days in the dark at 23°C in multiwell plates containing half-strenght murashige skoog medium without added sucrose. Sample was subsequently kept for 6h under anoxia in the presence of 90mM sucrose.  RNA was extracted using a Ambion RNaqueous kit. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  Each independent experiment consisted of four replicated seedlings cultures, pooled after RNA extraction.
Keywords = Arabidopsis, anoxic, sucrose, seedling, dark grown


title: ANOXIA EXPERIMENT 2


title: ANOXIA+SUCROSE EXPERIMENT 1


title: lec1-1 Floral Bud

status: Public on Jan 01 2005

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Microarray Methods: Total RNA was extracted using the Hot Borate Method (ref.).  Fifteen micrograms of biotinylated complementary RNA (cRNA) was prepared as described (Le et. al., 2004, PNAS).  cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips.  The scanned array images were analyzed using Affymetrix Microarray Suite 5.0 (MAS 5.0) with a global scaling intensity set at 500.

source_name: Genotype: Ws-0, lec1-1; Organ: Floral Bud


title: WT Post-Mature Green Seed 2

description:
Growth Condition: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20oC and 50% - 70% relative humidity. Experiments were performed as described (Le et. al., 2003, PNAS).

Microarray Methods: Total RNA was extracted using the Hot Borate Method (ref.). Fifteen micrograms of biotinylated complementary RNA (cRNA) was prepared as described (Le et. al., 2003, PNAS). cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips. The scanned array images were analyzed using Affymetrix Microarray Suite 5.0 (MAS 5.0) with a global scaling intensity set at 500.
Keywords = Arabidopsis
Keywords = seed development

source_name: Genotype: Ws-0, Wild Type; Stage: Post-Mature Green Seed; Biological Replica: 2 of 2


title: lec1-1 Root

source_name: Genotype: Ws-0, lec1-1; Organ: Root


title: WT Rosette Leaf

source_name: Genotype: Ws-0, Wild Type; Organ: Rosette Leaf


title: WT Stem

source_name: Genotype: Ws-0, Wild Type; Organ: Stem


title: WT Root

source_name: Genotype: Ws-0, Wild Type; Organ: Root


title: WT Seedling 2

source_name: Genotype: Ws-0, Wild Type; Stage: 3-Day-After-Imbibition Seedling; Biological Replica: 2 of 2


title: AIR EXPERIMENT 1

description:
Arabidopsis thaliana ecotype Columbia glabra were grown for 4 days in the dark at 23°C in multiwell plates containing half-strenght murashige skoog medium without added sucrose. Sample was subsequently kept for 6h under the same conditions (aerobic)  RNA was extracted using a Ambion RNaqueous kit. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  Each independent experiment consisted of four replicated seedlings cultures, pooled after RNA extraction.
Keywords = Arabidopsis, aerobic, seedling, dark grown


title: AIR EXPERIMENT 2


title: WT Mature Green Seed 1

description:
Growth Condition: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20oC and 50% - 70% relative humidity. Experiments were performed as described (Le et. al., 2003, PNAS).

Microarray Methods: Total RNA was extracted using the Hot Borate Method (ref.). Fifteen micrograms of biotinylated complementary RNA (cRNA) was prepared as described (Le et. al., 2003, PNAS). cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips. The scanned array images were analyzed using Affymetrix Microarray Suite 5.0 (MAS 5.0) with a global scaling intensity set at 500.
Keywords = Arabidopsis
Keywords = seed development
Lot batch = 2003282

source_name: Genotype: Ws-0, Wild Type; Stage: Mature Green Seed; Biological Replica: 1 of 2


title: WT Seedling 1

source_name: Genotype: Ws-0, Wild Type; Stage: 3-Day-After-Imbibition Seedling; Biological Replica: 1 of 2


title: WT Floral Bud

source_name: Genotype: Ws-0, Wild Type; Organ: Floral bud


title: WT Mature Green Seed 2

source_name: Genotype: Ws-0, Wild Type; Stage: Mature Green Seed; Biological Replica: 2 of 2


title: WT 24-Hr Seed 2

source_name: Genotype: Ws-0, Wild Type; Stage: 24-Hr Fertilized Seed; Biological Replica: 2 of 2


