title: Lung - 403738

description:
Quality metric = 28S to 18S: 1.6
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?: No
Presenting Symptoms: Hemoptysis
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Prostate - 403734

status: Public on Sep 28 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: 1.6
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Nocturia
PSA: Elevated
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

molecule: total RNA

organism: Homo sapiens

source_name: Prostate


title: Vulva - 403730

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 39
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Primary Site: Vulva
Histology: Squamous cell carcinoma, NOS

source_name: Vulva


title: Prostate - 404992

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: 50
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Clinical T: 3b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 4
Clinical Gleason Score: 8-10
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Kidney - 388951

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 76
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Primary Site: Kidney
Histology: Chromophobe renal carcinoma

source_name: Kidney


title: Breast - 388891

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
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: 1c
Pathological N: 1mi
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma

source_name: Breast


title: Ovary - 403728

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
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 Adenocarcinoma

source_name: Ovary


title: Kidney - 388909

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?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Thyroid - 388953

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Difficulties in swallowing
Pathological T: 1
Pathological N: 1a
Pathological M: X
Pathological Stage: Unknown
Primary Site: Thyroid
Histology: Papillary carcinoma

source_name: Thyroid


title: Soft Tissue of arm - 388980

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 70-80
Gender: Male
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
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 2b
Retreatment N: 0
Retreatment M: 0
Retreatment Stage: 3
Retreatment Grade: 3
Primary Site: Soft Tissue of arm
Histology: Pleomorphic sarcoma

source_name: Soft Tissue of arm


title: Ovary - 388908

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
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
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 3
Retreatment N: 1
Retreatment M: 1
Retreatment Metastatic Sites: Other
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Colon
Histology: Metastatic Adenocarcinoma


title: Colon - 388907

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-90
Gender: Male
Ethnic Background: African-American
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: 21
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Mucinous Carcinoma

source_name: Colon


title: Stomach - 388950

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 3
Have you ever had esophagitis/reflux?: No
Clinical Question: Stage
Clinical Value: No AJCC Scheme for this site and histology
Primary Site: Stomach
Clinical Question: Histology
Clinical Value: Solitary fibrous tumor, benign

source_name: Stomach


title: Cervical lymph node - 403729

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: 1
Retreatment M: X
Retreatment Stage: Unknown
Retreatment Grade: X
Primary Site: Oral cavity
Histology: Metastatic Squamous cell carcinoma, NOS

source_name: Cervical lymph node


title: Small intestine - 403725

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Clinical Stage: Unknown
Clinical Symptoms: A
Primary Site: Small intestine
Histology: Malignant lymphoma, large B-cell, diffuse, immunoblastic, NOS

source_name: Small intestine


title: Colon - 388935

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Male
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
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 1
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Primary Site: Colon
Histology: Mucinous Carcinoma


title: Prostate - 388954

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
PSA: Elevated
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Liver - 388936

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: 60
Pathological Question: T
Pathological Value: 3
Pathological Question: N
Pathological Value: 0
Pathological Question: M
Pathological Value: 0
Pathological Question: Stage
Pathological Value: 3A
Pathological Question: Grade
Pathological Value: 3
Pathological Question: Symptoms
Primary Site: Liver
Pathological Question: Histology
Pathological Value: Cholangiocarcinoma

source_name: Liver


title: Rectum - 388893

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
Days from Patient Diagnosis to Excision: 19
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 2
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: Colon - 403739

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
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?: Yes
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Primary Site: Colon
Histology: Mucinous Carcinoma


title: Kidney - 388892

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3b
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Pulmonary
Pathological Stage: 4
Pathological Grade: 4
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Breast - 383911

description:
Quality metric = 28S to 18S: 1.8
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: 11
Mammogram: Yes
Number of years in which a mammogram was obtained?: 26-30
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: Yes
Fibrocystic disease?: Yes
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Kidney - 383404

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Ovary - 388900

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?: Yes
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Serous Adenocarinoma


title: Urinary Bladder - 366609

description:
Quality metric = 28S to 18S: 1.4
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?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Primary Site: Urinary Bladder
Histology: Urothelial (transitional cell) carcinoma

source_name: Urinary Bladder


title: Ovary - 383413

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Bloating
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1A
Primary Site: Ovary
Histology: Mucinous cystic tumor of low malignant potential


title: Uterus - 384490

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: 39
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 2
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Uterus


title: Breast - 383913

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?: No
Days from Patient Diagnosis to Excision: 15
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: Yes
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 0-5
Pathological T: 3
Pathological N: 1a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 2
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: Ovary - 384509

description:
Quality metric = 28S to 18S: 1.4
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: 7
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma


title: Retroperitoneum - 384494

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?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Primary Site: Retroperitoneum
Histology: Leiomyosarcoma

source_name: Retroperitoneum


title: Kidney - 383408

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?: No
Days from Patient Diagnosis to Excision: 210
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 4
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Breast - 383909

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: 15
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: Yes
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 26-30
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Ovary - 384508

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 37
Presenting Symptoms: Abdominal pain
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1A
Clinical Grade: 3
Primary Site: Ovary
Histology: Sertoli-Leydig cell tumor, poorly differentiated


title: Colon - 384504

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
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: 41
Presenting Symptoms: Abdominal Pain
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: Mucinous Carcinoma


title: Colon - 366598

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
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: 4
Primary Site: Colon
Histology: Adenocarcinoma


title: Ureter - 383399

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 3
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 3
Clinical Multiple Tumours: Yes
Primary Site: Renal Pelvis
Histology: Papillary transitional cell carcinoma

source_name: Ureter


title: Lung - 366614

description:
Quality metric = 28S to 18S: 1.4
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?: No
Days from Patient Diagnosis to Excision: 8
Presenting Symptoms: SOB
Workplace or household smokers?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Primary Site: Lung
Histology: Squamous cell carcinoma

source_name: Lung


title: Kidney - 383890

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-70
Gender: Female
Ethnic Background: American Indian
Tobacco Use : Yes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Primary Site: Kidney
Histology: Papillary renal cell carcinoma


title: Ovary - 384496

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-70
Gender: Female
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: 17
Presenting Symptoms: Vaginal bleeding
Clinical T: 3b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3B
Clinical Grade: 3
Primary Site: Ovary
Histology: Clear cell adenocarcinoma, NOS


title: Colon - 366602

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?: Yes
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
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


title: Kidney - 384507

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
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: 7
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Colon - 366620

