title: Lymph Node - 143669

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 4
Retreatment N: 1
Retreatment M: 0
Retreatment Stage: 4
Primary Site: Eye, NOS
Histology: Metastatic Malignant melanoma, NOS


title: Breast - 151607

status: Public on Jan 03 2007

type: RNA

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

country: USA

institute: IGC

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-90
Gender: Female
Ethnic Background: Other
Ethnic Background: Unknown
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 50
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Hormonal therapy (# of Years)?: 26-30
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Primary Site: Breast
Histology: Lobular Carcinoma

molecule: total RNA

organism: Homo sapiens

source_name: Breast


title: Pelvic tumor - 143653

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
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 2b
Retreatment N: X
Retreatment M: 0
Retreatment Stage: Unknown
Retreatment Grade: X
Primary Site: Ovary
Histology: Metastatic Endometrioid adenocarcinoma

source_name: Pelvic tumor


title: Colon - 129666

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 22
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Colon - 129670

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: 9
Presenting Symptoms: Diarrhea
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma


title: Liver - 133637

description:
Quality metric = 28S to 18S: 1
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigars
Alcohol Consumption?: Yes
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Diarrhea
Presenting Symptoms: Nausea
Presenting Symptoms: Vomiting
Screening studies performed?: Yes
Clinical T: X
Clinical N: X
Clinical M: 1
Clinical Metastatic Sites: Hepatic
Clinical Stage: 4
Clinical Grade: X
Primary Site: Colon
Histology: Metastatic Adenocarcinoma

source_name: Liver


title: Colon - 127830

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Abdominal Pain
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Breast - 127826

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 49
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: Yes
Fibrocystic disease?: Yes
Mammogram calcifications?: Yes
Hormonal therapy (# of Years)?: 0-5
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Breast - 1234

description:
Quality metric = 28S to 18S: 1
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: 30
Mammogram: Yes
Number of years in which a mammogram was obtained?: 21-25
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 3a
Pathological M: X
Pathological Stage: 3C
Pathological Grade: X
Primary Site: Breast
Histology: Ductal and Lobular carcinoma


title: Ureter - 112886

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
Clinical T: 1
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Primary Site: Ureter
Histology: Urothelial (transitional cell) carcinoma

source_name: Ureter


title: Rectosigmoid - 127827

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Days from Patient Diagnosis to Excision: 30
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: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Cervix Uteri - 129668

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 20-30
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 10
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 1b2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B2
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma, spindle cell type

source_name: Cervix Uteri


title: Omentum - 129663

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 10
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: X
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: Breast - 127820

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 35
Mammogram: Yes
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 0(i-)
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Breast
Histology: Ductal Carcinoma


title: Omentum - 1231

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 150
Prior Therapy: Chemotherapy
Presenting Symptoms: Bloating
Clinical T: 3c
Clinical N: 0
Clinical M: 0
Clinical Stage: 3C
Clinical Grade: 3
Clinical Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Metastatic Serous Adenocarinoma


title: Testis - 101154

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 24
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 2B
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Pathological Serum Tumor Markers: S0
Primary Site: Testis
Histology: Seminoma, NOS

source_name: Testis


title: Omentum - 127835

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Hispanic
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 15
Presenting Symptoms: Abdominal pain
Pathological Question: Stage
Pathological Value: 3C
Primary Site: Peritoneum
Pathological Question: Histology
Pathological Value: Metastatic Papillary serous carcinoma


title: Cervical Lymph Node - 1013

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
Have you ever had mononucleousis?: No
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Clinical Stage: 1
Clinical Symptoms: A
Primary Site: Lymph Nodes
Histology: Diffuse large B-cell lymphoma

source_name: Cervical Lymph Node


title: Breast - 101144

description:
Quality metric = 28S to 18S: 1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Hormonal Treatment
Prior Therapy: Radiation
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?: 26-30
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: Yes
Retreatment T: 2
Retreatment N: X
Retreatment M: X
Retreatment Stage: Unknown
Retreatment Grade: X
Retreatment ER: Positive
Retreatment PR: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: H1993 High dose 5-aza treatment group (1000 nM)

city: South San Francisco

first: David

middle: S

last: Shames

state: CA

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

hyb_protocol: please see the Southwestern Medical Center Microarray Core Facility website for details

data_processing: Raw signal data without normalization

label: biotin

source_name: NSCLC cell line

label_protocol: Affymetrix

growth_protocol: See publication for details.

extract_protocol: Trizol

treatment_protocol: High dose treatment group (1000 nM).  5-aza-2'-deoxycytidine qod for 6 days.

tag: See publication for details.


title: H460 Low dose treatment group (100 nM)

description: H460 Low dose treatment group (100 nM)

scan_protocol: please see the Southwestern Medical Center Microarray Core Facility website for details

treatment_protocol: H460 Low dose treatment group (100 nM).  5-aza-2'-deoxycytidine qod for 6 days.


title: H1299 Low dose 5-aza treatment group (100 nM)

source_name: NSCLC Cell line

treatment_protocol: Control treatment group.  DMSO qod for 6 days.


source_name: Immortalized Bronchial Epithelial Cells (HBEC)

treatment_protocol: HBEC2 Low dose treatment group (100 nM).  5-aza-2'-deoxycytidine qod for 6 days.


title: H1993 Control treatment group (DMSO)

description: H1993 Control treatment group (DMSO)

growth_protocol: See pulication for details.

tag: See pulication for details.


source_name: Immortalized human bronchial epithelial cells

treatment_protocol: HBEC4 Low dose treatment group (100 nM).  5-aza-2'-deoxycytidine qod for 6 days.


title: H2347 High dose 5-aza treatment group (1000 nM)

treatment_protocol: High dose (1000 nM) treatment group.  5-aza-2'-deoxycytidine qod for 6 days.


title: A549 Low dose treatment group (100 nM).

description: A549 Low dose treatment group (100 nM).

treatment_protocol: A549 Low dose treatment group (100 nM).  5-aza-2'-deoxycytidine qod for 6 days.


title: H1299 Control group treatment

description: H1299 Control group treatment


title: B6D2 2CELL PARTHENOGENIC EMBRYOS SAMPLE3

status: Public on Jan 01 2007

city: Philadelphia

first: Keith

middle: E

last: Latham

state: PA

address: 3307 N Broad St

department: The Fels Institute for Cancer Research and Molecular Biology

institute: Temple University School of Medicine

hyb_protocol: EukGE-WS2v5_450 script for Affymetrix Fluidics Station

scan_protocol: default Affymetrix GCOS settings for GeneChip 3000 7G scanner

data_processing: Microarray Analysis Suite 5.0 (MAS, Affymetrix) was used to quantify microarray signals with default analysis parameters and global scaling to target MEAN = 150

label: BIOTIN

molecule: polyA RNA

organism: Mus musculus

source_name: B6D2 2CELL PARTHENOGENIC EMBRYOS

label_protocol: ENZO RNA LABELLING KIT. ACCORDING TO MANUFACTURER SPECIFICATION

extract_protocol: PICOPURE RNA EXTRACTION KIT. ACCORDING TO MANUFACTURER SPECIFICATION

tag: B6D2 FEMALE. CULTURED IN MEMa


title: B6D2 2CELL PARTHENOGENIC EMBRYOS SAMPLE4


title: H1993 Low dose 5-aza treatment group (100 nM)

treatment_protocol: Low dose treatment group (100 nM).  5-aza-2'-deoxycytidine qod for 6 days.


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLEA3

source_name: B6D2 2CELL FERTILIZED EMBRYOS

tag: B6D2 FEMALE. CULTURED IN KSOM+AMANITIN


title: B6D2 2CELL PARTHENOGENIC EMBRYOS SAMPLE2


title: HBEC3 Low dose treatment group (100 nM).

source_name: Immortalized human bronchial epithelial cells (HBEC)


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLEA4


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLE4

tag: B6D2 FEMALE. CULTURED IN KSOM


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLEA1


title: B6D2 2CELL PARTHENOGENIC EMBRYOS SAMPLE1


title: H2347 5-aza treatment (100nM)

description: H2347 5-aza treatment (100nM)

treatment_protocol: Low dose treatment group.  5-aza-2'-deoxycytidine qod for 6 days.


