title: Colon - 143664

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal Pain
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
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: Thyroid - 143660

status: Public on Jul 07 2006

type: RNA

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

country: USA

institute: IGC

description:
Quality metric = 28S to 18S: 1
Patient Age: 20-30
Gender: Female
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Primary Site: Thyroid
Histology: Follicular adenocarcinoma

molecule: total RNA

organism: Homo sapiens

source_name: Thyroid


title: Pancreas - 143659

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 1
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Exocrine Pancreas
Histology: Ductal adenocarcinoma

source_name: Pancreas


title: Endometrium - 143657

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
Days from Patient Diagnosis to Excision: 60
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Endometrium


title: Breast - 143654

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 180
Prior Therapy: Chemotherapy
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: Yes
Mammogram calcifications?: Yes
Hormonal therapy (# of Years)?: 41-45
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 1
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Breast
Histology: Mucinous Carcinoma

source_name: Breast


title: Kidney - 143658

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 1
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional(clear cell) renal carcinoma

source_name: Kidney


title: Omentum - 143662

description:
Quality metric = 28S to 18S: 1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 3c
Retreatment N: X
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Grade: X
Primary Site: Fallopian Tube
Histology: Metastatic Papillary serous adenocarcinoma

source_name: Omentum


title: Cervix - 135187

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 1b1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B1
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Cervix Uteri
Histology: Endometrioid carcinoma

source_name: Cervix


title: Lung - 138193

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Male
Ethnic Background: Hispanic
Tobacco Use : Yes
Years of Tobacco Use: 51-55
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 40
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma

source_name: Lung


title: Colon - 143650

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 13
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Lung - 138204

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: Yes
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Endometrium - 133677

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Asian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Adenocarcinoma


title: Pancreas - 143661

description:
Quality metric = 28S to 18S: 1.6
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
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 90
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Exocrine Pancreas
Histology: Adenocarcinoma, NOS


title: Endometrium - 133649

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 11
Pathological T: 1c
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: Endometrium
Histology: Endometrioid carcinoma


title: Brain - 133635

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 12
Presenting Symptoms: Headaches
Presenting Symptoms: Memory Problems
Clinical Question: Grade
Clinical Value: WHO Grade IV
Clinical Question: Stage
Clinical Value: No AJCC Staging Scheme for this Site/Histology
Primary Site: Brain
Clinical Question: Histology
Clinical Value: Glioblastoma multiformae

source_name: Brain


title: Colon - 143655

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 28
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Endometrium - 133648

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: 49
Pathological T: 1b
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Breast - 133647

description:
Quality metric = 28S to 18S: 1.1
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: 14
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 0(i-)
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Endometrium - 133632

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Fallopian tube - 129674

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Fallopian tube


title: Omentum - 133672

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Clinical T: 3c
Clinical N: X
Clinical M: 0
Clinical Stage: 3C
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Metastatic Serous Adenocarinoma


title: Lung - 133683

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 17
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma


title: Soft Tissue of Retroperitoneum - 133650

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Female
Ethnic Background: Asian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical Question: Stage
Clinical Value: No AJCC Scheme for this Site/Histology
Primary Site: Soft Tissue of Retroperitoneum
Clinical Question: Histology
Clinical Value: Cellular Schwannoma

source_name: Soft Tissue of Retroperitoneum


title: Breast - 129693

description:
Quality metric = 28S to 18S: 1
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 17
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: 3
Pathological N: 1a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: Endometrium - 129673

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
Pathological T: 2a
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: Endometrium
Histology: Endometrioid carcinoma


title: Breast - 129701

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 30-40
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: 12
Mammogram: Yes
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 21-25
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: Yes
Pathological T: 3
Pathological N: 2a
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Endometrium - 112870

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-90
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 1b
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Breast - 104351

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 10
Mammogram: Yes
Number of years in which a mammogram was obtained?: 21-25
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 11-15
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: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Breast - 112875

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 19
Mammogram: Yes
Number of years in which a mammogram was obtained?: 26-30
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: Yes
Mammogram calcifications?: Yes
Pathological T: 2
Pathological N: 0(i-)
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: Cervix Uteri - 101086

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 30-40
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 3b
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma, keratinizing

source_name: Cervix Uteri


title: Rectum - 152490

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 120
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological Dukes Stage: A
Primary Site: Rectum
Histology: Carcinoma in situ arising in a villous adenoma

source_name: Rectum


title: Rectum - 104340

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 41
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Rectum
Histology: Adenocarcinoma in adenomatous polyp


title: Liver - 144576

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Clinical Question: Grade
Clinical Value: 4
Clinical Question: Multiple Tumors
Clinical Value: No
Clinical Question: Stage
Clinical Value: Insufficient information for staging - Biopsy only
Primary Site: Liver
Clinical Question: Histology
Clinical Value: Hepatocellular carcinoma

source_name: Liver


title: Ileum_Mouse-microbiota-colonized_rep5_9790

city: Chapel Hill

first: John

middle: F

last: Rawls

state: NC

address: 111 Mason Farm Rd.

department: Department of Cell and Molecular Physiology

institute: University of North Carolina at Chapel Hill

description: Ileum of adult mouse colonized for 14 days with a conventional mouse microbiota

data_processing: Raw expression values were normalized using RMA (RMAExpress); Present/absent calls were generated using MAS5.0

label: Biotin

organism: Mus musculus

tag: Strain

value: NMRI,

tag: Age

value: Adult,

tag: Tissue

value: Ileum,

tag: Microbial colonization state

value: colonized with conventional mouse microbiota,

tag: Days post-colonization

tag: Replicate

value: 5 of 5


title: Ileum_Mouse-microbiota-colonized_rep4_9789

source_name: Ileum of adult mouse colonized for 14 days with a conventional mouse microbiota

value: 4 of 5


title: Ileum_Zebrafish-microbiota-colonized_rep3_9793

source_name: Ileum of adult mouse colonized for 14 days with a conventional zebrafish microbiota

value: colonized with conventional zebrafish microbiota,

value: 3 of 3


title: Ileum_Zebrafish-microbiota-colonized_rep2_9792

value: 2 of 3


title: Ileum_Zebrafish-microbiota-colonized_rep1_9791

value: 1 of 3


title: Ileum_Mouse-microbiota-colonized_rep2_9787

value: 2 of 5


title: Ileum_Germ-free_rep2_9772

description: Ileum of adult germ-free mouse

source_name: Ileum of adult germ-free mouse

value: Germ-free,

value: N/A,


title: Ileum_PA01-colonized_rep1_9776

description: Ileum of adult mouse colonized for 14 days with P. aeruginosa PA01

value: colonized with Pseudomonas aeruginosa PAO1,

value: 1 of 5


title: Ileum_PA01-colonized_rep2_9777

source_name: Ileum of adult mouse colonized for 14 days with P. aeruginosa PA01


title: Ileum_PA01-colonized_rep3_9778

value: 3 of 5


title: Ileum_Germ-free_rep4_9774

description: Ileum of adult germ-free mouse


title: Ileum_PA01-colonized_rep5_9780


title: Ileum_PA01-colonized_rep4_9779


title: Ileum_Germ-free_rep5_9775

description: Ileum of adult germ-free mouse


title: Ngn3 ES3 ON replicate 2

status: Public on Jul 01 2006

city: Morristown

first: Nathan

middle: R

last: Treff

state: NJ

address: 111 Madison Ave

department: Molecular Biology

institute: RMA of NJ

description: 16 embryonic stem cell (ESC) samples (8 groups in duplicate) were processed for microarray analysis using the Affymetrix Mouse Genome 430 2.0 GeneChip.  The samples included the parental Ainv15 ESC line (1) undifferentiated (Ainv15 ESC), (2) differentiated for 3 days as embryoid bodies (Ainv15 EB3) or (3) for 10 days as embryoid bodies (Ainv15 EB10).  The remaining samples included tetracycline inducible Ngn3 ESC line derived from the parental Ainv15 ESC line (4) after differentiation and addition of doxycycline for 3 days without embryoid body formation (Ngn3 ES3 ON), (5 and 6) after differentiation as embryoid bodies for 3 days with (Ngn3 EB3 ON) or without (Ngn3 EB3 OFF) doxycycline, and (7 and 8) after differentiation as embryoid bodies for 10 days with (Ngn3 EB10 ON) or without (Ngn3 EB10 OFF) doxycycline.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Stratagene ArrayAssist GCRMA Normalization

label: biotin

source_name: tetracycline inducible Ngn3 ESC differentiated for 3 days without feeder cells or LIF and with doxycycline

