title: B-ALL-17-0h

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 14.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.
Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.


title: Mouse-in vivo-4h-GC

status: Public on Nov 14 2005

type: RNA

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: mus musculus, three CD-1 mice (males, aged 4-6 weeks), pooled thymic cell suspensions, 4h after intraperitoneal injection of 0.2mg dexamethasone per mouse.

hyb_protocol: On rotation (60 rpm) hybridization at 45C for 16 hours

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.

label: R-Phycoerythrin

molecule: total RNA

organism: Mus musculus

source_name: Mouse, thymus

label_protocol: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.

extract_protocol: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.


title: B-ALL-13-24h

description:
biological source:
homo sapiens, childhood ALL patient (male, aged 5.9 years), peripheral blood taken  after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.

Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.

organism: Homo sapiens

source_name: Patient 13, peripheral blood


title: B-ALL-13-0h

description:
biological source:
homo sapiens, childhood ALL patient (male, aged 5.9 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.

Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.


title: Mouse-in vivo-4h-PBS

description: mus musculus, three CD-1 mice (males, aged 4-6 weeks), pooled thymic cell suspensions, 4h after intraperitoneal injection of PBS


title: B-ALL-31-6h

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 17.2 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.

source_name: Patient 31, peripheral blood


title: B-ALL-13-8h

description:
biological source:
homo sapiens, childhood ALL patient (male, aged 5.9 years), peripheral blood taken after 8 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.

Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.


title: B-ALL-24-6h

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 2.6 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.

source_name: Patient 24, peripheral blood


title: B-ALL-24-24h

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 2.6 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).

Technical protocols: Target hybridization preparation
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization
Measurement data /specifications
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing and presentation. Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry


title: B-ALL-24-0h

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 2.6 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.


title: T-ALL-25-0h

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.
Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.

source_name: Patient 25, peripheral blood


title: T-ALL-2-0h

description:
biological source:
homo sapiens, childhood ALL patient (male, aged 8.5 years), peripheral blood taken prior to treatment, leukocyte isolation without enrichment for malignant blasts.
Technical protocols: Target hybridization preparation:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.

Hybridization:
Measurement data /specifications:
The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.

source_name: Patient 2, peripheral blood


title: 13_25US_75Placenta_2_HG_U133_Plus_2

status: Public on Nov 08 2005

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

country: USA

institute: Cincinnati Childrens Hospital Medical Center

description: Technical labeling replicate of 5_25US_75Placenta_HG_U133_Plus_2 (GSM66945)

data_processing: RMA via Bioconductor

label: Affymetrix standard protocol

source_name: PBMC and Placenta

tag: Approximately 50 mL whole blood was collected from 30 adult, apparently healthy, volunteers using Acid Citrate Dextrose (ACD) as an anti-coagulant. Samples were processed immediately following blood draw. Cells were isolated by Ficoll gradient centrifugation and total RNA was isolated using Trizol (Invitrogen Life Technologies; Carlsbad, CA) according to manufacturer’s protocol, aliquoted and stored at -80°C until use. Whole placenta was collected and immediately frozen in liquid nitrogen. RNA was extracted using TRI reagent, purified using RNeasy columns (Qiagen; Valencia, CA), aliquoted and stored at -80°C until use. RNA mixtures (100:0, 95:5, 75:25, 50:50, 25:75, 0:100; PBMC

value: placenta) were prepared in single aliquots.


title: 3_75US_25Placenta_HG_133_Plus_2

description: Technical labeling replicate of 11_75US_25Placenta_HG_U133_Plus_2 (GSM66940)


title: 5_25US_75Placenta_HG_U133_Plus_2

description: Technical labeling replicate of 13_25US_75Placenta_HG_U133_Plus_2 (GSM66944)


title: 12_50US_50Placenta_HG_U133_Plus_2

description: Technical labeling replicate of 4_50US_50Placenta_HG_U133_Plus_2 (GSM66941)


title: 4_50US_50Placenta_HG_U133_Plus_2

description: Technical labeling replicate of 12_50US_50Placenta_HG_U133_Plus_2 (GSM66942)