title: B6D2 2CELL SCNT EMBRYOS SAMPLEA3

source_name: B6D2 2CELL SCNT EMBRYOS

tag: B6D2 FEMALE. DONOR CELL

value: CUMULUS CELL. CULTURED IN MEMa+AMANITIN


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLE3


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLE2


title: B6D2 2CELL SCNT EMBRYOS SAMPLEA4


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLEA2


title: B6D2 1CELL SCNT EMBRYOS SAMPLE2

source_name: 1CELL SCNT EMBRYOS CULTURED IN MEMa

label_protocol: ENZO BIOTIN LABELLING KIT. PROTOCOL ACCORDING TO MANUFACTURER SPECIFICATION

extract_protocol: PICOPURE KIT FROM ARCTURUS. PROTOCOL ACCORDING TO MANUFACTURER SPECIFICATION

value: CUMULUS CELL. CULTURED IN MEMa


title: B6D2 2CELL SCNT EMBRYOS SAMPLE2

tag: B6D2 FEMALE. DONOR CELL:CUMULUS CELL. CULTURED IN MEMa


title: B6D2 2CELL SCNT EMBRYOS SAMPLE1


title: B6D2 1CELL PARTHENOGENIC EMBRYOS SAMPLE4

source_name: B6D2 1CELL PARTHENOGENIC EMBRYOS

label_protocol: ENZO BIOTIN LABELLING KIT. PROTOCOL ACCORDING TO MAUFACTURER SPECIFICATION

extract_protocol: PICOPURE RNA EXTRACTION KIT. PROTOCOL ACCORDING TO MANUFACTURER SPECIFICATION


title: B6D2 1CELL FERTILIZED EMBRYOS SAMPLEA1

source_name: B6D2 1CELL FERTILIZED EMBRYOS


title: B6D2 2CELL SCNT EMBRYOS SAMPLE4


title: B6D2 2CELL SCNT EMBRYOS SAMPLE A2


title: B6D2 2CELL SCNT EMBRYOS SAMPLE3


title: B6D2 1CELL FERTILIZED EMBRYOS SAMPLE A2


title: B6D2 1CELL PARTHENOGENIC EMBRYOS SAMPLE1


title: B6D2 1CELL SCNT EMBRYOS SAMPLE4

source_name: B6D2 1CELL SCNT EMBRYOS


title: B6D2 2CELL SCNT EMBRYOS SAMPLEA1


title: B6D2 2CELL FERTILIZED EMBRYOS SAMPLE1


title: B6D2 1CELL FERTILIZED EMRBYOS SAMPLEA4


title: B6D2 1CELL FERTILIZED EMBRYOS SAMPLEA3


title: B6D2 1CELL SCNT EMBRYOS SAMPLE A4

tag: B6D2 FEMALE. DONOR CELL:CUMULUS CELL. EMBRYOS CULTURED IN MEMa+AMANITIN


title: B6D2 1CELL PARTHENOGENIC EMBRYOS SAMPLE3


title: B6D2 1CELL SCNT EMBRYOS SAMPLE3


title: Ovary - 129660

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Presenting Symptoms: Bloating
Pathological T: 3b
Pathological N: X
Pathological M: 0
Pathological Stage: Unknown
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Serous Adenocarinoma

source_name: Ovary


title: B6D2 1CELL SCNT EMBRYOS SAMPLE A3

value: CUMULU CELL. CULTURED IN MEMa+AMANITIN


title: B6D2 1CELL FERTILIZED EMBRYOS SAMPLE1

source_name: 1CELL EMBRYOS

label_protocol: ENZO RNA LABELLING KIT. PROTOCOL ACCORDING TO MANUFACTURER SPECIFICATION

extract_protocol: PICOPURE RNA EXTRACTION KIT, ARCTURUS. PROTOCOL ACCORDING TO MANUFACTURER SPECIFICATION

tag: B6D2 FEMALE


title: B6D2 1CELL FERTILIZED EMBRYO SAMPLE3

source_name: 1CELL EMBRYO


title: B6D2 1CELL PARTHENOGENIC EMBRYOS SAMPLE2

source_name: B6D2 1 CELL PARTHENOGENIC EMBRYOS


title: B6D2 1CELL SCNT EMBRYOS SAMPLE1

source_name: 1CELL SCNT EMBRYOS

value: CUMULUS CELL


title: B6D2 1CELL FERTILIZED EMBRYOS SAMPLE2


title: B6D2 1CELL SCNT EMBRYOS SAMPLE A1

source_name: 1CELL SCNT EMBRYOS. DONOR CELL:CUMULUS CELL


title: Prostate - 127839

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
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?: Yes
Days from Patient Diagnosis to Excision: 59
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Current status of disease: Under Therapy
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 8-10
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Breast - 127841

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 0-5
Pathological T: 3
Pathological N: 1a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 2
Pathological Multiple Tumors: No
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: B6D2 1CELL SCNT EMBRYO SAMPLE A2

source_name: B6D2 1CELL SCNT EMBRYO CULTURED IN MEMa_AMANITIN

tag: FEMALE B6D2. DONOR CELL

value: CUMULUS CELL. EMBRYOS CULTURED IN MEMa+AMANITIN


title: B6D2 1CELL FERTILIZED EMBRYO SAMPLE4

source_name: 1CELL EMBRYO CULTURED IN KSOM

tag: B6D2 FEMALE MICE


title: mKS1

city: Miami

first: Enrique

last: Mesri

state: FL

address: 1550 NW 10th Ave, PAP-109B

department: Microbiology and Immunology

institute: University of Miami

description: Mouse KS tumor. Sample number 1

hyb_protocol: Standard affymetrix protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf

scan_protocol: Standard affymetrix protocol-GeneChip Scanner 3000 using the protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf

data_processing: Affymetrix Microarray Suite version 5.0

label: Biotin

extract_protocol: RNA extration using TRIzol reagent(http://www.invitrogen.com/content/sfs/manuals/15596026.pdf) and purified using Qiagen Rneasy Mini Kit (http://www1.qiagen.com/literature/protocols/pdf/RY20.pdf)

tag: Mouse KS tumor. Sample number 1


title: mEC-V 3

description: Mouse EC cells transfected with empty-BAC. Control sample number 3

source_name: mEC-V 3

label_protocol: Standard affymetrix protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf


title: Muscle Control 2

city: Boston

first: Michael

last: Huntgeburth

state: MA

address: 99 Brookline Ave.

department: Endocrinology, Diabetes and Metabolism

institute: Beth Israel Deaconess Medical Center

description: second control, M. quadriceps sample

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using a confocal laser scanner

data_processing: Micoarray analysis was performed using dChip software

source_name: Quadriceps muscle, control mouse

label_protocol: Standard Affymetrix procedures

extract_protocol: RNA was extracted using the Qiagen RNeasy Midi Kit according to manufacturer guidelines

tag: Strain

value: C57BL/6; Tissue:quadricpes muscle


title: mEC-V 1

description: Mouse EC cells transfected with empty-BAC. Control sample number 1

source_name: mEC-V 1

extract_protocol: RNA extration using TRIzol reagent. (http://www.invitrogen.com/content/sfs/manuals/15596026.pdf) and purified using Qiagen Rneasy Mini Kit (http://www1.qiagen.com/literature/protocols/pdf/RY20.pdf)


title: mKS3

description: Mouse KS tumor. Sample number 3

tag: Mouse KS tumor. Sample number 3


title: Muscle Experiment 2

description: second experimental M. quadriceps sample

source_name: Quadricpes muscle, PGC1beta mutant mouse

value: C57BL/6; PGC1beta mutant mouse; Tissue:quadriceps muscle


title: Muscle Control 3

description: third control, M. quadriceps sample

value: C57BL/6; Tissue:quadriceps muscle


title: Liver Experiment 2

description: second experimental liver sample from PGC1beta mouse

scan_protocol: Standard Affymetrix procedures using confocal laser scanner

data_processing: Microarray analysis was performed using dChip software

source_name: Liver experimental mouse

extract_protocol: RNA was extracted using Qiagen RNeasy Midi Kit according to manufacturer guidelines

value: C57BL/6; PGC1beta mutant; Tissue:liver


title: Muscle Experiment 1

description: first experimental M. quadriceps sample

source_name: Quadriceps muscle, PGC1beta mutant mouse


title: mECK36 1

source_name: mECK36 1

tag: Mouse EC cells transfected with KSHVBac36. Sample number 1.


title: mEC-V 2

description: Mouse EC cells transfected with empty-BAC. Control sample number 2

source_name: mEC-V 2


title: Muscle Control 1

description: first control, M. quadriceps sample

source_name: Quadricpes muscle, control mouse


title: Liver Control 2

description: second control, liver sample

scan_protocol: Standard Affymetrix procedures using confocal laser scanner.

source_name: liver control mouse

extract_protocol: RNA was extracted using the Qiagen RNeasy Midi Kit according to the manufacturers guidelines

value: C57Bl/6; Tissue:liver


title: H2347 DMSO Control

description: H2347 DMSO Control

source_name: NSCLC Cell Line

treatment_protocol: Control treatment group.  Dimethylsulfoxide qod for 6 days.


title: Liver Control 3

description: third control, liver sample

value: C57BL/6; Tissue:liver


title: mKS2

description: Mouse KS tumor. Sample number 2

tag: Mouse KS tumor. Sample number 2


title: mECK36 3

source_name: mECK36 3

tag: Mouse EC cells transfected with KSHVBac36. Sample number 3


title: Muscle Experiment 3

description: third experimental M. quadriceps sample

scan_protocol: Standard Affymetrix procedures usinf a confocal laser scanner

value: C57BL/6; PGC1beta mutant mopuse, Tissue:quadriceps muscle


title: Placenta Preeclampsia

city: Berlin

first: Florian

last: Herse

address: Wiltbergstr. 50

country: Germany

institute: Charite

description: Preeclampsia complicates more than 3% of all pregnancies in the United States and Europe. High-risk populations include women with diabetes, dyslipidemia, thrombotic disorders, hyperhomocysteinemia, hypertension, renal diseases, previous preeclampsia, twin pregnancies, and low socioeconomic status. In the latter case, the incidence may increase to 20% to 25%. Preeclampsia is a major cause of maternal and fetal morbidity and mortality. Preeclampsia is defined by systolic blood pressure of more than 140 mm Hg and diastolic blood pressure of more than 90 mm Hg after 20 weeks gestation in a previously normotensive patient, and new-onset proteinuria. Abnormal placentation associated with shallow trophoblast invasion (fetal cells from outer cell layer of the blastocyst) into endometrium (decidua) and improper spiral artery remodeling in the decidua are initial pathological steps.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GCOS

source_name: placenta

label_protocol: 20 µg RNA were transcribed in double-stranded cDNA by cDNA Synthesis System (Roche Diagnostics GmbH, Mannheim, Germany). cRNA was produced by MEGAscript TM High Yield Transcription Kit (Ambion, Austin, USA) and labelled with biotin-11-CTP and biotin-16-UTP nucleotides (Perkin Elmer Life Sciences, Boston, USA).