label_protocol: 10ug total RNA

extract_protocol: TRIzol extraction, RNeasy column purification


title: Ainv15 EB3 replicate 2

source_name: parental Ainv15 ESC differentiated as EB for 3 days


title: Ileum_Germ-free_rep3_9773

description: Ileum of adult germ-free mouse


title: Ileum_Mouse-microbiota-colonized_rep3_9788


title: Ngn3 EB10 OFF replicate 2

source_name: tetracycline inducible Ngn3 ESC differentiated for 10 days as EB without doxycycline


title: Ileum_Germ-free_rep1_9771

description: Ileum of adult germ-free mouse


title: Ngn3 EB10 OFF replicate 1

tag: tetracycline inducible Ngn3 ESC differentiated for 10 days as EB without doxycycline


title: Ngn3 ES3 ON replicate 1

tag: tetracycline inducible Ngn3 ESC differentiated for 3 days without feeder cells or LIF and with doxycycline


title: Ainv15 EB3 replicate 1

tag: parental Ainv15 ESC differentiated as EB for 3 days


title: Ileum_Mouse-microbiota-colonized_rep1_9786


title: Ngn3 EB10 ON replicate 1

source_name: tetracycline inducible Ngn3 ESC differentiated for 10 days as EB with doxycycline for 3 days


title: Ngn3 EB3 ON replicate 2

source_name: tetracycline inducible Ngn3 ESC differentiated for 3 days as EB with doxycycline


title: Ngn3 EB3 OFF replicate 2

source_name: tetracycline inducible Ngn3 ESC differentiated for 3 days as EB without doxycycline


title: Ngn3 EB3 ON replicate 1

tag: tetracycline inducible Ngn3 ESC differentiated for 3 days as EB with doxycycline


title: Ngn3 EB3 OFF replicate 1

tag: tetracycline inducible Ngn3 ESC differentiated for 3 days as EB without doxycycline


title: Rectosigmoid - 144558

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

source_name: Rectosigmoid


title: Ainv15 EB10 replicate 1

source_name: parental Ainv15 ESC differentiated as EB for 10 days


title: Ainv15 EB10 replicate 2

tag: parental Ainv15 ESC differentiated as EB for 10 days


title: Ainv15 ES0 replicate 2

source_name: parental Ainv15 undifferentiated ESC

tag: parental Ainv15 undifferentiated ESC


title: thyroid_tumor_7

status: Public on Jun 30 2006

city: Valhalla

first: Ismael

last: Reyes

state: NY

address: Microbiology department BSB room 311

institute: New York Medical College

description: papillary thyroid carcinoma tissue

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: dChip v 1.3 was used for normalization, model-based gene expression estimatation and outlier detection ; Affymetrix Microarray Suite version 5.0 was used to calculate the present call of each transcript

source_name: human thyroid

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

tag: thyroid sample containing tumor cells


title: thyroid_tumor_2

description: papillary thyroid carcinoma tissue


title: thyroid_normal_3

description: normal thyroid tissue extracted adyacent to tumor tissue

tag: thyroid sample containing normal cells


title: thyroid_normal_6


title: thyroid_normal_5


title: thyroid_tumor_4

description: papillary thyroid carcinoma tissue


title: thyroid_tumor_1

description: papillary thyroid carcinoma tissue


title: thyroid_tumor_5

description: papillary thyroid carcinoma tissue


title: thyroid_tumor_6

description: papillary thyroid carcinoma tissue


title: Conventionalized Paneth cell 1

status: Public on Jun 28 2006

city: Dallas

first: Lora

middle: V

last: Hooper

state: TX

address: 5323 Harry Hines Blvd.

department: Immunology

institute: The University of Texas Southwestern Medical Center at Dallas

description: Laser capture microdissected Paneth cell from conventionalized NMRI mice

data_processing: Affymetrix GeneChip software; arrays were scaled to a target intensity of 500

source_name: laser capture microdissected Paneth cell from mouse

label_protocol: RNAs from three mice were pooled in equal amounts. Duplicate 10 ng RNA aliquots were amplified for each condition using the Arcturus RiboAmp HS kit. Biotinylated cRNAs were generated by substituting the Enzo T7 BioArray Transcript Kit during the last step.

extract_protocol: Total RNA was prepared from captured cells (harvested from 3 mice per group) using the Arcturus PicoPure RNA isolation kit, and was quantitated using the RiboGreen RNA quantitation reagent (Invitrogen).

treatment_protocol: Germ-free mice were conventionalized for 10 days with an intestinal microflora recovered from a conventionally-raised mouse. Small intestines were snap frozen in OCT and sectioned for laser capture microdissection. Paneth cells were isolated from small intestine by laser capture microdissection.

value: NMRI, sex:Male, age:8 weeks, colonization status:conventionalized (10 days), Tissue:laser capture microdissected Paneth cell


title: Conventionalized Paneth cell 2


title: Ainv15 ES0 replicate 1


title: Germfree Paneth cell 1

description: Laser capture microdissected Paneth cell from germ-free NMRI mice

treatment_protocol: Mice were maintained under germ-free conditions until sacrifice. Small intestines were snap frozen in OCT and sectioned for laser capture microdissection. Paneth cells were isolated from small intestine by laser capture microdissection.

value: NMRI, sex:Male, age:8 weeks, colonization status:germ-free, Tissue:laser capture microdissected Paneth cell


title: thyroid_normal_2


title: thyroid_normal_1


title: Germfree Paneth cell 2


title: thyroid_tumor_3

description: papillary thyroid carcinoma tissue


title: Breast - 112876

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Family History of Cancer?: Yes
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 21-25
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: CD rep 3

status: Public on Jun 15 2006

city: Davis

first: Sailaja

last: Peddada

state: CA

address: 3426 Tupper Hall, One Shields Avenue

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from experimental treatment D-CD = Differentiated and control decoy transfected cells.

hyb_protocol: Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C  in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.

data_processing: The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.

source_name: SH-SY5Y neuronal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).

tag: SH-SY5Y neuroblastoma cells obtained from ATCC.

tag: differentiated and control decoy transfected SH-SY5Y cells


title: MD rep 1

description: Gene expression data from experimental treatment D-MD = differentiated and MeCP2 decoy transfected cells.

tag: differentiated and MeCP2 decoy transfected SH-SY5Y cells


title: CD rep 2


title: thyroid_normal_7


title: MD rep 3


title: UT rep 3

description: Gene expression data from experimental treatment D-UT = 48h after PMA induced differentiated SH-SY5Y cells.

tag: 48h after PMA addition


title: MD rep 2


title: UD rep 3

description: Gene expression data from experimental treatment UD = Undifferentiated SH-SY5Y cells, i.e. before PMA induced differentiation (UD).

tag: UD -Undifferentiated cells (before PMA addition).


title: UT rep 2


title: CD rep 1


title: UT rep 1


title: Ngn3 EB10 ON replicate 2

tag: tetracycline inducible Ngn3 ESC differentiated for 10 days as EB with doxycycline for 3 days


title: NIH3T3_7h_FGF_U0126_exp1

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h. U0126 (20 uM) was added 30 min before stimulation.

data_processing: MAS 5.0, scaled to 500

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: RNeasy total RNA extraction protocol (Qiagen)


title: NIH3T3_4h_FGF_U0126_exp2

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h. U0126 (20 uM) was added 30 min before stimulation.


title: GM15850 patient cells treated with FA2 at 2uM 2

status: Public on Jun 14 2006

city: La Jolla

first: Ryan

middle: Stephen

last: Burnett

address: 10550 N. Torrey Pines Road, MB-27

institute: The Scripps Research Institute

description: Normal and patient cells were treated with pyrrole-imidazole made to target GAA repeats.

data_processing: RMAExpress and BRBArraytools

label: Caltech core facility labeled

tag: GM15850 patient cells treated with FA2 at 2uM.


title: NIH3T3_4h_FGF_exp1

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h.

source_name: NIH3T3, FGF 4 h


title: NIH3T3_7h_FGF_U0126_1h_exp1

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h. U0126 (20 uM) was added 1 h after stimulation.

source_name: NIH3T3, FGF 7 h + U0126 at + 1 h


title: NIH3T3_4h_FGF_U0126_exp1


title: NIH3T3_12h_FGF_U0126_exp1

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h. U0126 (20 uM) was added 30 min before stimulation.


title: NIH3T3_0h_exp2

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum.

source_name: NIH3T3, 0 h


title: NIH3T3_7h_FGF_U0126_exp2


title: NIH3T3_0h_exp1_rep1


title: NIH3T3_12h_FGF_exp1

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h.

source_name: NIH3T3, FGF 12 h


title: NIH3T3_12h_FGF_exp2


title: NIH3T3_12h_FGF_U0126_7h_exp1

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h. U0126 (20 uM) was added 7 h after stimulation.

source_name: NIH3T3, FGF 12 h + U0126 at + 7 h


title: NIH3T3_12h_FGF_U0126_exp2


title: NIH3T3_1h_FGF_U0126_exp1

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 1 h. U0126 (20 uM) was added 30 min before stimulation.


