title: Kidney - 104345

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 1
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Ovary - 101150

status: Public on Mar 30 2006

type: RNA

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

country: USA

institute: IGC

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 15
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Carcinoma

molecule: total RNA

organism: Homo sapiens

source_name: Ovary


title: Kidney - 101193

description:
Quality metric = 28S to 18S: 1.2
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: 21
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Breast - 101145

description:
Quality metric = 28S to 18S: 1.1
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: 35
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: Yes
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Endometrium - 101148

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 90
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Endometrium


title: Thyroid - 101186

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Chewing Tobacco
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Clinical T: 1
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Multiple Tumours: No
Clinical Staged During or Following Multimodality Therapy: No
Primary Site: Thyroid
Histology: Papillary carcinoma

source_name: Thyroid


title: Rectum - 101188

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: Colon - 104346

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?: Yes
Days from Patient Diagnosis to Excision: 21
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Breast - 101135

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
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?: Yes
Days from Patient Diagnosis to Excision: 110
Prior Therapy: Chemotherapy
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Breast
Histology: Metaplastic squamous carcinoma


title: Rectosigmoid - 104350

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?: Yes
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Renal Pelvis - 101179

description:
Quality metric = 28S to 18S: 1.4
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: 210
Pathological T: 3
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 4
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Renal Pelvis and Ureter
Histology: Papillary transitional cell carcinoma

source_name: Renal Pelvis


title: Lung - 101184

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
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: 60
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma

source_name: Lung


title: Lung - 101183

description:
Quality metric = 28S to 18S: 1.1
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?: Yes
Days from Patient Diagnosis to Excision: 12
Workplace or household smokers?: No
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Mucinous adenocarcinoma


title: Kidney - 101147

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
Pathological T: 3a
Pathological N: 0
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional(clear cell) renal carcinoma


title: Bladder - 101130

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Chewing Tobacco
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Cigars
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 32
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 4
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Urinary Bladder
Histology: Urothelial (transitional cell) carcinoma

source_name: Bladder


title: Prostate - 101128

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Urgency
PSA: Elevated
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: No
Clinical T: 2c
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Kidney - 101126

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 30-40
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: 80
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Transverse colon nodule - 101146

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: Hispanic
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Retreatment T: 3c
Retreatment N: X
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Grade: X
Primary Site: Ovary
Histology: Metastatic Papillary Serous Carcinoma

source_name: Transverse colon nodule


title: Axillary lymph node - 104341

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Retreatment T: 1c
Retreatment N: 2a
Retreatment M: 0
Retreatment Stage: 3A
Retreatment Grade: X
Retreatment ER: Positive
Retreatment PR: Negative
Retreatment HER/2 Neu: Positive
Primary Site: Breast
Histology: Metastatic Lobular Carcinoma

source_name: Axillary lymph node


title: Lung - 101178

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Asian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Presenting Symptoms: Hemoptysis
Presenting Symptoms: Persistent Cough
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Lung - 101192

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Kidney - 104344

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-60
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 6
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Breast - 101141

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Kidney - 101133

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Chewing Tobacco
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: 32
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Kidney - 101119

description:
Quality metric = 28S to 18S: 1.5
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: 12
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Uterus - 101191

description:
Quality metric = 28S to 18S: 1.2
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: 300
Pathological T: 1c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Corpus Uteri
Histology: Endometrioid carcinoma

source_name: Uterus


title: Colon - 101129

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: 14
Presenting Symptoms: Abdominal Pain
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Mucinous Carcinoma


title: Bladder - 101127

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 53
Pathological T: 2a
Pathological N: 2
Pathological M: 0
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumours: Yes
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Urinary Bladder
Histology: Urothelial (transitional cell) carcinoma


title: Omentum - 101151

description:
Quality metric = 28S to 18S: 1.3
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?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 18
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Metastatic Papillary Serous Carcinoma

source_name: Omentum


title: Lung - 101182

description:
Quality metric = 28S to 18S: 1.2
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?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 28
Presenting Symptoms: Hemoptysis
Presenting Symptoms: Persistent Cough
Presenting Symptoms: SOB
Presenting Symptoms: Weight Loss
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Uterus - 101099

description:
Quality metric = 28S to 18S: 1.2
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: 30
Pathological T: 2a
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Kidney - 101096

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 1
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Ovary - 101094

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Abdominal pain
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Endometrioid adenocarcinoma, secretory variant


title: Colon - 101097

description:
Quality metric = 28S to 18S: 1.4
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: 30
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Endometrium - 101093

description:
Quality metric = 28S to 18S: 1.2
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: 25
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Colon - 101116

description:
Quality metric = 28S to 18S: 1.3
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: 42
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Thyroid - 101092

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Pathological T: 3
Pathological N: 0
Pathological Multiple Tumours: Yes
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Thyroid
Histology: Papillary carcinoma, follicular variant


title: Soft Tissue L Thigh - 101095

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Primary Site: Soft Tissue Sarcoma
Histology: Pleomorphic sarcoma

source_name: Soft Tissue L Thigh


title: urethra_4

city: San Diego

first: Richard

middle: B

last: Roth

state: CA

address: 12790 El Camino Real

department: Molecular Medicine

institute: Neurocrine Biosciences, Inc.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA

label: biotin

source_name: urethra

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

extract_protocol: Total RNA extracted using standard Trizol protocol, followed by Qiagen RNeasy column clean-up