title: 6_Placenta_100_HG_U133_Plus_2

description: Technical labeling replicate of 14_Placenta_100_HG_U133_Plus_2 (GSM66945)

source_name: Placenta


title: 11_75US_25Placenta_HG_U133_Plus_2

description: Technical labeling replicate of 3_75US_25Placenta_HG_U133_Plus_2 (GSM66939)


title: 14_Placenta_100_HG_U133_Plus_2

description: Technical labeling replicate of 6_Placenta_100_HG_U133_Plus_2 (GSM66946)


title: 2_95US_5Placenta_HG_U133_Plus_2

description: Technical labeling replicate of 10_95US_5Placenta_HG_U133_Plus_2 (GSM66937)


title: 1_100US_HG_U133_Plus_2

description: Technical labeling replicate of 9_100US_HG_U133_Plus_2 (GSM66936)

label: Affymetrix Standard

source_name: Ficol separated PBMC


title: 9_100US_HG_U133_Plus_2

description: Technical labeling replicate of 1_US_100_HG_U133_Plus_2 (GSM66935).

source_name: PBMC


title: scrambled antagomir122 (mm-antagomir122)

status: Public on Nov 02 2005

city: New York

first: Markus

last: Stoffel

state: NY

address: 1230 York Avenue

department: Laboratory of Metabolic Diseases

institute: Rockefeller University

description: mice were treated with 3x 80mg/KG bodyweight/day mm-antagomir122

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

source_name: liver

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

extract_protocol: total RNA from 3 livers were combined


title: 10_95US_5Placenta_HG_U133_Plus_2

description: Technical labeling replicate of 2_95US_5Placenta_HG_U133_Plus_2 (GSM66938).


title: antagomir122

description: mice were treated with 3x 80mg/KG bodyweight/day antagomir122


title: aldosterone 12 hours

status: Public on Nov 01 2005

city: Boston

first: Alexander

last: Turchin

state: MA

address: 221 Longwood Avenue

department: Division of Endocrinology

institute: Brigham and Women's Hospital

description: mouse whole heart aldosterone-injected group 12 hours

data_processing: Affymetrix GCOS 1.2

source_name: heart

label_protocol: Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Whole hearts were removed upon the sacrifice of the animal and immediately frozen in liquid nitrogen. RNA was extracted using Trizol reagent.

tag: Male C57BL6, whole heart


title: aldosterone 5 hours

description: mouse whole heart aldosterone group 5 hours


title: aldosterone 4 hours

description: mouse whole heart aldosterone-injected group 4 hours


title: aldosterone 2 hours

description: mouse whole heart aldosterone-injected group 2 hours


title: aldosterone 3 hours

description: mouse whole heart aldosterone group 3 hours


title: retina_DBA_1024L_3mo_rep1

status: Public on Nov 04 2005

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

address: 20 South, 2030 East Rm. 320 BPRB

department: Neurobiology & Anatomy

institute: University of Utah

description: Three month old female DBA/2J mouse retina

data_processing: All preprocessing of Affymetrix data was performed using the Bioconductor Package in the R statistical environment. Data set analysis done under the R statistical environment version 1.9.0 on i686-pc-linux-gnu. Bioconductor package 'affy' version 1.4.32, 'gcrma' version 1.1.0, 'siggenes'(R sam analysis) version 1.0.6.

source_name: Animal id 1024, left retina, 3 months, female, DBA/2J

label_protocol: Total RNA was isolated using a Qiagen RNeasy Kit. The quantity and quality of the RNA was assessed using a Nanodrop ND1000 spectrophotometer and an Agilent 2100 Bioanalyzer. 20ng of each retinal RNA sample was amplified, fractionated, and labeled with a NuGEN Ovation Biotin kit to generate probe for Affymetrix microarray analysis.

extract_protocol: Whole retinas were removed from 3, and 8 month old DBA/2J mice and rinsed in ice-cold 0.1 M phosphate buffered saline to remove blood. Three individual retinas at each age were homogenized in Qiagen RLT buffer using a micro pestle and pulled five times through a 22G needle, then flash frozen in liquid nitrogen.