title: lec1-1 Stem

source_name: Genotype: Ws-0, lec1-1; Organ: Stem


title: Prostate - 2047

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
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: 106
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 2a
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate Gland


title: WT Post-Mature Green Seed 1

source_name: Genotype: Ws-0, Wild Type; Stage: Post-Mature Green Seed; Biological Replica: 1 of 2


title: WT Cotyledon Stage Seed 1

source_name: Genotype: Ws-0, Wild Type; Stage: Cotyledon Stage Seed; Biological Replica: 1 of 2


title: WT Ovule 1

description:
Growth Condition: Plants were grown in a Conviron chamber
under continuous light with fluorescent lamps at 20oC and 50% - 70% relative
humidity.  Experiments were performed as described (Le et. al., 2003, PNAS).

Microarray Methods: Total RNA was extracted using the Hot
Borate Method (ref.).  Fifteen micrograms of biotinylated complementary RNA
(cRNA) was prepared as described (Le et. al., 2003, PNAS).  cRNA was
subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips.  The scanned
array images were analyzed using Affymetrix Microarray Suite 5.0 (MAS 5.0) with
Keywords = Arabidopsis
Keywords = seed development
Lot batch = 2003282

source_name: Genotype: Ws-0, Wild Type; Stage: Unfertilized Ovule; Biological Replica: 1 of 2


title: WT Cotyledon Stage Seed 2

source_name: Genotype: Ws-0, Wild Type; Stage: Cotyledon Stage Seed; Biological Replica: 2 of 2


title: Breast - 8220

description:
Quality metric = 28S to 18S: 1.5
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: 22
Mammogram: Yes
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 16-20
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: Yes
Pathological T: 0
Pathological N: 0(i+)
Pathological M: 0
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: WT Ovule 2

source_name: Genotype: Ws-0, Wild Type; Stage: Unfertilized Ovule; Biological Replica: 2 of 2


title: WT 24-Hr Seed 1

source_name: Genotype: Ws-0, Wild Type; Stage: 24-Hr Fertilized Seed; Biological Replica: 1 of 2


title: mouse reference pRS 0.3 ng -1

status: Public on Dec 21 2004

city: Manhattan

first: Philine

last: Wangemann

state: KS

address: 1600 Dension Avenue

department: Anatomy and Physiology

institute: Kansas State University

description:
Universal Mouse Reference RNA from Strategene
This sample is also known as MUR pRS 0.3ng
Keywords = Universal mouse reference RNA
Keywords = mur pRS 0.3ng

organism: Mus musculus

source_name: Universal RNA


title: mouse reference pRS 10 ng -2

description:
Universal Mouse Reference RNA from Strategene
This sample is also known as MUR pRS 10ng
Keywords = Universal mouse reference RNA
Keywords = murpRS 10ng


title: mouse reference pRS 3 ng -3

description:
Universal Mouse Reference RNA from Strategene
This sample is also known as MUR pRS 3ng
Keywords = Universal mouse reference RNA
Keywords = murpRS 3ng


title: mouse reference pRS 10 ng -1


title: mouse Kidney pRS 10 ng -3

description:
Mouse Kidney RNA from Ambion
This sample is also known as MK pRS
Keywords = mouse Kidney RNA
Keywords = MK pRS

source_name: Mouse Kidney RNA


title: PGA-Hs_S-18

status: Public on Dec 03 2004

city: Cambridge

first: Martina

last: Schinke

state: MA

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

institute: Harvard University

description:
Human subjects with ischemic cardiomyopathy
Keywords = ischemic cardiomyopathy

source_name: left ventricle biopsy


title: mouse reference pRS 3 ng -1

description:
Universal Mouse Reference RNA from Strategene
This sample is also known as MUR pRS 3ng
Keywords = Universal mouse reference RNA
Keywords = mur pRS 3ng


title: mouse reference pRS 0.3 ng -2


title: PGA-Hs_S-20


title: PGA-Hs_V-3

description:
Human subjects with viral cardiomyopathy
Keywords = viral cardiomyopathy