tag: Normal tissue


title: vestibular_nuclei_superior_9


title: urethra_2


title: ventral_tegmental_area_9


title: vulva_8

source_name: vulva


title: urethra_1


title: vagina_10

source_name: vagina


title: vestibular_nuclei_superior_6


title: trigeminal_ganglia_9


title: trigeminal_ganglia_10


title: vulva_10


title: ventral_tegmental_area_8


title: ventral_tegmental_area_10


title: vestibular_nuclei_superior_8


title: vulva_9


title: trigeminal_ganglia_5


title: vagina_9


title: tongue_superior_part_w/_papillae_4


title: vagina_8


title: tongue_superior_part_w/_papillae_2


title: tonsil_5

source_name: tonsil


title: vulva_3


title: tonsil_3


title: trachea_2

source_name: trachea


title: trigeminal_ganglia_8


title: trachea_3


title: tongue_superior_part_w/_papillae_1


title: tongue_superior_part_w/_papillae_3


title: ventral_tegmental_area_5


title: vestibular_nuclei_superior_4


title: ventral_tegmental_area_3


title: trigeminal_ganglia_4


title: thalamus_10

source_name: thalamus


title: trigeminal_ganglia_3


title: thyroid_gland_3


title: substantia_nigra_8


title: thyroid_gland_2


title: thyroid_gland_4


title: vagina_3


title: ventral_tegmental_area_2


title: substantia_nigra_9


title: ventral_tegmental_area_1


title: substantia_nigra_10


title: vestibular_nuclei_superior_3


title: trigeminal_ganglia_2


title: ventral_tegmental_area_4


title: thyroid_gland_1


title: trigeminal_ganglia_1


title: testes_2

source_name: testes


title: vestibular_nuclei_superior_2


title: testes_5


title: subthalamic_nucleus_9


title: subthalamic_nucleus_8


title: temporal_lobe_10


title: thalamus_8


title: testes_1


title: thalamus_9


title: subthalamic_nucleus_10


title: vestibular_nuclei_superior_10


title: thalamus_5


title: temporal_lobe_5


title: temporal_lobe_4


title: prostate_gland_4


title: temporal_lobe_1


title: temporal_lobe_3


title: subthalamic_nucleus_5


title: subthalamic_nucleus_6


title: thalamus_2


title: spleen_3

source_name: spleen


title: thalamus_4


title: salivary_gland_2


title: subthalamic_nucleus_3


title: subthalamic_nucleus_4


title: temporal_lobe_2


title: substantia_nigra_1


title: salivary_gland_4


title: thalamus_3


title: temporal_lobe_9


title: substantia_nigra_5


title: substantia_nigra_3


title: substantia_nigra_4


title: tongue_main_corpus_3


title: salivary_gland_3


title: spleen_4


title: substantia_nigra_2


title: thalamus_1


title: temporal_lobe_8


title: subthalamic_nucleus_2


title: salivary_gland_1


title: pituitary_gland_2


title: stomach_pyloric_3


title: pituitary_gland_3


title: stomach_pyloric_4


title: stomach_pyloric_1


title: prostate_gland_2


title: stomach_pyloric_2


title: pituitary_gland_9


title: pituitary_gland_8


title: spinal_cord_10


title: pituitary_gland_10


title: stomach_fundus_4


title: stomach_fundus_1


title: spleen_1


title: spinal_cord_8


title: skeletal_muscle_5


title: stomach_fundus_2


title: spinal_cord_9


title: pituitary_gland_6


title: saphenous_vein_1


title: skeletal_muscle_2


title: pituitary_gland_4


title: skeletal_muscle_4


title: prostate_gland_1


title: spinal_cord_5


title: skeletal_muscle_3


title: spleen_2


title: spinal_cord_4


title: pituitary_gland_5


title: spinal_cord_1


title: skeletal_muscle_10


title: stomach_fundus_3


title: saphenous_vein_3


title: spinal_cord_3


title: stomach_cardiac_3


title: spinal_cord_2


title: ovary_3

source_name: ovary


title: stomach_cardiac_4


title: oral_mucosa_4


title: stomach_cardiac_1


title: oral_mucosa_1


title: nodose_nucleus_4


title: occipital_lobe_3


title: occipital_lobe_2


title: oral_mucosa_2


title: occipital_lobe_4


title: occipital_lobe_9


title: nodose_nucleus_2


title: occipital_lobe_1


title: oral_mucosa_3


title: nodose_nucleus_3


title: nodose_nucleus_1


title: nodose_nucleus_8


title: nodose_nucleus_9


title: parietal_lobe_10


title: occipital_lobe_8


title: ovary_8


title: ovary_9


title: occipital_lobe_10


title: parietal_lobe_8


title: nodose_nucleus_10


title: ovary_10


title: parietal_lobe_9


title: parietal_lobe_4


title: lymph_nodes_3


title: nodose_nucleus_5


title: nipple_cross-section_3


title: pharyngeal_mucosa_2


title: nipple_cross-section_1


title: parietal_lobe_5


title: liver_4

source_name: liver


title: kidney_medulla_3


title: occipital_lobe_5


title: parietal_lobe_2


title: lymph_nodes_2


title: lymph_nodes_1


title: parietal_lobe_7


title: kidney_medulla_4


title: lymph_nodes_4


title: pharyngeal_mucosa_3


title: parietal_lobe_3


title: parietal_lobe_1


title: nipple_cross-section_2


title: nipple_cross-section_4


title: kidney_medulla_2


title: kidney_medulla_1


title: liver_3


title: liver_1


title: mammary_gland_9


title: myometrium_3

source_name: myometrium


title: myometrium_10


title: medulla_10


title: medulla_7

source_name: medulla


title: myometrium_7


title: liver_2


title: myometrium_8


title: lung_1

source_name: lung


title: medulla_9


title: mammary_gland_10


title: medulla_3


title: mammary_gland_8


title: myometrium_9


title: medulla_8


title: medulla_5


title: midbrain_10


title: midbrain_9

source_name: midbrain


title: medulla_1


title: midbrain_1


title: lung_3


title: midbrain_4


title: midbrain_3


title: midbrain_5


title: heart_atrium_1


title: midbrain_6


title: midbrain_2


title: esophagus_1

source_name: esophagus


title: hypothalamus_2

source_name: hypothalamus


title: hippocampus_10


title: esophagus_3


title: esophagus_2


title: kidney_cortex_4


title: frontal_lobe_8


title: endometrium_3

source_name: endometrium


title: endometrium_10


title: frontal_lobe_7


title: endometrium_9


title: kidney_cortex_3


title: hypothalamus_10


title: hypothalamus_4


title: hippocampus_7

source_name: hippocampus


title: hypothalamus_3


title: frontal_lobe_9


title: esophagus_4


title: hippocampus_9


title: hypothalamus_9


title: endometrium_8


title: kidney_cortex_2


title: hippocampus_8


title: kidney_cortex_1


title: hypothalamus_1


title: midbrain_8


title: frontal_lobe_10


title: hypothalamus_5


title: frontal_lobe_6


title: hypothalamus_8


title: hippocampus_3


title: heart_atrium_3


title: frontal_lobe_3


title: frontal_lobe_5


title: hippocampus_2


title: heart_ventricle_3


title: heart_atrium_2


title: hippocampus_5


title: cerebral_cortex_4


title: cerebral_cortex_10


title: heart_atrium_4


title: hippocampus_1


title: corpus_callosum_10


title: hippocampus_4


title: cerebral_cortex_9


title: heart_ventricle_2


title: cerebral_cortex_3


title: cerebral_cortex_1


title: corpus_callosum_8


title: heart_ventricle_1


title: corpus_callosum_7


title: corpus_callosum_9


title: frontal_lobe_1


title: dorsal_root_ganglia_8


title: dorsal_root_ganglia_9


title: cerebral_cortex_8


title: cerebral_cortex_2


title: cerebral_cortex_7


title: colon_cecum_1


title: coronary_artery_5


title: cervix_8

source_name: cervix


title: dorsal_root_ganglia_10


title: corpus_callosum_3


title: cerebral_cortex_5


title: dorsal_root_ganglia_4


title: dorsal_root_ganglia_1


title: corpus_callosum_4


title: adrenal_gland_cortex_2


title: adrenal_gland_cortex_1


title: bone_marrow_9


title: colon_cecum_10


title: coronary_artery_4


title: corpus_callosum_2


title: adrenal_gland_cortex_3


title: dorsal_root_ganglia_5


title: corpus_callosum_1


title: coronary_artery_1


title: bone_marrow_8


title: adrenal_gland_cortex_4


title: bone_marrow_10


title: cervix_9


title: cervix_10


title: dorsal_root_ganglia_2


title: colon_cecum_3


title: corpus_callosum_5


title: cervix_3


title: dorsal_root_ganglia_3


title: putamen_9

source_name: putamen


title: putamen_8


title: accumbens_10


title: amygdala_10


title: putamen_7


title: adipose_tissue_subcutaneous_6


title: accumbens_8

source_name: accumbens


title: accumbens_9


title: accumbens_7


title: amygdala_8

source_name: amygdala


title: putamen_10


title: amygdala_5


title: adipose_tissue_3


title: accumbens_4


title: adipose_tissue_5


title: amygdala_9


title: bone_marrow_2


title: putamen_5


title: accumbens_3


title: putamen_1


title: amygdala_4


title: bronchus_2

source_name: bronchus


title: accumbens_2


title: accumbens_5


title: bone_marrow_1


title: putamen_4


title: accumbens_1


title: bronchus_3


title: adipose_tissue_subcutaneous_5


title: putamen_2


title: adipose_tissue_omental_1


title: adipose_tissue_omental_2


title: adipose_tissue_omental_3


title: amygdala_1


title: adipose_tissue_omental_4


title: amygdala_2


title: single cell from ICM E3.5, biological rep16

status: Public on Mar 20 2006

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

country: Japan

institute: Nara Medical University

description: Gene expression data from single ICM cells (E3.5)

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data obtained from the eight amplified samples (ES-10pg-amplified-rep1:8) were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

organism: Mus musculus

source_name: Single cell from ICM in blastocyst at E3.5

label_protocol: Biotinylated cRNA were prepared from the PCR-amplified double-starnded cDNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

extract_protocol: Single cell was lysed by adding to the tube containing cell lysis buffer, and the clude lysate was used for cDNA synthesis and amplification without purification.

tag: Strain


title: amygdala_3


title: ES 5ug nonamplified, technical rep3

description: Gene expression data to verify the PCR-based single-cell cDNA amplification method (the V1V3 method)

source_name: Total RNA from Embryonic Stem cell culture (5ug)

label_protocol: Biotinylated cRNA were prepared from total RNA from cultured ES cells according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

extract_protocol: The total RNA was prepared by the RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction

tag: Line


title: ES 5ug nonamplified, technical rep1


title: ES 10pg amplified, technical rep5

source_name: Total RNA from Embryonic Stem cell culture diluted to 10 pg


title: ES 5ug nonamplified, technical rep4


title: single cell from ICM E3.5, biological rep19


title: ES 5ug nonamplified, technical rep2


title: ES 10pg amplified, technical rep1


title: single cell from ICM E3.5, biological rep18


title: ES 10pg amplified, technical rep8


title: ES 5ug nonamplified, technical rep5


title: ES 10pg amplified, technical rep3


title: single cell from ICM E3.5, biological rep14


title: ES 5ug nonamplified, technical rep7


title: ES 5ug nonamplified, technical rep6


title: ES 10pg amplified, technical rep7


title: single cell from ICM E3.5, biological rep17


title: ES 10pg amplified, technical rep4


title: ES 10pg amplified, technical rep2


title: single cell from ICM E3.5, biological rep12


title: single cell from ICM E3.5, biological rep9


title: single cell from ICM E3.5, biological rep15


title: single cell from ICM E3.5, biological rep20


title: single cell from ICM E3.5, biological rep11


title: single cell from ICM E3.5, biological rep8


title: ES 10pg amplified, technical rep6


title: single cell from ICM E3.5, biological rep10


title: single cell from ICM E3.5, biological rep6


title: single cell from ICM E3.5, biological rep5


title: single cell from ICM E3.5, biological rep4


title: single cell from ICM E3.5, biological rep13


title: single cell from ICM E3.5, biological rep7


title: single cell from ICM E3.5, biological rep2


title: single cell from ICM E3.5, biological rep1


title: single cell from ICM E3.5, biological rep3


title: 61011AFFYPS1191

status: Public on Mar 15 2006

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Mouse HSC transcript levels from Young Cohort