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: American Indian
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: 26
Presenting Symptoms: Abdominal Pain
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


title: Colon - 383903

description:
Quality metric = 28S to 18S: 1.4
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: 20
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
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 arising in a villous adenoma


title: Kidney - 383906

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
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: 35
Pathological T: 1b
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Pulmonary
Pathological Stage: 4
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Uterus - 383405

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?: Yes
Days from Patient Diagnosis to Excision: 90
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 1
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Kidney - 366597

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
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: 13
Pathological T: 4
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Lymph Nodes
Pathological Stage: 4
Pathological Grade: 3
Primary Site: Kidney
Histology: Renal cell carcinoma, sarcomatoid


title: Colon - 384492

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?: Yes
Days from Patient Diagnosis to Excision: 28
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: Kidney - 384502

description:
Quality metric = 28S to 18S: 1.7
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: 58
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Kidney - 384499

description:
Quality metric = 28S to 18S: 1.5
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?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 11
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Pancreas - 384493

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Cigars
Type of Tobacco Use: Pipe
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 38
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 4
Primary Site: Exocrine Pancreas
Histology: Carcinoma with osteoclast-like giant cells

source_name: Pancreas


title: Kidney - 384503

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
Days from Patient Diagnosis to Excision: 64
Clinical T: 1a
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: Kidney - 341534

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 120
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Lung - 362593

description:
Quality metric = 28S to 18S: 1.6
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: 21
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 1
Primary Site: Lung
Histology: Neuroendocrine carcinoma


title: Kidney - 366592

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Clinical Multiple Tumors: Yes
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Kidney - 366583

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 3b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Breast - 366595

description:
Quality metric = 28S to 18S: 1.3
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?: No
Days from Patient Diagnosis to Excision: 182
Prior Therapy: Chemotherapy
Prior Therapy: Hormonal Treatment
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
Pathological T: 4b
Pathological N: 3a
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological ER: Negative
Pathological PR: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Lung - 346001

description:
Quality metric = 28S to 18S: 1.7
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?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 1
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Prostate - 362598

description:
Quality metric = 28S to 18S: 1.7
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: 21
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 2c
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


title: Lung - 362599

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-50
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: 14
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Primary Site: Lung
Histology: Large cell carcinoma


title: Liver - 345994

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Hepatic
Retreatment Stage: 4
Retreatment Grade: X
Primary Site: Rectum
Histology: Metastatic Adenocarcinoma


title: Breast - 346010

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 30-40
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 56
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
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Ovary - 345993

description:
Quality metric = 28S to 18S: 1.5
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?: No
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Pathological T: 2b
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Ovary
Histology: Endometrioid Carcinoma

source_name: Ovary


title: Supraclavicular lymph node - 366594

description:
Quality metric = 28S to 18S: 1.5
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
Presenting Symptoms: Lymphadenopathy
Have you ever had mononucleousis?: No
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Clinical Stage: 2
Clinical Symptoms: A
Primary Site: Lymph Nodes (Nodal Lymphoma)
Histology: Malignant lymphoma, small B-cell lymphocytic

source_name: Supraclavicular lymph node


title: Uterus - 362596

description:
Quality metric = 28S to 18S: 1.6
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: 60
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Prostate - 345976

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: African-American
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: 48
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 - 345971

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Diarrhea
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 arising in a villous adenoma

source_name: Colon


title: Breast - 345995

description:
Quality metric = 28S to 18S: 1.4
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: 48
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?: Yes
Pathological T: 1c
Pathological N: 3a
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Kidney - 345966

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
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
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Kidney - 345975

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Male
Ethnic Background: Hispanic
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
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: Lung - 366585

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
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: 17
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Lung - 362608

description:
Quality metric = 28S to 18S: 1.8
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: 30
Presenting Symptoms: SOB
Workplace or household smokers?: No
Pathological T: 2
Pathological N: 2
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 4
Primary Site: Lung
Histology: Large cell carcinoma


title: Breast - 362594

description:
Quality metric = 28S to 18S: 1.6
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: 50
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: No
Oophorectomy?: Yes
Hormonal therapy (# of Years)?: 0-5
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: Yes
Primary Site: Breast
Histology: Ductal Carcinoma


title: Prostate - 362584

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?: No
Days from Patient Diagnosis to Excision: 111
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Lung - 362609

description:
Quality metric = 28S to 18S: 2.7
Patient Age: 70-80
Gender: Male
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: 37
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: Yes
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 3
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Prostate - 345963

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
PSA: Elevated
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Lung - 344201

description:
Quality metric = 28S to 18S: 2.1
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Cigars
Type of Tobacco Use: Pipe
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 42
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Kidney - 362589

description:
Quality metric = 28S to 18S: 1.4
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?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 26
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Colon - 345961

description:
Quality metric = 28S to 18S: 1.6
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: 21
Presenting Symptoms: Black tarry stools
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
Presenting Symptoms: Nausea
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: Liver - 362591

description:
Quality metric = 28S to 18S: 1.6
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?: No
Days from Patient Diagnosis to Excision: 32
Clinical Question: T
Clinical Value: 2
Clinical Question: N
Clinical Value: 0
Clinical Question: M
Clinical Value: 0
Clinical Question: Stage
Clinical Value: 2
Clinical Question: Grade
Clinical Value: 2
Primary Site: Liver
Clinical Question: Histology
Clinical Value: Hepatocellular carcinoma


title: Kidney - 345968

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Breast - 346011

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 13
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 0-5
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Cervix - 311868

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 3a
Pathological N: 1
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma, non-keratinizing

source_name: Cervix


title: 24h_Estradiol_2

city: Jena

first: Friedemann

last: Gaube

address: Semmelweisstr. 10

department: Pharmacy

country: Germany

institute: Friedrich-Schiller-University Jena

description: Analysis of gene expression in MCF-7 cells after 24h stimulation with 17beta-Estradiol.