title: mouse Kidney pRS 10 ng -2


title: mouse reference pRS 10 ng -3


title: PGA-Hs_V-1


title: mouse reference pRS 3 ng -2


title: PGA-Hs_V-6


title: PGA-Hs_V-4


title: PGA-Hs_S-17


title: PGA-Hs_V-5


title: PGA-Hs_S-14


title: PGA-Hs_S-11


title: mouse Kidney pRS 10 ng -1


title: PGA-Hs_S-12


title: PGA-Hs_S-16


title: PGA-Hs_V-7


title: PGA-Hs_S-13


title: PGA-Hs_V-2


title: PGA-Hs_S-19


title: PGA-Hs_S-15


title: PGA-Hs_S-21


title: PGA-Hs_S-10


title: PGA-Hs_S-3


title: lec1-1 Rosette Leaf

source_name: Genotype: Ws-0, lec1-1; Organ: Rosette Leaf


title: PGA-Hs_S-8


title: PGA-Hs_S-9


title: PGA-Hs_S-7


title: PGA-Hs_P-6

description:
Human subjects with post-partum cardiomyopathy
Keywords = post-partum cardiomyopathy


title: PGA-Hs_H-2

description:
Human subjects with hypertrophic cardiomyopathy
Keywords = hypertrophic cardiomyopathy


title: PGA-Hs_S-1


title: PGA-Hs_H-3


title: PGA-Hs_F-6

description:
Human subjects with familial cardiomyopathy
Keywords = Familial Cardiomyopathy


title: PGA-Hs_P-5


title: PGA-Hs_H-5


title: PGA-Hs_P-4


title: PGA-Hs_F-4


title: PGA-Hs_S-5


title: PGA-Hs_F-3

description:
Human subjects with familial cardiomyopathy
Keywords = familial cardiomyopathy


title: PGA-Hs_D-13

description:
Human subjects with idiopathic cardiomyopathy
Keywords = idiopathic cardiomyopathy


title: PGA-Hs_F-2


title: PGA-Hs_D-12


title: PGA-Hs_S-6


title: PGA-Hs_H-4


title: PGA-Hs_D-15


title: PGA-Hs_P-7


title: PGA-Hs_D-7


title: PGA-Hs_D-10


title: PGA-Hs_H-1


title: PGA-Hs_F-1


title: PGA-Hs_S-2


title: PGA-Hs_D-5


title: PGA-Hs_D-1

description:
Human subjects with idiopathic cardiomyopathy
Keywords = Idiopathic Cardiomyopathy


title: PGA-Hs_D-4


title: brain, forebrain: VEH-HI 8_e1_le1

status: Public on Nov 24 2004

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

description:
Forebrain
Treatment, type=pharmacogenomic_treatment, description=Vehicle injection 1 hour before hypoxic ischemia

source_name: brain, forebrain


title: brain, forebrain: VEH-HI 9_e1_le1

description:
Forebrain
Treatment, type=pharmacogenomic_treatment, description=Vehicle injection 1 hr before hypoxic ischemia


title: brain, forebrain: VEH-HI 7_e1_le1


title: brain, forebrain: VEH-Sham 5_e1_le1

description:
Forebrain
Treatment, type=pharmacogenomic_treatment, description=Vehicle injection 1 hour before sham surgery


title: PGA-Hs_D-2


title: brain, forebrain: EPO-HI 13_e1_le1

description:
Forebrain
Treatment, type=pharmacogenomic_treatment, description=EPO (5U/g, i.p.) 1 hr before hypoxic ischemia