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

extract_protocol: Rossi_et_al_2005_sample_processing; Long-term hematopoietic stem cells (Lineage negative, c-kit positive, Sca1 positive, Flk2 negative and CD34 negative ie. KLSflk2-CD34-) from old mice (22-23 months). Cells were double FACS sorted for purity with the second sort done directly into Trizol (Gibco BRL, Gaithersburg, MD). mRNA from 22,000-25,000 cells were twice amplified using Arcturus RiboAmp RNA amplification kit (Arcturus, Mountain View, CA). Amplified material (cRNA) was biotin-labeled using Affymetrix IVT labelling kit (Affymetrix, Santa Clara, CA) and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.; Protocol Type = AffyExp; Performer: Rebecca,,Sonu

tag: Young Cohort


title: 60983AFFYPS1185

description: Mouse HSC transcript levels from Old Cohort

tag: Old Cohort


title: JKim Hypoxia 2a

status: Public on Mar 16 2006

city: Baltimore

first: Chi

middle: V.

last: Dang

state: MD

address: 720 Rutland Ave, Ross 1032

department: Medicine

institute: Johns Hopkins University, School of Medicine

description: JHMI Microarray Core

hyb_protocol: 16hrs at 45 C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.1.1, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

label: Biotin

source_name: Human Burkitt’s lymphoma cell line, P493-6

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: P493-6 cells were maintained in RPMI 1640 medium (GIBCO/BRL) with 10% fetal bovine serum (GIBCO/BRL) and 1% streptomycin and penicillin (Invitrogen) at 37C in a 5% CO2 incubator.

extract_protocol: Total RNA was isolated from P493-6 cells using Trizol (Invitrogen) according to manufacturer’s instruction.

treatment_protocol: Hypoxic cells were maintained in a control atmosphere chamber at 0.1% O2 with 5% C02 and 95% N2 at 37C for 29 hours


title: 60966AFFYPS1184

source_name: Mouse HSC transcript levels from Old Cohort


title: ES 5ug nonamplified, technical rep8


title: peripheral ganglion, dorsal root ganglion: sample-2_le2

status: Public on Mar 08 2006

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

description:
use total RNA extracted from the other level of freshly dissected DRGs to hybridize with MG 2.0 affymetrix chip.
Treatment, type=dissect, description=fresh DRG dissection


title: 60995AFFYPS1189

source_name: Mouse HSC transcript levels from Young Cohort


title: JKim Non-hypoxia 1a

description: JHMI Microarray Core

treatment_protocol: Non-hyopxic cells (20% O2) were incubated at 37C in a 5% CO2 incubator.

tag: Human Burkitt’s lymphoma cell line, P493-6


title: JKim Non-Hypoxia 2a

description: JHMI Microarray Core


title: skeletal muscle, tibialis anterior: Innvervated Control 1_e1_le1

description:
innervated tibialis anterior muscles from runx1f/- control mice
Treatment, type=add, description=runx1f/-

source_name: skeletal muscle, tibialis anterior


title: 60994AFFYPS1188


title: skeletal muscle, tibialis anterior: Innvervated Control 3_e1_le1


title: 60997AFFYPS1190


title: peripheral ganglion, dorsal root ganglion: sample-2_le1


title: 60992AFFYPS1186


title: 60993AFFYPS1187


title: JKim Hypoxia 1a

description: JHMI Microarray Core

treatment_protocol:
Hypoxic cells were maintained in a control atmosphere chamber at 0.1% O2 with 5% C02 and 95% N2 at 37C for 29 hours
Normoxic cells (20% O2) were maintained at 37C in a 5% CO2 incubator


title: peripheral ganglion, dorsal root ganglion: sample-1_le2

description:
use total RNA extracted from one level of freshly dissected DRGs to hybridize with MG 2.0 affymetrix chip.
Treatment, type=dissect, description=fresh DRG dissection


title: skeletal muscle, tibialis anterior: Denervated 3-day MCK::cre 2_e1_le1

description:
3-day-denervated tibialis anterior muscles from runx1f/-; MCK::cre mice
Treatment, type=remove, description=runx1f/-; MCK::cre


title: skeletal muscle, tibialis anterior: Innvervated Control 2_e1_le1


title: peripheral ganglion, dorsal root ganglion: sample-1_le1


title: skeletal muscle, tibialis anterior: Denervated 3-day MCK::cre 3_e1_le1


title: skeletal muscle, tibialis anterior: Denervated 3-day MCK::cre 1_e1_le1


title: skeletal muscle, tibialis anterior: Innverated MCK::cre 1_e1_le1

description:
innervated tibialis anterior muscles from runx1f/-; MCK::cre mice
Treatment, type=remove, description=MCK::cre; runx1f/-


title: skeletal muscle, tibialis anterior: Denervated 3-day Control 2_e1_le1

description:
3-day-denervated tibialis anterior muscles from runx1f/- control mice
Treatment, type=add, description=runx1f/-


title: skeletal muscle, tibialis anterior: Denervated 3-day Control 3_e1_le1

description:
3-day-denervated tibialis anterior muscles from runx1f/- control mice
Treatment, type=add, description=5-day-denervated tibialis anterior muscles from runx1f/- control mice


title: skeletal muscle, tibialis anterior: Innervated MCK::cre 2_e1_le1


title: skeletal muscle, tibialis anterior: Denervated 3-day Control 1_e1_le1


title: Src R388A/Y527F-12 hr

status: Public on Mar 07 2006

first: Philip

middle: A

last: Cole

address: 725 N Wolfe St

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins Medical School

description: Johns Hopkins JHMI Microarray Core

hyb_protocol: 18 hrs at 45 degree, with rotation 60 rpm

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS 1.1 software

data_processing: Affymetrix GCOS 1.3 TGT Target Intensity Value150

source_name: Src R388A/Y527F transfected SYF cells, 5 mM imidazole treated for 12 hr.

label_protocol: Affymetrix 1 round amplification protocol

growth_protocol: SYF cells stably transfected with Src constructs were cultured in DMEM media supplemented with 10% (v/v) FBS and 300 ug/ml of hygromycin B and incubated at 37°C in the presence of 5% CO2.

extract_protocol: RNeasy Miniprep (Qiagen)

treatment_protocol: SrcR388A/Y527F stably transfected SYF cells were serum-starved overnight and then treated with imidazole 5 mM for 12 h.

tag: SYF (Src, Yes, Fyn deleted) mouse embryonic fibroblast cell line, stably transfected with mutant Src R388A/Y527F gene


title: Src R388A/Y527F-1 hr

description: Johns Hopkins JHMI Microarray Core

source_name: Src R388A/Y527F transfected SYF cells, 5 mM imidazole treated for 1 hr.

treatment_protocol: SrcR388A/Y527F stably transfected SYF cells were serum-starved overnight and then treated with imidazole 5 mM for 1 h.


title: Src D386N/Y527F-1 hr

description: Johns Hopkins JHMI Microarray Core

source_name: Src D386N/Y527F transfected SYF cells, 5 mM imidazole treated for 1 hr.

treatment_protocol: SrcD386N/Y527F stably transfected SYF cells were serum-starved overnight and then treated with imidazole 5 mM for 1 h.

tag: SYF (Src, Yes, Fyn deleted) mouse embryonic fibroblast cell line, stably transfected with mutant Src D386N/Y527F gene


title: Src D386N/Y527F-0 hr

description: Johns Hopkins JHMI Microarray Core

source_name: Src D386N/Y527F transfected SYF cells, control group.

treatment_protocol: SrcD386N/Y527F stably transfected SYF cells were serum-starved overnight.


