title: homozygot FH P261

description: Gene expression data from the homozygous FH participant A

source_name: homozygot FH P261 (human CD3 positive T cells)

value: homozygote FH


title: heterozygot FH P265

status: Public on Apr 01 2008

type: RNA

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

country: Germany

institute: University Hospital Jena

description: Gene expression data from the heterozygous FH participant B

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133A2.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: heterozygot FH P265 (human CD3 positive T cells)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: the RNA was worked up using PLG Tubes and the Qiagen Rneasy Kit

treatment_protocol: T cells were precipitated untouched from 4 ml peripheral blood mononuclear cells, washed in PBS + 2mM EDTA, lysed in TriZol

tag: cell type

value: T cell

tag: disease state

value: heterozygote FH


title: TERT6-65, TERT transfected, Affymetrix

city: Hiroshima

first: Keiko

last: Hiyama

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Research Institute for Radiation Biology and Medicine

country: Japan

institute: Hiroshima University

description: immortal-competent lifespan

hyb_protocol: The synthesized 20 microgram of cRNA, quantified by spectrometry and qualified using an Agilent 2100 Bioanalyzer, was then fragmented and hybridized to each array.

scan_protocol: Each microarray was scanned using an Affymetrix GeneChip Scanner 3000 with Affymetrix GeneChip Operating System (GCOS) 1.2.

data_processing: Using Affymetrix GeneChip Operating System (GCOS) 1.2., scale factor was set as 500.

source_name: human fetal lung fibroblast TIG-1 clone TERT6 transfected with TERT

label_protocol: The first-strand cDNA was generated from 1 microgram of total RNA using reverse transcriptase and a T7 primer using the GeneGhip One-Cycle Target Labeling kit, and then second-strand cDNA was produced using DNA polymerase mix and RNase H. cRNA (complementary RNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and biotinilated ribonucleotide analog.

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's minimal essential medium (DMEM; Sigma-Aldrich Japan, Tokyo, Japan) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from the frozen cultured cell pellets using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA), respectively, according to the manufacturer's protocols. The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TERT expression vector was transfected to TIG-1 and isolated as a G418 resistant clone. Exponentially growing cultured cells were collected using trypsin followed by rinse with PBS, and frozen until use.

tag: human fetal lung fibroblast TIG-1 clone TERT6 at 65 PDL transfected with TERT


title: heterozygot FH P276

description: Gene expression data from the heterozygous FH participant E

source_name: heterozygot FH P276 (human CD3 positive T cells)


title: homozygot FH P269

description: Gene expression data from the homozygous FH participant C

source_name: homozygot FH P269 (human CD3 positive T cells)


title: homozygot FH P254

description: Gene expression data from the homozygous FH participant K2

source_name: homozygot FH P254 (human CD3 positive T cells)


title: heterozygot FH P387neu

description: Gene expression data from the heterozygous FH participant LW

source_name: human CD14 positive monopcytes

treatment_protocol: monocytes were precipitated untouched from 8ml peripheral blood mononuclear cells, washed in PBS + 2mM EDTA, lysed in TriZol

value: monocyte


title: heterozygot FH P250

description: Gene expression data from the heterozygous FH participant V

source_name: heterozygot FH P250 (human CD3 positive T cells)


title: control participant P351

description: Gene expression data from control participant RF

value: control participant


title: control participant P335

description: Gene expression data from control participant T5


title: control participant P333

description: Gene expression data from control participant T4


title: control participant P319

description: Gene expression data from control participant TL


title: control participant P327

description: Gene expression data from control participant T1


title: control participant P309

description: Gene expression data from control participant DB


title: control participant P331

description: Gene expression data from control participant T3


title: control participant P329

description: Gene expression data from control participant T2


title: control participant P303

description: Gene expression data from control participant BL


title: homozygot FH P270wh


title: heterozygot FH P282

description: Gene expression data from the heterozygous FH participant M


title: control participant P313

description: Gene expression data from control participant SH


title: control participant P317

description: Gene expression data from control participant MO


title: heterozygot FH P279

description: Gene expression data from the heterozygous FH participant F


title: control participant P311

description: Gene expression data from control participant LF


title: heterozygot FH P266

description: Gene expression data from the heterozygous FH participant B


title: homozygot FH P253

description: Gene expression data from the homozygous FH participant K2


title: heterozygot FH P560

description: Gene expression data from the heterozygous FH participant DW


title: homozygot FH P251

description: Gene expression data from the homozygous FH participant K1


title: control participant P307

description: Gene expression data from control participant KP


title: homozygot FH P262

description: Gene expression data from the homozygous FH participant A


title: Col-0-SH-rep3

city: La Jolla

first: Joanne

last: Chory

state: CA

address: 10010 N. Torrey Pines Road.

department: Plant Biology Laboratory

country: USA

institute: The Salk Institute for Biological Studies

description: The purpose of this experiment is to study the underlying molecular mechanism that leads to the different responses of Col-0, sav3 and sav1-1 to shade.

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: All 18 arrays were processed using gcRMA method provided by bioconductor

organism: Arabidopsis thaliana

source_name: 7-day old, Col-0 treated with 1hr of low R:FR light

label_protocol: Affymetrix protocol

extract_protocol: Spectrum™ Plant Total RNA Kit (Sigma)

treatment_protocol: Seeds were surface sterilized and plated on 1/2 Murashige Skoog (MS) medium Seedlings were grown at 22 degree, under simulated continuous white light, mixture of Red: 13 µ mol m-2 s-1, Blue (B): 1.23 µ mol m-2 s-1 for 7-day, then treated with low R:FR light (mixture of Red: 13 µ mol m-2 s-1, Blue (B): 1.23 µ mol m-2 s-1,FR: 20.2 µ mol m-2 s-1 )for 1hr

tag: Ecotype

tag: Age

value: 7 days

tag: Tissue

value: whole seedling


title: sav1-1-SH-rep2

source_name: 7-day old, sav1-1 treated with 1hr of low R:FR light

growth_protocol: Seedlings were grown at 22 degree, under simulated continuous white light, mixture of Red: 13 µ mol m-2 s-1, Blue (B): 1.23 µ mol m-2 s-1

tag: Genotype


title: sav1-1-Wc-rep3

source_name: 7-day old, sav1-1 grown under simulated Wc

treatment_protocol: Seeds were surface sterilized and plated on 1/2 Murashige Skoog (MS) medium Seedlings were grown at 22 degree, under simulated continuous white light, mixture of Red: 13 µ mol m-2 s-1, Blue (B): 1.23 µ mol m-2 s-1 for 7-day


title: sav1-1-SH-rep3


title: Col-0-SH-rep2


title: sav3-2-SH-rep2

source_name: 7-day old, sav3-2 treated with 1hr of low R:FR light


title: sav3-2-Wc-rep3

source_name: 7-day old, sav3-2 grown under simulated Wc


title: sav1-1-Wc-rep2


title: sav3-2-Wc-rep2


title: heterozygot FH P249

description: Gene expression data from the heterozygous FH participant V


title: Col-0-Wc-rep2

source_name: 7-day old, Col-0 grown under simulated Wc


title: Col-0-Wc-rep1


title: sav1-1-SH-rep1


title: sav3-2-Wc-rep1


title: Col-0-SH-rep1


title: sav3-2-SH-rep1


title: Col-0-Wc-rep3


title: sav1-1-Wc-rep1


title: sav3-2-SH-rep3


title: Trasnsformed Lymphocytes Schizophrenia Affected discordant twin (TP4)