title: NIH3T3_7h_FGF_exp2

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h.

source_name: NIH3T3, FGF 7 h


title: NIH3T3_7h_FGF_exp1


title: NIH3T3_1h_FGF_exp1

description: NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 1 h.

source_name: NIH3T3, FGF 1 h


title: GM15850 patient cells treated with FA2 at 2uM 3


title: NIH3T3_0h_exp1_rep2


title: UD rep 2


title: NIH3T3_4h_FGF_exp2


title: UD rep 1


title: thyroid_normal_4

description: normal thyroid tissue extracted adyacent to tumor tissue


title: GM15850 patient cells treated with FA2 at 2uM 1


title: GM15850 patient cells treated with FA1 at 1uM 3

tag: GM15850 patient cells treated with FA1 at 1uM.


title: GM15850 patient cells treated with FA1 at 1uM 2


title: GM15850 patient cells untreated 3

tag: GM15850 patient cells untreated


title: GM15851 control cells treated with FA2 at 2uM 1

tag: GM15851 control cells treated with FA2 at 2uM.


title: GM15850 patient cells untreated 2


title: GM15850 patient cells treated with FA1 at 1uM 1


title: GM15850 patient cells untreated 1


title: GM15851 control cells treated with FA1 at 2uM 2

tag: GM15851 control cells treated with FA1 at 2uM.


title: GM15851 control cells treated with FA1 at 1uM 2

tag: GM15851 control cells treated with FA1 at 1uM.


title: GM15851 control cells treated with FA1 at 2uM 1


title: GM15851 control cells treated with FA2 at 2uM 2


title: GM15851 control cells treated with FA1 at 1uM 1


title: GM15851 control cells untreated 3

tag: GM15851 control cells untreated


title: GM15851 control cells untreated 2


title: GM15851 control cells treated with FA2 at 2uM 3


title: GM15851 control cells untreated 1


title: GM15850 patient cells treated with FA1 at 2uM 2

tag: GM15850 patient cells treated with FA1 at 2uM.


title: GM15850 patient cells treated with FA1 at 2uM 3


title: GM15850 patient cells treated with FA1 at 2uM 1


title: spinal cord, ventral spinal cord: D28WTMN2_e1_le1

status: Public on Jun 09 2006

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

description: Motor neurons obtained from a wild type mouse by laser capture microdissection.

source_name: spinal cord, ventral spinal cord


title: spinal cord, ventral spinal cord: D28SDMN1_e1_le1

description: Motor neurons obtained from a SOD1 mutant mouse by laser capture microdissection.


title: spinal cord, ventral spinal cord: D28WTSP3_e1_le1

description: total spinal cord from a wild type mouse.


title: spinal cord, ventral spinal cord: D28WTMN1_e1_le1


title: brain, brainstem: D60WTFNMN3_e1_le1

description:
Motor neurons from the facial nucleus of  wildtype mice
Treatment, type=linear_amplification, description=T7-based RNA amplification

source_name: brain, brainstem


title: spinal cord, ventral spinal cord: D28SDMN2_e1_le1


title: spinal cord, ventral spinal cord: D28WTSP1 e1 le1


title: brain, brainstem: D60SODFNMN1_e1_le1

description:
Motor neurons from the facial nucleus of  SOD1 mutant  mice
Treatment, type=linear_amplification, description=T7-based RNA amplification


title: spinal cord, ventral spinal cord: D28WTSP2 e1_le1


title: brain, brainstem: D60SODFNMN2_e1_le1


title: spinal cord, ventral spinal cord: D60SODSPMN3_e1_le1

description:
Motor neurons from the spinal cord of  SOD1 mutant  mice
Treatment, type=linear_amplification, description=T7-based RNA amplification


title: brain, brainstem: D60SODFNMN3_e1_le1


title: spinal cord, ventral spinal cord: D60WTSPMN2_e1_le1

description:
Motor neurons from the spinal cord of  wildtype mice
Treatment, type=linear_amplification, description=T7-based RNA amplification


title: brain, brainstem: D60WTFNMN2_e1_le1


title: spinal cord, ventral spinal cord: D28WTMN3_e1_le1


title: spinal cord, ventral spinal cord: D28SDMN3_e1_le1


title: brain, brainstem: D60WTFNMN1_e1_le1


title: spinal cord, ventral spinal cord: D60WTSP3_e1_le1

description:
Spinal cord tissue from wildtype mice
Treatment, type=linear_amplification, description=T7-based RNA amplification


title: spinal cord, ventral spinal cord: D60WTSP1_e1_le1


title: spinal cord, ventral spinal cord: D60SODSPMN2_e1_le1


title: spinal cord, ventral spinal cord: D60WTSPMN1_e1_le1


title: spinal cord, ventral spinal cord: D60SODSP3_e1_le1

description:
Spinal cord tissue from SOD1 mutant  mice
Treatment, type=linear_amplification, description=T7-based RNA amplification


title: spinal cord, ventral spinal cord: D60SODSP1_e1_le1


title: spinal cord, ventral spinal cord: D60SODSP2_e1_le1


title: spinal cord, ventral spinal cord: D60WTSP2_e1_le1


title: spinal cord, ventral spinal cord: D60SODSPMN1_e1_le1


title: spinal cord, ventral spinal cord: D60WTSPMN3_e1_le1


title: brain, hindbrain and spinal cord: R1 aRNA

description: aRNA probe from T7-based amplification

source_name: brain, hindbrain and spinal cord


title: brain, hindbrain and spinal cord: R0 aRNA

description: aRNA probe from T7-based amplification


title: brain, hindbrain and spinal cord: P0WT2_e1_le1

description:
Total RNA from brain sample of wild type mice at P0
Treatment, type=purify, measurement=0.0 years


title: brain, hindbrain and spinal cord: P5WT1_e1_le1

description:
Total RNA from brain sample of wild type mice at P5.
Treatment, type=purify, measurement=0.0 years


title: brain, hindbrain and spinal cord: P5WT3_e1_le1


title: brain, hindbrain and spinal cord: N1 cDNA

description: amplified by Nugen kit


title: brain, hindbrain and spinal cord: P5KO3_e1_le1

description:
Total RNA from brain sample of NR3B knockout mice at P5.
Treatment, type=purify, measurement=0.0 years


title: brain, hindbrain and spinal cord: P5KO1_e1_le1


title: brain, hindbrain and spinal cord: P0WT1_e1_le1

description:
Total RNA from brain sample of wild type mice at P0.
Treatment, type=purify, measurement=0.0 years


title: brain, hindbrain and spinal cord: P0KO3_e1_le1

description:
Total RNA from brain sample of NR3B knockout mice at P0.
Treatment, type=purify, measurement=0.0 years


title: brain, hindbrain and spinal cord: P5WT2_e1_le1


title: brain, hindbrain and spinal cord: P0WT3_e1_le1


title: brain, hindbrain and spinal cord: P0KO1_e1_le1


title: brain, hindbrain and spinal cord: P5KO2_e1_le1


title: brain, unknown: Sample64_e1_le1

status: Public on Jun 06 2006

description:
Meningioma Recurrent Grade 3
Treatment, type=harvest, description=There is no treatment.  Tumors were flash frozen in liquid nitrogen within 1 minute of removal.  Recurrent tumor grade 3.

source_name: brain, unknown


title: brain, unknown: Sample63_e1_le1

description:
Meningioma Primary Grade 3
Treatment, type=harvest, description=There was no treatment.  Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal.  Meningioma Primary Grade 2.


title: brain, unknown: Sample47_e1_le1

description:
Meningioma Primary Grade 1
Treatment, type=harvest, description=There was no treatment.  Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal.


title: brain, hindbrain and spinal cord: P0KO2_e1_le1


title: brain, unknown: 00ZP_e1_le2

description:
Meningioma Primary Grade 1
Treatment, type=harvest, description=There was no treatment.  Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal.  Meningioma Primary Grade 1.


title: brain, unknown: Sample61_e1_le1

description:
Meningioma Primary Grade 2
Treatment, type=harvest, description=There was no treatment.  Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal.  Meningioma Primary Grade 2.


title: brain, unknown: Sample55_e1_le1


title: brain, unknown: Sample49_e1_le1


title: brain, unknown: Sample43_e1_le1


title: brain, unknown: Sample60_e1_le1


title: brain, unknown: Sample57_e1_le1


title: brain, unknown: Sample58_e1_le1


title: brain, hindbrain and spinal cord: N0 cDNA

description: cDNA probe amplified by Nugen kit


title: brain, unknown: Sample59_e1_le1


title: GM15851 control cells treated with FA1 at 1uM 3

description: Normal and patient cells were treated with pyrrole-imidazole made to target GAA repeats.


title: brain, unknown: Sample56_e1_le1


title: brain, unknown: 04JZ_e1_le1

description:
Meningioma Recurrent Grade 1
Treatment, type=harvest, description=There is no treatment.  Tumors were flash frozen in liquid nitrogen within 1 minute of removal.


title: brain, unknown: Sample46_e1_le1


title: brain, unknown: 00ME_e1_le1

description: Meningioma Primary Grade 1


title: brain, unknown: Sample53_e1_le1


title: brain, unknown: Sample51_e1_le1


title: brain, unknown: 00HN_e1_le1

description: Meningioma Primary Grade 1


title: brain, unknown: Sample42_e1_le1


title: brain, unknown: 03CU_e1_le1

description:
Meningioma Primary Grade 2
Treatment, type=harvest, description=There was no treatment.  Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal.


title: brain, unknown: Sample45_e1_le1


title: brain, unknown: 04HM_e1_le1

description: Meningioma Primary Grade 1


title: brain, unknown: 00YZ_e1_le1


title: brain, unknown: 03DO_e1_le1

description: Meningioma


title: brain, unknown: Sample50_e1_le1


title: brain, unknown: 00UO_e1_le1


title: brain, unknown: Sample52_e1_le1


title: brain, unknown: 00DLR_e1_le1


title: brain, unknown: Sample48_e1_le1

description:
Meningioma Recurrent Grade 1
Treatment, type=harvest, description=There was no treatment.  Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal.


title: brain, unknown: Sample62_e1_le1

description:
Meningioma Recurrent Grade 2
Treatment, type=harvest, description=There was no treatment.  Tissue/cells must be flash frozen in liquid nitrogen within 1 minute of removal.  Meningioma Primary Grade 2.


title: brain, unknown: 00BFR_e1_le1


title: brain, unknown: 4222-99_e1_le1


title: brain, unknown: 00ZP_e1_le1


title: brain, unknown: 03EH_e1_le1


title: brain, unknown: 03DD_e1_le1


title: brain, unknown: 03DM_e1_le1


title: brain, unknown: 00BD_e1_le1


title: brain, unknown: 03BV_e1_le1


title: brain, unknown: Sample44_e1_le1


title: brain, unknown: 00JO_e1_le1

description: Meningioma Primary Grade 1


title: brain, unknown: 00PXR_e1_le1


title: brain, unknown: 00SI_e1_le1

description: Meningioma Primary Grade 1


title: brain, unknown: 5238-99_e1_le1


title: brain, unknown: 5634-99_e1_le1


title: brain, unknown: 03BY_e1_le1


title: brain, unknown: 13786-00_e1_le1


title: brain, unknown: 2292-99_e1_le1


title: brain, unknown: 3090-00_e1_le1


title: brain, unknown: 9708-99_e1_le1


title: brain, unknown: 03CQ_e1_le1


title: brain, unknown: 14897-98_e1_le1


title: brain, unknown: 03CX_e1_le1


title: brain, unknown: 03BI_e1_le1


title: brain, unknown: 3317-99_e1_le1


title: brain, unknown: R2A_e1_le1

description:
rotenone 2 weeks A
Treatment, type=time_course, measurement=2.0 weeks


title: brain, unknown: R1A_e1_le1

description:
rotenone 1 week A
Treatment, type=time_course, measurement=1.0 weeks


title: brain, unknown: 03DE_e1_le1


title: brain, unknown: C4B_e1_le1

description:
control 4 weeks B
Treatment, type=time_course, measurement=4.0 weeks


title: brain, unknown: R2A_e1_le2


title: brain, unknown: R4B_e1_le1

description:
rotenone 4 weeks C
Treatment, type=time_course, measurement=4.0 weeks


title: brain, unknown: C4C_e1_le1

description:
control 4 weeks C
Treatment, type=time_course, measurement=4.0 weeks


title: brain, unknown: C2B_e1_le1

description:
control 2 weeks B
Treatment, type=time_course, measurement=2.0 weeks


title: brain, unknown: R4A_e1_le1

description:
rotenone 4 weeks A
Treatment, type=time_course, measurement=4.0 weeks


title: brain, unknown: 03CA_e1_le1


title: brain, unknown: R2C_e1_le1

description:
rotenone 2 weeks C
Treatment, type=time_course, measurement=2.0 weeks


title: brain, unknown: C1C_e1_le1

description:
control 1 week C
Treatment, type=time_course, measurement=1.0 weeks


title: brain, unknown: R1C_e1_le1

description:
rotenone 1 week C
Treatment, type=time_course, measurement=1.0 weeks


title: brain, unknown: C4A_e1_le1

description:
control 4 weeks
Treatment, type=time_course, measurement=4.0 weeks


title: brain, unknown: R1B_e1_le1

description:
rotenone 1 week B
Treatment, type=time_course, measurement=1.0 weeks


title: brain, unknown: UTA_e1_le1

description:
untreated A
Treatment, type=time_course, measurement=1.0 weeks


title: brain, unknown: C2A_e1_le1

description:
control 2 weeks A
Treatment, type=time_course, measurement=2.0 weeks


title: brain, unknown: C1B_e1_le1

description:
control 1 week B
Treatment, type=time_course, measurement=1.0 weeks


title: brain, unknown: R4C_e1_le1


title: brain, unknown: C2C_e1_le1

description:
control 2 weeks C
Treatment, type=time_course, measurement=2.0 weeks


title: brain, unknown: UTB_e1_le1

description:
untreated B
Treatment, type=time_course, measurement=1.0 weeks


title: brain, unknown: UTC_e1_le1

description:
untreated C
Treatment, type=time_course, measurement=1.0 weeks


title: Bone marrow, Mesenchymal stem cells: T1-210404_e1_le1

description: Sample 1 at Time 1

source_name: Bone marrow, Mesenchymal stem cells


title: E10.5 craniofacial tissue, first branchial arch: WT_MXA2-2_e1_le1

description:
We will separately dissect the maxillary and mandibular branches of the E10.5 first branchial arch from wild type, dlx2, dlx1/2 and Dlx5/6 mutants. The tissues wil be flash frozen within 1 min of removal.We have not performed the dissections yet so we dont know how much RNA will be get from each sample, but previous experience suggests that we will need ~10 branchial arches/experiment.
Treatment, type=nucleic_acid_extraction, description=We anticipate using this method as it was recommended by TGEN for small amounts of tissue.


title: E10.5 craniofacial tissue, first branchial arch: WT_MXA-3_e1_le1


title: Bone marrow, Mesenchymal stem cells: T2-1-101103_e1_le1

description: Sample 2 at Time 2


title: Bone marrow, Mesenchymal stem cells: T2-2-101103_e1_le1

description: Sample 2 at Time 2


title: E10.5 craniofacial tissue, first branchial arch: WT_MNA-2_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: WT_MXA-1_e1_le1


title: Bone marrow, Mesenchymal stem cells: T3-2-101103_e1_le1

description: Sample 3 at Time 3


title: Bone marrow, Mesenchymal stem cells: T4-1-101103_e1_le1

description: Sample 4 at Time 4


title: E10.5 craniofacial tissue, first branchial arch: WT_MXA-2_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: WT_MNA-1_e1_le1


title: Bone marrow, Mesenchymal stem cells: T4-2-101103_e1_le1

description: Sample 4 at Time 4


title: Bone marrow, Mesenchymal stem cells: T3-101103_e1_le1

description: Sample 3 at Time 3


title: E10.5 craniofacial tissue, first branchial arch: WT_MXA2-3_e1_le1


title: Bone marrow, Mesenchymal stem cells: T3-1-101103_e1_le1

description: Sample 3 at Time 3


title: E10.5 craniofacial tissue, first branchial arch: KO_MXA-3_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: KO_MXA-1_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: 5_6_MNA-3_e1_le1


title: Bone marrow, Mesenchymal stem cells: T1-181203_e1_le1

description: Sample 1 at Time 1


title: E10.5 craniofacial tissue, first branchial arch: WT_MNA-3_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: KO_MXA-2_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: 5_6_MNA-2_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: 5_6_MNA-1_e1_le1


title: E10.5 craniofacial tissue, first branchial arch: WT_MXA2-1_e1_le1


title: Col-LUC_WT_no treatment_Rep4

status: Public on Jun 01 2006

city: Riverside

first: Jian-Kang

last: Zhu

address: 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: University of California

description: Target value (TGT value) was set to 500 global scaling.

hyb_protocol: Followed users manual: http://www.affymetrix.com/support/downloads/manuals/expression_s21_manual.pdf

data_processing: Microaray data were extracted from scanned GeneChip images and analyzed by use of Microarray Suite version 5.0.1

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: The wild-type and sta1 mutant seeds were plated on MS agar plates supplemented with 3% sucrose. Seedlings were grown at 22C with 16h light and 8h dark cycles for 2 weeks before being harvested.

extract_protocol: RNeasy Plant Mini Kit, Qiagen

treatment_protocol: No treatment.

tag: Columbia ecotype containing RD29A promoter-driven luciferase transgene.


title: Col-LUC_WT_no treatment_Rep3

scan_protocol: Followed users manual: http://www.affymetrix.com/support/downloads/manuals/expression_s21_manual.pdf


title: Col-LUC_WT_no treatment_Rep2

label_protocol: Followed users manual: http://www.affymetrix.com/support/downloads/manuals/expression_s21_manual.pdf

treatment_protocol: No Treatment


title: sta1_no treatement_Rep2

data_processing: Microarray data were extracted from scanned GeneChip images and analyzed by use of Microarray Suite version 5.0.1

growth_protocol: The wild-type and ice1 mutant seeds were plated on MS agar plates supplemented with 3% sucrose. Seedlings were grown at 22C with 16-h light and 8-h dark cycles for 2 weeks before being treated.

treatment_protocol: No treatment

tag: STA1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover and stress tolerance in Arabidopsis


title: C24-LUC_WT_no treatment_Rep5

tag: C24 ecotype containing RD29A promoter-driven luciferase transgene.


title: Bone marrow, Mesenchymal stem cells: T5-181203_e1_le1

description: Sample 5 at Time 5


title: TH_GFP2

status: Public on May 30 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

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.

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: stimulated with irradiated  allogenic EBV B-cells

extract_protocol: Qiagen, RNAeasy

tag: genetic modification

value: alloreactive TH cells were transduced using pMSCV-based retroviral vector encoding an IRES-driven GFP

tag: tissue

value: T-cells


title: TH_UBD2

value: alloreactive TH cells were transduced using pMSCV-based retroviral vector encoding the human UBD coupled to an IRES-driven GFP


title: TH_UBD1


title: Col-LUC_WT_no treatment_Rep1

growth_protocol: The wild-type and sta1 mutant seeds were plated on MS agar plates supplemented with 3% sucrose.  Seedlings were grown at 22C with 16h light and 8h dark cycles for 2 weeks before being harvested.


title: Acromegaly case A20

status: Public on May 26 2006

city: Helsinki

first: Antti

last: Kokko

address: POBOX 63 (Haartmaninkatu 8)

department: Dept of Medical Genetics

country: Finland

institute: University of Helsinki

description: peripheral blood

data_processing: Affymetrix GeneChip® Operating Software (GCOS)

source_name: blood

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

extract_protocol: Total RNA extracted from whole blood with PAXgene Blood RNA Kit (PreAnalytiX) and concentrated with RNeasy MinElute Cleanup columns (Qiagen).

tag: peripheral blood


title: Acromegaly case A16

description: peripheral blood


title: sta1_no treatement_Rep1

source_name: Seedllings


title: endometrium 619

status: Public on May 24 2006

city: San Francisco

first: Said

last: Talbi

address: 500 Parnassus

institute: UCSF

description: Gene expression data from normal human endometrium specimen in proliferative phase.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG 133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner HR3000.

data_processing: The data were analyzed with Gene Chip Operating System GCOS version 1.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: uterus

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

tag: Late secretory phase LSE

tag: Age

value: 44 Diagnostics:Leiomyomata (TAH) Caucasian


title: Acromegaly case A8

description: peripheral blood


title: Acromegaly case A22

description: peripheral blood


title: Acromegaly control C7

description: peripheral blood


title: Acromegaly control C8

description: peripheral blood


title: TH_GFP1

value: alloreactive TH cells were transduced using pMSCV-based retroviral vector encoding  IRES-driven GFP


title: Acromegaly control C9

description: peripheral blood


title: Acromegaly case A2

description: peripheral blood


title: endometrium 449

value: 39 Diagnostics:Leiomyomata (LAVH) Caucasian


title: endometrium 462

value: 39 Diagnostics:Leiomyomata (TAH) Asian


title: Acromegaly control C1

description: peripheral blood


title: Acromegaly control C4

description: peripheral blood


title: endometrium 614

value: 43 Diagnostics:TVH for uterine prolapse Other Detrol LA


title: Acromegaly case A18

description: peripheral blood


title: endometrium 407

tag: Ambiguous histology reading

value: 43 Diagnostics:Leiomyomata (LAVH3TAH) Black None/secretorya


title: endometrium 576

value: 41 Diagnostics:Right ovarian cyst, endometrial biopsy, Unknown ethnicity


title: Acromegaly case A21

description: peripheral blood


title: Acromegaly case A14

description: peripheral blood


title: Acromegaly case A6

description: peripheral blood


title: endometrium 442

value: 43 Diagnostics:Leiomyomata; adenomyosis (TAH) Black Astelin, flonase


title: Acromegaly control C3

description: peripheral blood


title: endometrium 648

value: 45 Diagnostics:Leiomyomata (SCH) Caucasian Lexapro, ambion/MSE, LSEb


title: endometrium 494

value: 45 Diagnostics:Leiomyomata (TAH) Black Norvasc, HCTZ/MSE, uncertainb


title: endometrium 659

tag: Mid secretory phase MSE

value: 46 Diagnostics:TVH for uterine prolapse/SUI Caucasian


title: endometrium 650

tag: Early secretory phase ESE

value: 48 Diagnostics:Leiomyomata (TAH) Caucasian


title: endometrium 626

value: 42 Diagnostics:TVH for uterine prolapse Caucasian Allegra, advil


title: endometrium M163

value: 33 Diagnostics:Pipelle endometrial biopsy-nml volunteer Caucasian


title: endometrium M153

value: 34 Diagnostics:Pipelle endometrial biopsy-nml volunteer Caucasian


title: endometrium M158

value: 23 Diagnostics:Pipelle endometrial biopsy-nml volunteer Black


title: endometrium 610

value: 49 Diagnostics:Leiomyomata (LAVH no endo) Caucasian


title: endometrium G98A

value: 30 Diagnostics:Pipelle endometrial biopsy-nml volunteer Caucasian


title: endometrium 598

tag: Proliferative phase PE

value: 33 Diagnostics:Leiomyomata (TAH)


title: endometrium M165

value: 31 Diagnostics:Pipelle endometrial biopsy-nml volunteer Caucasian


title: endometrium 642

value: 48 Diagnostics:Atrophic/no hormone/leiomyomata (SCH) Caucasian OCP/atrophicb


title: endometrium M169

value: 32 Diagnostics:Pipelle endometrial biopsy-nml volunteer Caucasian


title: endometrium M182


title: endometrium 617

value: 42 Diagnostics:Pelvic pain (no endo at laparoscopy) TVH/TAH Caucasian


title: endometrium 629

value: 46 Diagnostics:Leiomyomata (SCH) Caucasian Celexa


title: endometrium 389

value: 41 Diagnostics:Leiomyomata (TAH) Caucasian None/uncertaina


title: endometrium 664

value: 44 Diagnostics:TVH for uterine prolapse; adenomyosis Other


title: endometrium 421

value: 37 Diagnostics:Adenomyosis (TAH) Black Ranitidine, tramadol/uncertaina


title: Gaido_Testes_gd11_17_14Dec2005

status: Public on May 12 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: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2184

hyb_protocol: Affymetrix standard protocol (701021 Rev 4) Amount labeled  target hybridization to array: 10 ug

data_processing: Analysis method: Affymetrix GCOS and SAS Microarray Solutions GCOS Tgt value: 500

source_name: testes

extract_protocol: Gaido protocol: 'RNA isolation from whole testes'

treatment_protocol:
pool size: 2
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design:  CD-1 mice are time-mated within a 2 hour window.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal gonads are removed from fetuses at gestation days 11, 12, 14, 16, 18, and postnatal day 2, snap frozen in liquid nitrogen and stored at -80ºC.

tag: gene reported

value: wild-type

tag: strain

tag: Sex

value: Male

tag: developmental stage

value: gd 11

tag: theiler stage

tag: somite count

tag: developmental landmark


title: Gaido_Testes_gd11_20_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2187


title: Gaido_Testes_gd14_11_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2178

treatment_protocol:
pool size: NA
Pooled sample: No
Dissection Method: Whole organ excision
Experimental Design:  CD-1 mice are time-mated within a 2 hour window.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal gonads are removed from fetuses at gestation days 11, 12, 14, 16, 18, and postnatal day 2, snap frozen in liquid nitrogen and stored at -80ºC.

value: gd 14


title: Gaido_Testes_gd11_18_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2185


title: Gaido_Testes_gd11_19_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2186


title: Gaido_Testes_gd14_12_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2179


title: Gaido_Testes_gd12_13_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2180

treatment_protocol:
pool size: 5
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design:  CD-1 mice are time-mated within a 2 hour window.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal gonads are removed from fetuses at gestation days 11, 12, 14, 16, 18, and postnatal day 2, snap frozen in liquid nitrogen and stored at -80ºC.

value: gd 12


title: Gaido_Testes_gd11_16_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2183


title: Gaido_WholeLitterReference_pnd0.5_21_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2188

treatment_protocol:
pool size: 8 whole embryos (4 male & 4 female)
Pooled sample: Yes
Dissection Method: NA
Experimental Design: P0.5 whole embryo RNA (4 male & 4 female) provided by Steve Potter.  This sample represents the universal standard for cross comparison of microarray data.

tag: strain:

value: Both (male & female)

value: pnd 0.5


title: Gaido_Testes_gd12_15_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2182


title: Gaido_Testes_gd12_14_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2181


title: Gaido_Testes_gd16_9_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2176

value: gd 16


title: 25B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2199

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

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

source_name: wild-type postnatal day 1 bladder

extract_protocol: Qiagen: RNeasy

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: whole bladder
FVB/N female mice are time-mated to control males.  Pregnant FVB/N mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses and newborn mice are killed by decapitation with a scalpel. Tissues are harvested and used whole or placed in OCT in a mold, frozen and stored at -80 °C.  Blocks are sectioned, stained and used for laser capture micro-dissection.

value: FVB/N

tag: sex

value: postnatal day 1


title: 23B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2195

source_name: SMAA/EYFP postnatal day 1 bladder

treatment_protocol:
pool size: N/A
Pooled sample: no
Dissection Method: whole bladder
FVB/N female mice are time-mated to SMGA/EGFP or SMAA/EYFP transgenic males.  Pregnant FVB/N mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses and newborn mice are killed by decapitation with a scalpel. Tissues are harvested and used whole or placed in OCT in a mold, frozen and stored at -80 °C.  Blocks are sectioned, stained and used for laser capture micro-dissection.

value: SMAA/EYFP transgenic / PMID:14713859


title: Gaido_Testes_gd16_8_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2175


title: Gaido_Testes_gd18_4_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2171

value: gd 18


title: Gaido_Testes_pnd2_1_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2168

treatment_protocol:
pool size: NA
Pooled sample: No
Dissection Method: Whole organ excision
Experimental Design: CD-1 mice are time-mated within a 2 hour window.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal gonads are removed from fetuses at gestation days 11, 12, 14, 16, 18, and postnatal day 2, snap frozen in liquid nitrogen and stored at -80ºC.

value: pnd 2


title: 43B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2192


title: Gaido_Testes_pnd2_2_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2169


title: 26B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2200


title: Gaido_Testes_gd14_10_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2177


title: Gaido_Testes_gd18_6_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2173


title: Gaido_Testes_gd16_7_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2174


title: Acromegaly control C2

description: peripheral blood


title: 13B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2189

source_name: SMGA/EGFP postnatal day 1 bladder

value: SMGA/EGFP transgenic / PMID:14713859


title: 27B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2196


title: 32B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2197


title: 15B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2190


title: Gaido_Testes_gd18_5_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2172


title: 61B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2194


title: Gaido_Testes_pnd2_3_14Dec2005

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: NA
Target Amplified protocol: NA
Rounds of amplification: NA
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2170


title: 45B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2193


title: 40B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2191


title: U87_1

status: Public on May 10 2006

city: Bethesda

first: Howard

last: Fine

state: MD

address: 9030 Old Georgetown Rd

department: Neurological Disorders and Stroke

institute: National Cancer Institute

description: Tumor cell line U87, cultured in serum

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.2 with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Tumor cell line U87

tag: commonly used glioma line


title: U87_2

description: Tumor cell line U87, cultured in serum


title: U87_SC_2

description: Tumor cell line U87, cultured in serum


title: 24B

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Epicentre
Target Amplified protocol: Potter protocols
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:2198


title: U387_2

description: Tumor cell line U387, cultured in serum

source_name: Tumor cell line U387


title: HF0445_U133P2

description: Brain tissue from GBM patient

source_name: Brain tissue from GBM patient

tag: GBMs


title: U251_IC_2

description: Tumor cell line U251, cultured in serum

source_name: Tumor cell line U251


title: U387_1

description: Tumor cell line U387, cultured in serum


title: U118_1

description: Tumor cell line U118, cultured in serum

source_name: Tumor cell line U118


title: U373_2

description: Tumor cell line U373, cultured in serum

source_name: Tumor cell line 373


title: U138_2

description: Tumor cell line U138, cultured in serum

source_name: Tumor cell line U138


title: U118_2

description: Tumor cell line U118, cultured in serum


title: NOB0308_S_p25_IC_2

description: Tumor cell line NOB0308, cultured in serum at passage 25, were injected into intracranial tissue in mice

source_name: Tumor cell line NOB0308

tag: primary GBM-deriven cells


title: U87_SC_1

description: Tumor cell line U87, cultured in serum


title: U251_SC_2

description: Tumor cell line U251, cultured in serum


title: T98_1

description: Tumor cell line T98, cultured in serum

source_name: Tumor cell line T98


title: T98_2

description: Tumor cell line T98, cultured in serum


title: U251_IC_1

description: Tumor cell line U251, cultured in serum


title: U251_1

description: Tumor cell line U251, cultured in serum


title: NOB1228_S_p3_1

description: Tumor cell line NOB1228, cultured in serum at passage 3

source_name: Tumor cell line NOB1228


title: U251_SC_1

description: Tumor cell line U251, cultured in serum


title: NOB0308_NBE_p1_IC

description: Tumor cell line NOB0308, cultured in NBE at passage 1, were injected into intracranial tissue in mice


title: NOB0308_S_p25_IC_1


title: NOB1228_S_p3_2


title: NOB0308_NBE_p20_1

description: Tumor cell line NOB0308, cultured in NBE at passage 20


title: U373_1

description: Tumor cell line U373, cultured in serum


title: NOB0308_S_p20_2

description: Tumor cell line NOB0308, cultured in serum at passage 20


title: SW1088_1

description: Tumor cell line SW1088, cultured in serum

source_name: Tumor cell line SW1088


title: SW1088_2


title: NOB0308_NBE_p20_2


title: NOB0308_NBE_p35_IC

description: Tumor cell line NOB0308, cultured in NBE at passage 35, were injected into intracranial tissue in mice


title: NOB0308_S_p20_1


title: U251_2

description: Tumor cell line U251, cultured in serum


title: U138_1

description: Tumor cell line U138, cultured in serum


title: NOB0308_NBE_p10_IC

description: Tumor cell line NOB0308, cultured in NBE at passage 10, were injected into intracranial tissue in mice


title: NOB0308_NBE_ssc_IC

description: Tumor cell line NOB0308, clonally selected in NBE, were injected into intracranial tissue in mice


title: NOB1228_NBE_p3_2

description: Tumor cell line NOB1228, cultured in NBE at passage 3


title: NOB1228_NBE_p3_1


title: NOB1228_NBE_P8_3

description: Tumor cell line NOB1228, cultured in NBE at passage 8


title: NOB1228_NBE_P8_1


title: NOB1228

description: Brain tissue from glioblastopma patient NOB1228

source_name: Brain tissue from patient NOB1228

tag: primary GBM


title: NOB1228_S_p8_4

description: Tumor cell line NOB1228, cultured in serum at passage 8


title: NOB0308_1

description: Brain tissue from glioblastopma patient NOB0308

source_name: Brain tissue from patient NOB0308


title: NOB1228_S_p3_4


title: NOB0308_2


title: NSC_p13_1

description: Normal neural stem cells, cultured in NBE at passage 13

source_name: Normal neural stem cells

tag: primary human fetal neural stem cells


title: NSC_p13_2


title: NOB1228_S_p13_3

description: Tumor cell line NOB1228, cultured in serum at passage 13


title: NOB0308_S_P20_4


title: NOB1228_NBE_P8_2


title: NOB0308_S_P35_2

description: Tumor cell line NOB0308, cultured in serum at passage 35


title: NOB1228_S_P13_1


title: NOB0308_NBE_P5_3

description: Tumor cell line NOB0308, cultured in NBE at passage 5


title: NOB0308_NBE_P5_4


title: NOB0308_NBE_P35_2

description: Tumor cell line NOB0308, cultured in NBE at passage 35


title: NOB0308_NBE_P35_1


title: NOB1228_S_P13_2


title: NOB1228_NBE_P13_1

description: Tumor cell line NOB1228, cultured in NBE at passage 13


title: NOB0308_S_P35_1


title: NOB1228_NBE_P13_2


title: NOB0308_S_P35_3


title: NOB1228_NBE_P3_4


title: NOB0308_S_P20_3


title: NOB1228_NBE_P3_3


title: NOB1228_S_P8_3


title: NOB0308_NBE_P20_4

description: Tumor cell line NOB0308, cultured in NBE at passage 20


title: NOB1228_NBE_P13_3


title: NOB1228_S_p3_3

description: Tumor cell line NOB1228, cultured in serum at passage 3


title: NOB0308_NBE_P20_3


title: NOB0308_S_p10_2

description: Tumor cell line NOB0308, cultured in serum at passage 10


title: LN229_2

description: Tumor cell line LN228, cultured in serum

source_name: Tumor cell line LN228


title: NOB1228_S_p8_2


title: NOB1228_S_p8_1


title: A172_1

description: Tumor cell line A172, cultured in serum

source_name: Tumor cell line A172


title: NSC_p19

description: Normal neural stem cells, cultured in NBE at passage 19


title: NOB0308_NBE_p5_1


title: NOB1228_NBE_p1_IC_4

description: Tumor cell line NOB1228, cultured in NBE at passage 1, were injected into intracranial tissue in mice


title: NOB0308_S_p10_1


title: NOB1228_NBE_p1_IC_2


title: LN229_1


title: brain, Whole brain: aSYN/70 #5_le1

status: Public on May 02 2006

description: 4 month aSYN/Hsp70  (whole mouse brain RNA)

source_name: brain, Whole brain


title: brain, Whole brain: aSYN/70 #6_le1


title: NOB1228_NBE_p1_IC_3


title: brain, Whole brain: wt #3_le1

description: 4 month wildtype (whole mouse brain RNA)


title: NOB1228_NBE_p1_IC_1


title: brain, Whole brain: aSYN/70 #1_le1


title: brain, Whole brain: wt #4_le1


title: brain, Whole brain: wt #6_le1


title: brain, Whole brain: wt #5_le1


title: A172_2

description: Tumor cell line A172, cultured in serum


title: NOB0308_NBE_p5_2


title: brain, Whole brain: aSYN/70 #2_le1


title: brain, Whole brain: aSYN/70 #4_le1


title: brain, Entorhinal Cortex: 99-33 normal_e1_le1

description: entorhinal cortex layer II stellate island cells

source_name: brain, Entorhinal Cortex


title: brain, Entorhinal Cortex: 99-33 tangle_e1_le1


title: brain, Whole brain: wt #2_le1


title: brain, Whole brain: wt #1_le1


title: brain, Whole brain: aSYN/70 #3_le1


title: brain, Entorhinal Cortex: 99-28 tangle_e1_le1


title: brain, Entorhinal Cortex: 99-28 normal_e1_le1


title: brain, Whole brain: Hsp70 #6_le1

description: 4 month Hsp70 only (whole mouse brain RNA)


title: brain, Whole brain: aSYN #6_le1

description: 4 month aSYN only (whole mouse brain RNA)


title: brain, Entorhinal Cortex: 99-21 tangle_e1_le1


title: brain, Entorhinal Cortex: 99-21 normal_e1_le1


title: brain, Entorhinal Cortex: 96-31 tangle_e1_le1


title: brain, Whole brain: Hsp70 #4_le1


title: brain, Whole brain: aSYN #4_le1


title: brain, Whole brain: Hsp70 #3_le1


title: brain, Whole brain: Hsp70 #2_le1


title: brain, Whole brain: aSYN #2_le1


title: brain, Entorhinal Cortex: 97-01 normal_e1_le1


title: brain, Entorhinal Cortex: 95-08 tangle_e1_le1


title: brain, Whole brain: aSYN #1_le1


title: brain, Whole brain: Hsp70 #1_le1


title: brain, Entorhinal Cortex: 96-31 normal_e1_le1


title: brain, Whole brain: aSYN #3_le1


title: brain, Whole brain: aSYN #5_le1


title: eye, retina: Ret Exp-4-ENZO

description:
RNA extracted from injected retina
Treatment, type=compound_based_treatment

source_name: eye, retina


title: brain, Entorhinal Cortex: 96-18 tangle_e1_le1


title: brain, Whole brain: Hsp70 #5_le1


title: eye, retina: Ret-Exp-2-ENZO


title: brain, Entorhinal Cortex: 01-22 tangle_e1_le1


title: eye, retina: Ret Exp-3-ENZO


title: brain, Entorhinal Cortex: 98-18 normal_e1_le1


title: brain, Entorhinal Cortex: 95-08 normal_e1_le1


title: brain, Entorhinal Cortex: 98-18 tangle_e1_le1


title: brain, Entorhinal Cortex: 96-18 normal_e1_le1


title: brain, Entorhinal Cortex: 97-01 tangle_e1_le1


title: eye, retina: Ret-C4-ENZO

description:
RNA ectracted from a fresh retina
Treatment, type=timepoint, measurement=0.0 d


title: eye, retina: Ret-C3-ENZO

description:
RNA extracted from fresh retina
Treatment, type=timepoint, measurement=0.0 d


title: brain, Entorhinal Cortex: 00-28 tangle_e1_le1


title: eye, retina: Ret-C2-ENZO


title: brain, Entorhinal Cortex: 00 28 normal_e1_le1


title: eye, retina: RetExp-1-ENZO

description:
RNA extracted from  injected retina
Treatment, type=compound_based_treatment


title: brain, Entorhinal Cortex: 01-22 normal_e1_le1


title: brain, cerebral cortex: Total RNA extraction_le1 261215

description: Egr1/Egr3 double knockout #1

source_name: brain, cerebral cortex


title: brain, cerebral cortex: Egr1/Egr3 double knockout 2_e1_le1 261231

description: Egr1/Egr3 double knockout #2


title: Wildtype embryonic E11.5 Metanephric Mesenchyme replicate 4

status: Public on May 01 2006

city: Cincinnati

first: Kristopher

middle: Robert

last: Schwab

state: OH

address: 3333 Burnett Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Research Foundation

description: Wild type embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 4

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Wild type E11.5 MM rep4

label_protocol: RNA collected from multiple sections of metanephric mesenchyme (3 to 4 different metanephric mesenchymes) was pooled and prepared from collected tissue using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI).

extract_protocol: E11.5 kidney rudiments were dissected in ice-cold PBS then quick-frozen in Tissue-Tek® OCT compound (Sakura, Torrence, CA) using liquid nitrogen cooled 2-methylbutane isopentan.  Serial sections (7 microns) were made using a Microm HM 550 cryostat (Richard-Allan Scientific, Kalamazoo, MI), collected on Fisher Superfrost plus precleaned slides (Hampton, NH), and stored at –80 C. Alternate sections were hematoxylin and eosin stained and used to help identify the UB and MM. For LCM the remaining sections were air dried at room temperature for 3 min, acetone fixed for 2 min, rinsed in ice cold 1/10 PBS for 3 min and then dehydrated in 75%, 95%, 100%, 100% ethanol, followed by two five minute rinses with xylene. Laser capture microdissection was performed using the Arcturus Pixcell II system, according to Arcturus protocols (Mountain View, California). RNA was prepared from collected tissue using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI), and hybridized to Affymetrix MOE430_v2 microarrays.

tag: Wild type embryonic metanephric mesenchyme at E11.5 isolated by laser capture microdissection, Cd-1 strain


title: Wild type embryonic E11.5 Ureteric Bud replicate 1

description: Wild type embryonic E11.5 Ureteric bud isolated fine manual microdissection replicate 1

source_name: Wild type E11.5 UB rep1

extract_protocol: Ureteric bud was isolated by treating dissected E11.5 kidney rudiments, up to T-shaped stage, with 0.5 mg/ml collagenase B (Roche, Indianapolis, IN), in D-MEM (Invitrogen, Carlsbad, CA) for thirty minutes at 37° C and carefully dissecting the mesenchyme from the UB, followed by storage at -80° C. RNA from 3 to 9 dissected ureteric buds was prepared using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI), and hybridized to Affymetrix MOE430_v2 microarrays.

tag: Wild type embryonic ureteric bud at E11.5 isolated by fine manual microdissection, Cd-1 strain


title: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme replicate 5

description: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 5

source_name: HoxA11, D11 null E11.5 MM rep5

label_protocol: RNA collected from multiple sections of metanephric mesenchyme was prepared from collected tissue using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI).

extract_protocol: Urogenital ridges were dissected in ice-cold PBS then quick-frozen in Tissue-Tek® OCT compound (Sakura, Torrence, CA) using liquid nitrogen cooled 2-methylbutane isopentan.  Serial sections (7 microns) were made using a Microm HM 550 cryostat (Richard-Allan Scientific, Kalamazoo, MI), collected on Fisher Superfrost plus precleaned slides (Hampton, NH), and stored at –80 C. Alternate sections were hematoxylin and eosin stained and used to help identify the UB and MM. For LCM the remaining sections were air dried at room temperature for 3 min, acetone fixed for 2 min, rinsed in ice cold 1/10 PBS for 3 min and then dehydrated in 75%, 95%, 100%, 100% ethanol, followed by two five minute rinses with xylene. Laser capture microdissection was performed using the Arcturus Pixcell II system, according to Arcturus protocols (Mountain View, California). RNA was prepared from collected tissue using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI), and hybridized to Affymetrix MOE430_v2 microarrays.