title: Src D386N/Y527F-12 hr

description: Johns Hopkins JHMI Microarray Core

source_name: Src D386N/Y527F transfected SYF cells, 5 mM imidazole treated for 12 hr.

treatment_protocol: SrcD386N/Y527F stably transfected SYF cells were serum-starved overnight and then treated with imidazole 5 mM for 12 h.


title: Src R388A/Y527F-0 hr

description: Johns Hopkins JHMI Microarray Core

source_name: Src R388A/Y527F transfected SYF cells, control group.

treatment_protocol: SrcR388A/Y527F stably transfected SYF cells were serum-starved overnight.

tag: SYF (Src, Yes, Fyn deleted) mouse embryonic fibroblast cell line, stably transfected with mutant Src R388A/Y527F gene.


title: BALB_Female_CF_rep3

status: Public on Mar 01 2006

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

country: Canada

institute: McGill University

description: Keywords = mouse, lung, cystic fribrosis, strain differences

data_processing: affyPLM in bioconductor

source_name: whole right lung

tag: BALB/c, Female, CF


title: B6_Female_CF_rep3

tag: C57BL/6, Female, CF


title: B6_Female_CF_rep2


title: BALB_Female_Control_rep2

tag: BALB/c, Female, Control


title: B6_Male_CF_rep2

tag: C57BL/6, Male, CF


title: BALB_Female_Control_rep3


title: BALB_Male_CF_rep3

tag: BALB/c, Male, CF


title: B6_Female_CF_rep1


title: BALB_Male_CF_rep2


title: BALB_Male_Control_rep2

tag: BALB/c, Male, Contol


title: B6_Male_Control_rep3

tag: C57BL/6, Male, Contol


title: B6_Female_Control_rep1

tag: C57BL/6, Female, Contol


title: B6_Male_CF_rep1


title: B6_Female_Control_rep3


title: BALB_Male_Control_rep3


title: BALB_Female_CF_rep1


title: B6_Female_Control_rep2


title: B6_Male_Control_rep1


title: BALB_Female_CF_rep2


title: B6_Male_Control_rep2


title: BALB_Male_Control_rep1


title: wt-Gfp P6 replicate 2

status: Public on Feb 28 2006

city: Ann Arbor

first: Swaroop

last: Anand

state: MI

address: 1000 Wall St.

department: Ophthalmology & Visual Sciences

institute: University of Michigan

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P6 replicate 2.

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

source_name: Gfp+ photoreceptor cells

label_protocol: Nugene kit protocol

extract_protocol: mRNA was amplified using Nugene kit

tag: wt-Gfp, Gfp+ photoreceptor cells


title: wt-Gfp P2 replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P2 replicate 4.


title: wt-Gfp P2 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P2 replicate 3.


title: wt-Gfp P6 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P6 replicate 3.


title: wt-Gfp P6 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P6 replicate 1.


title: wt-Gfp P10 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P10 replicate 3.


title: wt-Gfp E16 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp E16 replicate 1.


title: wt-Gfp P6 replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P6 replicate 4.


title: BALB_Male_CF_rep1


title: wt-Gfp E16 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp E16 replicate 3.


title: wt-Gfp P2 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P2 replicate 1.


title: wt-Gfp P10 replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P10 replicate 2.


title: BALB_Female_Control_rep1


title: wt-Gfp P10 replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P10 replicate 4.


title: wt-Gfp 4 weeks replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp 4 weeks replicate 2.


title: wt-Gfp E16 replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp E16 replicate 2.


title: wt-Gfp 4 weeks replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp 4 weeks replicate 4.


title: wt-Gfp P2 replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P2 replicate 2.


title: wt-Gfp E16 replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp E16 replicate 4.


title: wt-Gfp P10 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P10 replicate 1.


title: Nrl-ko-Gfp P6 replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P6 replicate 4.

tag: Nrl-ko-Gfp, Gfp+ photoreceptor cells


title: Nrl-ko-Gfp P2 replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.

This is Nrl-ko-Gfp P2 replicate 4.


title: Nrl-ko-Gfp P6 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P6 replicate 1.


title: Nrl-ko-Gfp P6 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P6 replicate 3.


title: Nrl-ko-Gfp P2 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P2 replicate 1.


title: Nrl-ko-Gfp P2 replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.

This is Nrl-ko-Gfp P2 replicate 2.


title: wt-Gfp 4 weeks replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp 4 weeks replicate 3.


title: Nrl-ko-Gfp P10 replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P10 replicate 4.


title: Nrl-ko-Gfp E16 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp E16 replicate 3.


title: Nrl-ko-Gfp P10 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P10 replicate 3.


title: Nrl-ko-Gfp E16 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp E16 replicate 1.


title: Nrl-ko-Gfp P10 replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P10 replicate 1.


title: Nrl-ko-Gfp P2 replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P2 replicate 3.


title: Nrl-ko-Gfp P6 replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.

This is Nrl-ko-Gfp P6 replicate 2.


title: Nrl-ko-Gfp P10 replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp P10 replicate 2.


title: Nrl-ko-Gfp 4 weeks replicate 4

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp 4 weeks replicate 4.


title: Nrl-ko-Gfp E16 replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp E16 replicate 2.


title: Nrl-ko-Gfp 4 weeks replicate 3

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp 4 weeks replicate 3


title: Nrl-ko-Gfp 4 weeks retina replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp 4 weeks sample.

source_name: Gfp purified cell

tag: Nrl-ko, purified Gfp+ photoreceptor cell


title: Cumulus Oocyte Complex eCG-treated 48h, no hCG replicate 2

status: Public on Feb 17 2006

city: Houston

first: JoAnne

middle: S

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Wild type eCG-primed expanded cumulus-oocyte complex

data_processing: Affymetrix GeneChip Mouse Genome 430 2.0 Array

source_name: cumulus-oocyte complex

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

extract_protocol: Immature female mice were stimulated with eCG for 48h. Expanded cumulus-oocyte complexes were isolated by needle puncture from eCG-primed ovaries, pooled, then lysed using the RNeasy kit (Qiagen) according to the manufacturer's instructions .Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: 23 d.o. C57BL/6 female, eCG stimulated cumulus-oocyte complex


title: Cumulus Oocyte Complex eCG-treated 48h, no hCG replicate 1


title: Cumulus Oocyte Complex eCG-treated 48h, hCG 16h replicate 2

description: Wild type eCG-, hCG-primed (16h) cumulus-oocyte complex

extract_protocol: Immature female mice were stimulated with eCG for 48h then stimulated for 16h with hCG. Cumulus-oocyte complexes were isolated from the oviduct by needle puncture, pooled, then lysed using the RNeasy kit (Qiagen) according to the manufacturer's instructions .Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: 23 d.o. C57BL/6 female, eCG stimulated 48h - hCG stimulated 16h, cumulus-oocyte complex


title: Nrl-ko-Gfp 4 weeks replicate 2

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is Nrl-ko-Gfp 4 weeks replicate 2

source_name: purified Gfp+ photoreceptor cells


title: Hereditary gingival fibromatosis(HGF) patient Gingiva replicate1

city: Shanghai

first: Kong

last: Xiangyin

address: South Chongqin Rd.225

country: China

institute: Institute of Health Sciences,SIBS,CAS/SJTU

description: HGF gingiva tissue removed during surgical procedures and stored in liquid nitrogen immediately

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes

source_name: HGF patient gingiva tissue

extract_protocol: Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen)

tag: Hereditary gingival fibromatosis (HGF) is a benign disorder manifested by a slowly progressive enlargement of the oral gingival tissues, which results in the teeth being partially or totally engulfed by keratinized gingiva.Affected gingiva tissues were removed from HGF volunteers during surgical procedure.