extract_protocol: RNA was extracted from the placental tissue using Qiagen RNeasy mini kit including DNase kit using standard protocol

tag: placenta tissue. RNA was pooled from 10 patients with preeclampsia


title: Placenta Control

tag: placenta tissue. RNA was pooled from 10 patients with uneventfull pregnancy


title: Fat Control

source_name: fat tissue

extract_protocol: RNA was extracted from the adipose tissue using Qiagen RNeasy mini kit including DNase kit using standard protocol

tag: fat tissue (abdominal), pooled from 10 patients with uneventfull pregnancy


title: Fat Preeclampsia

tag: fat tissue (abdominal). RNA was pooled from 10 patients with preeclampsia


title: Liver Experiment 1

description: first experimental liver sample from PGC1beta mouse

source_name: Liver_experimental mouse

value: C57BL/6:PGC1beta mutant; Tissue:liver


title: Decidua Control

source_name: decidua

extract_protocol: RNA was extracted from the decidua using Qiagen RNeasy mini kit including DNase kit using standard protocol

tag: decidua tissue (Decidual tissue was collected through vacuum suctioning of the placental bed). RNA was pooled from 10 patients with uneventfull pregnancy


title: Liver Experiment 3

description: third experimental liver sample from PGC1beta mouse


title: Decidua Preeclampsia

tag: decidua tissue (Decidual tissue was collected through vacuum suctioning of the placental bed). RNA was pooled from 10 patients with preeclampsia


title: Liver Control 1

description: first control liver sample

scan_protocol: Standard Affymetrix procedure using a confocal laser scanner.

data_processing: Microarray analsis was performed using dCHip software.

source_name: Liver_control mouse

extract_protocol: RNA was extracted using the Qiagen RNeasy Midi Kit according to the manufacturer guidelines

value: C57BL/6; Tissue:liver;


title: B6N embryo, alcohol-PK11195 counterexposure-6N-CoT-1

status: Public on Dec 31 2006

city: Louisville

first: Thomas

middle: B

last: Knudsen

state: KY

address: 501 S Preston St

department: Birth Defects Center

institute: University of Louisville

description: PK11195 counterexposure (Cy3), B6N headfold

hyb_protocol: 16h, 45°C, Affymetrix Mouse Genome 430A Array

scan_protocol: intensity, GeneChip 3000 scanner

data_processing: Probe-level data normalization used the robust multichip average (RMA). Data were analyzed by fitting to the linear model and computing the coefficients for each element and sample pair average (less control elements).

label: biotinylated nucleotide analogue

source_name: embryonic headfold

label_protocol: streptavidin-conjugated peroxidase and cyanine-3

growth_protocol: 3.0h after maternal treatment

extract_protocol: Total cellular RNA isolated with RNeasy (Qiagen) that removes small RNAs (<200 nucleotides); RNA passing QA/QC amplified with Agilent Low RNA Input Fluorescent Linear Amplification Kit labeling to cRNA.

tag: 8 days post-coitum, 4-8 somite pair stage


title: B6N embryo, alcohol exposure-6N-EtOH-1

description: alcohol exposure (Cy3), B6N headfold

treatment_protocol: 2.9g/kg EtOH in saline


title: B6N embryo, alcohol-PK11195 counterexposure-6N-CoT-2


title: B6J embryo, alcohol & PK11195-6J-CoT-1

description: PK11195 counterexposure (Cy3), B6J headfold


title: B6N embryo, saline control-6N-SAL-2

description: saline control (Cy3), B6N headfold

treatment_protocol: normal saline (vehicle, intraperitoneal)


title: B6N embryo, saline control-6N-SAL-1

description: saline control (Cy3), B6N headfold


title: B6J embryo, alcohol exposure-6J-EtOH-2

description: alcohol exposure (Cy3), B6J headfold


title: B6N embryo, alcohol exposure-6N-EtOH-2

description: alcohol exposure (Cy3), B6N headfold


title: B6J embryo, alcohol & PK11195-6J-CoT-2


title: B6J embryo, saline control-6J-SAL-2

description: saline control (Cy3), B6J headfold


title: Simvastatin treated 24h, sample 3, Simvastatin is anti-inflammatory in macrophages

city: Kuopio

first: Tiina

last: Tuomisto

address: Neulaniementie 2

department: Molecular Medicine

country: Finland

institute: A.I.Virtanen Institute

hyb_protocol: cRNAs (15 ug) were hybridized to Affymetrix HGU133 Plus 2.0 oligonucleotide arrays, which was processed and scanned according to manufacturer’s instructions.

scan_protocol: Standard Affymetrix protocoll.

data_processing: Affymetrix GeneChip® Operating Software (GCOS) analysis

source_name: human peripheral blood monocyte-derived macrophages

label_protocol: cDNAs were prepared from RNAs (5 ug of RNA) with reverse transcriptase (Superscript II primed by a poly (T) oligomer/T7 promoter). cDNAs were subsequently used as a template to make biotin-labeled cRNA with an in vitro transcription reaction according to Affymetrix standard protocol.

growth_protocol: HPBM Cells were isolated from buffy coats using Ficoll-Paque gradient centrifugation (as described Pietarinen-Runtti, et al. Am.J Physiol Cell Physiol. 2000;278:C118-125). During isolation, monocytes from 3 individuals were pooled. Adherent cells were cultured in standard medium (20% human serum, Cambrex for differentiation into macrophages. The macrophage-phenotype at day 7 after isolation was confirmed with the typical shape of macrophages and also by macrophage-immunostaining (mAB CD68, DAKO, Denmark, dilution 1:200), where macrophages presented >95% of the cell population. 36 hours prior to sample collection cell growth medium was changed to serum free medium.

extract_protocol: Total RNA was isolated from the cells using Trizol reagent (Gibco BRL, USA) according to manufacturers’ instructions. The quality and amount of RNA was assessed by spectrophotometry (NanoDrop, USA) and by agarose gel electrophoresis.

treatment_protocol: 24h before sample collection cells were stimulated with 10 um simvastatin in serum free medium.

tag: from unknown healthy blood-donor volunteers (Finnish Red Cross)


title: B6J embryo, saline control-6J-SAL-1

description: saline control (Cy3), B6J headfold


title: Simvastatin treated 24h, sample 1, Simvastatin is anti-inflammatory in macrophages


title: Simvastatin treated 12h, sample 3, Simvastatin is anti-inflammatory in macrophages

treatment_protocol: 12h before sample collection cells were stimulated with 10 um simvastatin in serum free medium.


title: Simvastatin treated 12h, sample 1, Simvastatin is anti-inflammatory in macrophages


title: Control 2, Simvastatin is anti-inflammatory in macrophages

label_protocol: cDNAs were prepared from RNAs (5 ug of RNA) with reverse transcriptase (Superscript II primed by a poly (T) oligomer/T7 promoter). cDNAs were subsequently used as a template to make biotin-labeled cRNA with an  in vitro transcription reaction according to Affymetrix standard protocol.

treatment_protocol: Untreated control sample


title: B6J embryo, alcohol exposure-6J-EtOH-1

description: alcohol exposure (Cy3), B6J headfold


title: Control 3, Simvastatin is anti-inflammatory in macrophages


title: RWV R1 after 3 days exposure

city: Atlanta

first: Mamta

last: Patel

state: GA

address: 101 Woodruff Circle #315

department: Biomedical Engineering

institute: Georgia Tech and Emory University

data_processing: Signal value from Affy, data was also analyzed with dChip

label: biotinylated SAPE

source_name: 2T3 cells, simulated microgravity, 3 days

tag: cell

value: 2T3 preosteoblasts

tag: Passage

tag: Simulator

value: RWV

tag: Length

value: 3 days


title: RWV R3 after 3 days exposure

tag: Cell


title: Simvastatin treated 12h, sample 2, Simvastatin is anti-inflammatory in macrophages


title: RWV Static 3 for 3 days exposure

value: Rotating Wall Vessel


title: RWV R2 after 3 days exposure

value: 2t3 preosteoblasts


title: Simvastatin treated 24h, sample 2, Simvastatin is anti-inflammatory in macrophages


title: RWV Static 1 3days exposure

source_name: 2T3 cells

tag: Cell type


title: Control 1, Simvastatin is anti-inflammatory in macrophages


title: RWV Static 2 3 days Exposure

tag: Cells


title: WT Globular Stage Seed 2

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Wild type seed containing globular stage embryo.  Two biological replicas were generated.

hyb_protocol: Following fragmentation, fifteen micrograms of cRNA were hybridized for 16 hr at 45¡C on GeneChip Arabidopsis ATH1 Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip array was scanned using the GeneChip Scanner 3000 7G System.

data_processing: Data were processed and analyzed with Affymetrix GeneChip Operating System 1.3 (GCOS1.3) using default analysis settings and global scaling as a normalization method.  The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Arabidopsis thaliana

source_name: Wild type globular stage seed biological replica 2

label_protocol: Biotinylated cRNA were prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit (Farmingdale, NY).