title: brain, forebrain: EPO-HI 14_e1_le1


title: brain, forebrain: EPO-HI 12_e1_le1


title: brain, forebrain: VEH-Sham 3_e1_le1


title: brain, forebrain: VEH-Sham 4_e1_le1


title: brain, forebrain: VEH-Sham 1_e1_le1


title: SimvaVeh3

status: Public on Oct 26 2004

city: Baltimore

first: Shwu-Fan

last: Ma

state: MD

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins University

description:
Mice treated with 2.5ug/kg LPS intratracheally, samples at 24hr.  Mice given simvastatin 20mg/kg for 48 hr prior to sample collection (2 doses of simvastatin).
Sample_age: 7-8 weeks old
Sample_hybridization: total RNA was converted to first-strand cDNA using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. Complementary DNA corresponding to 5-10 µg of total RNA was used in a cRNA amplification step using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was fragmented to a size of approximately 50 bp, and approximately 20-30 µg of the biotinylated cRNA was hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA). The bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Sample_RNA_Isolation: Tissues (~50 mg) were taken frozen and directly solubilized in chaotropic solubilization buffer using a Brinkman Polytron tissue disruptor. Larger tissue fragments (>100mg) were pulverized into frozen powder with a mortar and pestle, pre-chilled to liquid nitrogen temperature, and then the frozen powder was solubilized with the Polytron. RNA was purified using Trizol LS (Life Technologies) and an additional RNA purification step was conducted using the RNAeasy purification kit (Qiagen Inc., Valencia, CA). Approximately 10 µg of purified, total RNA was used for analyses.
Sample_sex: male
Sample_strain: C57BL6
Keywords = Murine, endothelial cell barrier function, inflammation, Simvastatin, LPS

source_name: murine lungs


title: SimvaLPS3


title: PGA-Hs_D-9


title: PGA-Hs_D-3


title: VehLPS


title: SimvaLPS2


title: SimvaVeh1


title: brain, forebrain: VEH-Sham 2_e1_le1


title: SimvaVeh2


title: VehLPS1


title: brain, forebrain: EPO-HI 11_e1_le1


title: brain, forebrain: VEH-HI 6_e1_le1


title: VehLPS2


title: SimvaLPS1


title: PGA-Hs_D-6


title: brain, forebrain: EPO-HI 15_e1_le1


title: VehVeh3


title: brain, forebrain: VEH-HI 10_e1_le1


title: VehVeh1


title: VehVeh2


title: PGA-E18.5_3A

status: Public on Jun 24 2004

description:
C57BL/6 benchmark dataset:  Embryonic day 18.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart

source_name: Atrial chamber of heart


title: PGA-E14.5_1

description:
C57BL/6 benchmark dataset:  Embryonic day 14.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart

source_name: Both ventricles


title: eye, retina: Myoc 2_e1_le1

status: Public on Oct 14 2004

description:
retina
Treatment, type=pharmacogenomic_treatment, description=Retinas were dissected from control and transgenic animals. The transgenic animals expressed myocilin in their aqueous humor. A part of the aqueous humor also is present in the back of the eye. High levels of myocilin would be present around the retina.

source_name: eye, retina


title: PGA-E18.5_1A


title: PGA-E14.5_2A


title: eye, retina: Control 1_e1_le1


title: PGA-E18.5_1


title: eye, retina: Myoc 1_e1_le1


title: PGA-E18.5_2A


title: PGA-E16.5_2A

description:
C57BL/6 benchmark dataset:  Embryonic day 15.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart


title: PGA-E18.5_3


title: PGA-E13.5_2A

description:
C57BL/6 benchmark dataset:  Embryonic day 13.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart


title: PGA-E16.5_1A


title: PGA-E16.5_3


title: PGA-E13.5_3A


title: PGA-E14.5_3A


title: eye, retina: Control 2_e1_le1

description:
retina--technical replicate for Control 1
Treatment, type=pharmacogenomic_treatment, description=Retinas were dissected from control and transgenic animals. The transgenic animals expressed myocilin in their aqueous humor. A part of the aqueous humor also is present in the back of the eye. High levels of myocilin would be present around the retina.


title: PGA-E16.5_3A


title: PGA-E16.5_1


title: PGA-E16.5_2


title: PGA-E14.5_3


title: PGA-E18.5_2


title: PGA-E13.5_1A


title: PGA-E13.5_3


title: PGA-E13.5_2


title: PGA-E13.5_1


title: PGA-E12.5_2A

description:
C57BL/6 benchmark dataset:  Embryonic day 12.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart


title: PGA-E12.5_3A


title: PGA-E14.5_2


title: PGA-E12.5_1A


title: PGA-E12.5_3


title: PGA-E12.5_1


title: PGA-E11.5_3

description:
C57BL/6 benchmark dataset:  Embryonic day 11.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart

source_name: Whole heart


title: PGA-E11.5_2


title: PGA-E10.5_3

description:
C57BL/6 benchmark dataset:  Embryonic day 10.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart


title: PGA-E10.5_1

description:
C57BL/6 benchmark dataset:  Embryonic day 10.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stage 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart


title: IAA/B Treated - 3

status: Public on Jun 23 2004

city: Albany

first: Atsunari

last: Tsuchisaka

address: 800 Buchanan St.