title: Cumulus Oocyte Complex eCG-treated 48h, hCG 8h replicate 1

description: Wild type eCG-, hCG-primed (8h) cumulus-oocyte complex

extract_protocol: Immature female mice were stimulated with eCG for 48h then stimulated for 8h with hCG. Cumulus-oocyte complexes were isolated from the oviduct by needle puncture, pooled, then lysed using the RNeasy kit (Qiagen) according to the manufacturer's instructions .Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: 23 d.o. C57BL/6 female, eCG stimulated 48h - hCG stimulated 8h, cumulus-oocyte complex


title: Cumulus Oocyte Complex eCG-treated 48h, hCG 16h replicate 1


title: brain, pituitary: Non-invasive pituitary adenoma_e1_le1

status: Public on Feb 14 2006

description: RESECTED HUMAN PITUITARY TUMOR

source_name: brain, pituitary


title: brain, pituitary: Invasive pituitary adenoma_e1_le1

description: RESECTED HUMAN PITUITARY TUMOR


title: brain, pituitary: Non-recurrent pituitary adenoma_e1_le1

description: RESECTED HUMAN PITUITARY TUMOR


title: brain, pituitary: Sample7_e1_le1

description: RESECTED HUMAN PITUITARY TUMOR


title: Cumulus Oocyte Complex eCG-treated 48h, hCG 8h replicate 2


title: Normal Gingiva replicate1

description: normal gingiva tissue removed during surgical procedures and stored in liquid nitrogen immediately

source_name: Gingiva tissue

tag: normal gingiva tissue from volunteers


title: brain, pituitary: Sample5_e1_le1

description: RESECTED HUMAN PITUITARY TUMOR


title: brain, pituitary: Sample10_e1_le1

description: RESECTED HUMAN PITUITARY TUMOR


title: brain, pituitary: Recurrent Pituitary Adenoma_e1_le1

description: RESECTED HUMAN PITUITARY TUMOR


title: Normal Gingiva replicate2


title: brain, pituitary: Sample8_e1_le1

description: HP75- Tumor Cell Line


title: brain, pituitary: Sample6_e1_le1

description: RESECTED HUMAN PITUITARY TUMOR


title: E18.5_Mutant_Kidney_array2

status: Public on Feb 13 2006

first: You-Tzung

last: Chen

address: 1515 Holcombe Blvd. Unit 1006

department: Molecular Genetics

description: After scanning, all probe sets were scaled to a signal intensity of 250 and relative levels of expression of each transcript (signal) were determined using Microarray Suite 5.0 software (Affymetrix).  The images of all arrays were inspected for physical anomalies and for the presence of excessive background hybridization.  Generally, all array results used in this study were of good quality, and no major manufacturer’s defects or abnormalities were detected. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

hyb_protocol: The target was then fragmented and hybridized to Mouse Genome 430 2.0 Affymetrix GeneChip Arrays (Affymetrix, Santa Clara, CA) in duplicates using an Affymetrix GeneChip Fluidics Station 400, according to the manufacturer’s standard protocols. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

scan_protocol: The arrays were stained with phycoerythrin-coupled avidin and scanned using a GeneArray Scanner 3000.  The resultant output was analyzed using Affymetrix Microarray Suite software and examined for excessive background or evidence of RNA degradation.  All microarray processing was performed in the Murine Microarray and Affymetrix Facility at the University of Texas M. D. Anderson Cancer Center. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

data_processing: dChip2004, scaled to 250. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

label_protocol: Five to forty micrograms of total RNA from each pooled embryonic kidney sample was used to produce the cRNA target for the microarray.  The target was created using a reverse transcription reaction to produce cDNA (Supercript Choice System, Gibco), which was subsequently subjected to in vitro transcription with biotinylated cytidine-5’-triphosphate and uridine-5’-triphosphate using the ENZO BioArray High Yield RNA Transcript Labeling Kit to produce biotinylated cRNA. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

growth_protocol: To obtain mouse embryos with metanephric mesenchyme-specific Lim1 deficient (Lim1flox/lacZ; Rarb2-Cretg/+) kidneys, timed matings between Lim1+/lacZ; Rarb2-Cretg/+ males and Lim1flox/flox females were established.  Kidney samples of two different embryonic stages (E14.5 and E18.5) were isolated.  Their genotypes were assigned unambiguously using real time PCR assays detecting the presence of lacZ and Cre alleles, which were established in the M. D. Anderson Cancer Center DNA Analysis Core Facility.  For the E14.5 time point, a total of 71 embryos were collected, 17 of them were genotyped as conditional mutants (Lim1flox/lacZ; Rarb2-Cretg/+).  Kidneys from 23 Lim1flox/+; Rarb2Cretg/+ embryos were used as “control” kidneys.  For the E18.5 time point, a total of 39 embryos were harvested, 9 of them were genotyped as conditional mutants and 14 of them were genotyped as controls. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

extract_protocol: Embryonic kidney tissue from each individual was placed in a separate tube with 0.5 ml TRIzol (Invitrogen, Carlsbad, CA) and stored at –75oC until the corresponding visceral tissue could be genotyped.  After a genotype was unambiguously assigned to each individual, TRIzol preserved kidneys of the same genotype were pooled and total RNA was prepared as per the manufacturer’s instructions.  Total RNA was then processed using a QIAGEN RNeasy Midi Kit before in vitro transcription-labeling reaction per Affymetrix (Santa Clara, CA) recommendation.  Once purified, RNA quality was determined by electrophoretic methods using an agarose gel or analysis using an Agilent Bioanalyzer 2100 (Palo Alto, CA) and by spectroscopy at 260 and 280 nm. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

treatment_protocol: All procedures performed on animals were done in accordance with guidelines of the American Physiological Society and were approved by The University of Texas MD Anderson Cancer Center Institutional Animal Care and Use Committee (Richard R. Behringer, IACUC Protocol Number: 02-90-01735).  Mice carrying a targeted Lim1 null allele (Lim1lacZ), a Lim1 conditional null allele (Lim1flox) and an Rarb2-Cre transgene in which Cre is expressed in the metanephric mesenchyme of the developing kidney, were used in this study.  Lim1lacZ/+ and Lim1flox/flox mice were maintained on a C57BL/6J x 129/SvEv genetic background.  Rarb2-Cre transgenic mice were initially generated on a C57BL/6J x SJL/J genetic background. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

tag: Strain

value: 129 / C57BL/6 / SJL/J mixed, Genotype:Lim1flox/lacZ; Rarb2Cretg/+; Gender:mixed; Age:embryonic day 18.5; Tissue:whole kidneys from 9 embryos. (Reference:BMC Nephrol. 7(1):1, 2006, PMID:16464245)


title: E18.5_Control_Kidney_array2

institute: The University of Texas MD Anderson Cancer Center

value: 129 / C57BL/6 / SJL/J mixed, Genotype:Lim1flox/+; Rarb2Cretg/+; Gender:mixed; Age:embryonic day 18.5; Tissue:whole kidneys from 14 embryos. (Reference:BMC Nephrol. 7(1):1, 2006, PMID:16464245)


title: E18.5_Mutant_Kidney_array1


title: E14.5_Mutant_Kidney_array2

value: 129 / C57BL/6 / SJL/J mixed, Genotype:Lim1flox/lacZ; Rarb2Cretg/+; Gender:mixed; Age:embryonic day 14.5; Tissue:whole kidneys from 17 embryos. (Reference:BMC Nephrol. 7(1):1, 2006, PMID:16464245)


title: E14.5_Control_Kidney_array1

value: 129 / C57BL/6 / SJL/J mixed, Genotype:Lim1flox/+; Rarb2Cretg/+; Gender:mixed; Age:embryonic day 14.5; Tissue:whole kidneys from 23 embryos. (Reference:BMC Nephrol. 7(1):1, 2006, PMID:16464245)


title: brain, pituitary: Sample9_e1_le1

description: HP75- Tumor Cell Line


title: Hereditary gingival fibromatosis(HGF) patient Gingiva replicate2


title: E18.5_Control_Kidney_array1


title: E14.5_Control_Kidney_array2


title: E14.5_Mutant_Kidney_array1


title: NB83 U133p2

status: Public on Feb 09 2006

city: Boston

first: Andrea

last: Richardson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: RNA from bulk normal breast or normal bresat organoid

data_processing: GCRMA


title: NB69 U133p2

tag: bulk normal breast or normal bresat organoid


title: NB87 U133p2


title: NB42 U133p2


title: wt-Gfp 4 weeks replicate 1

description:
Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp 4 weeks replicate 1.