scan_protocol: Standard Protocol: Affymetrix GeneChip expression Analysis Technical Manual, Version 701021, Rev. 4. Scanning was done using a GeneChip Scanner 3000 7G with default parameters.

data_processing: Initial data analysis was performed with Affymetrix MAS5.1 software, setting the scaling of all probe sets to a constant value of 500. Data were further normalized using RMAExpress sofware (release 0.4 alpha 7).

growth_protocol: cells were incubated in DMEM + 10% FCS for 24h before treatment

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturers protocol. RNA quality was checked by UV spectroscopy and agarose (1.5 %) gel electrophoresis (EtBR staining)

treatment_protocol: MCF-7 were incubated for 24h with extracts/compounds in DMEM containing 10% hormone-free dextran-charcoal stripped FCS

tag: human breast adenocarcinoma epithelial cell line, ER+, derived from pleural effusion of a 69year-old caucasian woman


title: Kidney - 305117

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 2
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: 24h_Tamoxifen_2

description:
Analysis of gene expression in MCF-7 cells after 24h stimulation with
the ER antagonist Tamoxifen.

hyb_protocol: Standard Protocol: Affymetrix GeneChip expression Analysis Technical Manual, Version 701021, Rev. 4


title: 24h_Tamoxifen_1

label_protocol: Standard Protocol: Affymetrix GeneChip expression Analysis Technical Manual, Version 701021, Rev. 4


title: 24h_DMSO_2

description: Control/Reference experiment for the gene expression analysis of different plant extracts and compounds. Stimulation with 0,1 % DMSO for 24h.


title: BMDM at ET 4h

city: Charlestown

first: Chun

last: Kim

state: MA

address: Bldg 149, 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description: Gene expression data from murine BMDM treated with ET for 4h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®  Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Mus musculus

source_name: Mouse BMDM at 4h after ET treatment

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

growth_protocol: In order to get macrophages, bone marrow cells from C57BL/6 were cultured for 7 days in the presence of 10 ng/ml of murine MCSF.

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

treatment_protocol: On the experiment day, macrophages were treated with 1 ug/ml of ET.


title: Prostate - 317490

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
PSA: Elevated
# of years PSA Tested?: 11-15
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 2
Clinical Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: 24h_Estradiol_1


title: BMDM at ET 2h

description: Gene expression data from murine BMDM treated with ET for 2h

source_name: Mouse BMDM at 2h after ET treatment


title: BMDM at ET 0h

description: Gene expression data from murine BMDM

source_name: Mouse BMDM


title: 24h_Cimicifuga_1

description: Analysis of gene expression in MCF-7 cells after 24h stimulation with a dichloromethane ASE-extract of Cimicifuga racemosa L. (NUTT.)


title: VT_Epidi_norm_50ans_queue

status: Public on Sep 25 2007

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: biological rep 3

hyb_protocol: Following fragmentaion, 15 µg of cRNA were hybridized for 16h at 45°C to GeneChip U133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (EukGE-WS2v5_450).

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 G7 and extracted by GCOS 1.2 software (Affymetrix).

data_processing: The data were analyzed with LimmaGUI software (Bioconductor). Data was normalized by RMA method.

label: biotin

source_name: Normal epididimus,50 years-old, tail segment

label_protocol: Biotinylated cRNA were prepared accordind to the standard Affymetrix protocol from 10 µg total  RNA (Expression Analysis technical Manual, 2001, Affymetrix).

growth_protocol: Tissues were collected under optimum conditions while artificial circulation was maintained to preserve organs assigned for transplantation. Epididymides were dissected in caput, corpus and cauda epididymidis and immediately frozen in liquid nitrogen and stored at -80°C until used for RNA extraction

extract_protocol: Total RNA was extracted by Trizol reagent according to manufacturer’s instructions.

tag: Seminal vesicles


title: Fallopian Tube - 309423

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?: Yes
Days from Patient Diagnosis to Excision: 4
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Primary Site: Fallopian Tube
Histology: Serous cystadenocarcinoma, NOS

source_name: Fallopian Tube


title: VT_Epidi_norm_47ans_tete

description: biological rep 1

source_name: Normal epididimus,47 years-old, head segment


title: Colon - 267100

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?: No
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: 24h_Cimicifuga_2

description: a dichloromethane ASE-extract of Cimicifuga racemosa L. (NUTT.)


title: VT_Epidi_norm_47ans_corps

description: biological rep 2

source_name: Normal epididimus,47 years-old, corpus segment


title: VT_Epidi_norm_26ans_tete

description: biological rep 1

source_name: Normal epididimus,26 years-old, head segment


title: VT_Epidi_norm_50ans_tete

description: biological rep 1

source_name: Normal epididimus,50 years-old, head segment


title: VT_Epidi_norm_47ans_queue

description: biological rep 3

source_name: Normal epididimus,47 years-old, tail segment


title: VT_Epidi_norm_26ans_corps

description: biological rep 2

source_name: Normal epididimus, 26 years-old, corpus segment


title: VT_Epidi_norm_50ans_corps

description: biological rep 2

source_name: Normal epididimus,50 years-old, corpus segment


title: VT_Epidi_norm_26ans_queue

description: biological rep 3

source_name: Normal epididimus,26 years-old, tail segment


title: 10T1/2 cells_control_rep2

city: Baltimore

first: M.

middle: Daniel

last: Lane

state: MD

address: 725 N. Wolfe St

institute: Johns Hopkins University

description: Cells were grown to postconfluence. Total RNA was harvested at postconfluence

data_processing: global scaling to a target intensity of 150, using GCOS 1.3

source_name: C3H10T1/2 tissue culture cells no treatment

tag: C3H10T1/2 tissue culture cells


title: Pparg-ldi_MUT3

status: Public on Sep 22 2007

city: Bar Harbor

first: Yaacov

last: Barak

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: One of a 3 WT vs. 3 Ppargldi/+ expression series for identifying gene expression changes in white adipose tissue of lipodystrophic mice

hyb_protocol: According to manufacturer's instructions (Affymetrix)

data_processing: Mas5.0 protocol

source_name: Epididymal Fat pads, MUT3

extract_protocol: Tri Reagent followed by DNase treatment and reextraction with phenol

tag: Strain

value: Ppargldi/+ C57BL6;129Sv

tag: Gender

value: male

tag: Age

value: 10 weeks

tag: Tissue

value: Epididymal white adipose tissue


title: Pparg-ldi_WT3

scan_protocol: According to manufacturer's instructions (Affymetrix)

source_name: Epididymal Fat pads, WT3

value: WT C57BL6;129Sv


title: 24h_DMSO_1


title: mutant_crypt_day2_sample2

status: Public on Sep 24 2007

city: Epalinges

first: Joerg

last: Huelsken

address: Ch. des Boveresses 155

country: Switzerland

institute: ISREC

description: Expression analysis of intestinal crypt mRNA of control mice vs. beta-catenin deleted mutant animals (2days of deletion).

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

source_name: intestinal crypt cells isolated by laser capture microdissection

label_protocol: IVT Affymetrix kit

extract_protocol: Pico PureTM RNA Isolation Kit, Arcturus

tag: villin-creERT2:beta-catenin-/lox, induced by tamoxifen for 2days


title: mutant_crypt_day2_sample1


title: 10T1/2 cells_treated_BMP4_rep3

description: Cells were treated with 50 ng/ml BMP4 during proliferation. Total RNA was harvested at postconfluence

source_name: C3H10T1/2 tissue culture cells treated with BMP4


title: 10T1/2 cells_treated_BMP4_rep2


title: 10T1/2 cells_control_rep1


title: aP2-nSREBP1c_MUT1

description: Part of a 3 WT vs. 3 aP2-nSrebp1c expression series for identifying gene expression changes in white adipose tissue of lipodystrophic mice

data_processing: MAS5.0 protocol

source_name: Epididymal Fat pads, MUT1

label_protocol: According to manufacturer's instructions (Affymetrix)

value: aP2-nSrebp1c Tg C57BL6;SJL


title: Pparg-ldi_WT1

source_name: Epididymal Fat pads, WT1


title: 10T1/2 cells_treated_BMP4_rep1

description: Cells were treated with 50 ng/ml BMP4 during proliferation.  Total RNA was harvested at postconfluence


title: aP2-nSREBP1c_WT1

value: WT C57BL6;SJL


title: 10T1/2 cells_control_rep3

tag: C3H10T1/2 cells


title: Pparg-ldi_MUT1


title: control_crypt_day2_sample2

tag: villin-creERT2:beta-catenin+/lox, induced by tamoxifen for 2days


title: aP2-nSREBP1c_MUT3

value: aP2-SREBP1c Tg - C57BL6;SJL


title: Pparg-ldi_WT2

source_name: Epididymal Fat pads, WT2


title: aP2-nSREBP1c_WT3


title: Pparg-ldi_MUT2

source_name: Epididymal Fat pads, MUT2


title: aP2-nSREBP1c_WT2


title: control_crypt_day2_sample1


title: PlagL2KO2

city: boston

first: zhao

last: chen

address: 1 jimmy fund way

institute: Dana Farber Cancer Institute

hyb_protocol: The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: dChip

source_name: mouse intestine pLagl2 knockout 2

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample

extract_protocol: Total RNA was extracted from wild-type mouse small intestines at 18.5 dpc using the Macherey-Nagel Nucleospin kit.

tag: 18.5 dpc mouse small intestine pLagl2 knockout


title: PlagL2KO3

source_name: mouse intestine pLagl2 knockout 3


title: PlagL2KO1

source_name: mouse intestine pLagl2 knockout 1


title: PlagL2KO4

source_name: mouse intestine pLagl2 knockout 4


title: aP2-nSREBP1c_MUT2

value: aP2-nSrebp1 Tg - C57BL6;SJL


title: PlagL2WT1

source_name: mouse intestine pLagl2 wild type 1

label_protocol:
RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample

tag: 18.5 dpc mouse small intestine wild type


title: EBs w/o doxy replica C

status: Public on Sep 19 2007

city: Oeiras

first: Moises

last: Mallo

address: Rua da Quinta Grande 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

description: Non induced, day 6 Embryoid bodies (EBs) made from iHoxB4 ES cells, experiment C

hyb_protocol: 15 µg of fragmented cRNA was used in a 300-µl hybridization containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (EukGE-WS2v5) were used on an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000  for gene expression profiling as set forth by the manufacturer’s recommendations.

data_processing: Scanned arrays were analyzed with Affymetrix MAS 5.0 software using default  settings from Affymetrix. Normalized by global scaling, trimmed mean target intensity  set to 500.

source_name: EBs day6 w/odoxycycline, experiment_C

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Mouse Genome 430 2.0 Arrays, according to the manufacturer’s One-Cycle Target Labeling Assay. Briefly, 4.3 µg of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (One-Cycle DNA synthesis kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA (GeneChip Expression 3’-Amplification Reagents for IVT-Labeling; Affymetrix). Size distribution of the cRNA and fragmented cRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: The Hoxb4i ES cell line (Kyba et al. 2002, Cell 109:29-37) was cultured in DMEM supplemented with 0.1 mM non-essential aminoacids, 2 mM glutamine, 15% FCS, 0,1 mM beta-mercaptoethanol and 103 U/ml of LIF. Embryoid bodies were made by trypsinizing ES cells and incubating them in IMDM supplemented with 15% FCS, 200 ug/ml transferrin, 4.5 mM monothioglycerol, 50 ug/ml ascorbic acid and 2 mM glutamine at a concentration of 3500 cells/ml in bacteriological plates. After 4 days in culture at 37ºC, Hoxb4 was induced by addition of doxycycline to 2 ug/ml, and further incubated for 48 hours.

extract_protocol: Total RNA was extracted from EBs using RNAzol according to the manufacturer´s recommendations. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies).