department: Plant Gene Expression Center

institute: University of California, Berkeley / USDA

description: 7 day old light grown seedlings from liquid culture simultaneously treated with 10 microM Compound B and 5 microM IAA for 1 h.

source_name: 7d L+ Arabidopsis Seedlings


title: IAA/A Treated - 3

description: 7 day old light grown seedlings from liquid culture simultaneously treated with 10 microM Compound A and 5 microM IAA for 1 h.


title: PGA-E10.5_2


title: IAA/B Treated - 1


title: IAA/A Treated - 2


title: B Treated - 1

description: 7 day old light grown seedlings from liquid culture treated with 10 microM Compound B for 1 h.


title: A Treated - 1

description: 7 day old light grown seedlings from liquid culture treated with 10 microM Compound A for 1 h.


title: A Treated - 2


title: A treated - 3


title: B Treated - 3


title: A Treated - 4


title: PGA-E11.5_1


title: B Treated - 2


title: PGA-E12.5_2


title: IAA Treated - 4

description: 7 day old light grown seedlings from liquid culture treated with 5 microM IAA for 1 h.


title: IAA Treated - 2


title: IAA/B Treated - 2


title: IAA Treated - 3


title: Negative Control - 3

description: 7 day old light grown seedlings from liquid culture treated with DMSO for 1 h.


title: Negative control - 1


title: Negative Control - 2


title: IAA/A Treated - 1


title: Negative Control - 4


title: mouse reference TwoRA 10 ng -1

status: Public on May 28 2004

description:
Universal Mouse Reference RNA from Strategene
This sample is also known as MUR TwoRA
Keywords = Universal mouse reference RNA
Keywords = mur TwoRA


title: mouse Kidney RS 3 ng -1

description:
Mouse Kidney RNA from Ambion
This sample is also known as MK RS
Keywords = mouse Kidney RNA
Keywords = MK RS


title: mouse Kidney RS 10 ng -3


title: mouse Kidney TwoRA 10 ng -2

description:
Mouse Kidney RNA from Ambion
This sample is also known as MK TwoRA
Keywords = mouse Kidney RNA
Keywords = MK TwoRA


title: mouse Kidney RS 10 ng -1


title: mouse reference RS 10 ng -2

description:
Universal Mouse Reference RNA from Strategene
This sample is also known as MUR RS 10ng
Keywords = Universal mouse reference RNA
Keywords = mur RS 10ng


title: IAA treated - 1


title: mouse Kidney RS 30 ng -2


title: mouse Kidney RS 100 ng -3


title: mouse Kidney TwoRA 10 ng -1


title: mouse Kidney OneRA 10 ug -1

description:
Mouse Kidney RNA from Ambion
This sample is also known as MK OneRA
Keywords = mouse Kidney RNA
Keywords = MK OneRA


title: mouse Kidney OneRA 10 ug -3

description:
Mouse Kidney RNA from Ambion
This sample is also known as MK OneRA
Keywords = mouse Kidney RNA
Keywords = MKOneRA


title: mouse Kidney RS 3 ng -3


title: mouse Kidney RS 100 ng -1


title: mouse Kidney TwoRA 10 ng -3


title: mouse reference RS 10 ng -1


title: mouse Kidney RS 30 ng -1


title: mouse Kidney RS 3 ng -2


title: PGA-E14.5_1A

description:
C57BL/6 benchmark dataset:  Embryonic day 14.5.  The most common congenital cardiac abnormalities are associated with the defects in cardiac septation and outflow tract development.  Specifically, atrial septal defects (ASDs) account for about one third of the cases detected in adults.  To address this question it is imperative to get insight into the genes expressed during normal heart development.  Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  These developmental stages have been selected as they encompass stages of septation of the atrial and ventricular chambers as well as the cardiac outflow tract.  Gene expression was further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stages 10.5 and 11.5, we have removed the rostral and caudal parts of the embryo and subjected the middle part, which includes the heart, for expression analysis.  From embryonic day 12.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.
Keywords = cardiac development, heart


title: mouse Kidney OneRA 10 ug -2


title: mouse reference RS 10 ng -3


title: mouse reference TwoRA 10 ng -3


title: mouse reference TwoRA 10 ng -2


title: mouse Kidney RS 10 ng -2


title: mouse reference OneRA 10 ug -2

description:
Universal Mouse Reference RNA from Strategene
This sample is also known as MUR OneRA
Keywords = Universal mouse reference RNA
Keywords = mur OneRA