title: T162 U133p2

description: bulk breast tumor RNA from patient T162

tag: breast tumor


title: T73 U133p2

description: bulk breast tumor RNA from patient T73


title: NB64 U133p2


title: T41 U133p2

description: bulk breast tumor RNA from patient T41


title: T92 U133p2

description: bulk breast tumor RNA from patient T92


title: NB60 U133p2


title: T175 U133p2

description: bulk breast tumor RNA from patient T175


title: T50 U133p2

description: bulk breast tumor RNA from patient T50


title: T4 U133p2

description: bulk breast tumor RNA from patient T4


title: T84 U133p2

description: bulk breast tumor RNA from patient T84


title: T145 U133p2

description: bulk breast tumor RNA from patient T145


title: T44 U133p2

description: bulk breast tumor RNA from patient T44


title: T115 U133p2

description: bulk breast tumor RNA from patient T115


title: NB58 U133p2


title: T74 U133p2

description: bulk breast tumor RNA from patient T74


title: T119 U133p2

description: bulk breast tumor RNA from patient T119


title: T81 U133p2

description: bulk breast tumor RNA from patient T81


title: T178 U133p2

description: bulk breast tumor RNA from patient T178


title: T37 U133p2

description: bulk breast tumor RNA from patient T37


title: T117 U133p2

description: bulk breast tumor RNA from patient T117


title: T30 U133p2

description: bulk breast tumor RNA from patient T30


title: T151 U133p2

description: bulk breast tumor RNA from patient T151


title: T152 U133p2

description: bulk breast tumor RNA from patient T152


title: T161 U133p2

description: bulk breast tumor RNA from patient T161


title: T183 U133p2

description: bulk breast tumor RNA from patient T183


title: T123 U133p2

description: bulk breast tumor RNA from patient T123


title: T144 U133p2

description: bulk breast tumor RNA from patient T144


title: T116 U133p2

description: bulk breast tumor RNA from patient T116


title: T130 U133p2

description: bulk breast tumor RNA from patient T130


title: T38 U133p2

description: bulk breast tumor RNA from patient T38


title: Pachytene spermatocytes replicate 1

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

description: Mouse 430 2.0

data_processing: Affymetrix Microarray Suite version 5.0

label: Biotin-dUTP

source_name: Pachytene spermatocytes


title: T147 U133p2

description: bulk breast tumor RNA from patient T147


title: T21 U133p2

description: bulk breast tumor RNA from patient T21


title: Type A spermatogonia replicate 1

description: Mouse 430 2.0

source_name: Type A spermatogonia


title: Type B spermatogonia replicate 2

description: Mouse 430 2.0

source_name: Type B spermatogonia


title: Type B spermatogonia replicate 1

description: Mouse 430 2.0


title: Round spermatids replicate 1

description: Mouse 430 2.0

source_name: Round spermatids


title: Round spermatids replicate 2

description: Mouse 430 2.0


title: T143 U133p2

description: bulk breast tumor RNA from patient T143


title: T137 U133p2

description: bulk breast tumor RNA from patient T137


title: T129 U133p2

description: bulk breast tumor RNA from patient T129


title: T141 U133p2

description: bulk breast tumor RNA from patient T141


title: T56 U133p2

description: bulk breast tumor RNA from patient T56


title: T146 U133p2

description: bulk breast tumor RNA from patient T146


title: T149 U133p2

description: bulk breast tumor RNA from patient T149


title: Pou5f1 RNAi replicate-1

status: Public on Feb 08 2006

city: Singapore

first: Huck Hui

last: Ng

state: Singapore

address: 60 Biopolis street, #02-01 Genome

department: Cell and Medical Biology

country: Singapore

institute: Genome Institute of Singapore

description: Pou5f1 RNAi replicate-1.

hyb_protocol: Prior to injection of hybridization cocktail, probes were primed by injection with hybridisation buffer (100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween-20 and placed in oven (45oC) for 10 minutes with rotation (60rpm). Hybridisation was performed by injection of the hybridization cocktail and incubating the probe in oven at 45oC with rotation (60rpm) for 16 hours. Probes were washed at the Fluidics FS-450 station with Buffer A (6X SSPE, 0.01% Tween 20) and B (100mM MES, 0.1M [Na+], 0.01% Tween-20). Staining of the probes was performed with 0.01mg/ml SAPE (Streptavidin Phycoerythrin) and biotinylated antibody (0.06mg/ml).

data_processing: RMA normalization

source_name: E14TG2a mouse embroyonic stem cells (ATCC, CRL-1841)

label_protocol: Total RNAs were extracted directly from the cells using TRIzol reagent (Invitrogen). DNA contamination was removed by Dnase (Ambion) treatment and the RNA was further purified by Rneasy column (Qiagen Cat# 75144).  Probes for hybridization were prepared by GeneChip One-Cycle target labeling kit (Affymetrix). Biotin-labeled cRNA was synthesizedusing the Enzo IVT labeling kit. 20 ug of the labeled cRNA was fragmented for target preparation in hybridization cocktail. Controls used in hybridization cocktail include Eukaryotic Hybridisation controls and Oligonucleotide B2 controls. SAPE (Streptavidin Phycoerythrin) and biotinylated antibody were used for microarray (Affymetrix Mouse Genome 430 2.0 Array) staining.

extract_protocol: Mouse embryonic stem cells were transfected with constructs expressing parental Pou5f1 RNAi, using Lipofectamine 2000 (Invitorgen protocol). The cells were selected with 1ug/ml of Puromycin (Sigma) 24-hours after transfection for 3 days.

tag: mouse embryonic stem cell


title: Pachytene spermatocytes replicate 2

description: Mouse 430 2.0


title: Type A spermatogonia replicate 2

description: Mouse 430 2.0


title: T133 U133p2

description: bulk breast tumor RNA from patient T133


title: T140 U133p2

description: bulk breast tumor RNA from patient T140


title: Pou5f1 RNAi replicate-4

description: Pou5f1 RNAi replicate-4.


title: Pou5f1 RNAi replicate-2

description: Pou5f1 RNAi replicate-2.


title: T134 U133p2

description: bulk breast tumor RNA from patient T134


title: T118 U133p2

description: bulk breast tumor RNA from patient T118


title: Pou5f1 RNAi replicate-3

description: Pou5f1 RNAi replicate-3.


title: Nanog RNAi replicate-4

description: Nanog RNAi replicate-4

extract_protocol: Mouse embryonic stem cells were transfected with constructs expressing parental Nanog RNAi, using Lipofectamine 2000 (Invitorgen protocol). The cells were selected with 1ug/ml of Puromycin (Sigma) 24-hours after transfection for 3 days.


title: Nanog RNAi replicate-3

description: Nanog RNAi replicate-3


title: Nanog RNAi replicate-5

description: Nanog RNAi replicate-5


title: Parental vector, pSUPER-puro replicate 4

extract_protocol: Mouse embryonic stem cells were transfected with constructs expressing parental vectors (2 ug), using Lipofectamine 2000 (Invitorgen protocol). The cells were selected with 1ug/ml of Puromycin (Sigma) 24-hours after transfection for 3 days.


title: Parental vector, pSUPER-puro replicate 5


title: Nanog RNAi replicate-2

description: Nanog RNAi replicate-2


description: Parental vector, pSUPER-puro replicate 1.


title: Germinal Center replicate 1

status: Public on Feb 02 2006

first: Irving

middle: L.

last: Weissman

email: irv@stanford.edu, deepta@stanford.edu

address: 279 Campus Dr.

institute: Stanford University

description: B220+  IgM-low/- Ig-lambda-low NP-PE+ CD38-low PNA+ CD11b- Ter119- Gr-1- CD3- CD4- CD5- CD8- cells harvested from spleen 14 days after immunization

data_processing: RMA normalized with other B cell subsets

source_name: spleen

treatment_protocol: Mice were immunized intraperitoneally with 100 ug alum-precipitated NP-CGG 14 days prior to harvest

tag: Gender

value: Male

tag: Age

value: 6-10 weeks

tag: Tissue

value: Spleen

tag: Immunogen

value: NP-CGG/alum


title: Memory B cell replicate 3

description: B220+ IgM- IgD- NP-PE+ CD38-high Ig-lambda+ PNA- CD11b- Ter119- Gr-1- CD3- CD4- CD5- CD8- cells were sorted from spleens 10-12 weeks after immunization

data_processing: RMA normalized against other B cell subsets

source_name: Spleen

treatment_protocol: Mice were immunized intraperitoneally with 100-ug alum-precipitated NP-CGG and cells were harvested 10-12 weeks post-immunization

value: 14-18 weeks


title: Memory B cell replicate 1


title: Germinal Center replicate 3


title: Naive B cell replicate 2

description: B220+ CD23+ IgM-low IgD+ Ig-lambda+ CD11b-negative Ter119-negative Gr-1-negative CD3-negative CD4-negative CD8-negative CD5-negative cells double sorted by FACS from spleen

value: 4-8 weeks


title: Germinal Center replicate 2


title: Parental vector, pSUPER-puro replicate 2


title: Memory B cell replicate 2


title: Plasma replicate 2

description: B220-low IgM-low Ig-lambda+ syndecan-1+ NP-PE+ CD11b- Ter119- Gr-1- CD3- CD4- CD5- CD8- PNA-negative cells harvested from spleen 7 days after immunization

treatment_protocol: Mice were immunized intraperitoneally with 100 ug alum-precipitated NP-CGG 7 days prior to harvest

value: 5-9 weeks


title: Naive B cell replicate 3


title: Wild type third repeat

status: Public on Jan 31 2006

city: East Lansing

first: Jianping

last: Yu

address: Michigan State University

department: Plant Research Laboratory

institute: Michigan State University

description: Wild type gl1 in the third of three repeats.