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20oC and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using the Hot Borate Method [Stones et. al. PNAS vol 98 no 20: 11806-11811 (2001)]

tag: Genotype

value: Ws-O, Wild Type; Stage:Globular Stage Seed; Biological Replica:2 of 2


title: lec1-1 Globular Stage Seed 2

description: lec1-1 seed containing globular stage embryo.  Two biological replicas were generated.

source_name: lec1-1 globular stage seed biological replica 2

value: Ws-O, lec1-1; Stage:Globular Stage Seed; Biological Replica:2 of 2


title: vte2-1(Col-0) 3 day, biological rep3

status: Public on Dec 29 2006

city: East Lansing

first: Scott

middle: E.

last: Sattler

state: MI

address: room 201 Biochem Bldg

department: Biochemistry and Molecular Boliogy

institute: Michigan State University

description: Gene expression data from 3 day-old seedlings of the tocopherol deficient mutant vte2

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on the ATH1 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Arabidopsis seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: seedlings were germinate under 12hr photoperiod (100 photons umol m-1 s-1) at 22C following 5 days at 6C to break dormancy.

extract_protocol: Approximately 100 mg of seedlings were frozen in liquid nitrogen and total RNA was extracted using the RNAqueous RNA extraction kit and the Plant RNA Isolation Aid (Ambion, Austin, TX) following the manufacturer's protocol.

treatment_protocol: seedlings were grown on Petri plates containing 0.5X Murashige and Skoog basal medium (MS salts; Sigma, St. Louis, MO) and 1.0% phytoagar.

value: vte2-1 (Columbia-0)

tag: Age

value: 3 days (72hr) at 22C after 5 days at 6C to break dormancy and synchronize germination


title: lec1-1 Globular Stage Seed 1

source_name: lec1-1 globular stage seed biological replica 1

value: Ws-O, lec1-1; Stage:Globular Stage Seed; Biological Replica:1 of 2


title: vte1-1(Col-0) 3 day, biological rep2

description: Gene expression data from 3 day-old seedlings of the tocopherol deficient mutant vte1

value: vte1-1 (Columbia-0)

value: 3 day (72hr) at 22C after 5 days at 6C to break dormancy and synchronize germination


title: vte2-1(Col-0) 1 day, biological rep3

description: Gene expression data from 1 day-old seedlings of the tocopherol deficient mutant vte2

value: 1 day (24hr) at 22C after 5 days at 6C to break dormancy and synchronize germination


title: vte2-1(Col-0) 1 day, biological rep2


title: WT Globular Stage Seed 1

scan_protocol: GeneChip array was scanned using the Affymetrix GeneChip Scanner 3000 7G System.

source_name: Wild type globular stage seed biological replica 1

value: Ws-O, Wild Type; Stage:Globular Stage Seed; Biological Replica:1 of 2


title: vte2-1(Col-0) 3 day, biological rep2


title: vte1-1(Col-0) 1 day, biological rep1

description: Gene expression data from 1 day-old seedlings of the tocopherol deficient mutant vte1


title: vte1-1(Col-0) 3 day, biological rep1


title: wild-type(Col-0) 3 day, biological rep3

description: Gene expression data from 3 day-old wild-type (Col-0) seedlings

value: wild-type (Columbia-0)


title: vte2-1(Col-0) 1 day, biological rep1


title: vte1-1(Col-0) 1 day, biological rep2


title: vte1-1(Col-0) 3 day, biological rep3


title: wild-type(Col-0) 1 day, biological rep3

description: Gene expression data from 1 day-old wild-type (Col-0) seedlings

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on ATH1 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: wild-type(Col-0) 1 day, biological rep2


title: vte2-1(Col-0) 3 day, biological rep1


title: mECK36 2

source_name: mECK36 2

tag: Mouse EC cells transfected with KSHVBac36-Sample number 2


title: vte1-1(Col-0) 1 day, biological rep3


title: wild-type(Col-0) 1 day, biological rep1

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on  ATH1 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: wild-type(Col-0) 3 day, biological rep2


title: wild-type(Col-0) 3 day, biological rep1


title: TC.DR+-4

status: Public on Dec 25 2006

city: bologna

first: pier paolo

last: piccaluga

address: via massarenti 9

country: Italy

institute: university of bologna

description: Gene expression data from PTCL/U patient at diagnosis

hyb_protocol: Following fragmentation, 15 mg of fragmented cRNA were hybridized to HG-U133 2.0 plus microarrays (Affymetrix, Inc.). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Human subject, Control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA and hybridized on the HG U133 2.0 plus GeneChip.

growth_protocol: Frozen samples

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

treatment_protocol: Frozen samples homogenized on ice in the Trizol solution (GibcoBRL).

tag: Lymph-node biopsy


title: TC.DR-6


title: TC.CD4-2

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


title: TC.CD4-5


title: TC.CD4-1


title: TC.CD8-3


title: TC.CD8-4


title: TC.DR-7


title: TC.CD8-1


title: TC.CD4-6


title: TC.DR+-3


title: TC.DR+-2A


title: TC.DR--3


title: ALCL_AV_001

source_name: Human subject, Patient


title: TC.DR-1


title: TC.DR+-1


title: ALCL_AV_003


title: TC.CD8-2


title: TC.DR-2


title: TC.CD8-5


title: ALCL_AV_002


title: TC.CD4-3


title: TC.DR+-5


title: ALCL_006

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


title: AILD_006


title: ALCL_AV_004


title: AILD_AV_005


title: AILD-03


title: ALCL_AV_005


title: AILD_AV_004


title: PTCL.BG.18


title: PTCL.PG.16


title: PTCL.BO-13


title: PTCL_AV_022


title: PTCL_021


title: AILD-02


title: PTCL.BO.10


title: PTCL_AV_024


title: PTCL.PG.15


title: PTCL_AV_020


title: AILD-01


title: PTCL.BO.11


title: PTCL.BO.02


title: PTCL_025


title: PTCL.PG.17


title: PTCL.BO-12


title: PTCL_028


title: PTCL.BO.03


title: PTCL_027


title: PTCL_AV_023


title: PTCL.BO.08


title: PTCL.PG.14


title: PTCL_AV_029


title: PTCL_AV_019


title: PTCL_026


title: PTCL.BO.06


title: PTCL_BO_001


title: PTCL.BO.04


title: PTCL.BO.05


title: Proxtubules 2_6_13_06

status: Public on Dec 23 2006

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7132

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 5ug

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: Early Proximal Tubule

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: approx 50 sections from 5 kidneys
Pooled sample: Yes
Dissection Method: Laser capture microdissection
CD-1 mice are time-mated.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses placed in OCT in a mold, frozen in liquid nitrogen and stored at -80°C. Blocks are sectioned, stained and used for laser capture micro-dissection.

tag: gene reported

value: wild-type

tag: strain

tag: Sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: Urothelium5_1_6_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7138

source_name: Urothelium


title: UreteralSmoothmuscle_2_7_07_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7135

source_name: Ureteral Smooth Muscle


title: CCD_1_7_07_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7129

source_name: Cortical Collecting Duct


title: Urothelium_1_4_11_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7137


title: Urothelium6_1_6_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7139


title: Cortical Collecting Duct

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7130


title: UreteralSmoothmuscle3_1_6_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7136


title: gh3.5-1D 48 hpi, biological replicate 1

status: Public on Dec 18 2006

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of plant physiology & ecology, SIBS, CAS

description: Gene expression data of mutant gh3.5-1D leaves after infection with Pst DC3000(avrRpt2)

hyb_protocol: Affymetrix standard protocol

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

source_name: Arabidopsis thaliana mutant gh3.5-1D leaves, 48 hpi with Pst DC3000(avrRpt2)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit and Genechip Sample Cleanup Module (Affymetrix)

extract_protocol: Total RNA was extracted from the leaves using the Trizol method (Invitrogen) and purified with RNeasy MiniKit (Qiagen). cDNA was synthesized and purified with one-cycle cDNA Synthesis Kit (Affymetrix) and GeneChip Sample Cleanup Module (Affymetrix), respectively.