treatment_protocol: After 4 days in culture at 37ºC, Hoxb4 was induced by addition of doxycycline to 2 ug/ml, and further incubated for 48 hours. After 48 hours the celly were lysed in RNAzol and total RNA  was purified.

tag: HoxB4-inducible ES cells


title: PlagL2WT4

source_name: mouse intestine pLagl2 wild type 4


title: EBs with doxy replica C

description: Doxycycline-induced, day 6 Embryoid bodies (EBs) made from iHoxB4 ES cells, experiment C

source_name: EBs day6 withdoxycycline, experiment_C


title: EBs w/o doxy replica A

description: Non induced, day 6 Embryoid bodies (EBs) made from iHoxB4 ES cells, experiment A

source_name: EBs day6 w/odoxycycline, experiment_A


title: EBs with doxy replica A

description: Doxycycline-induced, day 6 Embryoid bodies (EBs) made from iHoxB4 ES cells, experiment A

source_name: EBs day6 withdoxycycline, experiment_A


title: MO_control_180min_Patient5

status: Public on Sep 18 2007

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

description: healthy subject

hyb_protocol: cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 and GeneSpring 5.0.  Normalization protocol as follows.  1. Data transformation: set measurements less than 0.0 to 0.0.  2. Per Chip: Normalize to a constant value of 150.0 (MAS scaling factor).  3. Per Gene: Normalize to median.

source_name: peripheral blood mononuclear cells, control, 180min, Patient5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: PMNs and PBMCs were isolated from venous blood of each participant in accordance with a protocol approved by the Institutional Review Board for Human Subjects, National Institute of Allergy and Infectious Diseases as described in Methods.  PMNs or PBMCs (107) were combined on ice with or without IgG- and C3bi-coated latex beads (IgG-C3bi LBs) (8 x 107) in tissue culture plates pre-coated with 20% normal human serum (12-well plates) and centrifuged at 350 x g for 8 min at 4oC to synchronize phagocytosis. Following centrifugation, samples were either processed immediately (0 h) or plates were incubated at 37oC in a CO2 incubator for 3 h or 6 h.


title: PlagL2WT2

source_name: mouse intestine pLagl2 wild type 2


title: MO_control_180min_Patient16

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 180min, Patient16


title: EBs with doxy replica B

description: Doxycycline-induced, day 6 Embryoid bodies (EBs) made from iHoxB4 ES cells, experiment B

source_name: EBs day6 withdoxycycline, experiment_B


title: MO_control_180min_Patient3

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient3


title: MO_control_180min_Patient18

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 180min, Patient18


title: MO_control_180min_Patient17

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 180min, Patient17


title: MO_control_180min_Patient7

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient7


title: EBs w/o doxy replica B

description: Non induced, day 6 Embryoid bodies (EBs) made from iHoxB4 ES cells, experiment B

source_name: EBs day6 w/odoxycycline, experiment_B


title: MO_control_180min_Patient9

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient9


title: MO_control_180min_Patient4

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient4


title: MO_control_180min_Patient6

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 180min, Patient6


title: MO_control_180min_Patient12

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient12


title: MO_control_180min_Patient2

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 180min, Patient2


title: MO_control_180min_Patient10

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient10


title: Clements control sample

city: Nottingham

first: Simon

middle: R.

last: Johnson

address: Queen's Medical Centre

department: Therapeutics and Molecular Medicine

country: United Kingdom

institute: University of Nottingham

description: control

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

value: tumour tissue

tag: Extraction Protocol

value: Tumour tissue derived by passaging primary subcutaneous SV7tertAML-derived tumour into nude mice.


title: MO_control_180min_Patient8

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient8


title: Clements oestrogen-treated sample

description: estrogen treatment

source_name: oestrogen

treatment_protocol: 0.36mg 60 day release oestrogen pellets implanted sub-cutaneously into mouse host


title: PlagL2WT3

source_name: mouse intestine pLagl2 wild type 3


title: MO_control_180min_Patient13

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient13


title: MO_control_180min_Patient14

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 180min, Patient14


title: MO_control_180min_Patient15

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 180min, Patient15


title: MO_control_180min_Patient1

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 180min, Patient1


title: MO_LB_180min_Patient18

description: Job's patient

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient18


title: MO_LB_180min_Patient17

description: Job's patient

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient17


title: MO_LB_180min_Patient15

description: Job's patient

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient15


title: MO_LB_180min_Patient16

description: Job's patient

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient16


title: MO_LB_180min_Patient13

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient13


title: MO_LB_180min_Patient4

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient4


title: MO_LB_180min_Patient14

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient14


title: MO_LB_180min_Patient10

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient10


title: MO_LB_180min_Patient1

description: Job's patient

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient1


title: MO_LB_180min_Patient3

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient3


title: MO_LB_180min_Patient5

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient5


title: MO_control_0min_Patient15

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 0min, Patient15


title: MO_LB_180min_Patient9

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient9


title: MO_LB_180min_Patient12

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient12


title: MO_control_0min_Patient16

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 0min, Patient16


title: MO_LB_180min_Patient2

description: Job's patient

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient2


title: MO_control_0min_Patient13

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient13


title: MO_LB_180min_Patient7

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient7


title: MO_control_0min_Patient18

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 0min, Patient18


title: MO_control_0min_Patient17

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 0min, Patient17


title: MO_LB_180min_Patient6

description: Job's patient

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient6


title: MO_LB_180min_Patient8

description: healthy subject

source_name: peripheral blood mononuclear cells, treated with IgG-coated latex beads, 180min, Patient8