data_processing: Alpha1 o.o5. Alpha2 0.065.

organism: Arabidopsis thaliana

source_name: Leaves

tag: Arabidopsis thaliana gl1 wild-type leaves from 5 week old plants.


title: S5 second repeat

description: Over-expresser S5 in the second of three repeats.


title: Memory B cell replicate 4


title: Nanog RNAi replicate-1

description: Nanog RNAi replicate-1


title: Wild type second repeat

description: Wild type gl1 in the second of three repeats.


title: Plasma replicate 4


title: S5 third repeat

description: Over-expresser S5 in the third of three repeats.

tag: Alternative oxidase over-expresser line S5 leaves from 5 week old plants.


title: Plasma replicate 3

description: B220-low IgM-low Ig-lambda+ syndecan-1+ NP-PE+ CD11b- Ter119- Gr-1- CD3- CD4- CD5- CD8- PNA- cells harvested from spleen 7 days after immunization


title: Parental vector, pSUPER-puro replicate 3


title: S5 first repeat

description: Over-expresser S5 in the first of three repeats.


title: Naive B cell replicate 1

source_name: Naive B cell

value: C57Bl/Ka mice


title: Plasma replicate 1

description:
B220-low IgM-low Ig-lambda+
syndecan-1+ NP-PE+ CD11b-negative Ter119-negative Gr-1-negative CD3-negative CD4-negative CD8-negative CD5-negative PNA-negative cells double sorted by FACS from spleen at 7 days post-immunization with NP-CGG


title: A1-1 third repeat

description: Antisense line A1-1 in the third of three repeats.

tag: Alternative oxidase antisense line A1-1 leaves from 5 week old plants.


title: A1-1 second repeat

description: Antisense line A1-1 in the second of three repeats.


title: Wild type first repeat

description: Wild type gl1 in the first of three repeats.

tag: Arabidopsis thaliana gl1 leaves from 5 week old plants.


title: A1-1 first repeat

description: Antisense line A1-1 in the first of three repeats.


title: M8C

status: Public on Jan 27 2006

city: Chicago

first: Mingyuan

last: Zhou

state: IL

address: 303 E. Chicago Ave.

department: Dermatology

description: Wild type, cornea, limbus, epithelial basal cells

data_processing: Affymetrix Gene Operating System 1.2

source_name: anterior eye

extract_protocol: limbal and corneal epithelial basal cells are isolated using laser cupture microdissection (LCM). 300 cells from each location were collected and total RNA were extracted, mRNA were amplified using Arcturus (CA) cRNA amplification kit and the cRNAs were subjected to gene microarray hybridization (Affymetrix).

tag: Balb/c mouse

tag: Wild type, cornea


title: M7C

tag: Wild type, cornea, limbus


title: M7L

tag: Wild type, limbus


title: M5L


title: M8L


title: M4L


title: M5C


title: M3L


title: M6C


title: M2C


title: M2L


title: M1L


title: M6L


title: brain, brainstem: cRNA-SOD-3

status: Public on Jan 13 2006

description:
RNA sample 3 from motor neurons of SOD1 mice
Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification

source_name: brain, brainstem


title: brain, hippocampus: inhibitor-1 KO 2_e1_le1

description: inhibitor-1 knock-out mouse

source_name: brain, hippocampus


title: M1C


title: M3C


title: brain, brainstem: cRNA-WT1

description:
RNA sample 1 from motor neurons of wild type mice
Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification


title: brain, hippocampus: wildtype 1_e1_le1

description: wild-type mouse


title: brain, brainstem: cRNA-SOD-2

description:
RNA sample 2 from motor neurons of SOD1 mice
Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification


title: M4C


title: brain, hippocampus: inhibitor-1 KO 1_e1_le1

description: inhibitor-1 knock-out mouse


title: brain, brainstem: cRNA-WT2

description:
RNA sample 2 from motor neurons of wild type mice
Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification


title: brain, hippocampus: wildtype 3_e1_le1

description: wild-type mouse


title: brain, brainstem: cRNA-SOD-1

description:
RNA sample 1 from motor neurons of SOD1 mice
Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification


title: brain, hippocampus: wildtype 2_e1_le1

description: wild-type mouse


title: brain, hippocampus: inhibitor-1 KO 3_e1_le1

description: inhibitor-1 knock-out mouse


title: brain, brainstem: cRNA-WT3

description:
RNA sample 3 from motor neurons of wild type mice
Treatment, type=double_round_amplification, description=T7-based two round of RNA amplification


title: brain, cerebellum: RNA#7S_le1

description:
total RNA from biosource CC#7S
Treatment, type=dissect, description=dissection from cerebellar tissue

source_name: brain, cerebellum


title: brain, cerebellum: RNA#41_le1

description:
total RNA from biosource CC#41
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, hippocampus: Hippocampus 4_e1_le1

description: Hippocampus, Low Freezing Male, Line 24


title: brain, hippocampus: Hippocampus 12_e1_le1

description: Hippocampus, High Freezing Male, Line 25


title: brain, hippocampus: Hippocampus 1_e1_le1

description: Hippocampus, Low Freezing Male, Line 24


title: brain, cerebellum: RNA#11S_le1

description:
total RNA from biosource CC#11S
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, hippocampus: Hippocampus 5_e1_le1

description: Hippocampus, Low Freezing Male, Line 24


title: brain, cerebellum: RNA#36_le1

description:
total RNA from biosource CC#36
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, cerebellum: RNA#42a_le1

description:
total RNA from biosource CC#42a
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, cerebellum: RNA#1S_le1


title: brain, hippocampus: Hippocampus 2_e1_le1

description: Hippocampus, Low Freezing Male, Line 24


title: brain, hippocampus: Hippocampus 8_e1_le1


title: brain, amygdala: Amygdala 11_e1_le1

description: Amygdala, High Freezing Male, Line 25

source_name: brain, amygdala


title: brain, hippocampus: Hippocampus 7_e1_le1


title: brain, amygdala: Amygdala 9_e1_le1

description: Amygdala, High Freezing Male, Line 25


title: brain, hippocampus: Hippocampus 6_e1_le1

description: Hippocampus, Low Freezing Male, Line 24


title: brain, cerebellum: RNA#3S_le1

description:
total RNA from biosource CC#3S
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, cerebellum: RNA#39*_le1

description:
total RNA from biosource CC#1
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, amygdala: Amygdala 10_e1_le1

description: Amygdala, High Freezing Male, Line 25


title: brain, amygdala: Amygdala 7_e1_le1

description: Amygdala, High Freezing Male, Line 25


title: brain, hippocampus: Hippocampus 9_e1_le1


title: brain, amygdala: Amygdala 12_e1_le1

description: Amygdala, High Freezing Male, Line 25


title: brain, hippocampus: Hippocampus 3_e1_le1

description: Hippocampus, Low Freezing Male, Line 24


title: brain, hippocampus: Hippocampus 10_e1_le1


title: brain, amygdala: Amygdala 5_e1_le1

description: Amygdala, Low Freezing Male, Line 24


title: brain, amygdala: Amygdala 8_e1_le1

description: Amygdala, High Freezing Male, Line 25


title: brain, cerebellum: RNA#5S_le1

description:
total RNA from biosource CC#5S
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, hippocampus: Hippocampus 11_e1_le1


title: brain, amygdala: Amygdala 6_e1_le1

description: Amygdala, Low Freezing Male, Line 24


title: brain, amygdala: Amygdala 4_e1_le1

description: Amygdala, Low Freezing Male, Line 24


title: brain, cerebellum: RNA#18_le1

description:
total RNA from biosource CC#18
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, cerebellum: RNA#2_le1

description: total RNA from biosource CC#2


title: brain, cerebellum: RNA#31_le1

description:
total RNA from biosource CC#31
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, amygdala: Amygdala 2_e1_le1

description: Amygdala, Low Freezing Male, Line 24


title: brain, cerebellum: RNA #5_le1

description:
total RNA from biosource CC#5
Treatment, type=dissect, description=dissection from cerebellar tissue