value: gh3.5-1D, mutant Age:5 week-old Tissue:48 hpi with Pst DC3000(avrRpt2) leaves


title: Col-0 48 hpi, biological replicate 3

description: Gene expression data of wild type Columbia-0 leaves after infection with Pst DC3000(avrRpt2)

source_name: Arabidopsis thaliana Col-0 leaves, 48 hpi with Pst DC3000(avrRpt2)

value: Columbia-0, wild-type (Col-0) Age:5 week-old Tissue:48 hpi with Pst DC3000(avrRpt2) leaves


title: Proxtubules_1_6_13_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7133


title: Proxtubules _1_7_07_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7131


title: gh3.5-1D 48 hpi, biological replicate 2


title: UreteralSmoothmuscle_2_4_11_06

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7134


title: gh3.5-1D uninoculated, biological replicate 2

description: Gene expression data of mutant gh3.5-1D leaves, uninoculated

source_name: Arabidopsis thaliana mutant gh3.5-1D leaves, uninoculated

value: gh3.5-1D, mutant Age:5 week-old Tissue:uninoculated leaves


title: gh3.5-1D uninoculated, biological replicate 3


title: gh3.5-1D uninoculated, biological replicate 1


title: Col-0 uninoculated, biological replicate 1

description: Gene expression data of wild type Columbia-0 leaves, uninoculated

source_name: Arabidopsis thaliana Col-0 leaves, uninoculated

value: Columbia-0, wild-type (Col-0) Age:5 week-old Tissue:uninoculated leaves


title: gh3.5-1D 48 hpi, biological replicate 3


title: Col-0 uninoculated, biological replicate 3


title: Col-0 48 hpi, biological replicate 1


title: 4CNP M

status: Public on Dec 15 2006

city: London

first: Claudine

last: James

email: claudinegj@hotmail.com, fbeier@uwo.ca

state: Ontario

address: 1151 Richmond Street, Suite 2

department: Physiology and Pharmacology

country: Canada

institute: University of Western Ontario

description:
culture time: 6 days
media: minimal
treatment regime: treat on days 1, 3 and 5
microdissect: day 6
number of tibiae per treatment: 24

hyb_protocol: According to standard protocols used in London Regional Genomics Facility. Ontario, Canada

data_processing: Gene Spring GX

label: SAPE

growth_protocol: 6 days in minimal media

extract_protocol: Qiagen RNeasy lipid extraction kit

treatment_protocol: CNP at 10exp(-6) M

tag: stage

tag: organ

value: tibiae

tag: mouse strain

tag: gender

value: male and female


title: 4CNP R/P

scan_protocol: According to standard protocols used in London Regional Genomics Facility. Ontario, Canada


title: 4BSA M

label_protocol: According to standard protocols used in London Regional Genomics Facility. Ontario, Canada

treatment_protocol: vehicle: BSA/HCL 1.0 Mm


title: 4BSA H


title: 4CNP H


title: PTCL.BO.09

description: Gene expression data from PTCL/U patient at diagnosis


title: 4BSA R/P


title: 2BSA M


title: Col-0 uninoculated, biological replicate 2


title: 3CNP R/P


title: 2BSA R/P


title: 2CNP R/P


title: 3BSA M


title: 2CNP M


title: 2BSA H


title: 3CNP H


title: 2CNP H


title: 3CNP M


title: MCF7_inhibitor_HRG_AG1478_45min

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN RCAI

description: Early gene expression (up to 90min) induced by growth hormone stimulation with an EGFR kinase inhibitor.

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: The data were analyzed with GeneChip Operating System (GCOS) (ver.1.2) using Affymetrix default analysis settings and global scaling as normalization method. The Single-Array Expression Analysis function was used and the trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: breast epithelial cell, adherent, HRG, AG1478, 45min

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment. The inhibitor, AG1478 (an EGFR kinase inhibitor) was added to 20 min prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: Cell line

value: MCF-7 (Obtained from ATCC (American Type Culture Collection)), Organ:mammary gland; breast, Cell type:epithelial, Disease:adenocarcinoma, Derived from metastatic site:pleural effusion, Age:69 years adult, Gender:female, Ethnicity:Caucasian


title: MCF7_inhibitor_HRG_AG1478_10min

source_name: breast epithelial cell, adherent, HRG, AG1478, 10min


title: MCF7_inhibitor_AG1478_15min

description: Early gene expression (up to 90min) induced by an EGFR kinase inhibitor stimulation.

source_name: breast epithelial cell, adherent, AG1478, 15min

growth_protocol: Prior to the inhibitor treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the inhibitor treatment


title: MCF7_inhibitor_HRG_AG1478_5min

source_name: breast epithelial cell, adherent, HRG, AG1478, 5min


title: 3BSA R/P


title: MCF7_inhibitor_AG1478_90min

source_name: breast epithelial cell, adherent, AG1478, 90min


title: MCF7_inhibitor_HRG_AG1478_60min

source_name: breast epithelial cell, adherent, HRG, AG1478, 60min


title: MCF7_inhibitor_AG1478_30min

source_name: breast epithelial cell, adherent, AG1478, 30min


title: MCF7_inhibitor_HRG_AG1478_90min

source_name: breast epithelial cell, adherent, HRG, AG1478, 90min


title: MCF7_inhibitor_AG1478_45min

source_name: breast epithelial cell, adherent, AG1478, 45min


title: MCF7_inhibitor_AG1478_60min

source_name: breast epithelial cell, adherent, AG1478, 60min


title: MCF7_inhibitor_HRG_AG1478_15min

source_name: breast epithelial cell, adherent, HRG, AG1478, 15min


title: 3BSA H


title: MCF7_inhibitor_HRG_U0126_60min

description: Early gene expression (up to 90min) induced by growth hormone stimulation with a MEK inhibitor.

source_name: breast epithelial cell, adherent, HRG, U0126, 60min

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment. The inhibitor, U0126 (a MEK inhibitor) was added to 20 min prior to the GF treatment.


title: MCF7_inhibitor_HRG_U0126_90min

source_name: breast epithelial cell, adherent, HRG, U0126, 90min


title: MCF7_inhibitor_AG1478_10min

source_name: breast epithelial cell, adherent, AG1478, 10min


title: MCF7_inhibitor_HRG_U0126_30min

source_name: breast epithelial cell, adherent, HRG, U0126, 30min


title: MCF7_inhibitor_AG1478_5min

source_name: breast epithelial cell, adherent, AG1478, 5min


title: MCF7_inhibitor_U0126_45min

description: Early gene expression (up to 90min) induced by a MEK inhibitor stimulation.

source_name: breast epithelial cell, adherent, U0126, 45min


title: MCF7_inhibitor_U0126_10min

source_name: breast epithelial cell, adherent, U0126, 10min


title: MCF7_inhibitor_HRG_U0126_5min

source_name: breast epithelial cell, adherent, HRG, U0126, 5min


title: MCF7_inhibitor_U0126_60min

source_name: breast epithelial cell, adherent, U0126, 60min


title: MCF7_inhibitor_HRG_U0126_15min

source_name: breast epithelial cell, adherent, HRG, U0126, 15min


title: MCF7_inhibitor_U0126_15min

source_name: breast epithelial cell, adherent, U0126, 15min


title: MCF7_inhibitor_U0126_5min

source_name: breast epithelial cell, adherent, U0126, 5min


title: MCF7_inhibitor_HRG_60min

description: Early gene expression (up to 90min) induced by growth hormone stimulation

source_name: breast epithelial cell, adherent, HRG, 60min

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.


title: MCF7_inhibitor_HRG_U0126_10min

source_name: breast epithelial cell, adherent, HRG, U0126, 10min


title: MCF7_inhibitor_U0126_90min

source_name: breast epithelial cell, adherent, U0126, 90min


title: MCF7_inhibitor_HRG_U0126_45min

source_name: breast epithelial cell, adherent, HRG, U0126, 45min


title: MCF7_inhibitor_HRG_90min

source_name: breast epithelial cell, adherent, HRG, 90min


title: MCF7_inhibitor_control_for_AG1478

description: Early gene expression (up to 90min) induced by growth hormone stimulation.

source_name: breast epithelial cell, adherent, without stimulus, control for AG1478


title: MCF7_inhibitor_HRG_15min

source_name: breast epithelial cell, adherent, HRG, 15min


title: MCF7_inhibitor_U0126_30min

source_name: breast epithelial cell, adherent, U0126, 30min


title: MCF7_inhibitor_HRG_5min

source_name: breast epithelial cell, adherent, HRG, 5min


title: MCF7_inhibitor_HRG_45min

source_name: breast epithelial cell, adherent, HRG, 45min


title: MOLT4_ctrl_C

city: Stockholm

last: Brodin

address: Halsovagen 7-9

department: Department of biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description:
MOLT4 cells (a human T-cell acute lymphoblastic leukemia cell line), with a mutation in the NOTCH 1 gene (Weng et al., 2004, Science, 306, 269-271).
Total RNA was harvested from three independent cultures of the MOLT4 cell line before and 48 hours after addition of the gamma-secretase inhibitor DAPT (5 uM).

hyb_protocol: standard Affymetrix EukGE-WS2v4 protocol

scan_protocol: standard Affymetrix procedures using a GeneChip Scanner 3000 7G with autoloader

data_processing: all probe sets scaling to target signal 100 (GCOS 1.4)

source_name: MOLT4 cell line, untreated

label_protocol: Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA.

growth_protocol: RPMI medium 1640 (Invitrogen) supplemented with 10 % FBS, 10 mM HEPES and penicillin-streptomycin (200 U/ml).

extract_protocol: cells were harvested and lysed using Trizol (Invitrogen), with an additional RNA clean-up step using the RNAeasy purification kit (Qiagen).