status: Public on Mar 30 2008

city: Brisbane

first: Nicholas

last: Matigian

state: Queensland

address: 170 Kessels Rd, Nathan

country: Australia

institute: National Adult Stem Cell Centre

hyb_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

data_processing: Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared

label: Biotin

source_name: Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin 2)

extract_protocol: LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software

tag: Sample ID:TP4

tag: Twin Pair ID:-

tag: Clinical Status

value: Schizophrenia

tag: Age of Onset:N/A

tag: Age at interview & blood sampling:26

tag: Current Age (2007):31

tag: Sex

value: Female

tag: Medication at interview (duration) :Nil


title: Trasnsformed Lymphocytes Schizophrenia Affected discordant twin (TP3)

scan_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

source_name: Trasnsformed Lymphocytes Schizophrenia (Affected pateint of MZ twin 2)

tag: Sample ID:TP3

tag: Age of Onset:21

tag: Medication at interview (duration) :Olanzapine


title: Trasnsformed Lymphocytes Unaffected Twin Pair 1 (TP2)

source_name: Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 1)

label_protocol: Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

tag: Sample ID:TP2

value: Unaffected

tag: Age at interview & blood sampling:61

tag: Current Age (2007):66

tag: Medication at interview (duration)

value: thyroxine


title: ovary - 440433

status: Public on Mar 28 2008

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 2.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Adenocarcinoma, endometrioid and papillary serous

source_name: ovary


title: RPE/choroid_old_rep1

status: Public on Mar 29 2008

city: Chicago

first: Huiyi

last: Chen

state: IL

address: 303 E Chicago Ave, Tarry 13-752

department: Ophthalmology

institute: Northwestern University School of Medicine

hyb_protocol: standard Affymetrix hybridization

scan_protocol: standard Affymetrix scanning

data_processing: Based on the affymetrix .cel files, invariant set normalization was performed using dchip2006 and PM-only model was used for generating gene signal intensities.

organism: Mus musculus

source_name: old retinal pigmental epithelium/choroid

label_protocol: standard Affymetrix labeling

extract_protocol: Total RNA was extracted by using RNeasy Minikit from Qiagen.

tag: Strain:C57BL/6, Gender

value: male, Age:26 months, Tissue:retinal pigmental epithelium/choroid


title: RPE/choroid_old_rep4


title: RPE/choroid_young_rep3

source_name: young retinal pigmental epithelium/choroid

value: male, Age:4 months, Tissue:retinal pigmental epithelium/choroid


title: Trasnsformed Lymphocytes Brief Psychotic Disorder Affected Twin Pair 1 (TP1)

source_name: Trasnsformed Lymphocytes Brief Psychotic Disorder (Affected pateint of MZ twin pair 1)

tag: Sample ID:TP1

value: Brief Psychotic Disorder

tag: Age of Onset:55

tag: Medication at interview (duration) :Thyroxine


title: Kidney - 440442

description:
Quality metric = 28S to 18S: 2.1
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: 2
Clinical Multiple Tumors: Yes
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Renal cell carcinoma

source_name: Kidney


title: Ovary - 440438

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Clinical T: 3c
Clinical N: 0
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: Papillary Serous Adenocarcinoma

source_name: Ovary


title: RPE/choroid_young_rep1


title: RPE/choroid_young_rep2


title: Omentum - 443473

description:
Quality metric = 28S to 18S: 1.4
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
Clinical T: 3c
Clinical N: 0
Clinical M: 0
Clinical Stage: 3C
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Fallopian Tube
Histology: Papillary serous adenocarcinoma

source_name: Omentum


title: Omentum - 443471

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
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma


title: RPE/choroid_old_rep2


title: Stomach - 438174

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 70-80
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 58
Have you ever had esophagitis/reflux?: Yes
Pathological T: 3
Pathological N: 3
Pathological M: 0
Pathological Stage: 4
Pathological Grade: 4
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Stomach
Histology: Signet Ring Cell Carcinoma

source_name: Stomach


title: Breast - 440439

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Mammogram: Yes
Number of years in which a mammogram was obtained?: 26-30
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Breast
Histology: Invasive Ductal Carcinoma

source_name: Breast


title: Foxj3 WT myoblasts P3

status: Public on Mar 31 2008

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

description: Gene expression data from Foxj3 WT skeletal myoblasts

hyb_protocol: Following fragmentation/labeling, 20ug of cRNA were hybridized for 16hours at 45C, on the Affymetrix murine genome U74A V.2 chip

scan_protocol: Gene chips were scanned using the Affymetrix Gene Chips Operating Software (GCOS) under standard automation.

data_processing: GeneSpring data analysis software was used to analyse the raw data.  Fold Changes greater than 2 fold in which the probe was present in both samples (P) were considered significant

source_name: Foxj3 WT skeletal myoblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in 20% FBS/DMEM supplemented with Pen/Strep antibiotics (Gibco).

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

treatment_protocol: Cells were grown to 80% confluency before harvest.

tag: normal


title: RPE/choroid_old_rep3


title: Foxj3 KO myoblasts P3

description: Gene expression data from Foxj3 KO skeletal myoblasts

source_name: Foxj3 KO skeletal myoblasts

tag: increased cellular proliferation


title: Pancreas - 443468

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
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: Mucinous Adenocarcinoma

source_name: Pancreas


title: Colon - 440432

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: D
Primary Site: Colon
Histology: Mucinous Carcinoma

source_name: Colon


title: RPE/choroid_young_rep4


title: Uterus - 433399

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Clear cell adenocarcinoma

source_name: Uterus


title: Inguinal Lymph Nodes - 438165

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 56-60
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: 3b
Retreatment N: 3
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Melanoma of Skin
Histology: Metastatic Malignant melanoma, NOS

source_name: Inguinal Lymph Nodes


title: Pancreas - 433405

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Exocrine Pancreas
Histology: Colloid Adenocarcinoma w/Intraductal Papillary Mucinous Tumor


title: Uterus - 433408

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
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: Uterus - 433394

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
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 Adenocarcinoma


title: Colon - 438159

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 13
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: Mucinous Carcinoma


title: Kidney - 433393

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Renal mixed papillary sarcomatoid


title: Kidney - 426420

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 16
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Chromophobe renal carcinoma


title: Uterus - 433390

description:
Quality metric = 28S to 18S: 1.6
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: 45
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Omentum - 433392