tag: Age

value: 3 months, Sex:Female, Retina:left, Final IOP (mm Hg):19.1, Strain:DBA/2J


title: retina_DBA_1026L_3mo_rep3

source_name: Animal id 1026, left retina, 3 months, female, DBA/2J

value: 3 months, Sex:Female, Retina:left, Final IOP (mm Hg):18.2, Strain:DBA/2J


title: slr-1 6h NAA replicate 1

city: Ghent

first: Steffen

last: Vanneste

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB-University of Ghent

description: lateral root inducible segment (between root meristem and hypocotyl)

organism: Arabidopsis thaliana

label_protocol: Approximately 5.8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Root segments as described in Himanen et al (2002; Plant Cell, 14, 2339-2351)  were dissected from 3 day old slr-1 seedlings, germinated on 10 µM NPA and an additional 6h 10µM NAA treatment. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: solitary root (slr-1) mutant, root segments of 3 day old seedlings, NPA grown plus 6h NAA treatment


title: control 12 hours

description: mouse whole heart control group 12 hours


title: retina_DBA_1025L_3mo_rep2

source_name: Animal id 1025, left retina, 3 months, female, DBA/2J

value: 3 months, Sex:Female, Retina:left, Final IOP (mm Hg):15.3, Strain:DBA/2J


title: control 5 hours

description: mouse whole heart control group 5 hours


title: retina_DBA_544R_8mo_rep2

description: Eight month old female DBA/2J mouse retina

source_name: Animal id 544, right retina, 8 months, female, DBA/2J

value: 8 months, Sex:Female, Retina:right, Final IOP (mm Hg):26.5, Strain:DBA/2J


title: retina_DBA_543L_8mo_rep1

source_name: Animal id 543, left retina, 8 months, female, DBA/2J

value: 8 months, Sex:Female, Retina:left, Final IOP (mm Hg):25.3, Strain:DBA/2J


title: retina_DBA_552R_8mo_rep3

source_name: Animal id 552, right retina, 8 months, female, DBA/2J

value: 8 months, Sex:Female, Retina:right, Final IOP (mm Hg):30.4, Strain:DBA/2J


title: slr-1 6h NAA replicate 2

source_name: lateral root inducible segment (between root meristem and hypocotyl)


title: Col-0 2h NAA replicate 2

extract_protocol: Root segments as described in Himanen et al (2002; Plant Cell, 14, 2339-2351)  were dissected from 3 day old seedlings, germinated on 10 µM NPA and an additional 2h 10µM NAA treatment. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Wild type, root segments of 3 day old seedlings, NPA grown plus 2h NAA treatment


title: slr-1 0h NAA replicate 2

extract_protocol: Root segments as described in Himanen et al (2002; Plant Cell, 14, 2339-2351)  were dissected from 3 day old slr-1 seedlings, germinated on 10 µM NPA. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: solitary root (slr-1) mutant, root segments of 3 day old seedlings, NPA grown


title: slr-1 2h NAA replicate 2

extract_protocol: Root segments as described in Himanen et al (2002; Plant Cell, 14, 2339-2351)  were dissected from 3 day old slr-1 seedlings, germinated on 10 µM NPA and an additional 2h 10µM NAA treatment. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: solitary root (slr-1) mutant, root segments of 3 day old seedlings, NPA grown plus 2h NAA treatment


title: slr-1 2h NAA replicate 1


title: Col-0 6h NAA replicate 2

extract_protocol: Root segments as described in Himanen et al (2002; Plant Cell, 14, 2339-2351)  were dissected from 3 day old seedlings, germinated on 10 µM NPA and an additional 6h 10µM NAA treatment. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Wild type, root segments of 3 day old seedlings, NPA grown plus 6h NAA treatment


title: aldosterone 1 hour

description: mouse whole heart aldosterone group 1 hour


title: Col-0 6h MOCK replicate 2

description: Wild type third instar larvae imaginal wing discs

extract_protocol: Root segments as described in Himanen et al (2002; Plant Cell, 14, 2339-2351)  were dissected from 3 day old seedlings, germinated on 10 µM NPA and an additional 6h mock-treatment. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Wild type, root segments of 3 day old seedlings, NPA grown plus 6h mock treatment


title: Col-0 6h MOCK replicate 1


title: aldosterone 0.5 hours

description: mouse whole heart aldosterone-injected group 0.5 hours


title: control 3 hours

description: mouse whole heart control group 3 hours


title: control 1 hour

description: mouse whole heart control group 1 hour


title: control 4 hours

description: mouse whole heart control group 4 hours


title: control 0.5 hours

description: mouse whole heart control group 0.5 hours


title: control 2 hours

description: mouse whole heart control group 2 hours


title: slr-1 0h NAA replicate 1


title: Col-0 0h NAA replicate 2

extract_protocol: Root segments as described in Himanen et al (2002; Plant Cell, 14, 2339-2351)  were dissected from 3 day old seedlings, germinated on 10 µM NPA. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Wild type, root segments of 3 day old seedlings, NPA grown


title: Col-0 6h NAA replicate 1


title: Col-0 0h NAA replicate 1

description: Wild type lateral root inducible segments of 3day old NPA grown seedlings


title: Col-0 2h NAA replicate 1


title: Col_+IAA_A2_2

status: Public on Oct 19 2005

city: Albany

first: Yoko

last: Okushima

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center, U. C. Berkeley

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: IAA treated

source_name: Light grown liquid cultured seedlings (7-day old)


title: arf2-6_+IAA_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf2-6 (ecotype Columbia)
Treatment: IAA treated
Replicate 1


title: Col_+IAA_A2_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 3


title: arf2-6_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf2-6 (ecotype Columbia)
Treatment: Control
Replicate 1


title: arf2-6_control_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf2-6 (ecotype Columbia)
Treatment: Control


title: arf2-6_+IAA_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf2-6 (ecotype Columbia)
Treatment: IAA treated


title: Col_+IAA_A2_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 1


title: Col_control_A2_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: Control
Replicate 2


title: nph4-1arf19-1_control_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 arf19-1 (ecotype Columbia)
Treatment: Control
Replicate 3


title: arf2-6_control_2


title: nph4-1arf19-1_+IAA_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 arf19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 3


title: nph4-1arf19-1_control_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 arf19-1 (ecotype Columbia)
Treatment: Control
Replicate 2


title: Col_control_A2_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: Control


title: arf19-1_+IAA_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 2


title: Col_control_A2_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: Columbia wild-type
Treatment: Control
Replicate 1


title: nph4-1arf19-1_+IAA_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 arf19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 2


title: arf2-6_+IAA_2


title: arf19-1_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf19-1 (ecotype Columbia)
Treatment: Control
Replicate 1


title: nph4-1arf19-1_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 arf19-1 (ecotype Columbia)
Treatment: Control
Replicate 1


title: nph4-1_+IAA_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 1


title: arf19-1_+IAA_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 1


title: nph4-1_+IAA_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 (ecotype Columbia)
Treatment:IAA treated
Replicate 3


title: nph4-1arf19-1_+IAA_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 arf19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 1


title: arf19-1_control_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf19-1 (ecotype Columbia)
Treatment: Control
Replicate 3


title: arf19-1_+IAA_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 3


title: nph4-1_+IAA_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 2


title: arf19-1_control_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: arf19-1 (ecotype Columbia)
Treatment: Control
Replicate 2


title: nph4-1_control_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 (ecotype Columbia)
Treatment: Control
Replicate 2


title: 50.Woodruff_19saA1.CEL

status: Public on Oct 04 2005

city: San Francisco

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

description: Total RNA from freshly isolated macrophages

hyb_protocol: Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChips. RNA was ampli?ed by performing two rounds of in vitro transcription (Ambion Message Amp aRNA kit no. 1750).

scan_protocol: Scanning was performed at the UCSF core facility (cat.ucsf.edu) as per Affymetrix's standard scanning protocol for this chip type (www.affymetrix.com)

data_processing: Bioconductor was used for quality control (affyPLM) and preprocessing (RMA).

source_name: isolated alveolar macrophages

label_protocol: Labeling was performed at the UCSF core facility (cat.ucsf.edu) as per Affymetrix's standard labeling protocol for this chip type (www.affymetrix.com)

extract_protocol: RNA was extracted from mouse and human alveolar macrophages and DNase-treated using the RNeasy RNA extraction kit (Qiagen). RNA concentration and quality were assessed using the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: status

value: Asthmatic


title: 48.Woodruff_3saA1.CEL


title: 44.Woodruff_2saA1.CEL


title: 51.Woodruff_20asA1.CEL


title: 37.Woodruff_36_N.CEL

value: Nonsmoker


title: nph4-1_control_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 (ecotype Columbia)
Treatment: Control
Replicate 3


title: 30.Woodruff_16saA1.CEL


title: 40.Woodruff_52_C.CEL

value: Smoker


title: 34.Woodruff_5saA1.CEL


title: 39.Woodruff_15saA1.CEL


title: 47.Woodruff_62_N.CEL


title: 36.Woodruff_54_C.CEL


title: 33.Woodruff_64_N.CEL


title: 26.Woodruff_47_C.CEL


title: 29.Woodruff_44_N.CEL


title: 41.Woodruff_9saA1.CEL


title: 49.Woodruff_11saA1.CEL


title: 45.Woodruff_55_HS.CEL


title: HCaRG-9 HG-U133 Plus 2.0

city: Montreal

first: Johanne

last: Tremblay

state: QUE

country: Canada

institute: CHUM Research Center, Hotel-Dieu

description:
HEK293 cells were transfected with pcDNAI/Neo (Invitrogen) plasmid containing HCaRG. Stable transfectants, overexpressing HCaRG, were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen).

Chip was normalized using all probe sets scaling option and target signal at 500.

source_name: HEK293 cells


title: 25.Woodruff_38_N.CEL


title: 38.Woodruff_6saA1.CEL


title: Neo-1 Ctl HG-U133 Plus 2.0

description:
HEK293 cells were transfected with pcDNAI/Neo (Invitrogen) as control plasmid. Stable transfectants were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen).

Chip was normalized using all probe sets scaling option and target signal at 500.


title: 24.Woodruff_46_C.CEL


title: 27.Woodruff_4saA1_SCAN1.CEL


title: nph4-1_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5µM IAA (IAA treated) or EtOH (control) for 2 h at 24 °C.

Line: nph4-1 (ecotype Columbia)
Treatment: Control
Replicate 1


title: 23.Woodruff_50_C.CEL


title: 32.Woodruff_48_C.CEL


title: 43.Woodruff_45_C.CEL


title: 14.Woodruff_33_N.CEL


title: 16.Woodruff_56_HS.CEL


title: 15.Woodruff_51_C.CEL


title: 10.Koth_60_HS.CEL


title: 20.Woodruff_18saA1.CEL


title: 18.Woodruff_8sA1.CEL


title: 21.Woodruff_25saA1.CEL


title: 09.Koth_59_HS.CEL


title: 17.Woodruff_57_N.CEL


title: 12.Woodruff_22_N.CEL


title: 03.Koth_29_HS.CEL


title: 04.Koth_61_N.CEL


title: 08.Koth_43_N.CEL


title: 06.Koth_27_N.CEL


title: 13.Woodruff_32_C.CEL


title: 07.Koth_40_N.CEL


title: 19.Woodruff_13saA1.CEL


title: 05.Koth_26_C.CEL


title: 11.Woodruff_20_N.CEL


title: 02.Koth_25_N.CEL


title: 01.Koth_24_N.CEL


title: ice1_24H Cold_Rep1

status: Public on Oct 01 2005

city: Riverside

first: Jian-Kang

last: Zhu

address: 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: University of California

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

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

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

label: Biotin

source_name: Seedlings

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

extract_protocol: RNeasy Plant Mini Kit, Qiagen

treatment_protocol: Treated at 0C for 24 hours just prior to harvesting.

tag: A mutant defective in an upstream transcription factor required for chilling and freezing tolerance as described in Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.H., Hong, X.H., Agarwal, M., and Zhu, J.K. (2003). ICE1

value: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 17, 1043-1054.


title: ice1_24H Cold_Rep2

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


title: ice1_no treatment_Rep1

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


title: ice1_3H Cold_Rep1

treatment_protocol: Treated at 0C for 3 hours just prior to harvesting.


title: ice1_no treatment_Rep2


title: ice1_6H Cold_Rep2

treatment_protocol: Treated at 0C for 6 hours just prior to harvesting.


title: Wildtype_3H Cold_Rep1

tag: Columbia ecotype containing CBF3 promoter-driven luciferase transgene. As described in Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.H., Hong, X.H., Agarwal, M., and Zhu, J.K. (2003). ICE1


title: Wildtype_6H Cold_Rep1


title: Wildtype_3H Cold_Rep2


title: ice1_3H Cold_Rep2


title: Liver - 8059

status: Public on Sep 30 2005

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological Question: Histology
Pathological Value: Hepatocellular Carcinoma
Pathological Question: T
Pathological Value: 1
Pathological Question: N
Pathological Value: 0
Pathological Question: M
Pathological Value: 0
Pathological Question: Metastatic Sites
Pathological Value: None
Pathological Question: Stage
Pathological Value: 1
Pathological Question: Multiple Tumors
Pathological Value: No
Pathological Question: Stage During or Following Multimodality Theraphy
Pathological Value: No
Primary Site: Liver

source_name: Liver


title: Soft Tissue Abdominal Wall - 8057

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Primary Site: Soft Tissue Sarcoma
Histology: Myxoid liposarcoma

source_name: Soft Tissue Abdominal Wall


title: Prostate - 8050

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 28
Presenting Symptoms: Nocturia
PSA: Elevated
# of years PSA Tested?: 0-5
Pathological T: 2c
Pathological N: 0
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 8-10
Primary Site: Prostate
Histology: Adenocarcinoma, Acinar Type

source_name: Prostate


title: Wildtype_24H Cold_Rep2


title: Wildtype_6H Cold_Rep2


title: Wildtype_24H Cold_Rep1


title: Prostate - 89224

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: Yes
Current status of disease: Under Therapy
Pathological T: 2c
Pathological N: 1
Pathological M: 0
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 8-10
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Wildtype_no treatment_Rep2

source_name: Seedling

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


title: Endometrium - 89227

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Days from Patient Diagnosis to Excision: 90
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Endometrium


title: Wildtype_no treatment_Rep1

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


title: Lung - 8067

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Workplace or household smokers?: No
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Pulmonary
Retreatment Stage: 4
Retreatment Grade: 2
Primary Site: Kidney
Histology: Metastatic Conventional (clear cell) renal carcinoma

source_name: Lung


title: Lymph node - 8058

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Pathological T: 3a
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Lymph Nodes
Pathological Stage: 4B
Pathological Grade: 3
Primary Site: Endometrium
Histology: Metastatic Mixed adenocarcinoma and small cell neuroendocrine carcinoma


title: ice1_6H Cold_Rep1


title: Retroperitoneum - 8051

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
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 pain
Presenting Symptoms: Bloating
Retreatment T: 3c
Retreatment N: X
Retreatment M: 0
Retreatment Stage: 3C
Retreatment Grade: 3
Primary Site: Ovary
Histology: Metastatic Papillary serous cystadenocarcinoma

source_name: Retroperitoneum


title: Endometrium - 78397

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 35
Pathological T: 1b
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Omentum - 7232

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Presenting Symptoms: Abdominal mass
Primary Site: Ovary
Histology: Metastatic Papillary Serous Carcinoma

source_name: Omentum


title: Colon - 78403

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 45
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Omentum - 8060

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Other
Retreatment Stage: 4B
Retreatment Grade: 3
Primary Site: Endometrium
Histology: Metastatic Endometrioid carcinoma


title: Endometrium - 7231

description:
Quality metric = 28S to 18S: 1
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 6
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Endometrium - 7005

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
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: Adenocarcinoma


title: Breast - 7233

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 40-50
Gender: Female
Ethnic Background: Other
Ethnic Background: Eastern Indian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 120
Prior Therapy: Chemotherapy
Mammogram: Yes
Number of years in which a mammogram was obtained?: 0-5
Oral contraceptives?: No
Pathological T: 3
Pathological N: 1a
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma

source_name: Breast


title: Ovary - 7008

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Carcinosarcoma

source_name: Ovary


title: Lung - 6991

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 60
Pathological T: 1
Pathological N: 1
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Neuroendocrine carcinoma


title: Breast - 6898

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 0-5
Primary Site: Breast
Histology: Lobular Carcinoma


title: Head of Pancreas - 7000

description:
Quality metric = 28S to 18S: 1
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 2
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Theraphy: No
Primary Site: Head of Pancreas
Histology: Ductal adenocarcinoma

source_name: Head of Pancreas


title: Kidney - 6891

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Clinical T: 1b
Clinical N: 0
Clinical M: 1
Clinical Metastatic Sites: Pulmonary
Clinical Stage: 4
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma

source_name: Kidney


title: Colon - 6910

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Male
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Presenting Symptoms: Abdominal Pain
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma


title: Omentum - 8061

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 120
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Primary Site: Ovary
Histology: Metastatic Papillary Serous Adenocarcinoma


title: Abdominal wall mass - 6519

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 80-90
Gender: Male
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
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: 4
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Other
Retreatment Stage: 4
Retreatment Grade: 2
Primary Site: Rectum
Histology: Metastatic Adenocarcinoma

source_name: Abdominal wall mass


title: Breast - 6894

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 0(i-)
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Ovary - 6515

description:
Quality metric = 28S to 18S: 1
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 120
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Bloating
Primary Site: Ovary
Histology: Adenocarcinoma


title: Vagina - 6517

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 75
Clinical Question: Histology
Clinical Value: Adenocarcinoma, mixed epithelial type (papillary serous and clear cell)
Clinical Question: Grade
Clinical Value: 3
Primary Site: Vagina

source_name: Vagina


title: Brain - 6312

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Brain
Retreatment Stage: 4
Retreatment Grade: 1
Primary Site: Lung
Histology: Metastatic Adenocarcinoma, NOS

source_name: Brain


title: Cervix - 59002

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 42
Have you ever been diagnosed as having HPV on your PAP smear?: No
Pathological T: 1b1
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Theraphy: No
Primary Site: Cervix Uteri
Histology: Squamous cell carcinoma, non-keratinizing

source_name: Cervix


title: Colon - 58991

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 30-40
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal Pain
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Primary Site: Colon
Histology: Adenocarcinoma


title: Breast - 6300

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: No
Pathological T: 2
Pathological N: 2a
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Positive
Primary Site: Breast
Histology: Ductal Carcinoma


title: Bone & Cartilage - 6304

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 90
Pathological Question: Histology
Pathological Value: Chondrosarcoma
Pathological Question: T
Pathological Value: 2
Pathological Question: N
Pathological Value: 0
Pathological Question: M
Pathological Value: 0
Pathological Question: Stage
Pathological Value: IIB
Pathological Question: Grade
Pathological Value: 4
Pathological Question: Stage During or Following Multimodality Theraphy
Pathological Value: Yes
Pathological Question: Multiple Tumors
Pathological Value: No
Primary Site: Bone & Cartilage

source_name: Bone & Cartilage


title: Thyroid - 58999

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 63
Primary Site: Thyroid
Histology: Papillary carcinoma, follicular variant

source_name: Thyroid


title: Lung - 6305

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Pipe
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: 1
Retreatment M: 1
Retreatment Metastatic Sites: Pulmonary
Retreatment Stage: 4
Retreatment Grade: 2
Primary Site: Lung
Histology: Metastatic Bronchioloalveolar carcinoma

source_name: Left Lower Lobe Lung


title: Colon - 6293

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Colon - 54077

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Abdominal Pain
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Mucinous Carcinoma


title: Cervix - 58990

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 20-30
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Have you ever been diagnosed as having HPV on your PAP smear?: No
Primary Site: Cervix Uteri
Histology: Adenosquamous carcinoma


title: Colon - 6295

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 80-90
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Constipation
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


title: Kidney - 54071

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 150
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Breast - 59000