title: mouse reference OneRA 10 ug -3


title: PGA_PA-S_386

status: Public on Mar 24 2004

description:
To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.http://cardiogenomics.med.harvard.edu/project-detail?project_id=229
Keywords = human, idiopathic, ischemic, cardiac, hypertrophy

source_name: Left Ventricle Biopsy


title: mouse Kidney RS 30 ng -3


title: PGA_PA-S_281


title: PGA_PA-S_464


title: mouse Kidney RS 100 ng -2


title: PGA_PA-N_294


title: PGA_PA-S_242


title: PGA_PA-S_342


title: PGA_PA-S_267


title: PGA_PA-S_233


title: PGA_PA-N_325


title: PGA_PA-S_224


title: PGA_PA-S_297


title: PGA_PA-N_326


title: PGA_PA-N_291


title: PGA_PA-S_314


title: PGA_PA-S_115


title: PGA_PA-N_322


title: PGA_PA-N_249


title: mouse reference OneRA 10 ug -1


title: PGA_PA-N_118


title: PGA_PA-N_148


title: PGA_PA-N_200


title: PGA_PA-D_98


title: PGA_PA-N_112


title: PGA_PA-D_93


title: PGA_PA-D_319


title: PGA_PA-D_216


title: PGA_PA-D_206


title: PGA_PA-D_225


title: PGA_PA-D_229


title: Dexamethasone

status: Public on Dec 18 2003

city: Philadelphia

first: Doris

last: Wagner

state: PA

department: Biology

institute: University of Pennsylvania

description:
8hr dexamethasone treated LEAFY-GR seedlings
Lot batch = 1

source_name: 9 day old seedlings (total RNA)


title: Landsberg erecta - replicate

description:
untreated Landsberg erecta seedlings
Lot batch = 2


title: Mock - replicate

description:
8hr mock treated LEAFY-GR seedlings
Lot batch = 2


title: PGA_PA-D_82


title: Dexamethasone plus cycloheximide

description:
8hr dexamethasone and cycloheximide treated LEAFY-GR seedlings
Lot batch = 1


title: Cycloheximide - replicate

description:
8hr cycloheximide treated LEAFY-GR seedlings
Lot batch = 2


title: Cycloheximide

description:
8hr cycloheximide treated LEAFY-GR seedlings
Lot batch = 1


title: PGA_PA-D_132


title: PGA_PA-D_85


title: PGA_PA-D_64


title: PGA_PA-D_348


title: 35S::LFY

description:
untreated 35S::LFY seedlings
Lot batch = 1


title: PGA_PA-D_374


title: Landsberg erecta

description:
untreated Landsberg erecta seedlings
Lot batch = 1


title: Dexamethasone plus cycloheximide - replicate

description:
8hr dexamethasone and cycloheximide treated LEAFY-GR seedlings
Lot batch = 2