treatment_protocol: untreated control

tag: genotype


title: MOLT4_GSI_B

source_name: MOLT4 cell line, treated with GSI

treatment_protocol: addition of the gamma-secretase inhibitor DAPT (5 uM) and incubation for 48h

value: mutation in the NOTCH 1 gene (Weng et al., 2004, Science, 306, 269-271)


title: MOLT4_ctrl_B


title: Col-0 48 hpi, biological replicate 2

source_name: Arabidopsis thaliana Col-0 leaves, 48 hpi with Pst DC3000(avrRpt2)

tag: Genotype


title: MOLT4_ctrl_A

description:
MOLT4 cells, a human T-cell acute lymphoblastic leukemia cell line. Contains a mutation in the NOTCH 1 gene (Weng et al., 2004, Science, 306, 269-271).
Total RNA was harvested from three independent cultures of the MOLT4 cell line before and 48 hours after addition of the gamma-secretase inhibitor DAPT (5 uM).


title: MCF7_inhibitor_HRG_10min

source_name: breast epithelial cell, adherent, HRG, 10min


title: MCF7_inhibitor_control_for_U0126

source_name: breast epithelial cell, adherent, without stimulus, control for U0126


title: MOLT4_GSI_C


title: MOLT4_GSI_A


title: MCF7_inhibitor_HRG_30min

source_name: breast epithelial cell, adherent, HRG, 30min


title: SLWF uninfested arabidopsis rosette tissue, replicate 2

city: Riverside

first: Linda

middle: L.

last: Walling

address: 3401 Watkins Drive

department: Botany and Plant Sciences, CEPCEB

institute: University of California, Riverside

description: Gene expression data from uninfested 7-week old short day Arabidopsis thaliana plants

hyb_protocol: The labeled cRNA was hybridized to Affymetrix Arabidopsis genome ATH1 Chip arrays using standard Affymetrix protocols.

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

source_name: Arabidopsis rosette tissue, uninfested

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Eukaryotic One-Cycle Target Labeling Assay protocol (Affymetrix GeneChip Expression, Analysis Technical Manual, Affymetrix, Santa Clara, CA)

growth_protocol: Tissue collected from developmentally matched control leaves after 7 weeks.

extract_protocol: RNAwiz extraction of total RNA, pooled from 2 biological replicates (total 20 plants), was performed according to the manufacturer's instructions.

treatment_protocol: 10 Three-week old Arabidopsis plants were infested with 100 Silverleaf whiteflies (SLWF) (or not infested); contained by a nylon-mesh bag.  Tissue was collected from infested leaves 28 days post-infestation. Developmentally matched uninfested tissue was also collected.

tag: Ecotype

value: Columbia

tag: Age

value: 7 week old short-day plants


title: SLWF uninfested arabidopsis rosette tissue, replicate 1

treatment_protocol: 10 21-day old Arabidopsis plants, grown under short-day conditions, were infested with 100 Silverleaf whiteflies (SLWF) (or not infested); contained by a nylon-mesh bag.  Tissue was collected from infested leaves 28 days post-infestation. Developmentally matched uninfested tissue was also collected.


title: SLWF infested arabidopsis rosette tissue, replicate 1

description: Gene expression data from SLWF infested 7-week old short day Arabidopsis thaliana plants

source_name: Arabidopsis rosette tissue, infested

growth_protocol: Tissue collected from SLWF infested leaves 28 days post-infestation.


title: NS3-7

status: Public on Dec 12 2006

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
airway epithelial cells obtained by bronchoscopy and brushing
Time: Day 7; Smoking status: non-smoker

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and Robust Multi-array Average (RMA).

source_name: Time: Day 7; Smoking status: non-smoker

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Time

value: Day 7

tag: Smoking status

value: non-smoker

tag: Pack-years

value: M

tag: Ethnic group

value: white


title: Expression data from ankle tissue of C57BL/6 IL10KO mice at 1 week of infection

status: Public on Dec 14 2006

city: Salt Lake City

first: Janis

last: Weis

state: UT

address: 15 North Medical Drive East

department: Pathology

institute: University of Utah

description: expression during the development of arthritis

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=4.678364753723 SFGene=All
Background=Avg:44.11,Stdev:0.47,Max:45.3,Min:43.1  Noise=Avg:2.17,Stdev:0.08,Max:2.4,Min:2.0  RawQ=1.36  Corner+=Avg:68,Count:32 Corner-=Avg:9936,Count:32 Central-=Avg:10854,Count:9

source_name: ankle tissue at 1 week of infection

label_protocol: standard Affymetrix procedure

extract_protocol: total RNA extracted from ankle tissues

tag: C57BL/6 IL10KO mice


title: Expression data from ankle tissue of C57BL/6 IL10KO mice at 4 week of infection

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=4.356542587280 SFGene=All
Background=Avg:39.98,Stdev:0.53,Max:41.0,Min:38.5  Noise=Avg:1.92,Stdev:0.05,Max:2.1,Min:1.8  RawQ=1.23  Corner+=Avg:66,Count:32 Corner-=Avg:9949,Count:32 Central-=Avg:10700,Count:9

source_name: ankle tissue at 4 weeks of infection


title: S5-14

description:
airway epithelial cells obtained by bronchoscopy and brushing
Time: Day 14; Smoking status: smoker

source_name: Time: Day 14; Smoking status: smoker

value: Day 14

value: smoker

tag: Sex

value: F

value: black


title: Expression data from ankle tissue of C57BL/6 mice at 1 week of infection

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=5.669344425201 SFGene=All
Background=Avg:44.50,Stdev:0.58,Max:46.1,Min:43.3  Noise=Avg:2.10,Stdev:0.08,Max:2.4,Min:2.0  RawQ=1.37  Corner+=Avg:60,Count:32 Corner-=Avg:9029,Count:32 Central-=Avg:10004,Count:9

source_name: ankle tissue at 1 weeks of infection

tag: C57BL/6 mice


title: NS2-7


title: Expression data from ankle tissue of C57BL/6 mice at 4 week of infection

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=6.638023853302 SFGene=All
Background=Avg:41.07,Stdev:0.37,Max:42.2,Min:40.6  Noise=Avg:1.86,Stdev:0.05,Max:2.1,Min:1.8  RawQ=1.27  Corner+=Avg:60,Count:32 Corner-=Avg:8321,Count:32 Central-=Avg:9297,Count:9


title: NS4-14

description:
airway epithelial cells obtained by bronchoscopy and brushing
Time: Day 14; Smoking status: non-smoker


title: S2-7

description:
airway epithelial cells obtained by bronchoscopy and brushing
Time: Day 7; Smoking status: smoker

source_name: Time: Day 7; Smoking status: smoker


title: NS3-14

source_name: Time: Day 14; Smoking status: non-smoker


title: S3L-14


title: S3L-0

description:
airway epithelial cells obtained by bronchoscopy and brushing
Time: Day 0; Smoking status: smoker

source_name: Time: Day 0; Smoking status: smoker

value: Day 0


title: S4-14


title: S5-7


title: Expression data from ankle tissue of C57BL/6 mice at 2 week of infection

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=5.598697662354 SFGene=All
Background=Avg:49.44,Stdev:0.72,Max:51.1,Min:47.9  Noise=Avg:2.42,Stdev:0.08,Max:2.7,Min:2.3  RawQ=1.56  Corner+=Avg:63,Count:32 Corner-=Avg:8472,Count:32 Central-=Avg:9513,Count:9

source_name: ankle tissue at 2 weeks of infection


title: Expression data from ankle tissue of C57BL/6 IL10KO mice at 2 week of infection

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=5.894421577454 SFGene=All
Background=Avg:40.36,Stdev:0.47,Max:41.7,Min:39.5  Noise=Avg:1.93,Stdev:0.08,Max:2.1,Min:1.8  RawQ=1.25  Corner+=Avg:54,Count:32 Corner-=Avg:6847,Count:32 Central-=Avg:8103,Count:9


title: Adult male bladder J_244G

status: Public on Dec 08 2006

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7123

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10 ug

source_name: bladder

extract_protocol: Qiagen: RNeasy

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Gross dissection of entire bladder.
An adult SMGA/EGFP male was euthanized by carbon dioxide inhalation.  Bladders were removed by dissection, rapidly frozen and stored in liquid nitrogen until RNA was extracted for gene expression analysis.

tag: gene reported

value: SMGA/EGFP transgenic / PMID:14713859

tag: strain

value: FVB/N

tag: sex

value: male

tag: developmental stage

value: adult

tag: theiler stage

tag: somite count

tag: developmental landmark

value: Adult animal


title: Expression data from ankle tissue of C57BL/6 IL10KO mice at 0 week of infection (uninfected)

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=7.376115798950 SFGene=All
Background=Avg:43.57,Stdev:0.49,Max:44.4,Min:42.1  Noise=Avg:1.76,Stdev:0.06,Max:1.9,Min:1.6  RawQ=1.26  Corner+=Avg:56,Count:32 Corner-=Avg:8959,Count:32 Central-=Avg:9309,Count:9

source_name: ankle tissue at 0 weeks of infection


title: Adult male bladder J_271G

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7124


title: S3R-7


title: Expression data from ankle tissue of C57BL/6 mice at 0 week of infection (uninfected)

data_processing:
MAS 5
Algorithm: Statistical
HZ=4 VZ=4 BG=4 SmoothFactorBG=100 Epsilon=0.5 BF= Alpha1=0.05 Alpha2=0.065 Tau=0.015 Gamma1H=0.002 Gamma1L=0.002 Gamma2H=0.002667 Gamma2L=0.002667 Perturbation=1.1 TGT=500 NF=1.000000000000 SF=6.670738220215 SFGene=All
Background=Avg:44.37,Stdev:0.55,Max:46.0,Min:43.4  Noise=Avg:2.17,Stdev:0.07,Max:2.4,Min:2.0  RawQ=1.39  Corner+=Avg:51,Count:32 Corner-=Avg:7398,Count:32 Central-=Avg:8583,Count:9


title: Postnatal day 1 male bladder J_15B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7126