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Abdominal pain
Clinical T: 3c
Clinical N: 0
Clinical M: 0
Clinical Stage: 3C
Clinical Grade: X
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Malignant mixed muellerian tumor


title: Kidney - 426429

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Pipe
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 23
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Common Bile Duct - 432618

description:
Quality metric = 28S to 18S: 1.5
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
Clinical Question: T
Clinical Value: 3
Clinical Question: N
Clinical Value: 0
Clinical Question: M
Clinical Value: 0
Clinical Question: Stage
Clinical Value: 2a
Clinical Question: Grade
Clinical Value: 2
Clinical Question: Multiple Tumors
Clinical Value: No
Clinical Question: Stage During or Following Multimodality Therapy
Clinical Value: No
Clinical Question: Symptoms
Clinical Value: Jaundice
Primary Site: Common Bile Duct
Clinical Question: Histology
Clinical Value: Cholangiocarcinoma

source_name: Common Bile Duct


title: Ovary - 423081

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma


title: Ovary - 426414

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Presenting Symptoms: Abdominal pain
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 4
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Mixed Adenocarcinoma, Endometrioid and Clear Cell Types


title: Cecum - 426411

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 19
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma arising in a villous adenoma

source_name: Cecum


title: Ovary - 426418

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 30-40
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: 21
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 3b
Retreatment N: 0
Retreatment M: 0
Retreatment Stage: 3B
Retreatment Grade: 3
Retreatment Staged During or Following Multimodality Therapy: Yes
Primary Site: Cervix Uteri
Histology: Adenosquamous carcinoma


title: Breast - 421742

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Mammogram: Yes
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: Yes
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 16-20
Pathological T: 4b
Pathological N: 0(i-)
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Primary Site: Breast
Histology: Metaplastic squamous carcinoma


title: Uterus - 426419

description:
Quality metric = 28S to 18S: 1.7
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: 20
Pathological T: 1b
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Mixed clear cell and endometrioid adenocarcinoma


title: Kidney - 426412

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Renal cell carcinoma


title: Ovary - 426417

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: 2
Retreatment M: 1
Retreatment Metastatic Sites: Other
Retreatment Stage: 4
Retreatment Grade: X
Retreatment Stage During or Following Multimodality Therapy: Yes
Retreatment Dukes Stage: C
Primary Site: Colon
Histology: Metastatic Mucinous Adenocarcinoma


title: thyroid - 421735

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 4a
Pathological N: 1b
Pathological M: 0
Pathological Stage: 4A
Pathological Multiple Tumours: Yes
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Thyroid
Histology: Carcinoma, anaplastic

source_name: thyroid


title: skin from abdomen - 421736

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Mammogram: Yes
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Skin
Retreatment Stage: 4
Retreatment Grade: 2
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Retreatment ER: Positive
Retreatment PR: Positive
Retreatment HER/2 Neu: Negative
Primary Site: Breast
Histology: Metastatic Lobular Carcinoma

source_name: skin from abdomen


title: Renal Pelvis - 421739

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 54
Clinical T: 1
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumours: No
Clinical Staged During or Following Multimodality Therapy: No
Primary Site: Renal Pelvis
Histology: Transitional cell carcinoma

source_name: Renal Pelvis


title: Kidney - 416808

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigars
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 62
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Pelvic Lymph Node - 421718

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Have you ever been diagnosed as having HPV on your PAP smear?: No
Clinical T: 1b1
Clinical N: 1
Clinical M: 0
Clinical Stage: 3B
Clinical Grade: 2
Clinical Multiple Tumours: No
Clinical Staged During or Following Multimodality Therapy: No
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma

source_name: Pelvic Lymph Node


title: Uterus - 426410

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 2a
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma


title: Prostate - 403711

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
PSA: Elevated
Cancer discovered by digital exam?: No
Clinical T: 2a
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Omentum - 383917

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical Metastatic Sites: Omentum
Clinical Stage: Unknown
Clinical Grade: 2
Primary Site: Unknown Primary
Histology: Metastatic Carcinoma, NOS


title: Cecum - 416807

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Bright red stools
Pathological T: 4
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Pancreas - 421716

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 49
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Exocrine Pancreas
Histology: Adenocarcinoma, NOS


title: Colon - 383910

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 90-100
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 16
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Ovary - 421727

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3c
Pathological N: X
Pathological M: 1
Pathological Metastatic Sites: Pleura
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma

source_name: Ovary


title: Rectosigmoid - 421744

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
Days from Patient Diagnosis to Excision: 22
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Uterus - 416793

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: 41
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Lung - 416790

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
Presenting Symptoms: Persistent Cough
Presenting Symptoms: SOB
Workplace or household smokers?: No
Clinical T: 1
Clinical N: 0
Clinical M: 0
Clinical Stage: 1A
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma

source_name: Lung


title: Breast - 383901

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 56-60
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 31
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2A
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical ER: Positive
Clinical PR: Positive
Clinical HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Lung - 405008

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 28
Workplace or household smokers?: No
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Omentum - 416792

description:
Quality metric = 28S to 18S: 1.4
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: 28
Prior Therapy: Radiation
Presenting Symptoms: Bloating
Presenting Symptoms: Vaginal bleeding
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma

source_name: Omentum


title: Colon - 383907

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 5
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Vomiting
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: Breast - 383918

description:
Quality metric = 28S to 18S: 1.6
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: 23
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Oophorectomy?: No
Fibrocystic disease?: Yes
Hormonal therapy (# of Years)?: 11-15
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: breast - 383914

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 40-50
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 26
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 16-20
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: Yes
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: breast


title: Rectosigmoid Colon - 383898

description:
Quality metric = 28S to 18S: 1.6
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: 30
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: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid Colon


title: Kidney - 383894

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 1
Clinical Multiple Tumors: Yes
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma

source_name: Kidney


title: Liver - 383899

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Hepatic
Retreatment Stage: 4
Retreatment Grade: X
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Retreatment Dukes Stage: D
Primary Site: Colon
Histology: Metastatic Adenocarcinoma

source_name: Liver


title: Breast - 366601

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 8
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: No
Hormonal therapy (# of Years)?: 11-15
Pathological T: 3
Pathological N: 1a
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: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Colon - 362604

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Mucinous Adenocarcinoma

source_name: Colon


title: Prostate - 383893

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-60
Gender: Male
Ethnic Background: American Indian
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: 39
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Breast - 383895

description:
Quality metric = 28S to 18S: 1.2
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: 22
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Breast - 383892

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 39
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?: Yes
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 16-20
Pathological T: 3
Pathological N: 3a
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Lobular Carcinoma


title: Breast - 346007

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: American Indian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 27
Mammogram: Yes
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 16-20
Oophorectomy?: Yes
Fibrocystic disease?: No
Hormonal therapy (# of Years)?: 6-10
Pathological T: 2
Pathological N: 1a
Pathological M: 0
Pathological Stage: 2B
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: Lung - 346006

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 35
Presenting Symptoms: Hemoptysis
Workplace or household smokers?: No
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: Squamous cell carcinoma


title: Uterus - 426431

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 48
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma

source_name: Uterus


title: Wild type, water treatment, biological rep1

status: Public on Mar 27 2008

city: Columbia

first: Gary

last: Stacey

state: MO

address: 1201 Rollins Road

department: Plant Sciences

institute: University of Missouri-Columbia

description: Gene expression in response to chitooctaose

hyb_protocol: Following fragmentation, cRNA were hybridized with the Affymetrix Arabidopsis Whole Genome Array ATH1 according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using a Hewlett-Packard GeneArray Scanner

data_processing: The data were analyzed with DNA-CHIP (dChip) (Version, September 23, 2005) using the default settings.

source_name: Two-week-old whole seedlings of Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Seedlings were grown in the MS liquid medium for 14 days under constant light at 23 degree and then treated with water

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

treatment_protocol: Seedlings grown hydroponically were treated wtih water for 30 minutes (as a contro). The collected seedlings were frozen in liquid nitrogen for RNA isolation uisng the Trizol solution (Invitrogen).

tag: Genotype

value: WT Col-0

tag: Two-week-old seedlings


title: Wild type, chitooctaose treatment, biological rep1

growth_protocol: Seedlings were grown in the MS liquid medium for 14 days under constant light at 23 degree and then treated with chitooctaose

treatment_protocol: Seedlings grown hydroponically were treated wtih chitooctaose at a final concentration of 1 um for 30 minutes. The collected seedlings were frozen in liquid nitrogen for RNA isolation uisng the Trizol solution (Invitrogen).


title: Wild type, water treatment, biological rep2


title: Chitin receptor mutant, water treatment, biological rep2

treatment_protocol: Seedlings grown hydroponically were treated wtih water for 30 minutes (as a control). The collected seedlings were frozen in liquid nitrogen for RNA isolation uisng the Trizol solution (Invitrogen).

value: Mutant Col-0 with mutation in the chitin receptor


title: Chitin receptor mutant, water treatment, biological rep3


title: Chitin receptor mutant, water treatment, biological rep1


title: cumulus_PCOS_Obese_rep5

city: Toronto

first: Shlomit

last: Kenigsberg

state: Ontario

address: 790 Bay st.

department: Research

country: Canada

institute: Create Fertility Centre

description: All the participants included in the study were women undergoing In-Vitro Fertilization with intracytoplasmatic sperm injection (IVF-ICSI) at the IVF unit. The IVF-ICSI cycles included in the study were conducted according to the long mid luteal GnRH agonist (Diphereline 3.75 mg PharmaBiotech, France) protocol. Controlled ovarian hyperstimulation was conducted with either recombinant follicular stimulating hormone (rFSH- Follitropin Alfa, Serono, UK) or human menopausal gonadotropin (hMG - Menotropin, Ferring, Germany). Following oocyte retrieval, cumulus cells were stripped from the oocyte, in preparation for the ICSI process, with a micropipette.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner (Affymetrix)

data_processing: Data was preprocessed using Robust Multiarray Average (RMA) with default parameters, through the Affy package of bioconductor.

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Obese, rep5

label_protocol: Biotinylated cRNA were prepared according to the Small Sample Target Labeling Assay v.2' protocol from 50 ng total RNA from Affymetrix, (Santa Clara, CA)

growth_protocol: Cells were cultured for 48h in the original IVF plate, washed 3 times with DMEM/Ham's F12 (1:1) supplemented with penicillin, streptomycin and amphotericin and resuspended in the same medium supplemented with 10% Fetal calf serum. Cells were incubated for 48h at 37°C with 5% CO2, medium was replaced after 24h.

extract_protocol: Total RNA was extracted using Trizol (Molecular Research) according to the manufacturer's instructions

treatment_protocol: Patients were treated with gonadotropins

tag: Gender

value: Female, Age:27, BMI:29, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Obese_rep7

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Obese, rep7

value: Female, Age:37, BMI:31, Tissue:luteinized cumulus cells


title: Prostate - 345962

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
PSA: Elevated
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: Yes
Pathological T: 3a
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: cumulus_PCOS_Obese_rep4

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Obese, rep4

value: Female, Age:31, BMI:37, Tissue:luteinized cumulus cells


title: Wild type, chitooctaose treatment, biological rep2


title: Chitin receptor mutant, chitooctaose treatment, biological rep2


title: Chitin receptor mutant, chitooctaose treatment, biological rep3


title: Wild type, chitooctaose treatment, biological rep3


title: Chitin receptor mutant, chitooctaose treatment, biological rep1


title: cumulus_PCOS_Obese_rep6

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Obese, rep6

value: Female, Age:25, BMI:32, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Obese_rep2

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Obese, rep2

tag: gender

value: Female, Age:35.8, BMI:30, Tissue:luteinized cumulus cells


title: Wild type, water treatment, biological rep3


title: cumulus_PCOS_Lean_rep4

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Lean, rep4

value: Female, Age:32, BMI:25, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Lean_rep5

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Lean, rep5

value: Female, Age:28, BMI:17.1, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Obese_rep5

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep5

value: Female, Age:28, BMI:30, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Obese_rep4

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep4

value: Female, Age:32, BMI:30, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Obese_rep1

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Obese, rep1

value: Female, Age:25, BMI:31, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Lean_rep3

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Lean, rep3

value: Female, Age:25, BMI:23, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Lean_rep2

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Lean, rep2

value: Female, Age:35, BMI:22, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Lean_rep6

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep6

value: Female, Age:29, BMI:22, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Lean_rep1

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Lean, rep1

value: Female, Age:27, BMI:19, Tissue:luteinized cumulus cells


title: cumulus_PCOS_Obese_rep3

source_name: luteinized human cumulus cells, cultured 48h, PCOS, Obese, rep3


title: cumulus_nonPCOS_Obese_rep3

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep3

value: Female, Age:28, BMI:34, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Lean_rep3

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep3

value: Female, Age:30, BMI:24, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Obese_rep2

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep2

value: Female, Age:33, BMI:33, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Lean_rep5

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep5

value: Female, Age:31, BMI:21, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Obese_rep1

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep1

value: Female, Age:35, BMI:27, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Lean_rep4

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep4

value: Female, Age:25, BMI:16, Tissue:luteinized cumulus cells


title: cumulus_nonPCOS_Lean_rep2

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep2

value: Female, Age:27, BMI:21, Tissue:luteinized cumulus cells


title: beta-catenin conditional knockout mouse kidney E12.5, biological rep 1

status: Public on Mar 25 2008

first: Brian

middle: Joseph

last: Cox

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

description: Expression data for normal mousee embryonic day E12.5 kidney

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Hoxb7-Cre,Gfp;beta-catenin deficient mouse embryonic kidney day E12.5

label_protocol: one cycle amplification as per Affymetrix protocol from 1ug of total RNA

extract_protocol: Samples were stored in RNAlater RNA stabilization reagent (Qiagen, Canada) and then isolated using the RNeasy Micro kit (Qiagen, Canada).

treatment_protocol: tissue was disected, imaged by digital microscopy and randomly sorted into one of three sample vials

tag: 6 kidneys from a cross of beta-catenin loxP with Hoxb7-Cre,GFP


title: beta-catenin conditional knockout mouse kidney E12.5, biological rep 2


title: WT hippocampus 3 (Affymetrix)

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Affymetrix default hyb protocol

scan_protocol: Affymetrix default scan protocol

data_processing: MAS5 summarization and subsequent VSN transformation and normalization

source_name: Hippocampus WT mice

label_protocol: Ambion's amplification and labelling kit for Illumina

extract_protocol: Trizol

tag: Male C57/BL6j


title: TG hippocampus 3 (Affymetrix)

source_name: Hippocampus DLCK transgenic mice


title: Immortalized baby mouse kidney cells - tumor derived cell line 5D

city: Piscataway

first: Cristina

middle: M

last: Karp

state: NJ

address: 679 Hoes lane

institute: Rutgers University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneGPL339 (Affymetrix GeneChip  Mouse Expression Array 430A and Mouse Genome 430A 2.0 Array).

data_processing: Initial scaling was done using the Affymetrix  Microarray Suite Expression Software version 5.0 and subsequent analysis was done using GeneSpring Software version 6.1 ( Silicon Genetics).

source_name: Tumor derived cell line

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

growth_protocol: All cell lines were maintained in DMEM (Gibco/InVitrogen) containing 10% fetal bovine serum (FBS).

tag: Genoytpe

value: wild type


title: cumulus_nonPCOS_Lean_rep1

source_name: luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep1

value: Female, Age:28, BMI:17, Tissue:luteinized cumulus cells


title: TG hippocampus 4 (Affymetrix)


title: WT hippocampus 4 (Affymetrix)


title: beta-catenin conditional knockout mouse kidney E12.5, biological rep 3


title: WT hippocampus 6 (Affymetrix)


title: TG hippocampus 1 (Affymetrix)


title: TG hippocampus 5 (Affymetrix)


title: TG hippocampus 2 (Affymetrix)


title: WT hippocampus 1 (Affymetrix)


title: WT hippocampus 2 (Affymetrix)


title: RAW264.7_Infected with MSCV_Puro-selected_Rep1

status: Public on Mar 24 2008

city: Pasadena

first: David

last: Baltimore

address: 1200 E California Blvd

institute: Caltech

description: RAW264.7 infected with MSCV and Puro selected

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix STATISTICAL_ALGORITHM_TYPE

label_protocol: standard Affymetrix procedures

growth_protocol: Cultured in Dulbecco Modification of Eagle's Medium (DMEM) supplemented with fetal bovine serum to a final concentration of 10%. Incubated at 37 degrees in the presence of 5% CO2.

extract_protocol: Total RNA extracted using RNEasy from Qiagen.

treatment_protocol: Infected with MSCV using 10% polybrene during infection. Selected with Puromycin at 7 ug/ml. Single clones were obtained through limiting dilution. RNA was extracted from five individual clones and pooled.

tag: Monocyte/macrophage cell line obtained from the ascites fluid of a male adult Balb/c mouse; Abelson murine leukemia virus transformed.


title: Group 4 siRNA#3 for RIP140 with RA

city: Urbana

first: Michael

last: Spinella

address: 2001 South Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois

description: see above

hyb_protocol: standard affymetrix guidelines, Affy gene chip workstation

scan_protocol: strandard affy guidelines, Affy gene chip workstation

data_processing: Affy gene chip workstation

label: biotin cRNA

source_name: nT2 cells with RIP140 siRNA#3 with RA

label_protocol: standard affymetrix guidelines

growth_protocol: Standard DMEM high glucose media

extract_protocol: RNAeasy columns Qiagen.

treatment_protocol: Transfected with 90 nM of RIP140 siRNA#3 then treated for 24 hours with RA

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with RIP140#3 siRNA and treated with 10 uM retinoic acid (RA) for 24 hours


title: Group 1 replicate 2 RISC-free siRNA from Dharmacon no RA

description: see above

source_name: NT2 cells with RISC-free siRNA no RA

treatment_protocol: Transfected with 90 nM of the Dharmacon RISC-free siRNA then treated for 24 hours with DMSO

tag: human embryonal carcinoma cells tranfected with RISC-free darmacon siRNA and then treated with vehicle (DMSO)


title: Group 3 siRNA#1 for RIP140  no RA

description: see above

source_name: nT2 cells with RIP140 siRNA#1 no RA

treatment_protocol: Transfected with 90 nM of RIP140 siRNA#1 then treated for 24 hours with DMSO

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with RIP140 siRNA#1 and treated with vehicle (DMSO)


title: RAW264.7_Infected with MSCV encoding mir-155_Puro-selected_Rep1

description: RAW264.7 infected with MSCV encoding mir-155 and Puro selected

treatment_protocol: Infected with MSCV encoding mir-155 using 10% polybrene during infection. Selected with Puromycin at 7 ug/ml. Single clones were obtained through limiting dilution. RNA was extracted from five individual clones and pooled.


title: Group 3 siRNA#2 for RIP140  no RA

description: see above

source_name: NT2 cells with RIP140 siRNA#2 no RA

treatment_protocol: Transfected with 90 nM of RIP140 siRNA#2 then treated for 24 hours with DMSO

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with RIP140 siRNA#2 and treated with vehicle (DMSO)


title: Group 4 siRNA#2 for RIP140 with RA

description: see above

source_name: nT2 cells with RIP140 siRNA#2 with RA

treatment_protocol: Transfected with 90 nM of RIP140 siRNA#2 then treated for 24 hours with RA

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with RIP140 siRNA#2 and treated with 10 uM retinoic acid (RA) for 24 hours


title: Group 2 scramble siRNA from Dharmacon treated with RA

description: see above

source_name: NT2 cells with scramble siRNA treated with RA

treatment_protocol: Transfected with 90 nM ofscrambled siRNA then treated for 24 hours with RA

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with scrambled II siRNA and treated with 10 uM retinoic acid (RA) for 24 hours


title: Group 3 siRNA#3 for RIP140  no RA

description: see above

source_name: NT2 cells with RIP140 siRNA#3 no RA

treatment_protocol: Transfected with 90 nM of RIP140 siRNA#3 then treated for 24 hours with DMSO

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with RIP140 siRNA#3 and treated with vehicle (DMSO)


title: Group 2 RISC-free replicate siRNA with RA

description: see above

source_name: nT2 cells with RISC-free siRNA with RA

treatment_protocol: Transfected with 90 nM of RISC-free siRNA then treated for 24 hours with RA

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with RISC-free siRNA and treated with 10 uM retinoic acid (RA) for 24 hours


title: Group 2 RISC-free siRNA from Dharmacon treated with RA

description: see above

source_name: NT2 cells with RISC-free siRNA with RA


title: BCR/ABL_treated_2

status: Public on Mar 22 2008

city: Bar Harbor

first: Shaoguang

last: Li

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: HSC transfected with BCR/ABL and treated.

hyb_protocol: Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C.  Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays are scanned with a GeneChip Scanner 3000.  Images are acquired and cel files generated which are then used for analysis.

data_processing: Affymetrix Expression Console, MAS5 algorithm

source_name: BCR/ABL transduced HSC treated with imatinib

label_protocol: Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence.  The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA.  Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.  The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.

extract_protocol: Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA).

tag: Transfected with BCR/ABL and treated


title: Duodenum-D2WT-Biological rep3

city: Toulouse

first: Marie-Paule

last: Roth

address: Chu Purpan

country: France

institute: Inserm

description: Duodenum-D2WT-Biological rep3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue kit (Qiagen) according to the manufacturer's instructions.

tag: Strain

value: DBA/2, Gender:male, Age:7 weeks, Tissue:duodenum, Genotype:wild-type


title: Duodenum-D2KO-Biological rep2

description: Duodenum-D2KO-Biological rep2

value: DBA/2, Gender:male, Age:7 weeks, Tissue:duodenum, Genotype:Hfe-deficient


title: BCR/ABL_2

description: HSC transfected with BCR/ABL.

source_name: HSC transduced with BCR/ABL

tag: HSC transduced with BCR/ABL


title: BCR/ABL_1

description: HSC transfected with BCR/ABL.

source_name: BCR/ABL transduced HSC

tag: Transfected with BCR/ABL


title: Group 4 siRNA#1 for RIP140  with RA

description: see above

source_name: nT2 cells with RIP140 siRNA#1 with RA

treatment_protocol: Transfected with 90 nM of RIP140 siRNA#1 then treated for 24 hours with RA

tag: human embyonal carcinoma, NT2/D1 cell line tranfected with RIP140 siRNA#1 and treated with 10 uM retinoic acid (RA) for 24 hours


title: Vector_2

description: HSC transfected with empty vector.

source_name: HSC transfected with empty vector

tag: Transfected with empty vector


title: BCR/ABL_treated_1


title: Duodenum-D2WT-Biological rep1

description: Duodenum-D2WT-Biological rep1


title: Duodenum-D2KO-Biological rep1

description: Duodenum-D2KO-Biological rep1


title: Group 1 replicate scramble siRNA no RA

description: see above

source_name: NT2 cells with scramble siRNA no RA

treatment_protocol: Transfected with 90 nM of the Dharmacon scramble II siRNA then treated for 24 hours with DMSO

tag: Human embryonal carcinoma cells tranfected with scramble siRNA from Dharmacon and then treated with vehicle (DMSO)


title: Vector_1

description: HSC transfected with empty vector.


title: Group 1 replicate RISC-free siRNA from Dharmacon no RA

description: see above

tag: Human embryonal carcinoma cells, NT2/D1 transfected with RISC-Free siRNA and treated for 24 hours with vehicle (DMSO)


title: Duodenum-D2WT-Biological rep2

description: Duodenum-D2WT-Biological rep2


title: Duodenum-B6KO-Biological rep2

description: Duodenum-B6KO-Biological rep2

value: C57BL/6, Gender:male, Age:7 weeks, Tissue:duodenum, Genotype:Hfe-deficient


title: Duodenum-B6KO-Biological rep3

description: Duodenum-B6KO-Biological rep3


title: Duodenum-D2KO-Biological rep3

description: Duodenum-D2KO-Biological rep3


title: Duodenum-B6WT-Biological rep3

description: Duodenum-B6WT-Biological rep3

value: C57BL/6, Gender:male, Age:7 weeks, Tissue:duodenum, Genotype:wild-type


title: Duodenum-B6KO-Biological rep1

description: Duodenum-B6KO-Biological rep1


title: Duodenum-B6WT-Biological rep2

description: Duodenum-B6WT-Biological rep2


title: Liver-D2WT-Biological rep3

description: Liver-D2WT-Biological rep3

value: DBA/2, Gender:male, Age:7 weeks, Tissue:liver, Genotype:wild-type


title: Liver-D2KO-Biological rep2

description: Liver-D2KO-Biological rep2

value: DBA/2, Gender:male, Age:7 weeks, Tissue:liver, Genotype:Hfe-deficient


title: Liver-D2WT-Biological rep2

description: Liver-D2WT-Biological rep2


title: Liver-D2KO-Biological rep1

description: Liver-D2KO-Biological rep1


title: Liver-D2KO-Biological rep3

description: Liver-D2KO-Biological rep3


title: Liver-B6KO-Biological rep1

description: Liver-B6KO-Biological rep1

value: C57BL/6, Gender:male, Age:7 weeks, Tissue:liver, Genotype:Hfe-deficient


title: Liver-B6KO-Biological rep3

description: Liver-B6KO-Biological rep3


title: Liver-B6WT-Biological rep1

description: Liver-B6WT-Biological rep1

value: C57BL/6, Gender:male, Age:7 weeks, Tissue:liver, Genotype:wild-type


title: Liver-B6KO-Biological rep2

description: Liver-B6KO-Biological rep2


title: decidualizing Bmp2 f/f uterus horn-3

status: Public on Mar 21 2008

city: Houston

middle: J

last: Large

state: TX

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicine

description: Gene expression data from decidualizing Bmp2 f/f uterus horn

hyb_protocol: The fragmented, labeled cRNA (15 ug) was hybridized to Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: Scanning was done using an Affymetrix 3000 with autoloading scanner performed using Affymetrix protocols.

data_processing: A DNA-Chip analyzer dChIP version 1.3 was utilized to adjust arrays to a common baseline using invariant set normalization. All Genechips (n=6) were normalized together to the same baseline and modeled together.

source_name: decidualizing uterus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: QIAGEN RNeasy total RNA isolation kit.

tag: BMP2 f/f

tag: female

tag: 10 weeks old

tag: mixed background


title: Liver-B6WT-Biological rep3

description: Liver-B6WT-Biological rep3


title: decidualizing Bmp2 f/f uterus horn-1


title: decidualizing Bmp2 d/d uterus horn-1

description: Gene expression data from decidualizing Bmp2 d/d uterus horn

tag: BMP2 d/d


title: Liver-B6WT-Biological rep2

description: Liver-B6WT-Biological rep2


title: decidualizing Bmp2 d/d uterus horn-3


title: Normal control PBMCs, 0h after IL-2 withdrawal, biological replicate 2

city: Sao Paulo

first: Joao

middle: Bosco

last: Oliveira

state: Sao Paulo

address: Av. Dr. Eneas de carvalho Aguiar, 500 IMT Bldg. II 3rd Floor

department: Dermatology

country: Brazil

institute: University os São Paulo

description: Normal control PBMCs activated for 3 days with anti-CD3 + IL-2, then cycled for  3 more days in IL-2 only, lysed for analysis 0h after IL-2 withdrawal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized (in the presence of DMSO) for 16 hr at 45C on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetric Scanner 3000 6G model

source_name: Human T cells-cultured and activated

label_protocol: Affymetix GeneChip Expression 3' amplification reagents for IVT labeling (P/N 900449) was used to prepare Biotinylated cRNA according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ficoll isolated PBMCs were activated for 3 days in culture media (RPMI-1640 + 10% FBS + Pen/Strep + L-glu) in the presence of 1 ug/ml anti-CD3 (OKT3) + IL-25 25 u/ml. Cells were then washed in PBS and cultured for 3 more days in 100 U/ml of IL-2 before cytokine withdrawal

extract_protocol: Qiagen RNeasy mini kit with Dnase treatment (P/N 74104)

treatment_protocol: At the 6th day in culture, IL-2 was washed from the cultures and cells lysed for RNA extraction at 0h or 24h later.

tag: Lymphocytes activated for 3 days, cycled in IL-2 for 3 more days


title: decidualizing Bmp2 f/f uterus horn-2


title: Duodenum-B6WT-Biological rep1

description: Duodenum-B6WT-Biological rep1


title: P58 PBMCs, 24h after IL-2 withdrawal

description: P58 PBMCs activated for 3 days with anti-CD3 + IL-2, then cycled for  3 more days in IL-2 only, lysed for analysis24h after IL-2 withdrawal

tag: Lymphocytes activated for 3 days, cycled in IL-2 for 3 more days, then subjected to IL-2 withdrawal for 24h


title: Normal control PBMCs, 24h after IL-2 withdrawal, biological replicate 2

description: Normal control PBMCs activated for 3 days with anti-CD3 + IL-2, then cycled for  3 more days in IL-2 only, lysed for analysis 24h after IL-2 withdrawal


title: Normal control PBMCs, 24h after IL-2 withdrawal, biological replicate 1


title: ALPS 1A PBMCs, 0h after IL-2 withdrawal

description: ALPS 1A PBMCs activated for 3 days with anti-CD3 + IL-2, then cycled for  3 more days in IL-2 only, lysed for analysis  0h after IL-2 withdrawal


title: SG_Fkh_14APF_rep2

status: Public on Mar 20 2008

city: Fayetteville

last: Lehmann

state: AR

address: SCEN 601

department: Biological Sciences

institute: University of Arkansas

description: Salivary glands from P{hs-Fkh111} animals heat shocked at 9.5 hours after puparium formation and dissected at 14 hours after puparium formation.

hyb_protocol: Hybridization was performed following the instructions provided in the Affymetrix Manual (Section 2), using a Fluidics Station 450 and the Midi_euk2 v3 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip 3000 Scanner 7G and Genechip Operation Software (GCOS) v. 1.4.

data_processing: The data were processed and normalized using dChip 2006. The median intensity of the baseline assay used for normalization was 134.

organism: Drosophila melanogaster

source_name: fkh-expressing salivary glands, heat shocked, dissected 14 hours after puparium formation

label_protocol: Biotin-labeled cRNA was produced using the One-Cycle Eukaryotic Target Labeling Assay recommended by Affymetrix. Labeling was carried out exactly as specified in the instructions manual, section 2.

growth_protocol: Animals were kept at 25 °C, except during heat shock period.

extract_protocol: Salivary glands were dissected on ice and directly transferred to TRIzol Reagent (Invitrogen, Carlsbad, California). To support lysis of the tissue, the mixture was subjected to vigorous vortexing. Total RNA was isolated according to the instructions of the manufacturer. As a last step of the extraction procedure, the RNA was purified using an RNeasy Minikit (Qiagen, Hilden, Germany).

treatment_protocol: Animals were subjected to a 30-min heat shock treatment at 37 °C at 9.5 hours after puparium formation. Salivary glands were dissected for RNA extraction at 14 hours after puparium formation.

tag: Salivary glands of strain P{hs-Fkh111}, heat shocked, dissected at 14 hours after puparium formation.


title: Normal control PBMCs, 0h after IL-2 withdrawal, biological replicate 1


title: SG_Fkh_14APF_rep3


title: ALPS 1A PBMCs, 24h after IL-2 withdrawal

description: ALPS 1A PBMCs activated for 3 days with anti-CD3 + IL-2, then cycled for  3 more days in IL-2 only, lysed for analysis 24h after IL-2 withdrawal


title: decidualizing Bmp2 d/d uterus horn-2


title: SG_Fkh_14APF_rep1

source_name: fkh-expressing salivary glands, heat shocked, dissected at 14 hours after puparium formation


title: P58 PBMCs, 0h after IL-2 withdrawal

description: P58 PBMCs activated for 3 days with anti-CD3 + IL-2, then cycled for  3 more days in IL-2 only, lysed for analysis 0h after IL-2 withdrawal


title: U937_ROS_curcumin_18h_rep3

city: Horsham

first: Paul

last: Kirkham

state: west Sussex

address: Wimblehurst Road

country: United Kingdom

institute: Novartis Institutes for Biomedical Research

description: no additional information

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

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

source_name: differentiated U937 cells, ROS exposed, 1uM curcumin treated, 18h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: The human monocytic cell line (U937) was obtained from the American Type Culture Collection (ATTC, Rockville, MD, USA) and maintained in complete growth media (RPMI 1640 media supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin and 100 g/ml streptomycin) at +37C in a humidified atmosphere with 5% CO2.  U937 were differentiated into an adherent “macrophage-like” morphology by exposure to  PMA (40 ng/ml) for 4 hours in complete growth media at +37C, then cultured for a further 48hrs.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Promega).

treatment_protocol: After differentiation, the U937 cells were starved overnight in phenol red free RPMI 1640 media with 0.5% FCS. The cells were then subjected to oxidative stress for 4 hours with the addition of H2O2 (100 uM). The media was then replaced with fresh complete growth media, and then incubated with/without curcumin (1uM) for a further 4hrs or 18 hrs, whereupon the cells were then harvested and total RNA extracted.

tag: Immortilised monocyte cell line


title: U937_naive_curcumin_18h_rep3

description: no additional information

source_name: differentiated U937 cells, 1uM curcumin treated, 18h


title: U937_naive_untreated_4h_rep3

description: no additional information

source_name: differentiated U937 cells, untreated, 4h


title: U937_ROS_curcumin_18h_rep2

description: no additional information


title: U937_ROS_untreated_4h_rep3

description: no additional information

source_name: differentiated U937 cells, ROS exposed, 4h


title: U937_ROS_curcumin_4h_rep3

description: no additional information

source_name: differentiated U937 cells, ROS exposed, 1uM curcumin treated, 4h


title: U937_ROS_curcumin_4h_rep2

description: no additional information


title: U937_ROS_untreated_4h_rep2

description: no additional information


title: U937_ROS_curcumin_18h_rep1

description: no additional information


title: U937_naive_untreated_18h_rep1

description: no additional information

source_name: differentiated U937 cells, untreated, 18h


title: U937_naive_untreated_18h_rep2

description: no additional information


title: U937_naive_curcumin_18h_rep2

description: no additional information


title: U937_naive_untreated_4h_rep2

description: no additional information


title: U937_naive_untreated_18h_rep3

description: no additional information


title: U937_ROS_untreated_18h_rep3

description: no additional information

source_name: differentiated U937 cells, ROS exposed, 18h


title: U937_naive_curcumin_18h_rep1

description: no additional information


title: U937_naive_curcumin_4h_rep3

description: no additional information

source_name: differentiated U937 cells, 1uM curcumin treated, 4h


title: U937_naive_curcumin_4h_rep2

description: no additional information


title: U937_ROS_curcumin_4h_rep1

description: no additional information


title: U937_ROS_untreated_18h_rep1

description: no additional information


title: U937_ROS_untreated_18h_rep2

description: no additional information


title: U937_ROS_untreated_4h_rep1

description: no additional information


title: U937_naive_untreated_4h_rep1

description: no additional information


title: U937_naive_curcumin_4h_rep1

description: no additional information


title: Vehicle 2 hrs Donor 5

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

description:
Sample_Treatment_[C] = Vehicle
Sample_Treatment_amount_[C] = (Not applicable)
Sample_Treatment_2_[C] = (Not applicable)
Sample_Treatment_2_amount_[C] = (Not applicable)
Sample_Treatment_Source = (Not applicable)
Sample_Treatment_2_Source = (Not applicable)
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.

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

scan_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: GeneChips were scanned using the Affymetrix 3000 Scanner

label_protocol: Microarray on Affymetrix Human Genome U133_plus 2.0 arrays was performed according to established protocols

growth_protocol: Human monocytes were purified from anonymous healthy donor Buffycoats obtained from Massachusetts General Hospital. Buffycoats were stored at 4°C overnight for cell isolation the following day. Monocytes were isolated by negative selection using RosetteSep (Stem Cell Technologies, 15068) according to the manufacturer’s protocol by density centrifugation over Histopaque (SIGMA, H8889).  Monocytes were maintained in RPMI 1640 (Mediatech, Inc., 15-040-CV) supplemented with 10% fetal bovine serum (SIGMA, F-9423) that had been heat-inactivated. All incubations were at 37°C in a tissue culture incubator maintained at 5% CO2.

extract_protocol: Total RNA was isolated after 2 hour treatment using QIAshredders and RNeasy miniprep kits according to the manufacturer’s protocol (QIAGEN, 79654 and 74104, respectively). Total RNA yields ranged from 1-6 mg. Residual genomic DNA was removed by DNase treatment and phenol/chloroform extraction followed by ethanol precipitation using standard techniques.

tag: Anonymous Donor


title: Vehicle 2 hrs Donor 2


title: Vehicle 2 hrs Donor 1


title: Control 2 hrs Donor 2

description:
Sample_Treatment_[C] = Control Ab
Sample_Treatment_amount_[C] = 5 ug/ml
Sample_Treatment_2_[C] = (Not applicable)
Sample_Treatment_2_amount_[C] = (Not applicable)
Sample_Treatment_Source = a-E.tenella, Wyeth
Sample_Treatment_2_Source = (Not applicable)
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.


title: Control 2 hrs Donor 7


title: Vehicle 2 hrs Donor 9


title: Control 2 hrs Donor 3


title: Control 2 hrs Donor 10


title: Vehicle 2 hrs Donor 4


title: Control 2 hrs Donor 1


title: Control 2 hrs Donor 8


title: Vehicle 2 hrs Donor 7


title: Vehicle 2 hrs Donor 3


title: Control 2 hrs Donor 11


title: Vehicle 2 hrs Donor 11


title: Control 2 hrs Donor 9


title: Control 2 hrs Donor 6


title: Vehicle 2 hrs Donor 8


title: Control 2 hrs Donor 4


title: Anti-Trem1/LPS 2 hrs Donor 11

description:
Sample_Treatment_[C] = Anti-Trem1
Sample_Treatment_amount_[C] = 5 ug/ml
Sample_Treatment_2_[C] = Lipopolysaccharide
Sample_Treatment_2_amount_[C] = 1 ng/ml
Sample_Treatment_Source = R&D Systems Cat MAB1278
Sample_Treatment_2_Source = Sigma Cat L2262
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.


title: Anti-Trem1/LPS 2 hrs Donor 5


title: Anti-Trem1/LPS 2 hrs Donor 10


title: Anti-Trem1/LPS 2 hrs Donor 3


title: Vehicle 2 hrs Donor 6


title: Control 2 hrs Donor 5


title: Anti-Trem1/LPS 2 hrs Donor 7


title: Anti-Trem1/LPS 2 hrs Donor 6


title: Anti-Trem1/LPS 2 hrs Donor 1


title: Anti-Trem1/LPS 2 hrs Donor 2


title: Liver-D2WT-Biological rep1

description: Liver-D2WT-Biological rep1

tag: Strain


title: Anti-Trem1/LPS 2 hrs Donor 9


title: LPS Low 2 hrs Donor 2

description:
Sample_Treatment_[C] = Lipopolysaccharide
Sample_Treatment_amount_[C] = 1 ng/ml
Sample_Treatment_2_[C] = (Not applicable)
Sample_Treatment_2_amount_[C] = (Not applicable)
Sample_Treatment_Source = Sigma Cat L2262
Sample_Treatment_2_Source = (Not applicable)
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.


title: Anti-Trem1/LPS 2 hrs Donor 4


title: LPS Low 2 hrs Donor 1


title: LPS Low 2 hrs Donor 7


title: LPS Low 2 hrs Donor 6


title: LPS Low 2 hrs Donor 10


title: LPS Low 2 hrs Donor 9


title: Control/LPS 2 hrs Donor 6

description:
Sample_Treatment_[C] = Control Ab
Sample_Treatment_amount_[C] = 5 ug/ml
Sample_Treatment_2_[C] = Lipopolysaccharide
Sample_Treatment_2_amount_[C] = 1 ng/ml
Sample_Treatment_Source = a-E.tenella, Wyeth
Sample_Treatment_2_Source = Sigma Cat L2262
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.


title: LPS Low 2 hrs Donor 3


title: Control/LPS 2 hrs Donor 7


title: LPS Low 2 hrs Donor 8


title: Control/LPS 2 hrs Donor 10


title: LPS Low 2 hrs Donor 11


title: LPS Low 2 hrs Donor 4


title: Control/LPS 2 hrs Donor 4


title: Control/LPS 2 hrs Donor 8


title: Control/LPS 2 hrs Donor 5


title: Anti-Trem1 2 hrs Donor 8

description:
Sample_Treatment_[C] = Anti-Trem1
Sample_Treatment_amount_[C] = 5 ug/ml
Sample_Treatment_2_[C] = (Not applicable)
Sample_Treatment_2_amount_[C] = (Not applicable)
Sample_Treatment_Source = R&D Systems Cat MAB1278
Sample_Treatment_2_Source = (Not applicable)
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.


title: Control/LPS 2 hrs Donor 2


title: Anti-Trem1 2 hrs Donor 10


title: Anti-Trem1 2 hrs Donor 4


title: Control/LPS 2 hrs Donor 3


title: Control/LPS 2 hrs Donor 9


title: Anti-Trem1 2 hrs Donor 6


title: Anti-Trem1 2 hrs Donor 11


title: Anti-Trem1 2 hrs Donor 9


title: Anti-Trem1 2 hrs Donor 1


title: Anti-Trem1 2 hrs Donor 2


title: Anti-Trem1 2 hrs Donor 5


title: Anti-Trem1 2 hrs Donor 7