title: brain, amygdala: Amygdala 3_e1_le1

description: Amygdala, Low Freezing Male, Line 24


title: brain, cerebellum: RNA #1_le1


title: brain, amygdala: Amygdala 1_e1_le1

description: Amygdala, Low Freezing Male, Line 24


title: brain, amygdala: Amygdala 12_le1

description: High Freezing


title: brain, amygdala: Amygdala 11_le1

description: High Freezing


title: brain, amygdala: Amygdala 10_le1

description: High Freezing


title: brain, amygdala: Amygdala 6_le1

description: Low Freezing


title: brain, amygdala: Amygdala 8_le1

description: High Freezing


title: brain, amygdala: Amygdala 9_le1

description: High Freezing


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 329 Passage 3_le1

description:
Human Sural Nerve Schwann Cell Donor 317 Passage 1
Treatment, type=add, description=growth factors heregulin and forskolin added

source_name: nerve, HumanSuralNerve


title: brain, amygdala: Amygdala 7_le1

description: High Freezing


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 330 Passage 3_le1


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 351 Passage 1_le1


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 330 Passage 1_le1


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 329 Passage 1_le1


title: brain, amygdala: Amygdala 5_le1

description: Low Freezing


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 317 Passage 1_le1


title: brain, amygdala: Amygdala 4_le1

description: Low Freezing


title: brain, amygdala: Amygdala 3_le1

description: Low Freezing


title: brain, hippocampus: Hippocampus 8_le1

description: High Freezing


title: brain, amygdala: Amygdala 1_le1

description: Low Freezing


title: whole animal, whole head: Sample10_e1_le1

description:
OR 24-hr after conditioning
Treatment, type=behavioral_stimulus

organism: Drosophila melanogaster

source_name: whole animal, whole head


title: whole animal, whole head: Sample12_e1_le1

description:
OR 24-hr after non-conditioning
Treatment, type=behavioral_stimulus


title: whole animal, whole head: extract#7_le1


title: whole animal, whole head: Sample9_e1_le1

description:
OR 0-hr after conditioning (biological duplicate of sample#1
Treatment, type=behavioral_stimulus


title: brain, hippocampus: Hippocampus 11_le1

description: High Freezing


title: brain, hippocampus: Hippocampus 12_le1

description: High Freezing


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 317 Passage 3_le1


title: brain, hippocampus: Hippocampus 7_le1

description: High Freezing


title: whole animal, whole head: extract#6_le1

description:
OR 0-hr after non-conditioning
Treatment, type=behavioral_stimulus


title: whole animal, whole head: sample#8_le1


title: whole animal, whole head: Sample11_e1_le1


title: whole animal, whole head: extract#5_le1


title: brain, hippocampus: Hippocampus 9_le1

description: High Freezing


title: brain, hippocampus: Hippocampus 10_le1

description: High Freezing


title: brain, amygdala: Amygdala 2_le1

description: Low Freezing


title: whole animal, whole head: extract#4_le1

description:
OR 24-hr after conditioning (biological duplicate of sample#3)
Treatment, type=behavioral_stimulus


title: brain, hippocampus: Hippocampus  5_le1

description: Low Freezing


title: brain, hippocampus: Hippocampus 6_le1

description: Low Freezing


title: whole animal, whole head: extract#2_le1


title: whole animal, whole head: extract#3_le1


title: brain, hippocampus: Hippocampus 2_le1

description: Low Freezing


title: brain, hippocampus: Hippocampus 4_le1

description: Low Freezing


title: brain, hippocampus: Hippocampus 1_le1

description: Low Freezing


title: brain, hippocampus: Hippocampus 3_le1

description: Low Freezing


title: nerve, HumanSuralNerve: Human Schwann cell RNA extracts 351 Passage 3_le1


title: Wild-Type WS-O Seedling 4h Dex 1

status: Public on Jan 04 2006

city: Davis

first: Siobhan

last: Braybrook

address: 1 Shields Ave

department: Plant Biology

institute: University of California, Davis

description: 8 day old wild-type WS-O seedlings 4 hour Dexamethasone induction

data_processing: MAS 5.0

molecule: polyA RNA

source_name: Wild-Type WS-O Seedling

label_protocol: standard Affymetrix procedures

growth_protocol: As per Braybrook et al (PNAS, 2006)

extract_protocol: As per Stone et al (PNAS, 2001)

treatment_protocol: As per Braybrook et al (PNAS, 2006)

tag: Genotype

value: Ws-0, Wild-Type; Tissue:8 day old seedling;  Replicate:1 of 2


title: Transgenic LEC2GR Seedling 0h Dex 2

description: 8 day old LEC2-GR seedlings no treatment

source_name: Transgenic LEC2-GR Seedling

value: Ws-0, 35S:LEC2-GR; Tissue:8 day old seedling; Replicate:2 of 2


title: whole animal, whole head: extract#1_le1

description:
OR 0-hr after conditioning
Treatment, type=behavioral_stimulus


title: Scd1+/+ on chow diet replicate 3

status: Public on Dec 23 2005

city: Madison

first: Alan

middle: D

last: Attie

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

description: Scd1 wild type mice, liver, total RNA processed to biotin-labeled cRNA

data_processing: Affymetrix Microarray Suite version 5.0 was used to generate .CEL files. The .CEL files was processed by Robust Multi-Array Analysis (RMA) in R/Bioconductor to generate expression values represented by RMA

source_name: liver

label_protocol: Approximately 15 ?g of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: For each individual sample, about 10-50mg flash frozen liver tissue piece was transfeered to -80oC cold RNALater-ICE (Ambion) and placed at -20oC overnight. Tissue was processed according to manufacture's protocol. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Mus musculus (backcrossed to C57BL/6J mice for 5+ generations)

tag: Scd1 wild type mouse, chow diet, liver


title: Wild-Type WS-O Seedling 4h Dex 2

value: Ws-0, Wild-Type; Tissue:8 day old seedling;  Replicate:2 of 2


title: Transgenic LEC2GR Seedling 4h Dex 2

description: 8 day old LEC2-GR seedlings 4 hour Dexamethasone induction

value: Ws-0, 35S:LEC2-GR; Tissue:8 day old seedling;  Replicate:2 of 2


title: Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 3

tag: Scd1 wild type mouse, Harlan Teklad TD03045 diet, liver


title: Transgenic LEC2GR Seedling 0h Dex 1

value: Ws-0, 35S:LEC2-GR; Tissue:8 day old seedling; Replicate:1 of 2


title: Scd1+/+ on chow diet replicate 2


title: Transgenic LEC2GR Seedling 1h Dex 1

description: 8 day old LEC2-GR seedlings 1 hour Dexamethasone induction

value: Ws-0, 35S:LEC2-GR; Tissue:8 day old seedling;  Replicate:1 of 2


title: Scd1-/- on chow diet replicate 2

description: Scd1 knock out mice, liver, total RNA processed to biotin-labeled cRNA

tag: Scd1 knock out mouse, chow diet, liver


title: Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 4


title: Scd1-/- on chow diet replicate 5


title: Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 1


title: Scd1+/+ on chow diet replicate 5


title: Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 5


title: Scd1-/- on chow diet replicate 4


title: Scd1+/+ on chow diet replicate 4


title: Scd1-/- on chow diet replicate 3


title: Scd1+/+ on chow diet replicate 1


title: Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 2


title: Transgenic LEC2GR Seedling 1h Dex 2


title: Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 4

tag: Scd1 knock out mouse, Harlan Teklad TD03045 diet, liver


title: Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 2


title: Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 3


title: Transgenic LEC2GR Seedling 4h Dex 1


title: Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 5


title: Scd1-/- on chow diet replicate 1


title: Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 1


title: Colon - 89232

status: Public on Dec 22 2005

first: Erin

last: Curley

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Rectum - 89225

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 98
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological Dukes Stage: C
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: Rectosigmoid - 89234

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological Grade: 2
Primary Site: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Rectum - 89228

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 44
Presenting Symptoms: Bright red stools
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Rectum
Histology: Adenocarcinoma


title: Ovary - 89191

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: Bloating
Presenting Symptoms: Vaginal bleeding
Pathological T: 3c
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Osseous
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Clear cell adenocarcinoma, NOS

source_name: Ovary


title: Kidney - 89233

description:
Quality metric = 28S to 18S: 1.2
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?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
Clinical T: 1b
Clinical N: 0
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma

source_name: Kidney


title: Kidney - 95096

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: 14
Pathological T: 3b
Pathological N: X
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 4
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Adenocarcinoma, clear cell type


title: Endometrium - 89171

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Endometrium


title: Rectum - 89229

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Rectum
Histology: Adenocarcinoma


title: Breast - 89263

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 40
Pathological T: 4d
Pathological N: 1a
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast