title: Liver 12

city: Oulu

first: Mirella

last: Hietaniemi

address: Aapistie 5A

department: Department of Internal Medicine, Biocenter Oulu

country: Finland

institute: University of Oulu

description: Gene expression data from a liver biopsy obtained from an obese woman

hyb_protocol: Biotinylated cRNA was cleaned with an GeneChip Sample Cleanup Module (Qiagen), fragmented to 35 to 200 nt, and hybridized to Affymetrix Human Genome U133 Plus 2 arrays.

scan_protocol: After being washed, the array was stained with streptavidin-phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories) and second staining with streptavidin-phycoerythrin, and then scanned on GeneChip Scanner 3000.

data_processing: Affymetrix CEL files were imported into GeneSpring 7.2 software (Silicon Genetics) and RMA normalization was performed.

source_name: Liver sample

label_protocol: Using 8 µg of total RNA as template double-stranded DNA was synthesized by means of the One-cycle cDNA synthesis kit (Affymetrix) and T7-(dT)24 primer. The DNA was purified using GeneChip Sample Cleanup Module (Qiagen). In vitro transcription was performed to produce biotin labeled cRNA using a IVT labeling kit (Affymetrix) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from liver tissue using the RNeasy  mini kit (Qiagen).  RNA concentration and purity were assessed spectrophotometrically at wavelengths 260 and 280 nm. RNA integrity was checked by agarose gel electrophoresis.

treatment_protocol: Hypocaloric, low-fat AHA step I diet

tag: group

value: diet intervention, age:60 years, wigth loss:-7 kg


title: Liver 1

status: Public on Jul 23 2008

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Liver sample from control subject

treatment_protocol: Weight maintenance, keeping up habitual diet

value: control, age:61 years, weight loss:0 kg


title: Liver 26

treatment_protocol: Hypocaloric, low fat AHA step I diet

value: diet intervention, age:60 years, weight loss:-3 kg


title: MHLiv

value: control, age:77 years, weight loss:0 kg


title: Liver 2

value: diet intervention, age:58 years, weight loss:-3.4 kg


title: 2 hr Non-Stress IP RNA Rep 3

status: Public on Jul 22 2008

city: Riverside

first: Charles

last: Jang

state: CA

address: 2215 Batchelor Hall

department: Botany and Plant Sciences

country: USA

institute: UC Riverside

description: Comparison of 2 and 9 hour hypoxia stress and 9 hour hypoxia stess with 1 hour recovery to non-stress seedlings

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 oC for 16 h, in a rotating platform, using 15 µg of Biotin-labeled cRNA.

scan_protocol: Affymetrix scan protocol

data_processing: Expression data obtained in .cel files was extracted by use of the Bioconductor package of the R statistical software. Low-level normalization followed and was carried out using Robust Multichip Average (RMA). Present, Marginal or Absent (P/M/A) calls, a

label: Biotin

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: 7 day old Arabidopsis Seedling  2hr Non-Stress IP RNA

label_protocol: Total and polysomal RNA samples derived from three independent biological replicate experiments were used for microarray hybridization analysis. RNA samples (3 µg) were used to synthesize double stranded cDNA, using One-Cycle cDNA synthesis Kit (Affymetri

growth_protocol: Seeds from single copy transgene 35S:His6FLAG-RPL18B (Col-0) (Zanetti et al., 2005) were surface sterilized with 95 % (v/v) ethanol for 5 min, followed by 10 min submergence in bleach solution (20 % (v/v) bleach and 0.1 % (v/v) Tween-20), rinsed ad vernal

extract_protocol: Whole seedlings were harvested into liquid nitrogen within < 3 min from release from treatment.  All mRNA extraction procedures were performed at 4 oC or on ice. Approximately 5 mL of pulverized tissue was extracted in 10 mL of Polysome Extraction Buffer

treatment_protocol: Seven-day old seedlings were subjected to short and long  hypoxia stress (HS) treatments (2h and 9h) or allowed to recover after 9h HS for 1h in air (re-oxygenation). Treatments started at the end of the light period and took place 6.5 µM m-1 s-1 light, i

tag: Age

value: 7 day old seedlings

tag: Genotype

value: 35S:His6FLAG-RPL18B (Col-0)


title: 9 hr Hypoxia Stress 1 hr recovery IP RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  9hr Hypoxia Stress + 1 hr recovery IP RNA


title: 9 hr Hypoxia Stress 1 hr recovery Total RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  9hr Hypoxia Stress + 1 hr recovery Total RNA


title: 9 hr Non-Stress Total RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  9hr Non-Stress Total RNA


title: 2 hr Hypoxia Stress IP RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  2hr Hypoxia Stress IP RNA


title: 9 hr Non-Stress IP RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  9hr Non-Stress IP RNA


title: 9 hr Hypoxia Stress IP RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  9hr Hypoxia Stress IP RNA


title: Liver 25

value: control, age:55 years, weight loss:-1 kg


title: Liver 9

value: control, age:51 years, weight loss:-0.6 kg


title: Liver 3

value: diet intervention, age:55 years, weight loss:-5.0 kg


title: 2 hr Non-Stress Total RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  2hr Non-Stress Total RNA


title: 2 hr Hypoxia Stress Total RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  2hr Hypoxia Stress Total RNA


title: 9 hr Hypoxia Stress Total RNA Rep 3

source_name: 7 day old Arabidopsis Seedling  9hr Hypoxia Stress Total RNA


title: 9 hr Non-Stress Total RNA Rep 2


title: 2 hr Hypoxia Stress IP RNA Rep 2


title: 9 hr Hypoxia Stress 1 hr recovery Total RNA Rep 2


title: 9 hr Hypoxia Stress 1 hr recovery IP RNA Rep 2


title: 9 hr Non-Stress IP RNA Rep 2


title: 9 hr Hypoxia Stress IP RNA Rep 2


title: 2 hr Non-Stress IP RNA Rep 2


title: 9 hr Hypoxia Stress 1 hr recovery IP RNA Rep 1


title: 2 hr Hypoxia Stress Total RNA Rep 2


title: 9 hr Hypoxia Stress IP RNA Rep 1


title: 2 hr Non-Stress Total RNA Rep 2


title: 2 hr Hypoxia Stress IP RNA Rep 1


title: 9 hr Non-Stress IP RNA Rep 1


title: 9 hr Hypoxia Stress Total RNA Rep 1


title: classIIhiMECs NODaireWT rep1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: MHC class II high thymic medullary epithelial cells, NODaireWT jos3384

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

organism: Mus musculus

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: Gender

value: male Age:3-4.5 weeks Isolation:FACS of CD45-G8.8+Ly51intclassIIhi TECs Strain:NOD


title: classIIhiMECs NODaireKO rep2

description: MHC class II high thymic medullary epithelial cells, NODaireKO jos3787


title: classIIhiMECs BALBaireKO rep2

description: MHC class II high thymic medullary epithelial cells, BALBaireKO jos3130

value: male Age:3-4.5 weeks Isolation:FACS of CD45-G8.8+Ly51intclassIIhi TECs Strain:BALB/c


title: 9 hr Hypoxia Stress 1 hr recovery Total RNA Rep 1


title: 9 hr Hypoxia Stress Total RNA Rep 2


title: classIIhiMECs NODaireWT rep3

description: MHC class II high thymic medullary epithelial cells, NODaireWT jos3788


title: classIIhiMECs NODaireKO rep1

description: MHC class II high thymic medullary epithelial cells, NODaireKO jos3385


title: classIIhiMECs BALBaireKO rep3

description: MHC class II high thymic medullary epithelial cells, BALBaireKO jos3381


title: classIIhiMECs NODaireKO rep3

description: MHC class II high thymic medullary epithelial cells, NODaireKO jos3789


title: classIIhiMECs BALBaireWT rep4

description: MHC class II high thymic medullary epithelial cells, BALBaireWT jos3382


title: classIIhiMECs NODaireWT rep2

description: MHC class II high thymic medullary epithelial cells, NODaireWT jos3786


title: B16 at doxorubicine 4h

status: Public on Jul 18 2008

city: Charlestown

first: Chun

last: Kim

address: Bldg 149, 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

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

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

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

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

source_name: B16 Mouse Melanoma Cell at 4h after ET treatment

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

growth_protocol: B16 mouse melanoma cells were cultured in DMEM medium containing antibiotics and 10% FBS.

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

treatment_protocol: On the experiment day, B16 cells were treated with 1 microgram/ml of doxorubicin.


title: B16 at doxorubicine 2h

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

source_name: B16 Mouse Melanoma Cell at 2h after ET treatment


title: classIIhiMECs BALBaireWT rep2

description: MHC class II high thymic medullary epithelial cells, BALBaireWT jos3129


title: classIIhiMECs BALBaireWT rep3

description: MHC class II high thymic medullary epithelial cells, BALBaireWT jos3380


title: 2 hr Non-Stress IP RNA Rep 1


title: 2 hr Non-Stress Total RNA Rep 1


title: classIIhiMECs BALBaireKO rep1

description: MHC class II high thymic medullary epithelial cells, BALBaireKO jos3128


title: MCF-7

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Human Genetics

country: Denmark

institute: University of Aarhus

description: Gene expression data from breast cancer cell line MCF-7.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on 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 GeneChip 3000 scanner.

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

source_name: Breast cancer cell line (MCF-7)

growth_protocol: Cells were routinely cultured in DMEM medium supplemented with 10% fetal bovine serum and collected during the growth phase before confluence.

tag: Human mammary malignant epithelium cell line

tag: Cell line was established from metastatic cells in pleural effusions collected from an individual ductal invasive breast cancers


title: B16 at doxorubicnie 0h

description: Gene expression data from murine BMDM

source_name: B16 Mouse Melanoma Cell at 0h


title: classIIhiMECs BALBaireKO rep4

description: MHC class II high thymic medullary epithelial cells, BALBaireKO jos3383


title: 2 hr Hypoxia Stress Total RNA Rep 1

description: Comparison of 2 and 9 hour hypoxia stress and 9 hour hypoxia stess with 1 hour recovery to non-stress seedlings


title: ES LUC esiRNA day4 rep4

city: Dresden

first: Li

last: Ding

address: Pfotenhauerstr. 108

country: Germany

institute: MPI-CBG

description: lipofection mediated esiRNA knockdown

hyb_protocol: 15 µg fragmented cRNA was hybridised for 16 h at 45 °C to Mouse Genome 430 2.0 arrays which carry probes representing 45101 probe sets. Following hybridisation arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 450.

scan_protocol: scanned using the Hewlett-Packard GeneChip Scanner 3000 7G.

data_processing: The image data were analysed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalisation method. After RMA normalisation (Irizarry et al., 2003) and outlier removement using the Nalimov test (p< 0.001) have been performed.

source_name: ES cells

label_protocol: One-cycle target labeling and control reagent package (Affymetrix)

extract_protocol: Total RNA was isolated by using the RNeasy Mini kit (Qiagen) and treated with DNase (Qiagen).

tag: Strain

tag: Passage


title: ES Ctr9 esiRNA day4 rep1

description: lipofection mediated esiRNA knockdown


title: MDA-MB-231

description: Gene expression data from breast cancer cell line MDA-MB-231.

source_name: Breast cancer cell line (MDA-MB-231)


title: ES Ctr9 esiRNA day4 rep4

description: lipofection mediated esiRNA knockdown


title: ES Ctr9 esiRNA day4 rep3

description: lipofection mediated esiRNA knockdown


title: pool of thyroids from 6 months old RET-PTC transgenic mice

city: Brussels

first: Vincent

last: Detours

address: 808 Route de Lennik

department: School of Medicine

country: Belgium

institute: Free University of Brussels

description: To understand the different steps leading to thyroid carcinoma, we analyzed thyroid gene expression in two transgenic strains at different ages (2, 6, 10 months) by microarray technology

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: GCRMA normalized data (Wu et al. Journal of the American Statistical Association, 2004 vol 99 page 909)

label_protocol: Standard Affymetrix procedure

extract_protocol: Standard Affymetrix procedure

tag: RET-PTC, 6 months


title: pool of thyroids from 10 months old RET-PTC transgenic mice

tag: RET-PTC, 10 months


title: ES LUC esiRNA day4 rep3

description: lipofection mediated esiRNA knockdown


title: ES Ctr9 esiRNA day4 rep2

description: lipofection mediated esiRNA knockdown


title: ES LUC esiRNA day4 rep1

description: lipofection mediated esiRNA knockdown


title: pool of thyroids from 10 months old E7 transgenic mice

tag: E7, 10 months


title: pool of wild type thyroids from 2 months old wild type mice

data_processing: GCRMA (Wu et al. Journal of the American Statistical Association, 2004 vol 99 page 909)

tag: wild type; 2 months


title: 9 hr Non-Stress Total RNA Rep 1


title: pool of thyroids from 6 months old E7 transgenic mice

tag: E7, 6 months


title: ES LUC esiRNA day4 rep2

description: lipofection mediated esiRNA knockdown


title: pool of thyroids from 2 months old RET-PTC transgenic mice

tag: RET-PTC, 2 months


title: EWS primary tumor no evidence of disease (R69)

status: Public on Jul 15 2008

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

description: Gene expression data from EWS primary tumor

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

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

data_processing: Single samples were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Data were then rescaled within each array and between arrays through an affine transformation (Bengtsson and Hossjer 2006).

source_name: EWS human sample

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

tag: EWS primary tumor (NED -no evidence of disease)


title: EWS primary tumor no evidence of disease (R78)


title: EWS metastasis tumor metastasis (R81)

description: Gene expression data from EWS metastasis tumor

tag: EWS metastasis tumor (MET - metastasis)


title: EWS primary tumor relapse (R67)

tag: EWS primary tumor (REL - relapse)


title: EWS metastasis tumor metastasis (R84)


title: EWS primary tumor relapse (R64)


title: classIIhiMECs BALBaireWT rep1

description: MHC class II high thymic medullary epithelial cells, BALBaireWT jos3127

value: male Age:3-4.5 weeks Isolation:FACS of CD45-G8.8+Ly51intclassIIhi TECs

value: BALB/c


title: EWS primary tumor relapse (R72)


title: EWS primary tumor relapse (R80)


title: pool of thyroids from 10 months old wild type mice

tag: wild type; 10 months


title: EWS metastasis tumor metastasis (R83)


title: pool of thyroids from 6 months old wild type mice

tag: wild type; 6 months


title: pool of thyroids from 2 months old E7 transgenic mice

tag: E7, 2 months


title: EWS primary tumor no evidence of disease (R79)


title: EWS primary tumor no evidence of disease (R74)


title: EWS primary tumor relapse (R65)


title: EWS primary tumor no evidence of disease (R62)


title: EWS primary tumor no evidence of disease (R63)


title: EWS primary tumor no evidence of disease (R60)


title: EWS primary tumor relapse (R58)


title: EWS primary tumor no evidence of disease (R61)


title: EWS metastasis tumor metastasis (R55)


title: EWS primary tumor no evidence of disease (R53)


title: EWS primary tumor no evidence of disease (R41)


title: EWS metastasis tumor metastasis (R49)


title: EWS primary tumor relapse (R40)


title: EWS primary tumor no evidence of disease (R42)


title: EWS primary tumor no evidence of disease (R34)


title: EWS metastasis tumor metastasis (R50)


title: EWS primary tumor relapse (R57)


title: EWS primary tumor relapse (R46)


title: EWS primary tumor relapse (R35)


title: EWS primary tumor relapse (R33)


title: EWS primary tumor relapse (R37)


title: EWS primary tumor relapse (R38)


title: EWS primary tumor relapse (R194)


title: EWS metastasis tumor metastasis (R48)


title: EWS primary tumor relapse (R39)


title: EWS primary tumor relapse (R51)


title: NELF depleted 0610_Dm_S2_NELF-depleted_2

status: Public on Jul 14 2008

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using Drosophila Genome 2.0 Genechip® arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 5.1).  This system performs data pre-processing and error modeling as described in Weng (2004).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster S2 cells that have been depleted of the NELF complex using dsRNA targeting NELF-B and NELF-E, 72 hour treatment

growth_protocol: Cells were grown in Shields and Sang medium, supplemented with bactopeptone and yeast extract, plus 10% Fetal Bovine Serum, as recommended by the Drosophila Genomics Resource Center

extract_protocol: The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer’s protocol.

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-80

tag: Drosophila melanogaster S2 cells, male, largely tetraploid


title: EWS primary tumor relapse (R29)


title: NELF depleted 0610_Dm_S2_NELF-depleted_3

hyb_protocol: 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-81


title: NELF depleted 0610_Dm_S2_NELF-depleted_1

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-79


title: EWS primary tumor no evidence of disease (R30)


title: LacZ treated 0610_Dm_S2_LacZ-treated_2

source_name: Drosophila melanogaster S2 cells that have been treated for 72 hours with dsRNA targeting Beta-galactosidase (mock-treated control)

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-77


title: LacZ treated 0610_Dm_S2_LacZ-treated_3

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-78


title: LacZ treated 0610_Dm_S2_LacZ-treated_1

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-76


title: Untreated 0610_Dm_S2_untreated_3

source_name: Drosophila melanogaster S2 cells (no treatment control)

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-75


title: E14.5

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

description: Whole lung E14.5

hyb_protocol: Standard Affymetrix Procedures

scan_protocol: Standard Affymetrix Procedures

data_processing: Standard RMA normalization, Affy package (Bioconductor), www.bioconductor.org

source_name: Whole lung E14.5

label_protocol: Standard Affymetrix Procedures

extract_protocol: Ambion, miRVana miRNA isolation kit (yields total RNA including small RNAs)


title: E16.5

description: Whole lung E16.5

source_name: Whole lung E16.5


title: Untreated 0610_Dm_S2_untreated_ 2

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-74


title: E13.5

description: Whole lung E13.5

source_name: Whole lung E13.5


title: E11.5

description: Whole lung E11.5

source_name: Whole lung E11.5

value: C57BL/6J, pooled sample


title: lymphoblast_Control_rhodopsin_001-204

first: Dyonne

middle: T.

last: Hartong

address: 243 Charles Street

department: Massachusetts Eye and Ear Infirmary

hyb_protocol: RNA was further processed at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. 2. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. 3. Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

scan_protocol: Affymetrix Microarray Suite 5.0 was used as scanning software. The target mRNA from the cell sample of interest is fragmented, fluorescently labeled, and washed over the array. Ideally, the components of the target mRNA sample will specifically hybridize to the intended PM strand. The MM strand serves as a control for non-specific cross-hybridization. The fluorescence levels at each PM and MM are then measured using a scanning microscope. MAS software outputs detected fluorescence levels at each probe. When the scanning microscope reads fluorescence activity, it dissects each probe cell (that is, each individual PM and MM cell) into a 6x6 square of pixels, and records the fluorescence levels at each pixel in a file with extension .DAT. To summarize the fluorescence at each cell, MAS ignores the 20 border pixels and returns the 75th percentile fluorescence level of the remaining 16 pixels as the Average Intensity of the probe cell, and records these values in the .CEL file.

data_processing: Raw data reflecting hybridization intensities, from individual probes of 25 different chips were provided as Microarray Suite (MAS) 5.0 experiment data files: .CHP, .TXT, .RPT, .EXP, .CEL (the .TXT and .CEL files are linked below as supplementary files), and were normalised using d-Chip. Background information is provided on the website: http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm  The normalized data were extracted into a Microsoft Excel file and hybridization intensities from all probes of the affected patients in individual families were compared to all of the other samples. Significance in multiplex families was tested using a one-tailed Student’s t-test assuming unequal variance, a Bonferroni correction and P-value < 0.05. In families with only one available patient, the transcript in that patient had to have a hybridization signal more than two standard deviations below the mean hybridization intensity in all other patients.

source_name: Lymphoblast cell line from transformed lymphocytes.

label_protocol: RNA was labeled at the Dana Farber Cancer Institute Microarray Core Facility using their standard protocol detailed below. 1. RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. 2. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. 3. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 4. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Lymphoblasts were immortalized and grown at the Harvard Partners Center for Genetics and Genomics. Prior to harvesting for mRNA isolation, cells were grown to confluence in T25 flasks (10 ml media/flask), and then transferred to T75 flasks with an additional 15 ml of fresh media. When the cells reached confluence (typically after 3 - 6 weeks), another 25 ml of media was added, for a total of 50 ml.  The cells were harvested 24 hours after adding media.

extract_protocol: Harvested lymphoblast cell lines were pelleted by centrifugation at 1200 RPM at room temperature and washed twice with PBS buffer and repelleted. Cell pellet was suspended in 2 ml of Trizol, divided into 4 aliquots, and kept at -80 C.  An aliquot of the lymphoblast-Trizol suspension was thawed and RNA was purified using the Promega SV Total RNA Isolation kit and resuspended in RNAse-free water.

tag: human_male_dominant retinitis pigmentosa_transformed lymphocyte


title: lymphoblast_RPisolate_003-173

tag: human_male_recessive retinitis pigmentosa_transformed lymphocyte


title: lymphoblast_Control_Usher_184-135


title: lymphoblast_RPisolate_003-162


title: Untreated 0610_Dm_S2_untreated_1

treatment_protocol: Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73


title: lymphoblast_RPisolate_003-152

tag: human_female_recessive retinitis pigmentosa_transformed lymphocyte


title: lymphoblast_Control_Usher_184-137


title: NAB1

first: Peter

last: Oettgen

address: Harvard Institutes of Medicine, 4 Blackfan Circle

department: Department of Medicine

institute: Beth Israel Deaconess Medical Center

description: CD144 NEGATIVE CELLS AT DAY 3.5

scan_protocol: GeneChips were scanned using the Affymetrix standrad scanner.

source_name: CD144 NEGATIVE CELLS AT DAY 3.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES Cell Medium - DMEM (high glucose) Media supplements: Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol, LIF Culture conditions: 37 C, 5% CO2

extract_protocol: RNAEasy kit from QIAGEN.

tag: CD144 NEGATIVE CELLS AT DAY 3.5


title: P5

description: Whole lung P5

source_name: Whole lung P5

tag: Strain


title: lymphoblast_RPfamily_6_219-003


title: NHP2

description: CD41 NEGATIVE CELLS AT DAY 3.5

source_name: CD41 NEGATIVE CELLS AT DAY 3.5

tag: CD41 NEGATIVE CELLS AT DAY 3.5


title: NET2

description: CD144 NEGATIVE CELLS AT DAY 6.5

source_name: CD144 NEGATIVE CELLS AT DAY 6.5

tag: CD144 NEGATIVE CELLS AT DAY 6.5


title: lymphoblast_Control_normal_226-1823


title: lymphoblast_RPisolate_003-146


title: lymphoblast_RPisolate_003-115


title: lymphoblast_RPfamily_6_219-004


title: NET1

description: CD144 NEGATIVE CELLS AT DAY 6.5


title: lymphoblast_RPisolate_003-053


title: NHB1

description: VEGFR2 NEGATIVE cells at day 2.5

source_name: VEGFR2 NEGATIVE CELLS AT DAY 2.5

tag: VEGFR2 NEGATIVE cells at day 2.5


title: lymphoblast_RPisolate_003-131


title: NAB2

description: CD144 NEGATIVE CELLS AT DAY 3.5


title: NHB2

description: VEGFR2 NEGATIVE cells at day 2.5


title: lymphoblast_RPfamily_6_219-002


title: ET2

description: CD144 POSITIVE CELLS AT DAY 6.5

source_name: CD144 POSITIVE CELLS AT DAY 6.5

tag: CD144 POSITIVE CELLS AT DAY 6.5


title: ET1

description: CD144 POSITIVE CELLS AT DAY 6.5


title: AB2

description: CD144 POSITIVE CELLS AT DAY 3.5

source_name: CD144 POSITIVE CELLS AT DAY 3.5

tag: CD144 POSITIVE CELLS AT DAY 3.5


title: NHP1

description: CD41 NEGATIVE CELLS AT DAY 3.5


title: lymphoblast_RPfamily_5_226-065


title: lymphoblast_RPfamily_6_003-046


title: lymphoblast_RPfamily_5_003-050


title: lymphoblast_RPfamily_4_218-340


title: HP2

description: CD41 POSITIVE CELLS AT DAY 3.5

source_name: CD41 POSITIVE CELLS AT DAY 3.5

tag: CD41 POSITIVE CELLS AT DAY 3.5


title: lymphoblast_RPfamily1_218-237


title: lymphoblast_RPfamily_3_003-174


title: AB1

description: CD144 POSITIVE CELLS AT DAY 3.5


title: HB1

description: VEGFR2 POSITIVE cells at day 2.5

source_name: VEGFR2 POSITIVE CELLS AT DAY 2.5

tag: VEGFR2 POSITIVE cells at day 2.5


title: HP1

description: CD41 POSITIVE CELLS AT DAY 3.5


title: lymphoblast_RPfamily_2_003-166


title: HB2

description: VEGFR2 POSITIVE cells at day 2.5


title: lymphoblast_RPfamily_2_218-304


title: lymphoblast_RPfamily1_003-116


title: Chromophobe: OB04-20A1

status: Public on Jul 12 2008

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

hyb_protocol: Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.

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

data_processing: Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.

source_name: renal cell carcinoma tissue obtained surgically

label_protocol: RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)

extract_protocol: Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization.  Approximately 30 mg of fresh tissues was used for each sample.  For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization.  Approximately 30 mg of fresh tissues was used for each sample.  For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization.  Approximately 30 mg of fresh tissues was used for each sample.  For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.

tag: renal cell carcinoma


title: Oncocytoma: OB03-78A1


title: lymphoblast_RPfamily_4_003-019


title: lymphoblast_RPfamily_3_003-175


title: Chromophobe: OB04-210A4


title: Chromophobe: OB03-1A1


title: Oncocytoma: OB03-97A1


title: Chromophobe: 0B05-335_U133


title: Oncocytoma: 0B05-305_U133


title: Oncocytoma: 0B03-123_U133


title: Chromophobe: 0B05-268_U133


title: Oncocytoma: OB04-133A1


title: Oncocytoma: OB03-44A1


title: Oncocytoma: 0B04-340_U133


title: Oncocytoma: OB04-123A1


title: Chromophobe: OB03-59A1


title: Chromophobe: OB05-178_U133


title: Chromophobe: OB03-110A1


title: Chromophobe: OB04-65A1


title: Oncocytoma: OB04-22A1


title: MDA-MB-231_TR6194: transfected with a vector containing a shRNAs against CD146

status: Public on Jul 11 2008

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description: MDA-MB-231 transfected with a vector containing a shRNAs against CD146

hyb_protocol: Preparation of cRNA, hybridizations, washes and detection were done as recommended by the supplier. www.affymetrix.com

extract_protocol: Total RNA was isolated from 1 to 2 x 106 cells using an RNA extraction kit (Macherey-Nagel GmBH & Co, Düren, Germany)

tag: MDA-MB-231 (human, Caucasian, breast, adenocarcinoma)


title: T3-4 (HCC stage 3-4)

city: Taipei

first: Ann-Ping

last: Tsou

address: No. 155, Sec. 2, Li-Nong St., Beitou District

country: Taiwan

institute: National Yang-Ming University

description: Tissue

hyb_protocol: see Affymetrix GeneChip Human Genome U133 Plus 2.0 Array manufacturer's web site

data_processing: The arrays were scanned using an Affimetrix GeneChip scanner 3000. The resulting image data was captured and converted to digital output using GeneChip Operating Software v.1.1.1. The absolute results (*.chp) from different experiments (probe arrays of the same type) that are scaled to the same target signal using the All Probe Sets scaling option (scaling factor, 500) may be directly compared. Parameter: Alpha1=0.05, Alpha2=0.065, Tau=0.015.

source_name: Human Liver

extract_protocol: Total RNA was prepared by Trizol extraction

tag: HCC stage 3


title: T3-1 (HCC stage 3-1)

description: Tissue

scan_protocol: see Affymetrix GeneChip Human Genome U133 Plus 2.0 Array manufacturer's web site


title: T3-2 (HCC stage 3-2)

description: Tissue

label_protocol: see Affymetrix GeneChip Human Genome U133 Plus 2.0 Array manufacturer's web site


title: MDA-MB-231_TR6196: transfected with a vector containing a shRNAs against CD146

scan_protocol: Preparation of cRNA, hybridizations, washes and detection were done as recommended by the supplier. www.affymetrix.com


title: T3-5 (HCC stage 3-5

description: Tissue


title: T1-3 (HCC stage 1-3)

description: Tissue

tag: HCC stage 1


title: MDA-MB-231_TR20003: transfected with the original vector plasmid

description: MDA-MB-231 transfected with the original vector plasmid

label_protocol:
Preparation of cRNA, hybridizations, washes and detection were done as recommended by the supplier.
www.affymetrix.com


title: 12.5 Valve Cells 1

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

description: Samples used for hybridization consisted of pooled RNA extracts from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells.

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.034 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45?C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine MOE 430 2.0  gene chips were used. GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.3.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and ?-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring Gx 7.3 (Agilent technologies) was used to normalization, clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using PANTHER gene classification system.

source_name: Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells

label_protocol: Samples used for hybridization consisted of pooled RNA extracts from the E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells. Therefore, 6 hybridization experiments were performed in biological duplicates on pooled RNA extracts. The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

extract_protocol:
Embryos were collected at E12.5 for isolation of AV cushion and E17.5 for isolation of AV valves. Dissected cushions and valves were washed in 1XPBS and collected in TRIzol Reagent (Invitrogen) for total RNA isolation.
Quality control steps: Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).


title: MC3T3 Cell Line 2

tag: Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells


title: 12.5 Valve Cells 2


title: MDA-MB-231_Native Cell

description: Native MDA-MB-231

source_name: MDA-MB-231_Native Cell


title: T1-4 (HCC stage 1-4)

description: Tissue


title: lens_wildtype_rep3

city: Göteborg

first: Henrik

last: Landgren

address: Medicinaregatan 9E

department: Cell and molecularbiology

country: Sweden

institute: Goteborg university

description: lens wildtype replicate 3

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw data normalised with GEPAS Expresso, rma background correction, quantiles normalization, median polish summary method using perfect match values only.

label: Phycoerythrin via Biotin-Streptavidin

source_name: whole lens

label_protocol: IVT

extract_protocol: total RNA extraction with GenElute mammalian total RNA kit according to manufacturers instructions.

value: Balb/c

tag: Age

value: 2 days


title: T3-6 (HCC stage 3-6)

description: Tissue


title: 17.5 Valve Cells 2


title: 17.5 Valve Cells 1


title: T3-3 (HCC stage 3-3)

description: Tissue


title: MC3T3 Cell Line 1


title: lens_trangene_rep1

description: lens trangene replicate 1


title: T1-2 (HCC stage 1-2)

description: Tissue


title: lens_wildtype_rep2

description: lens wildtype replicate 2


title: Huh7

description: HCC cell line

source_name: HCC cell line

tag: human


title: HNL-1 (normal liver)

description: Tissue

source_name: human liver

tag: human liver


title: lens_wildtype_rep1

description: lens wildtype replicate 1


title: HNL-2 (normal human liver)

description: Tissue


title: T1-1 (HCC stage 1-1)

description: Tissue

tag: Human


title: lens_trangene_rep2

description: lens trangene replicate 2

tag: Strain


title: lens_trangene_rep3

description: lens trangene replicate 3


title: MDA-MB-231_TR30003: transfected with a vector containing a non-effective shRNA cassette against GFP

description: MDA-MB-231 transfected with a vector containing a non-effective shRNA cassette against GFP


title: Cornea, stroma, P1

status: Public on Jul 09 2008

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

source_name: total RNA

label_protocol: cDNA was subjected to in vitro transcription in the presence of biotinylated nucleoside triphosphates using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences), according to the manufacturer's protocol (One-Cycle Target Labeling and Control Reagent package).

extract_protocol: Total cellular RNA was isolated with the RNeasy Mini Kit (Qiagen), according to manufacture's instructions.). Genomic DNA was eliminated by DNase I (TAKARA BIO INC.) treatments.

tag: Cornea, stroma, passage 1 (EY1407Cor-st)


title: Wildtype no treatement rep 1

first: Jian-Kang

last: Zhu

address: 2150 Batchelor Hall

institute: University of California

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

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

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

source_name: Seedlings

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

extract_protocol: RNeasy Plant Mini Kit, Qiagen

treatment_protocol: No treatment.

tag: Columbia-0 ecotype


title: kn muscle 3, biological rep 3

status: Public on Jul 10 2008

city: LUND

first: Mattias

middle: Carl

last: Häger

state: M

address: BMC, B12

department: Expreimental Biology

institute: Lunds University

description: gene expression data from 4 weeks old laminin alpah 2 chain deficient mouse hind limb skeletal muscle

hyb_protocol: After fragmentation of the cRNA, 15 μg cRNA in 200 μl hybridisation cocktail was hybridised onto Affymetrix MOE430 2.0 microarray chip for 16 h at 45 °C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with dChip 2004. After array normalization (default analysis settings)  the model-based expression values were calculated using the PM-only model

source_name: laminin alpha 2 chain deficient mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Swegene Microarray Resource Centre (Lund, Sweden).

extract_protocol: TRIzol extraction of total RNA and further purified using the RNeasy Mini Kit (Qiagen) was used according to the manufacturers’ instructions.

tag: dy3K/dy3K, mouse model for congenital muscular dystrophy type 1 A


title: wt muscle 1, biological rep 1

description: gene expression data from 4 weeks old wildtype mouse hind limb skeletal muscle

source_name: wild type mouse

tag: normal


title: Jejunum_wild type mouse

first: Ann-Hwee

last: Lee

address: 651 Huntington Ave, FXB/205

institute: Harvard School of public health

description: unknown

hyb_protocol: 16 h hybridization following the standard protocol provided by Affymetrix

scan_protocol: unknown

source_name: Jejunum_wild type mouse

label_protocol: Double-stranded cDNA was synthesized from total RNA by using SuperScript II, Invitrogen Life Technologies. An in-vitro transcription (IVT) reaction was then done to produce biotin-labeled cRNA from the cDNA. The cRNA was fragmented before hybridization.

extract_protocol: Total RNA was isolated from intestinal scraping samples by Trozol

tag: Total RNA was isolated from jejunum of mice with XBP1+/+ genotype on mixed background


title: Jejunum_XBP1 knock-out mouse

description: unknown

source_name: Jejunum_XBP1 knock-out mouse

tag: Total RNA was isolated from jejunum of mice with XBP1flox/flox;Villin-cre genotype (XBP1-/-) on mixed background


title: kn muscle 2, biological rep 2


title: kn muscle 1, biological rep 1


title: wt muscle 3, biological rep 3


title: Wildtype no treatement rep 2

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


title: human oocyte, biological rep1

city: East Lansing

first: Arif

middle: Murat

last: Kocabas

email: kocabas@msu.edu, hotu@bidmc.harvard.edu

state: MI

address: B270 Anthony Hall

department: Animal Science

institute: Michigan State University

description: Gene expression data from human oocyte.

hyb_protocol: Hybridization cocktails of 300 ml containing 15 mg of fragmented biotin-labeled aRNA and biotinylated exogenous hybridization controls (50 pM control Oligo B2, Eukaryotic hybridization controls) (BioB at 1.5 pM, BioC at 5 pM, BioD at 25 pM, and CreX at 100 pM), herring sperm DNA (0.1 mg/ml), BSA (0.5 mg/ml) in buffer (100 mM Mes/1M NaCl/20 mM EDTA/0.01% Tween 20) were hybridized to the GeneChip Human Genome U133 plus 2.0 array (Affymetrix, Santa Clara, CA). Hybridizations were performed automatically, and each array was prehybridized with all components except the fragmented biotin-labeled aRNA in a chamber at 45°C for 15 min with rotation at 60 rpm. The prehybridized array was then hybridized with the aRNA mixture for 16 h under the prehybridization conditions.

scan_protocol: The arrays were scanned using Affymetrix's high density GeneArray Scanner 3000 and imaged using Affymetrix GeneChip Operating Software (GCOS).

data_processing: The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.

source_name: Pool of 10 human oocytes

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

growth_protocol: Three hours after retrieval, oocytes were denuded from surrounding corona and cumulus cells by a brief incubation (10-30 s) in 80 units/ml hyaluronidase solution (LifeGlobal, Guilford, CT) and subsequent pipetting to completely eliminate other cells. Oocytes were then observed at high magnification to confirm maturity (metaphase II stage) and to confirm the absence of other cells. Each oocyte was rinsed in sterile PBS and lysed in 100 ml of extraction buffer (XB, Arcturus, Mountain View, CA) in an RNase/DNase/Pyrogen-free 0.5-ml microcentrifuge tube. Each sample was incubated for 30 min at 42°C, centrifuged at 3,000 ´ g for 2 min, and stored in liquid nitrogen until use.

extract_protocol: Total RNA was isolated following the guanidium thiocyanate method by using the PicoPure RNA isolation kit (Arcturus, Sunnyvale, CA) following the manufacturer's instructions. However, only 6.5 ?l of elution buffer (Arcturus) was used, and the elution was repeated at least three times by using the first eluate. All RNA samples within the purification column were treated with the RNase-Free DNase (Qiagen, Valencia, CA). Extracted RNA was stored at ?80°C until used as template for cDNA synthesis.

treatment_protocol: Ovarian stimulation was performed under Gn-RH analog suppression [leuprolide acetate (Lupron); Abbott, Abbott Park, IL] in a daily s.c. dose of 0.5 mg. Recombinant FSH (rFSH, Gonal-f-Serono or Puregon; Organon, Roseland, NJ) was administered in daily doses that ranged between 200 and 300 units, starting the second day of the mense. Follicular growth and estradiol levels were monitored every 2 to 3 days until follicles had a mean diameter between 18 and 20 mm. Oocyte maturation was achieved by an injection of 10,000 units of hCG (Pregnyl; Organon). Oocytes were retrieved from the ovary by aspiration using guided transvaginal ultrasound 36 h after hCG administration.

tag: Genotype

value: Human Oocytes from reproductively healthy individuals with regular ovulatory cycles, male factor as the only cause for infertility


title: human reference, biological rep2

description: Gene expression data from pool of 10 normal human tissue.

source_name: Pool of ten normal human tissues for reference

growth_protocol: Samples are obtained from Ambion.

extract_protocol: The samples are processed using Ambion's RNA isolation reagents to produce highly pure, intact RNA. A stringent DNase treatment is performed to ensure that the RNA is ready for use in any downstream application, including RT-PCR.

treatment_protocol: Samples are obtained from Ambion

value: 10 different normal human tissues, including skeletal muscle, kidney, lung, colon, liver, spleen, breast, brain, heart, and stomach.


title: wt muscle 2, biological rep 2


title: human reference, biological rep3


title: human reference, biological rep1


title: Irradiated EL08-1D2, biological rep 1

status: Public on Jul 07 2008

city: Muenchen

first: Robert

last: Oostendorp

address: Ismaningerstrasse 22

department: Klinikum rechts der Isar

institute: Technische Universitaet Muenchen

description: Gene expression data from embryo-deived stromal cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on MOE430 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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: Embryonic E11.5 liver cell line EL08-1D2

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: Embryo-derived stromal cell lines were grown to confluence as described (Oostendorp et al., Stem Cells. 2005;23:842:50)

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

treatment_protocol: Confluent cultures were irradiated (30 Gy), medium exchanged completely and grown for another week. One day prior to harvest, medium was again completely refreshed.

tag: Embryonic liver stromal cell clone


title: Astrocyte_wt_rep2

status: Public on Jul 06 2008

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

description: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

data_processing: GCOS version 1.4, default parameters

source_name: Murine in vitro differentiated astrocytes

extract_protocol: Trizol according to the manufacturer's recommendations

treatment_protocol: ES cells were differentiated into neural precursor cells (NPCs) through embryoid body formation for 4 days and selection in ITSFn media for 5–7 days, and maintained in FGF2 and EGF2 (R&D Systems). After 18 passages from EB formation, the NPCs were differentiated into astrocytes by growth factor withdrawal and addition of 5% FBS for 5 days.

tag: Genotype 129SvJae x C57BL/6; male


title: Astrocyte_wt_rep1

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: human oocyte, biological rep3

description: Gene expression data from human oocyte.


title: Irradiated EL08-1D2, biological rep 2


title: Astrocyte_wt_rep3

scan_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: human oocyte, biological rep2

description: Gene expression data from human oocyte.


title: Col-0 plants overexpressing At1g54160 rep 1 no treatment

city: Riverside

department: Botany and Plant Sciences

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

tag: Col-0 ecotype plants transformed with an overexpression construct containing the gene for At1g54160. (NFYA5)  Vector used is pMDC32.


title: Irradiated UG26-1B6, biological rep 2

source_name: Embryonic E11.5 urogenital ridge cell line UG26-1B6

tag: Embryonic urogenital ridge stromal cell clone


title: Irradiated AM20-1B4

source_name: Embryonic E10.5 aorta/mesenchyme cell line AM20-1B4

tag: Embryonic aorta/mesenchyme stromal cell clone


title: Col-0 plants overexpressing At1g54160 rep 2 no treatment


title: Irradiated UG26-1B6, biological rep 1


title: M-62

status: Public on Jul 05 2008

city: Boston

first: Towia

middle: A

last: Libermann

address: 99 Brookline Ave.

description: Human Blood

hyb_protocol: Following fragmentation, 5 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: Standard Affymetrix Scanner

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

source_name: Long-term practitioner of daily RR practice

treatment_protocol: To measure the Relaxation Response (RR)  on Blood transcriptome. The series have data from three sets of subjects: Long RR practitioners Subjects [M], No RR Practice [N1], RR after 8 Weeks of Practice [N2]

tag: Effect of MIND and Body on Blood Transcriptome


title: M-28

description: Human Blood


title: M-22

description: Human Blood


title: M-29

description: Human Blood


title: M-24

description: Human Blood


title: M-21

description: Human Blood


title: M-20

description: Human Blood


title: M-58

description: Human Blood


title: M-43

description: Human Blood


title: M-19

description: Human Blood


title: M-18

description: Human Blood


title: M-56

description: Human Blood


title: M-25

description: Human Blood


title: M-52

description: Human Blood


title: M-05

description: Human Blood


title: M-38

description: Human Blood


title: M-42

description: Human Blood


title: M-16

description: Human Blood


title: M-55

description: Human Blood


title: M-57

description: Human Blood


title: M-13

description: Human Blood


title: M-44

description: Human Blood


title: M-10

description: Human Blood


title: M-15

description: Human Blood


title: M-27

description: Human Blood


title: N2-50

description: Human Blood

source_name: Healthy Subject with 8 weeks of  RR Practice


title: N2-49

description: Human Blood


title: N2-59

description: Human Blood


title: N2-51

description: Human Blood


title: N2-35

description: Human Blood


title: N2-01

description: Human Blood


title: N2-03

description: Human Blood


title: N2-46

description: Human Blood


title: N2-02

description: Human Blood


title: N2-41

description: Human Blood


title: N2-11

description: Human Blood


title: N2-23

description: Human Blood


title: N2-30

description: Human Blood


title: N2-39

description: Human Blood


title: N1-51

description: Human Blood

source_name: Healthy Subject with No RR Practice


title: N2-33

description: Human Blood


title: N2-07

description: Human Blood


title: N2-06

description: Human Blood


title: N2-14

description: Human Blood


title: N2-47

description: Human Blood


title: N2-40

description: Human Blood


title: N2-12

description: Human Blood


title: N2-36

description: Human Blood


title: N1-46

description: Human Blood


title: N2-32

description: Human Blood


title: N1-49

description: Human Blood


title: N1-41

description: Human Blood


title: N1-40

description: Human Blood


title: N1-47

description: Human Blood


title: N2-34

description: Human Blood


title: N1-39

description: Human Blood


title: N1-50

description: Human Blood


title: N1-59

description: Human Blood


title: N1-01

description: Human Blood


title: N1-02

description: Human Blood


title: N1-33

description: Human Blood


title: N1-32

description: Human Blood


title: N1-23

description: Human Blood


title: N1-12

description: Human Blood


title: N1-35

description: Human Blood


title: N1-03

description: Human Blood


title: N1-07

description: Human Blood


title: N1-30

description: Human Blood


title: N1-34

description: Human Blood


title: N1-06

description: Human Blood


title: N1-14

description: Human Blood


title: Tfh cells Roza2

status: Public on Jul 03 2008

city: Houston

first: Chen

last: Dong

state: TX

address: 7455 Fannin

department: Immunology

institute: MD Anderson Cancer Center

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were GCRMA normalized using R/Bioconductor

source_name: CXCR5+ TFH cells isolated from KLH-immunized mice

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

growth_protocol: TFH cells were restimulated in vitro with anti-CD3 for 4 hours before RNA prep

extract_protocol: Total RNA was prepared using Tri-zol reagent

treatment_protocol: splenic CD4+CXCR5+ T cells were FACS-sorted 7 days after immunization

tag: strain

tag: cell type

value: CXCR5+ TFH cells


title: Adult Salivary Gland rep2

status: Public on Jul 02 2008

city: Glasgow

first: Jing

last: Wang or Venkat Chintapalli

state: Scotland

address: Dumbarton Road

department: Molecular Genetics

country: United Kingdom

institute: University of Glasgow

description:
The Salivary glands
amplification: 1-round

hyb_protocol: Following fragmentation, 10 ug of cRNA (or according to the affy IVT protocol)  were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G.

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Adult Salivary Gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Wild-type Drosophila melanogaster (Canton S strain) were raised on standard medium on a 12:12 h L:D cycle, at 23C, and at 55% r.h. To facilitate the collection of accurately staged adults, a laying population of around 12 males and 12 females were transferred to fresh vials daily. When adults subsequently emerged, they were transferred to fresh vials on the day of emergence, and used 7 days later. Where larvae were used, these were third instar.

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Flies were anaesthetised briefly by chilling on ice, then immediately dissected.

tag: tissue

value: Canton-S, 60 female and  60 male flies, 7 days old


title: Adult Salivary Gland rep4


title: Tfh cells Roza1

value: C57BL/6 mice


title: Ovary - 458405

status: Public on Jul 01 2008

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 0
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: X
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Malignant mixed muellerian tumor

source_name: Ovary


title: Adult Salivary Gland rep1


title: Cecum - 458414

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 6
Presenting Symptoms: Abdominal Pain
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Cecum


title: Adult Salivary Gland rep3


title: KIdney - 458400

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: X
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Renal cell carcinoma

source_name: KIdney


title: Sigmoid Colon - 443483

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 80-89
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 10
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Sigmoid Colon


title: Prostate - 458393

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
PSA: Elevated
Cancer discovered by digital exam?: Yes
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
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

source_name: Prostate


title: Ovary - 443481

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Endometrioid adenocarcinoma


title: Uterus - 443489

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 300
Relapse Since Primary Treatment: No
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: Endometrioid Adenocarcinoma

source_name: Uterus


title: Abdominal Wall Soft Tissue - 443462

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-69
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
Clinical Question: T
Clinical Value: 3c
Clinical Question: N
Clinical Value: 0
Clinical Question: M
Clinical Value: 0
Clinical Question: Stage
Clinical Value: 3C
Clinical Question: Grade
Clinical Value: 3
Clinical Question: Multiple Tumors
Clinical Value: No
Clinical Question: Stage During or Following Multimodality Therapy
Clinical Value: No
Clinical Question: Symptoms
Clinical Value: Abdominal Pain
Primary Site: Peritoneum
Clinical Question: Histology
Clinical Value: Serous Adenocarcinoma

source_name: Abdominal Wall Soft Tissue


title: Upper Back Soft Tissue - 443482

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Soft Tissue Upper Back
Histology: Leiomyosarcoma

source_name: Upper Back Soft Tissue


title: Kidney - 440441

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-79
Gender: Male
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 75
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Clear cell adenocarcinoma

source_name: Kidney


title: Prostate - 443469

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
PSA: Elevated
# of years PSA Tested?: 11-15
Cancer discovered by digital exam?: Yes
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
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: Omentum - 443480

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Other
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: Omentum


title: Ovary - 440437

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Bloating
Pathological T: 1a
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: Ovary
Histology: Mixed endometrioid and papillary serous adenocarcinoma


title: LUL Lung - 440426

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Workplace or household smokers?: Yes
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS

source_name: LUL Lung


title: Uterus - 440445

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Pathological T: X
Pathological N: X
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Malignant mixed Mullerian tumor


title: Ovary - 440440

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Bloating
Pathological T: 1a
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: Ovary
Histology: Papillary Serous Adenocarcinoma


title: Rectosigmoid - 443479

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Black tarry stools
Presenting Symptoms: Bright red stools
Screening studies performed?: No
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: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Pleural Nodule - 440429