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: Gross dissection of entire bladder.
Newborn (postnatal day 1) SMGA/EGFP male pups were euthanized by carbon dioxide inhalation, bladders were dissected out, rapidly frozen, and stored at -80 °C until RNA was extracted for gene expression analysis.

value: postnatal day 1

value: ND

value: postnatal day 1 mouse


title: S1-7

value: Day 7


title: Postnatal day 1 male bladder J_13B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7125


title: Adult male bladder J_238G

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7122


title: Postnatal day 1 male and female bladders J_Ref_1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7128

source_name: whole mouse

treatment_protocol:
pool size: whole mouse (4 male & 4 female)
Pooled sample: yes,
Dissection Method: whole animal used; four males and four females pooled.
This sample represents the universal standard for cross comparison of microarray data.

value: wild-type

value: both (male & female)


title: Postnatal day 1 male bladder J_40B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7127


title: Human lymphatic endothelial cells TNFalpha_Rep 2

status: Public on Dec 05 2006

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

institute: University of Oxford

description: Here we have addressed important question of inflammation-induced mechanism for leukocyte transmigration of lymphatic vessel endothelium by comparing global gene expression profile of normal dermal lymphatic endothelial cells with/without TNFa added to the culture.

hyb_protocol: Fragmented labeled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). A 200µl of this hybridization cocktail was used on the chip and incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v5, Affymetrix) of double-staining and post-hybridizations washes.

scan_protocol: Fluorescent images were captured using gene Array Scanner 3000 and GCOS1.2 software (Affymetrix).

data_processing: We have used the genechip robust multi-array average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 54,675 probe sets (transcripts) on each array.

source_name: Primary lymphatic endothelial cells, cultured in vitro with TNFalpha, derived from skin samples obtained from healthy human donors during elective surgery.

label_protocol: 8 microgram total RNA used in Affymetrix one cycle target labeling kit cat. no. 900493.

growth_protocol: HDLEC were cultured in complete EGM-2 MV medium(Cambrex Bio Science Walkersville Inc.) supplemened with 1ng/ml TNFalpha at 37ºC, 5 % CO2 in a humidified atmosphere, using plastic tissue culture flasks that had been pre-coated with gelatin (0.1%, Gibco)

extract_protocol: Total RNA extracted using Qiagen RNeasy.

treatment_protocol: Human skin biopsy was digested overnight (4ºC) with Dispase®, 2 mg/ml (Gibco) in PBS, pH 7.5, to remove the epidermis. Cells were released from human tissue by scraping, passed through a 70μm cell strainer (BD Falcon) and expanded in 0.1% gelatine-coated flasks in complete EGM-2 MV medium. HDLEC were lifted with Accutase (PAALaboratories) then immuno-selected with mouse anti-human LYVE-1 mAb, followed by magnetic retrieval with appropriate MACS bead preparations (Miltenyi Biotech). HDLEC were cultured for 48h in EGM2MV medium supplemented with TNFalpha, 1 ng/ml.

tag: Human dermal microvascular lymphatic endothelial cells (HDLEC) were prepared from healthy female adults undergoing elective surgery (breast reduction and abdominoplasty).


title: ß-catenin transduced LSK day 3

status: Public on Dec 06 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: ß-catenin transduced LSK day 3

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: β-catenin transduced linnegSca-1posc-kitpos cells (after 3 days of retroviral transduction)

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

growth_protocol: IMDM-Medium + 10% FCS + 1% Pen/Strep + 20mM Hepes + Non Essential Amino Acids + Sodium Pyruvate + Zytokine (IL-3, SCF, Flt3, IL-11)

extract_protocol: Rneasy

tag: genetic modification:

tag: tissue

value: Bone marrow


title: Mouse lymphatic endothelial cells TNFa treated

hyb_protocol: Fragmented labeled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). A 200µl of this hybridization cocktail was used on the chip and incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v5, Affymetrix) of double-staining and post-hybridisations washes.

data_processing: We have used the genechip robust multi-array average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 45,101 probe sets (transcripts) on each array.

source_name: normal murine dermal lymphatic edothelial cells, with TNFa treatment

growth_protocol: cells cultured overnight in complete EGM-2 MV medium. Resulting cells were cultured in EGM-2 MV, using plastic tissue culture flasks that had been pre-coated with gelatin (0.1%, Gibco)

treatment_protocol:
mouse skin biopsy was digested overnight (4ºC) with Dispase®, 2 mg/ml (Gibco) in PBS, pH 7.5, to remove the epidermis. Dermal cells
were released from mouse skin by digestion (30 min, 37ºC)
with a mixture of collagenase A (2 mg/ml), ovine testicular hyaluronidase (0.2mg/ml), DNase I (0.05 mg/ml) and elastase (0.05 mg/ml, all from Roche). Digests were filtered through a 70μm cell strainer. MDLEC were lifted with Accutase (PAA Laboratories) then immuno-selected with rat anti-mouse LYVE-1 mAb respectively, followed by magnetic retrieval with appropriate MACS bead preparations (Miltenyi Biotech). cells cultured with/without TNFalpha treatment at 1 ng/ml.

tag: murine dermal lymphatic edothelial cells prepared from Balb/c female pups– neonates (2-4 days post parturition)


title: DKmix cells day 50

description: DKmix cells day 50

source_name: ß-catenin transduced linnegSca-1posc-kitpos cells cultured for 50 days


title: DKmix cells day 300

description: DKmix cells day 300

source_name: ß-catenin transduced linnegSca-1posc-kitpos cells cultured for 300 days (DKmix)


title: Human lymphatic endothelial cells Control_Rep 3

source_name: Skin samples obtained from healthy human donors during elective surgery at the Radcliffe Infirmary Hospital_Oxford (with full ethical approval)

growth_protocol: HDLEC were cultured overnight in complete EGM-2 MV medium(Cambrex Bio Science Walkersville Inc.) at 37ºC, 5 % CO2 in a humidified atmosphere, using plastic tissue culture flasks that had been pre-coated with gelatin (0.1%, Gibco)

treatment_protocol: Human skin biopsy was digested overnight (4ºC) with Dispase®, 2 mg/ml (Gibco) in PBS, pH 7.5, to remove the epidermis. Cells were released from human tissue by scraping, passed through a 70μm cell strainer (BD Falcon) and expanded in 0.1% gelatine-coated flasks in complete EGM-2 MV medium. HDLEC were lifted with Accutase (PAALaboratories) then immuno-selected with mouse anti-human LYVE-1 mAb, followed by magnetic retrieval with appropriate MACS bead preparations (Miltenyi Biotech). HDLEC were cultured for 48h in EGM2MV medium alone.


title: Mouse lymphatic endothelial cells Control

source_name: normal murine dermal lymphatic edothelial cells, without TNFa


title: eGFP transduced LSK day 3

description: eGFP transduced LSK day 3

source_name: eGFP transduced linnegSca-1posc-kitpos cells (after 3 days of retroviral transduction)


title: Human lymphatic endothelial cells Control_Rep 1

source_name: skin samples obtained healthy human donars during elective surgery at the Radcliffe Infirmary Hospital_Oxford (with full ethical approval)

growth_protocol: cells cultured overnight in complete EGM-2 MV medium(Cambrex Bio Science Walkersville Inc.) at 37ºC, 5 % CO2 in a humidified atmosphere, using plastic tissue culture flasks that had been pre-coated with gelatin (0.1%, Gibco)

treatment_protocol:
Human skin biopsy was digested overnight (4ºC) with Dispase®, 2 mg/ml (Gibco) in PBS, pH 7.5, to remove the epidermis. Cells were released from human tissue by scraping, passed through a 70μm cell strainer
(BD Falcon) and expanded in 0.1% gelatine-coated flasks in complete EGM-2 MV medium. HDLEC were lifted with Accutase (PAALaboratories) then immuno-selected with mouse anti-human LYVE-1 mAb , followed by magnetic retrieval with appropriate MACS bead preparations (Miltenyi Biotech). cells cultured with/without TNFalpha treatment at 1 ng/ml.