title: MO_control_0min_Patient12

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient12


title: MO_control_0min_Patient14

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient14


title: MO_control_0min_Patient9

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient9


title: PMN_LB_360min_Patient18

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient18


title: MO_control_0min_Patient2

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 0min, Patient2


title: MO_control_0min_Patient1

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 0min, Patient1


title: MO_control_0min_Patient10

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient10


title: MO_control_0min_Patient7

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient7


title: PMN_control_360min_Patient16

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 360min, Patient16


title: PMN_control_360min_Patient18

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 360min, Patient18


title: MO_control_0min_Patient3

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient3


title: MO_control_0min_Patient4

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient4


title: MO_control_0min_Patient8

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient8


title: PMN_control_180min_Patient16

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 180min, Patient16


title: PMN_control_360min_Patient17

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 360min, Patient17


title: MO_control_0min_Patient5

description: healthy subject

source_name: peripheral blood mononuclear cells, control, 0min, Patient5


title: PMN_LB_360min_Patient17

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient17


title: PMN_control_180min_Patient15

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 180min, Patient15


title: MO_control_0min_Patient6

description: Job's patient

source_name: peripheral blood mononuclear cells, control, 0min, Patient6


title: PMN_control_360min_Patient15

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 360min, Patient15


title: PMN_LB_360min_Patient16

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient16


title: PMN_LB_360min_Patient15

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient15


title: PMN_LB_180min_Patient16

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient16


title: PMN_control_180min_Patient17

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 180min, Patient17


title: PMN_LB_180min_Patient18

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient18


title: PMN_control_0min_Patient18

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 0min, Patient18


title: PMN_LB_180min_Patient17

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient17


title: PMN_LB_180min_Patient15

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient15


title: PMN_control_180min_Patient18

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 180min, Patient18


title: PMN_control_0min_Patient17

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 0min, Patient17


title: PMN_control_0min_Patient16

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 0min, Patient16


title: PMN_control_360min_Patient14

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient14


title: PMN_control_360min_Patient12

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient12


title: PMN_control_360min_Patient13

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient13


title: PMN_control_0min_Patient15

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 0min, Patient15


title: PMN_control_360min_Patient11

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient11


title: PMN_LB_360min_Patient11

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient11


title: PMN_LB_360min_Patient13

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient13


title: PMN_LB_360min_Patient14

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient14


title: PMN_LB_180min_Patient13

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient13


title: PMN_LB_180min_Patient14

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient14


title: PMN_control_180min_Patient11

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient11


title: PMN_control_180min_Patient14

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient14


title: PMN_control_0min_Patient12

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient12


title: PMN_control_180min_Patient12

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient12


title: PMN_LB_180min_Patient12

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient12


title: PMN_LB_360min_Patient12

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient12


title: PMN_control_360min_Patient9

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient9


title: PMN_control_0min_Patient13

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient13


title: PMN_control_360min_Patient10

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient10


title: PMN_LB_360min_Patient10

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient10


title: PMN_LB_180min_Patient11

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient11


title: PMN_control_0min_Patient14

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient14


title: PMN_control_360min_Patient8

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient8


title: PMN_control_360min_Patient7

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient7


title: PMN_control_180min_Patient13

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient13


title: PMN_LB_360min_Patient9

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient9


title: PMN_control_360min_Patient6

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 360min, Patient6


title: PMN_control_0min_Patient11

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient11


title: PMN_LB_360min_Patient7

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient7


title: PMN_LB_360min_Patient8

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient8


title: PMN_LB_180min_Patient10

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient10


title: PMN_LB_180min_Patient6

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient6


title: PMN_control_0min_Patient10

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient10


title: PMN_control_180min_Patient7

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient7


title: PMN_control_180min_Patient9

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient9


title: PMN_control_0min_Patient9

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient9


title: PMN_control_0min_Patient6

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 0min, Patient6


title: PMN_control_180min_Patient8

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient8


title: PMN_control_180min_Patient10

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient10


title: PMN_LB_360min_Patient6

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient6


title: PMN_LB_180min_Patient9

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient9


title: PMN_control_360min_Patient2

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 360min, Patient2


title: PMN_LB_180min_Patient8

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient8


title: PMN_control_180min_Patient6

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 180min, Patient6


title: PMN_LB_180min_Patient7

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient7


title: PMN_control_0min_Patient7

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient7


title: PMN_control_360min_Patient4

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient4


title: PMN_LB_360min_Patient3

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient3


title: PMN_control_360min_Patient3

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient3


title: PMN_LB_360min_Patient5

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient5


title: PMN_control_180min_Patient4

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient4


title: PMN_control_360min_Patient1

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 360min, Patient1


title: PMN_control_0min_Patient8

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient8


title: PMN_control_180min_Patient5

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient5


title: PMN_LB_360min_Patient1

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient1


title: PMN_LB_360min_Patient2

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient2


title: PMN_control_180min_Patient2

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 180min, Patient2


title: PMN_LB_360min_Patient4

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 360min, Patient4


title: PMN_control_180min_Patient3

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 180min, Patient3


title: PMN_control_360min_Patient5

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 360min, Patient5


title: PMN_LB_180min_Patient5

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient5


title: PMN_control_180min_Patient1

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 180min, Patient1


title: PMN_LB_180min_Patient3

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient3


title: PMN_LB_180min_Patient4

description: healthy subject

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient4


title: PMN_LB_180min_Patient1

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient1


title: PMN_control_0min_Patient1

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 0min, Patient1


title: PMN_LB_180min_Patient2

description: Job's patient

source_name: polymorphonuclear leukocytes, treated with IgG-coated latex beads, 180min, Patient2


title: PMN_control_0min_Patient2

description: Job's patient

source_name: polymorphonuclear leukocytes, control, 0min, Patient2


title: hAT1R tg Replicate2

status: Public on Sep 15 2007

city: Cleveland

first: Venkata Suresh Kumar

last: surampudi

state: OH

address: 9500 Euclid Avenue

department: Molecular Cardiology

institute: Lerner Research Institute

description: Gene expression data from  C57BL/6 mouse over expressiong hAT1R

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

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

data_processing: The data were preprocessed with GCRMA package  provided in Bioconductor  and quantile normalization as normalization method.