title: PGA_PA-D_102


title: 35S::LFY - replicate

description:
untreated 35S::LFY seedlings
Lot batch = 2


title: Mock

description:
8hr mock treated LEAFY-GR seedlings
Lot batch = 1


title: Dexamethasone - replicate

description:
8hr dexamethasone treated LEAFY-GR seedlings
Lot batch = 2


title: PGA_PA-D_317


title: PI3

status: Public on Aug 15 2003

city: Stanford

first: Shauna

last: Somerville

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution of Washington

description:
Growth Conditions and Inoculations: All experiments were performed as previously described (Vogel and Somerville, 2000, Proc. Natl. Acad. 97: 1897-1902). Arabidopsis thaliana and Hybrid Kuta squash (Park Seed, Greenwood, SC) were grown in growth chambers at 22o C with a 14 hr photoperiod and a light intensity of approximately 125 µEinsteins m-2 s-1 provided by Phillips F32T8 fluorescent lamps. Powdery mildew (Erysiphe cichoracearum UCSC1) was cultured on squash for 10-12 days and was then applied to Arabidopsis using 1.3 m settling towers. Plants were 3 weeks old at the time of inoculation.
RNA and Microarray Methods: Total RNA was extracted from the plants using the Trizol method (Invitrogen, Ramonell et al. (2002) Mol. Plant Pathol. 3: 301) and purified with a silica membrane column (Qiagen, RNeasy). Twenty micrograms biotinylated complementary RNA (cRNA) was prepared as described (Hernan et al. (2003) Cancer Res. 63, 140) from the purified total RNA. The resulting cRNA was used to hybridize ATH1 Arabidopsis GeneChips (Affymetrix) using the manufacturer’s protocols. The array images were analyzed with the Affymetrix Microarray Suite 5.0 software with the target intensity set to 500. These data were imported into GeneSpring 4.2. To remove chip-to-chip signal variation, the reference data set, consisting of the intensity values for each gene averaged over four replicates of Columbia-1, uninoculated, was normalized by the intensity values of the top 50th percentile of genes on this array. The normalized values for the reference data set (Normalized Value of Control) are reported along with the intensity values for this array.
Keywords = callose, defense, disease, host-pathogen interaction, mutant, powdery mildew, salicylic acid
Lot batch = 1000854

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 3 of four


title: PI2

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 2 of four


title: CI4

source_name: Genotype: Columbia-0, wild-type; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 4 of four


title: PU4

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: uninoculated; Biological Replicate: 4 of four


title: PU3

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: uninoculated; Biological Replicate: 3 of four


title: PU2

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: uninoculated; Biological Replicate: 2 of four


title: CI3

source_name: Genotype: Columbia-0, wild-type; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 3 of four


title: PI4

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 4 of four


title: CU1

source_name: Genotype: Columbia-0, wild-type; Treatment: uninoculated; Biological Replicate: 1 of four


title: CU2

source_name: Genotype: Columbia-0, wild-type; Treatment: uninoculated; Biological Replicate: 2 of four


title: CI1

source_name: Genotype: Columbia-0, wild-type; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 1 of four


title: CU3

source_name: Genotype: Columbia-0, wild-type; Treatment: uninoculated; Biological Replicate: 3 of four


title: PI1

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 1 of four


title: PU1

source_name: Genotype: pmr4-1, callose synthase deficient mutant; Treatment: uninoculated; Biological Replicate: 1 of four


title: CI2

source_name: Genotype: Columbia-0, wild-type; Treatment: 3 days after inoculation with powery mildew; Biological Replicate: 2 of four


title: PGA_PA-N_300

source_name: Left Ventricle Biopsy


title: CU4

description:
Growth Conditions and Inoculations: All experiments were performed as previously described (Vogel and Somerville, 2000, Proc. Natl. Acad. 97: 1897-1902). Arabidopsis thaliana and Hybrid Kuta squash (Park Seed, Greenwood, SC) were grown in growth chambers at 22o C with a 14 hr photoperiod and a light intensity of approximately 125 µEinsteins m-2 s-1 provided by Phillips F32T8 fluorescent lamps. Powdery mildew (Erysiphe cichoracearum UCSC1) was cultured on squash for 10-12 days and was then applied to Arabidopsis using 1.3 m settling towers. Plants were 3 weeks old at the time of inoculation.

RNA and Microarray Methods: Total RNA was extracted from the plants using the Trizol method (Invitrogen, Ramonell et al. (2002) Mol. Plant Pathol. 3: 301) and purified with a silica membrane column (Qiagen, RNeasy). Twenty micrograms biotinylated complementary RNA (cRNA) was prepared as described (Hernan et al. (2003) Cancer Res. 63, 140) from the purified total RNA. The resulting cRNA was used to hybridize ATH1 Arabidopsis GeneChips (Affymetrix) using the manufacturer’s protocols.
The array images were analyzed with the Affymetrix Microarray Suite 5.0 software with the target intensity set to 500. These data were imported into GeneSpring 4.2. To remove chip-to-chip signal variation, the reference data set, consisting of the intensity values for each gene averaged over four replicates of Columbia-1, uninoculated, was normalized by the intensity values of the top 50th percentile of genes on this array. The normalized values for the reference data set (Normalized Value of Control) are reported along with the intensity values for this array.

Keywords = callose
Keywords = defense
Keywords = disease
Keywords = host-pathogen interaction
Keywords = mutant
Keywords = powdery mildew
Keywords = salicylic acid
Lot batch = 1000854

source_name: Genotype: Columbia-0, wild-type; Treatment: uninoculated; Biological Replicate: 4 of four