tag: Hoxa11, Hoxd11 double null targeted embryonic metanephric mesenchyme at E11.5 isolated by laser capture microdissection, mixed C57, C3H and CF1 strain


title: brain, cerebral cortex: Egr1/Egr3 double knockout 3_e1_le1 261247

description: Egr1/Egr3 double knockout #3


title: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme replicate 3

description: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 3

source_name: HoxA11, D11 null E11.5 MM rep3


title: Wild type embryonic E11.5 Ureteric Bud replicate 2

description: Wild type embryonic E11.5 Ureteric bud isolated fine manual microdissection replicate 2

source_name: Wild type E11.5 UB rep2

label_protocol: Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI), and hybridized to Affymetrix MOE430_v2 microarrays.


title: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme replicate 4

description: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 4

source_name: HoxA11, D11 null E11.5 MM rep4


title: eye, retina: Ret-C1-ENZO

description:
RNA extracted from a fresh disected retina.
Treatment, type=timepoint, measurement=0.0 d


title: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme replicate 1

description: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 1

source_name: HoxA11, D11 null E11.5 MM rep1


title: Wildtype embryonic E11.5 Metanephric Mesenchyme replicate 2

description: Wild type embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 2

source_name: Wild type E11.5 MM rep2


title: Wild type embryonic E11.5 Metanephric Mesenchyme replicate 5

description: Wild type embryonic E11.5 Metanephric Mesenchyme isolated fine manual microdissection replicate 5

source_name: Wild type E11.5 MM rep5

extract_protocol: Metanephric Mesenchyme were isolated by treating dissected E11.5 kidney rudiments, up to T-shaped stage, with 0.5 mg/ml collagenase B (Roche, Indianapolis, IN), in D-MEM (Invitrogen, Carlsbad, CA) for thirty minutes at 37° C and carefully dissecting the mesenchyme from the UB, followed by storage at -80° C. RNA from individual dissected metanephric mesenchyme was prepared using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI), and hybridized to Affymetrix MOE430_v2 microarrays.

tag: Wild type embryonic metanephric mesenchyme at E11.5 isolated by fine manual microdissection, Cd-1 strain


title: Wildtype embryonic E11.5 Metanephric Mesenchyme replicate 3

description: Wild type embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 3

source_name: Wild type E11.5 MM rep3


title: Wild type embryonic E11.5 Ureteric Bud replicate 3

description: Wild type embryonic E11.5 Ureteric bud isolated fine manual microdissection replicate 3

source_name: Wild type E11.5 UB rep3


title: Wild type embryonic E11.5 Metanephric Mesenchyme replicate 7

description: Wild type embryonic E11.5 Metanephric Mesenchyme isolated fine manual microdissection replicate 7

source_name: Wild type E11.5 MM rep7


title: brain, cerebral cortex: Total RNA extraction_le1 261199

description: Wild type replicate #3


title: brain, cerebral cortex: Total RNA extraction_le1 261167

description: Wild type replicate #1


title: Wild type embryonic E11.5 Metanephric Mesenchyme replicate 6

description: Wild type embryonic E11.5 Metanephric Mesenchyme isolated fine manual microdissection replicate 6

source_name: Wild type E11.5 MM rep6


title: Wild type embryonic E11.5 Ureteric Bud replicate 4

description: Wild type embryonic E11.5 Ureteric bud isolated fine manual microdissection replicate 4

source_name: Wild type E11.5 UB rep4


title: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme replicate 2

description: HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 2

source_name: HoxA11, D11 null E11.5 MM rep2


title: Wildtype embryonic E11.5 Metanephric Mesenchyme replicate 1

description: Wild type embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 1

source_name: Wild type E11.5 MM rep1


title: brain, cerebral cortex: Total RNA extraction_le1 261183

description: Wild type replicate #2

source_name: brain, cerebral cortex


title: mouselung_scid_12DPI_rep02

city: Baltimore

first: Joshua

middle: J

last: Reece

address: 615 N. Wolfe Street

department: MMI

institute: Johns Hopkins University BSPH

description: Intensity of hybridization for each probe pair was computed by GCOS 1.2 software (Affymetrix). (For more detailed methods, please refer to the website of the Malaria Research Institute Gene Array Core Facility (MRI-GACF) at the Johns Hopkins Bloomberg School of Public Health http://jhmmi.jhsph.edu)

scan_protocol: standard Affymetrix procedures using affy GCS3000

source_name: whole lung

label_protocol: standard Affymetrix procedures

extract_protocol: trizol extraction followed by qiagen RNeasy total RNA cleanup protocol

tag: strain:BALB/c scid, gender:male, age:8wks, tissue

value: whole lung, condition:12DPI


title: mouselung_scid_12DPI_rep03


title: mouselung_scid_12DPI_rep01


title: mouselung_scid_8DPI_rep03

value: whole lung, condition:8DPI


title: mouselung_wt_12DPI_rep01

tag: strain:BALB/c WT, gender:male, age:8wks, tissue


title: mouselung_wt_12DPI_rep02


title: mouselung_wt_8DPI_rep02


title: mouselung_wt_8DPI_rep03


title: mouselung_wt_12DPI_rep03


title: mouselung_scid_2DPI_rep03

value: whole lung, condition:2DPI


title: mouselung_scid_8DPI_rep01


title: mouselung_scid_3DPI_rep01

value: whole lung, condition:3DPI


title: mouselung_wt_8DPI_rep01


title: mouselung_scid_4DPI_rep03

value: whole lung, condition:4DPI


title: mouselung_scid_3DPI_rep02


title: mouselung_wt_4DPI_rep03


title: mouselung_scid_4DPI_rep01


title: mouselung_wt_2DPI_rep03


title: mouselung_scid_2DPI_rep01


title: mouselung_wt_3DPI_rep03


title: mouselung_wt_4DPI_rep01


title: mouselung_wt_3DPI_rep02


title: mouselung_wt_3DPI_rep01


title: mouselung_scid_2DPI_rep02


title: mouselung_scid_8DPI_rep02


title: mouselung_wt_2DPI_rep02


title: mouselung_scid_4DPI_rep02


title: mouselung_scid_control_rep02

tag: strain:BALB/c SCID, gender:male, age:8wks, tissue

value: whole lung, condition:uninfected control


title: mouselung_scid_control_rep03


title: mouselung_scid_control_rep01


title: mouselung_scid_3DPI_rep03


title: mouselung_wt_4DPI_rep02


title: mouselung_wt_2DPI_rep01


title: mouselung_wt_control_rep03


title: mouselung_wt_control_rep01


title: opr3_OPDA_22 hrs_Rep3

status: Public on Apr 27 2006

city: Pullman

first: Ajin

middle: D

last: Mandaokar

state: WA

address: 447, Clark hall

department: Institute of Biological Chemistry

institute: Washington State University

description: Target value (TGT value) was set to 125 global scaling

hyb_protocol: Array was hybridized for 15 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on an Agilent GeneArray Scanner 2500A (Agilent, Palo Alto, CA).

data_processing: Gene chip data files were processed using Affymetrix Microarray Suite MAS 5.0

source_name: Stamens

label_protocol: Labeling and hybridization of RNA was carried out according to standard Affymetrix protocols (Affymetrix, Santa Clara, CA). In brief, ten micrograms of total RNA for each replicate was converted to cDNA, from which biotinylated cRNA target was synthesized. The resulting cRNA was purified on RNeasy columns and then fragmented for hybridization to ATH1 Arabidopsis GeneChips (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown on soil under continuous illumination of 130 mmol m-2s-1 at 22 0C.

extract_protocol: Total RNA was isolated from stamens using Trizol reagent following instructions from the manufacturer (Invitrogen Corporation, Carlsbad, CA) and was then purified on RNeasy columns (Qiagen, Valencia, CA).

treatment_protocol: Flower buds at developmental stage 12 from opr3 mutants were treated with 0.03% 12-oxophytodienoic acid (OPDA) and stamens were harvested 22 hrs after treatment and immediately frozen in liquid nitrogen

tag: A mutation in the gene encoding 12-oxophytodienoic acid reductase (OPR3) results in male sterility in Arabidopsis due to defects in anther development and pollen maturation. Described in Stintzi, A., and Browse, J. (2000). Proc. Natl. Acad. Sci. USA 97, 10625-10630.


title: opr3_OPDA_8 hrs_Rep1

treatment_protocol: Flower buds at developmental stage 12 from opr3 mutants were treated with 0.03% 12-oxophytodienoic acid (OPDA) and stamens were harvested 8 hrs after treatment and immediately frozen in liquid nitrogen