source_name: heart tissue from C57BL/6 mouse over expressiong hAT1R

extract_protocol: RNEasy (Qiagen) Kit was used for total RNA extraction from heart tissue. For homogenization,

tag: hAT1R transgenic mouse heart


title: PMN_control_0min_Patient4

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient4


title: Non transgenic Replicate2

description: Gene expression data from  normal C57BL/6 mouse

source_name: heart tissue from normal C57BL/6 mouse

tag: non-transgenic mouse heart


title: A549, 48 h, 25 microM resveratrol, replicate 2

city: Chicago

first: Lorna

last: Whyte

state: IL

address: 10 W 35th Street

department: Division of Carcinogenesis and Chemoprevention

institute: IIT Research Institute

hyb_protocol: Hybridizations were performed at the Functional Genomics Facility, University of Chicago.Following fragmentation, 12 g of fragmented cRNA was hybridized to U133 Plus 2.0  Arrays for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 400 using the Affymetrix GeneChip protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Agilent GeneArray Scanner.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the University of Chicago Functional Genomics Facility according to  the Affymetrix GeneChip Expression Analysis Manual (Santa Clara, CA). Briefly, 10 g of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labeled anti-sense cRNA was synthesized using BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). After precipitation with 4M Lithium Chloride, 20 g of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, and 30 mM MgOAc) for 35 min at 94°C

extract_protocol: A549 cells were treated with ethanol control or resveratrol (25 mM) for 48 h. One replicate of control cells and three replicates of resveratrol treated cells were analyzed. At the 48 h time point TRIzol (1 ml) was added to each culture flask, incubated and insoluble material removed by centrifugation at 10,000 RPM for 10 min at 4°C. Chloroform (0.2 ml) was added to each sample which was shaken and incubated for phase separation. Samples were centrifuged at 10,000 RPM for 15 min at 4°C and the RNA (top aqueous phase) isolated. RNA was precipitated by mixing with isopropanol (0.8 ml) and centrifuging at 10,000 RPM for 10 min at 4°C. The RNA pellet was washed with 75% ethanol, dried and dissolved in Rnase-free water.  Cleanup of the RNA was performed using an RNeasy spin column (Qiagen).

tag: A549, epithelial, lung carcinoma


title: PMN_control_0min_Patient3

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient3


title: Non transgenic Replicate3


title: hAT1R tg Replicate1

description: Gene expression data from C57BL/6 mouse over expressiong hAT1R


title: Non transgenic Replicate1


title: AFFY-Ap1-B

status: Public on Sep 14 2007

city: Manchester

first: Junfeng

last: Chen

address: Kilburn Building, Oxford Road

department: School of Computer Science

institute: University of Manchester

description: RNA extraction in Meyers Lab (http://mpss.udel.edu/). Affymetrix Experiment in St. Clair Lab (http://stclairlab.ucdavis.edu/).

hyb_protocol: as per GeneChip Expression Analysis Technical Manual 701021 rev1

scan_protocol: Affymetrix GeneArray 2500

data_processing: MAS 5.0 software was used with Absence Calls calculated.

organism: Arabidopsis thaliana

source_name: ap1-10 infloresence - mixed stage, immature buds, Second Replica

label_protocol: started with 12 μg total RNA; biotin labeling using ENZO kit

extract_protocol: TRIzol extraction (Invitrogen), followed by RNeasy purification (Qiagen)

tag: Plants were grown in soil in growth chamber with 16 hours of light for 5 weeks. Immature inflorescence was harvested ~2 hours after dark. Tissue included inflorescence meristem and early stage floral buds (up to Stage 11/12). Total RNA was isolated using TRIzol reagent.


title: hAT1R tg Replicate3


title: AFFY-S52-B

label: as per GeneChip Expression Analysis Technical Manual 701021 rev1

source_name: Leaves, 52 hr after salicylic acid treatment, Second Replica

tag: Plants were grown in soil in a growth chamber at 20 degrees C with 8 hours of light for 46 days. Half-strength Hoagland's solution was used to bottom-water the plants. Plants were sprayed to run-off with 0.3 mM SA in 0.02% silwet in the light. Fifty-two hours post-treatment, rosettes were cut above the soil line and harvested (in the light), quick-frozen in liquid nitrogen, then stored at -80 degrees C. Total RNA was later extracted using TRIzol reagent.


title: AFFY-S04-A

source_name: Leaves, 4 hr after salicylic acid treatment, First Replica

tag: Plants were grown in soil in a growth chamber at 20 degrees C with 8 hours of light for 54 days. Half-strength Hoagland's solution was used to bottom-water the plants. Plants were sprayed to run-off with 0.3 mM SA in 0.02% silwet in the light. Four hours post-treatment, rosettes were cut above the soil line and harvested (in the light), quick-frozen in liquid nitrogen, then stored at -80 degrees C. Total RNA was later extracted using TRIzol reagent.


title: A549, 48 h, 25 microM resveratrol, replicate 1


title: A549, 48 h, 25 microM resveratrol, replicate 3


title: PMN_control_0min_Patient5

description: healthy subject

source_name: polymorphonuclear leukocytes, control, 0min, Patient5


title: AFFY-Ap3-B

source_name: ap3-6 infloresence - mixed stage, immature buds, Second Replica


title: AFFY-S52-A

source_name: Leaves, 52 hr after salicylic acid treatment, First Replica


title: AFFY-Sap-B

source_name: sup/ap1 infloresence - mixed stage, immature buds, Second Replica


title: AFFY-S04-B

source_name: Leaves, 4 hr after salicylic acid treatment, Second Replica


title: A549, 48 h, ethanol control

description: A549, 48 h, ethanol control

source_name: A549, 48 h, ethanol control


title: AFFY-Sap-A

source_name: sup/ap1 infloresence - mixed stage, immature buds, First Replica


title: AFFY-Ap3-A

source_name: ap3-6 infloresence - mixed stage, immature buds, First Replica


title: AFFY-Ap1-A

source_name: ap1-10 infloresence - mixed stage, immature buds, First Replica


title: AFFY-Le-B

source_name: Leaves - 21 day, untreated, Second Replica

tag: Plants were grown in 16 hours of light for 21 days, grown under sterile conditions in vermiculite or perlite. Tissue was harvested ~2 hours after dark. Equal amounts of leaf tissue from each growth condition were mixed and RNA was isolated using TRIzol reagent.