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: Abdominal mass
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Pleura
Retreatment Stage: 4
Retreatment Grade: 2
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Metastatic Adenocarcinoma

source_name: Pleural Nodule


title: Stomach - 438185

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Relapse Since Primary Treatment: No
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 4
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Therapy: No
Primary Site: Soft Tissue Stomach
Histology: Spindle Cell Sarcoma

source_name: Stomach


title: Ovary - 443454

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 40-49
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: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Endometrioid adenocarcinoma


title: Kidney - 438162

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Grade: 1
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Cyst-associated renal cell carcinoma


title: Rectosigmoid - 438176

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal Pain
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Rectosigmoid
Histology: Adenocarcinoma


title: Chest Wall - 438167

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
Gender: Male
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
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Hormonal therapy (# of Years)?: 0-5
Retreatment T: 4a
Retreatment N: 3a
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Grade: 3
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Retreatment ER: Positive
Retreatment PR: Positive
Retreatment HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Chest Wall


title: N1-11

description: Human Blood

source_name: Healthy Subject with No RR Practice


title: Breast - 438163

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 25
Mammogram: Yes
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: No
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: Breast - 438160

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 30-39
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?: 0-5
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 21-25
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 2
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Medullary Carcinoma, NOS


title: Uterus - 433124

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
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: Prostate - 432631

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
PSA: Elevated
Cancer discovered by digital exam?: No
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: breast - 438172

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 30-39
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Prior Therapy: Hormonal Treatment
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 6-10
Oophorectomy?: Yes
Fibrocystic disease?: No
Hormonal therapy (# of Years)?: 0-5
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Negative
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Metastatic Ductal Carcinoma

source_name: breast


title: Uterus - 433403

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
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: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma


title: Kidney - 433118

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 40-49
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 10
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
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: Kidney - 433116

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-59
Gender: Male
Ethnic Background: Hispanic
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Clinical T: 1a
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: Ovary - 433115

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 20
Presenting Symptoms: Bloating
Pathological T: 2c
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 cystadenocarcinoma

source_name: Ovary


title: Uterus - 432629

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-69
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: 72
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma


title: Adrenal Gland - 432614

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 365
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Presenting Symptoms: SOB
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Adrenals
Retreatment Stage: 4
Retreatment Grade: X
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Lung
Histology: Metastatic Small cell carcinoma

source_name: Adrenal Gland


title: Cecum - 423087

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Cecum


title: Ovary - 432628

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
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
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Endometrioid adenocarcinoma


title: Ovary - 432627

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-49
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: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Mucinous cystadenocarcinoma


title: Kidney - 421730

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-79
Gender: Male
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: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Ovary - 432616

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Abdominal pain
Clinical T: 3b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3B
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma


title: Lung - 433111

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 51-55
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: Yes
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Squamous cell carcinoma

source_name: Lung


title: Cecum - 423093

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Screening studies performed?: Yes
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Prostate - 423086

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
PSA: Elevated
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: No
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
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

source_name: Prostate


title: Breast - 421743

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 43
Mammogram: Yes
Mammogram calcifications?: No
Clinical T: 4b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3B
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical ER: Negative
Clinical PR: Negative
Clinical HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Prostate - 423080

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
PSA: Elevated
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: No
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
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 - 421747

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 24
Mammogram: Yes
Number of years in which a mammogram was obtained?: 21-25
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 26-30
Oophorectomy?: No
Fibrocystic disease?: No
Hormonal therapy (# of Years)?: 6-10
Pathological T: 2
Pathological N: 3a
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma


title: Kidney - 421734

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
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: Prostate - 432622

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Type of Tobacco Use: Pipe
Alcohol Consumption?: No
Family History of Cancer?: Yes
PSA: Elevated
Cancer discovered by digital exam?: No
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Ovary - 458391

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment Question: Stage
Retreatment Value: No AJCC Scheme for this Site/Histology
Retreatment Question: Stage During or Following Multimodality Therapy
Retreatment Value: Yes
Retreatment Question: Symptoms
Retreatment Value: Abdominal Pain
Primary Site: Unknown Primary
Retreatment Question: Histology
Retreatment Value: Metastatic Mucinous Adenocarcinoma w/Signet Ring Features


title: Ovary - 432624

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 3a
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma


title: Prostate - 423094

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Family History of Cancer?: Yes
PSA: Elevated
Cancer discovered by digital exam?: No
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
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: Kidney - 423092

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 3b
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
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: Abdominal Wall - 432615

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 3c
Retreatment N: X
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Grade: X
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Endometrioid adenocarcinoma

source_name: Abdominal Wall


title: Ovary - 421726

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
Pathological T: 3
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Metastatic Signet Ring Cell Carcinoma


title: Cervical Lymph Node - 366606

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 30-39
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Hormonal Treatment
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Retreatment T: 1
Retreatment N: 1b
Retreatment M: 0
Retreatment Stage: 1
Retreatment Multiple Tumours: No
Retreatment Staged During or Following Multimodality Therapy: Yes
Primary Site: Thyroid
Histology: Papillary carcinoma

source_name: Cervical Lymph Node


title: Androgen ablation, fiber model 12R_AA

city: vancouver

first: Gang

last: Wang

state: BC

address: 675 W10th Ave.

department: Genome Sciences Centre

country: Canada

institute: BC Cancer Agenecy

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneArray Scanner

data_processing: MAS 5.0 data submitted, Genespring 7.2 used to generate RMA data

source_name: fiber model, 12R, AA

label_protocol: biotin

extract_protocol: TRIZOL

tag: model

value: fiber model, cell:LNCaP, mouse ID:12R, stage:AA


title: Prostate - 421721

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
PSA: Elevated
# of years PSA Tested?: 6-10
Cancer discovered by digital exam?: Yes
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: MRC5

city: London

first: Tim

last: Forshew

address: 4 Newark Street

department: Centre for Neuroscience

institute: Queen Mary's School of Medicine and Dentistry

hyb_protocol: affymetrix hybridization

scan_protocol: affymetrix scan

data_processing: Affymetrix CEL files were processed using RMA

label: affymetrix labelling

source_name: MRC5 primary lung fibroblasts, untreated

label_protocol: affymetrix labelling

extract_protocol: QIagen RNeasy plus

tag: Cell

value: MRC5, Treatment:None


title: Androgen independent, fiber model 11L_AI

source_name: fiber model, 11L, AI

value: fiber model, cell:LNCaP, mouse ID:11L, stage:AI


title: Androgen dependent, fiber model 10R_AD

source_name: fiber model, 10R, AD

value: fiber model, cell:LNCaP, mouse ID:10R, stage:AD


title: Androgen dependent, fiber model 11L_AD

source_name: fiber model, 11L, AD

value: fiber model, cell:LNCaP, mouse ID:11L, stage:AD


title: Androgen dependent, fiber model 12R_AD

source_name: fiber model, 12R, AD

value: fiber model, cell:LNCaP, mouse ID:12R, stage:AD


title: Androgen independent, fiber model 12R_AI

source_name: fiber model, 12R, AI

value: fiber model, cell:LNCaP, mouse ID:12R, stage:AI


title: Androgen independent, fiber model 10R_AI

source_name: fiber model, 10R, AI

value: fiber model, cell:LNCaP, mouse ID:10R, stage:AI


title: Breast - 346008

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 112
Prior Therapy: Chemotherapy
Relapse Since Primary Treatment: No
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Fibrocystic disease?: No
Pathological T: 4c
Pathological N: 2a
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological ER: Negative
Pathological PR: Negative
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Ductal Carcinoma

source_name: Breast


title: MRC5+INF

source_name: MRC5 primary lung fibroblasts, IFN gamma treated

value: MRC5, Treatment:IFN gamma 24 hours (200 IU/ml