title: Human lymphatic endothelial cells Control_Rep 2


title: Lmna H222P homozygous male 5

status: Public on Dec 02 2006

first: antoine

last: Muchir

address: 630W 168th street

department: Medicine

institute: columbia university

description: 10 weeks

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GC-RMA

source_name: whole heart

label_protocol: standard Affymetrix procedures

extract_protocol: RNA was extracted using Rneasy kit (QIAGEN)


title: Human lymphatic endothelial cells TNFalpha_Rep 3


title: Lmna H222P homozygous male 4

description: 10 weeks


title: Lmna H222P homozygous male 6

description: 10 weeks


title: Lmna H222P homozygous male 2

description: 10 weeks


title: Lmna H222P heterozygous male 6

description: 10 weeks


title: Lmna H222P heterozygous male 4

description: 10 weeks


title: Lmna H222P heterozygous male 3

description: 10 weeks


title: NS1-7

source_name: Time: Day 7; Smoking status: non-smoker

tag: Time

tag: Smoking status

value: non-smoker

tag: Age

value: M


title: Lmna H222P heterozygous male 5

description: 10 weeks


title: Lmna H222P homozygous male 1

description: 10 weeks


title: Lmna H222P homozygous male 3

description: 10 weeks


title: SLWF infested arabidopsis rosette tissue, replicate 2

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Arabidopsis rosette tissue, infested

tag: Ecotype

value: Columbia

value: 7 week old short-day plants


title: Lmna H222P heterozygous male 2

description: 10 weeks


title: Emd KO male 2

description: 10 weeks


title: Control male 6

description: 10 weeks


title: Control male 1

description: 10 weeks


title: Emd KO male 5

description: 10 weeks


title: Emd KO male 6

description: 10 weeks


title: Control male 7

description: 10 weeks


title: Control male 3

description: 10 weeks


title: Emd KO male 4

description: 10 weeks


title: Control male 4

description: 10 weeks


title: Emd KO male 3

description: 10 weeks


title: Control male 2

description: 10 weeks


title: Control male 5

description: 10 weeks


title: 2.5uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate A

status: Public on Dec 01 2006

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug. At four hours prior to RNA isolation, 2.5uM sapphyrin PCI-2050 (final concentration) was added to the culture. After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.

scan_protocol: We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.

data_processing: RMA Normalization

label: Affymetrix single-stage biotin

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

extract_protocol: We used the RNA Stat-60 reagent (Tel-Test, Inc.) according to the manufacturer's recommended protocols.


title: 2.5uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate C

growth_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug. At four hours prior to RNA isolation, 2.5uM sapphyrin PCI-2050 (final concentration) was added to the culture. After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Emd KO male 1

description: 10 weeks


title: 2.5uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate B

treatment_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug. At four hours prior to RNA isolation, 2.5uM sapphyrin PCI-2050 (final concentration) was added to the culture. After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Mannitol control treated A549 human lung cancer cell cultures replicate C

description: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, mannitol (5% final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: 1.25uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate C

description: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, 1.25uM sapphyrin PCI-2050 (1.25uM final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Actinomycin D treated A549 human lung cancer cell cultures replicate B

description: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, actinomycin D (5 ug/mL final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols.

scan_protocol: We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recomended protocols.

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recomended protocols.

extract_protocol: We used the RNA Stat-60 reagent (Tel-Test, Inc.) according to the manufacturer's recomended protocols.


title: 1.25uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate B

growth_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, 1.25uM sapphyrin PCI-2050 (1.25uM final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: 1.25uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate A

treatment_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, 1.25uM sapphyrin PCI-2050 (1.25uM final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: chorion villus cells_trisomy18_rep1

city: Tuebingen

first: Oezge

last: Altug Teber

address: Calwerstr. 7

department: Medical Genetics

institute: University of Tuebingen

description: prenatal sample with a trisomy 18

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Call detection and signal intensities were generated by Affymetrix GCOS software. Raw data were imorted into ArrayAssist version 4.1 software. For normalization, GC-RMA normalization algorithm implemented in ArrayAssist were applied.

source_name: chorion villus cells, trisomy

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Primary cell cultures of the amniocytes were performed using slide flasks (with NunclonTM surface, 9 cm2, NUNCTM). Amniocytes were grown in Amnio Max C100 Basal Medium and Amnio Max C100 Supplement (Invitrogen) at 37°C in 5% CO2. The second successive subculture was set up in culture flasks (with CELLSTAR® surface, 25 cm2, Greiner bio-one) using the same medium.

extract_protocol: Cells were harvested by centrifugation and media was removed by suction. The cells were then resuspended in RLT-buffer provided in RNeasy mini kit (QIAGEN) and total RNA was isolated from each cell culture using RNeasy mini kit according to manufacturer’s instructions (QIAGEN).

treatment_protocol: No treatment

value: prenatal chorion villus cells

value: 13 gestational weeks

tag: gender

tag: karyotype

value: Trisomy 18


title: chorion villus cells_trisomy18_rep3

description: prenatal sample with a trisomy 18

value: 12 gestational weeks

value: female


title: Actinomycin D treated A549 human lung cancer cell cultures replicate C

growth_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, actinomycin D (5 ug/mL final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Mannitol control treated A549 human lung cancer cell cultures replicate B

growth_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, mannitol (5% final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: amniocytes_trisomy13_rep3

description: prenatal sample with a trisomy 13.

source_name: amniocytes, trisomy

growth_protocol: Primary cell cultures of the amniocytes were performed using slide flasks (with NunclonTM surface, 9 cm2, NUNCTM). Amniocytes were grown in Amnio Max II Complete Medium (Invitrogen) at 37°C in 5% CO2. The second successive subculture was set up in culture flasks (with CELLSTAR® surface, 25 cm2, Greiner bio-one) using the same medium.

value: prenatal amniocytes

value: 16 gestational weeks

value: male

value: trisomy 13


title: chorion villus cells_trisomy18_rep2

description: prenatal sample with a trisomy 18


title: Mannitol control treated A549 human lung cancer cell cultures replicate A

treatment_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, mannitol (5% final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: Control male 8

description: 10 weeks


title: chorion villus cells_trisomy21_rep3

description: prenatal sample with a trisomy 21

value: trisomy 21


title: chorion villus cells_normalkaryotype_rep6

description: prenatal euploid sample

source_name: chorion villus cells, normal karyotype

value: normal


title: amniocytes_trisomy13_rep1

description: prenatal sample with a translocation-trisomy 13. The translocation involves the whole chromosome 13.

value: 15 gestational weeks


title: chorion villus cells_normal karyptype_rep5

description: prenatal sample with a normal karyotype


title: amniocytes_trisomy13_rep2

description: prenatal sample with a trisomy 13.


title: chorion villus cells_normalkaryotype_rep3

description: prenatal sample with a normal karyotype


title: Actinomycin D treated A549 human lung cancer cell cultures replicate A

treatment_protocol: A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, actinomycin D (5 ug/mL final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.


title: chorion villus cells_trisomy21_rep2

description: prenatal sample with a trisomy 21


title: amnoicytes_trisomy21_rep3

description: amniocytes trisomy 21 replicate 3

growth_protocol: Primary cell cultures of the chorion villus cells were performed using slide flasks (with NunclonTM surface, 9 cm2, NUNCTM). Chorionic villi were grown in Amnio Max II Complete Medium (Invitrogen) at 37°C in 5% CO2. The second successive subculture was set up in culture flasks (with CELLSTAR® surface, 25 cm2, Greiner bio-one) using the same medium.


title: amniocyte_normalkaryotype_rep3

description: amniocyte euploid control sample replicate 3

source_name: amniocytes, normal karyotype


title: amniocytes_trisomy21_rep1

description: amniocytes trisomy 21 replicate 1


title: amniocytes_trisomy21_rep2

description: amniocytes trisomy 21 replicate 2


title: chorion villus cells_normalkaryotype_rep2

description: chorion villus cells euploid control sample replicate 2

growth_protocol: Primary cell cultures of the chorion villus cells were performed using slide flasks (with NunclonTM surface, 9 cm2, NUNCTM). Chorionic villi were grown in Amnio Max C100 Basal Medium and Amnio Max C100 Supplement (Invitrogen) at 37°C in 5% CO2. The second successive subculture was set up in culture flasks (with CELLSTAR® surface, 25 cm2, Greiner bio-one) using the same medium.


title: amniocyte_normalkaryotype_rep1

description: amniocyte euploid control sample replicate 1


title: amniocyte_normalkaryotype_rep2

description: amniocyte euploid control sample replicate 2


title: chorion villus cells_normalkaryotype_rep1

description: chorion villus cells euploid control sample replicate 1


title: chorion villus cells_trisomy21_rep1

description: chorion villus cells trisomy 21 replicate 1

growth_protocol: Primary cell cultures of the chorion villus cells were performed using slide flasks (with NunclonTM surface, 9 cm2, NUNCTM). Chorionic villi were grown in Amnio Max C100 Basal Medium and Amnio Max C100 Supplementary Medium (Invitrogen) at 37°C in 5% CO2. The second successive subculture was set up in culture flasks (with CELLSTAR® surface, 25 cm2, Greiner bio-one) using the same medium.

value: 14 gestational weeks


title: control_B3, empty vector

city: Boston

first: Kevin

last: Struhl

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix HG-U133 plus 2.0 GeneChip, washed, and stained according to manufacturer’s instructions.

data_processing: Data were processed by Affymetrix GeneChip Operating Software (GCOS), followed by global median normalization.

source_name: Cervical carcinoma

label_protocol: Total RNA was converted to cDNA using T7-oligo(dT) and in vitro transcribed to obtain biotin-labeled cRNA for hybridization.

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum.

extract_protocol: Trizol (Invitrogen), per manufacturer’s instructions.

treatment_protocol: Cells were transduced with lentiviral supernatant containing pLL p63shRNA or empty vector (control), and harvested ~65 hours later.

value: 66 yrs Gender:Female  Ethnicity:Caucasian


title: p63shRNA_B1, p63-depleted


title: p63shRNA_B2, p63-depleted