title: AFFY-Agm-A

source_name: agamous infloresence - mixed stage, immature buds, First Replica


title: AFFY-Ro-A

source_name: Root - 21 day, untreated, First Replica

tag: Plants were grown in 16 hours of light for 21 days, grown under sterile conditions in vermiculite or perlite. Tissue was harvested ~2 hours after dark, and roots were rinsed in water and frozen immediately. Equal amounts of root tissue from each growth condition were mixed and RNA was isolated using TRIzol reagent.


title: AFFY-Agm-B

source_name: agamous infloresence - mixed stage, immature buds, Second Replica


title: AFFY-Ca-A

source_name: Callus - actively growing, First Replica

tag: Callus was initiated from Col-0 seeds grown on media containing 1/2X MS salts, 3% sucrose in presence of 2,4D (0.5 mg/l), IAA (2 mg/l) and kinetin (0.1mg/l). Tissue was grown ~3 months in dark at 22C and transfered to fresh plates every ~10-14 days. Total RNA was isolated using TRIzol reagent.


title: AFFY-In-A

source_name: Infloresence - mixed stage, immature buds, First Replica


title: AFFY-Le-A

source_name: Leaves - 21 day, untreated, First Replica


title: AFFY-Ro-B

source_name: Root - 21 day, untreated, Second Replica


title: AFFY-In-B

source_name: Infloresence - mixed stage, immature buds, Second Replica


title: AFFY-Ca-B

source_name: Callus - actively growing, Second Replica


title: AFFY-Si-A

source_name: Silique - 24 to 48 hr post-fertilization, First Replica

tag: Plants were grown in soil in growth chamber with 16 hours of light for 5 weeks. Siliques were harvested ~24-48 hours after fertilization, when petals have begun to detach (Stage 16-17). Tissue was harvested ~2 hours after dark. Length of siliques was 5-10 mm. Total RNA was isolated using TRIzol reagent.


title: PP243_uninfected_DC

status: Public on Sep 13 2007

city: Indianapolis

first: Stanley

middle: M.

last: Spinola

state: IN

address: 545 Barnhill Dr.

department: Infectious Diseases

institute: Indiana University School of Medicine

description: Gene expression from Dendritic cells from human subject with pustule former phenotype uninfected.

hyb_protocol: Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.

source_name: Monocyte derived Dendritic Cells from healthy human subjects

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix 2-cycle protocol from 100 ng total RNA.

growth_protocol: Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time.  CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN).  After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry. For controls, DC were untreated for 24 hours.

extract_protocol: RNeasy® Mini Kit, according to the manufacturer's instructions.

treatment_protocol: Untreated Dendritic Cells(Control)

tag: Dendritic Cells uninfected (control) from pustule former, id 243


title: RR203_uninfected_DC

description: Gene expression from Dendritic cells from human subject with resolver phenotype uninfected.

source_name: Monocyte derived dendritic cells from healthy human subjects

treatment_protocol: Untreated Dendritic cells (Control)

tag: Dendritic cells uninfected (control) from resolver, id 203


title: RR216_uninfected_DC

tag: Dendritic Cells uninfected (control) from resolver, id 216


title: PP149_infected_Skin biopsy

description: Gene expression data from biopsy of infected skin of subject with pustule former phenotype.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip? Scanner 3000

source_name: Skin biopsy from healthy human subjects

extract_protocol: Skin biopsy specimens were submerged in RNA Later (Qiagen, Valencia, CA) for 30 minutes immediately upon biopsy.  Total RNA was isolated from the specimens using the RNeasy Fibrous Tissue mini kit (Qiagen) per manufacturer's instructions.  Tissues were homogenized in lysis buffer using a Mini Bead Beater (Research Products International, Mt. Prospect, IL) with 1 µm silica beads.  The homogenates were then digested with proteinase K and RNA was isolated using RNeasy spin columns per kit directions.

treatment_protocol: skin innoculated with H.ducreyi

tag: H. ducreyi infected skin from pustule former, id 149


title: RR216_infected_DC

description: Gene expression from Dendritic cells from human subject with resolver phenotype infected with H. ducreyi.

growth_protocol: Peripheral blood was obtained from the 3 PP and 3RR subjects several mo after they were infected a third time.  CD14+ peripheral blood monocytes were isolated from PBMC by positive selection magnetic beads (Miltenyi Biotec, Auburn, CA) and grown in the presence of recombinant human (rh) IL-4 (1 ng/ml) and rhGM-CSF (0.2 ng/ml) (R&D Systems, Minneapolis, MN).  After 7 d of culture, the cells were HLA-DR+, CD86+ CD40+, CD3-, CD14-, and CD19- by flow cytometry.  DC were incubated with nonopsonized H. ducreyi for 90 min at an MOI of 30:1, washed to remove non-associated bacteria and incubated an additional 22.5 h.

treatment_protocol: Dendritic cells incubated with H.ducreyi

tag: Dendritic cells infected with H. ducreyi from resolver, id 216


title: PP243_infected_Skin biopsy

tag: H. ducreyi infected skin from pustule former, id 243


title: RR203_infected_DC

tag: Dendritic Cells infected with H. ducreyi from resolver, id 203


title: PP164_infected_DC

description: Gene expression from Dendritic cells from human subject with pustule former phenotype infected with H. ducreyi.

treatment_protocol: Dendritic Cells incubated with H.ducreyi

tag: Dendritic Cells infected with H. ducreyi from pustule former, id 164


title: PP149_uninfected_DC

treatment_protocol: Untreated Dendritic Cells (Control)

tag: Dendritic Cells uninfected (control) from pustule former, id 149


title: PP149_infected_DC

tag: Dendritic Cells infected with H. ducreyi from pustule former, id 149


title: PP164_infected_Skin biopsy

tag: H. ducreyi infected skin from pustule former, id 164


title: PP164_uninfected_DC

tag: Dendritic Cells uninfected (control) from pustule former, id 164