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 70-80
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Oral contraceptives?: No
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Primary Site: Breast
Histology: Ductal Carcinoma


title: Colon - 54078

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Constipation
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma


title: Breast - 53962

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 180
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: Yes
Hormonal therapy (# of Years)?: 0-5
Primary Site: Breast
Histology: Lobular Carcinoma


title: Colon - 54070

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 11
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Black tarry stools
Presenting Symptoms: Constipation
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Lymph Nodes
Pathological Stage: 4
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma


title: Omentum - 6292

description:
Quality metric = 28S to 18S: 1
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Metastatic Papillary Serous Adenocarcinoma


title: Colon - 58992

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Diarrhea
Presenting Symptoms: Nausea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma


title: Colon - 59003

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 10
Presenting Symptoms: Nausea
Presenting Symptoms: Vomiting
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: D
Primary Site: Colon
Histology: Adenocarcinoma


title: Pelvic Mass - 5236

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Chemotherapy
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment Grade: 3
Primary Site: Ovary
Histology: Metastatic Papillary Serous Adenocarcinoma

source_name: Pelvic Mass


title: Ovary - 53963

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Clear cell adenocarcinoma


title: Ovary - 53957

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Pathological T: 3c
Pathological N: X
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 4
Primary Site: Ovary
Histology: Malignant mixed muellerian tumor


title: Kidney - 53960

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 40-50
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
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: Ureter - 53955

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Theraphy: No
Primary Site: Ureter
Histology: Papillary transitional cell carcinoma

source_name: Ureter


title: Ovary - 53954

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Presenting Symptoms: Bloating
Primary Site: Ovary
Histology: Papillary Serous Carcinoma


title: Lung - 5131

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 40
Presenting Symptoms: Persistent Cough
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 0
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Large cell neuroendocrine carcinoma

source_name: Lung


title: Colon - 53951

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
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?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 4
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Brain - 4457

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 100
Presenting Symptoms: Seizures
Pathological Question: Histology
Pathological Value: Astrocytoma
Pathological Question: Grade
Pathological Value: WHO Grade III
Pathological Question: Stage
Pathological Value: No AJCC Staging Scheme
Primary Site: Brain


title: Breast - 4910

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 42
Mammogram: Yes
Number of years in which a mammogram was obtained?: 16-20
Oral contraceptives?: Yes
Oophorectomy?: Yes
Fibrocystic disease?: Yes
Mammogram calcifications?: Yes
Hormonal therapy (# of Years)?: 21-25
Pathological T: 1c
Pathological N: 0(i-)
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma


title: Lung - 4449

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
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
Days from Patient Diagnosis to Excision: 70
Presenting Symptoms: Persistent Cough
Presenting Symptoms: SOB
Workplace or household smokers?: Yes
Pathological T: 2
Pathological N: 1
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Breast - 4222

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 0-5
Oophorectomy?: Yes
Fibrocystic disease?: No
Mammogram calcifications?: No
Hormonal therapy (# of Years)?: 6-10
Pathological T: 2
Pathological N: 0(i-)
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Breast
Histology: Ductal Carcinoma


title: Renal Pelvis - 38211

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 56
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 3
Pathological Multiple Tumours: No
Pathological Staged During or Following Multimodality Theraphy: No
Primary Site: Renal Pelvis
Histology: Urothelial (transitional cell) carcinoma

source_name: Renal Pelvis


title: Lung - 5132

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
Presenting Symptoms: Persistent Cough
Pathological T: 2
Pathological N: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Ovary - 5229

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-70
Gender: Female
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Bloating
Pathological T: 3c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Adenocarcinoma


title: Breast - 4914

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 76
Mammogram: Yes
Number of years in which a mammogram was obtained?: 6-10
Oral contraceptives?: Yes
Number of years of use? (Oral contraceptives): 11-15
Oophorectomy?: No
Fibrocystic disease?: Yes
Mammogram calcifications?: No
Primary Site: Breast
Histology: Ductal Carcinoma


title: Peritoneum - 4439

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
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: 120
Prior Therapy: Chemotherapy
Presenting Symptoms: Abdominal mass
Presenting Symptoms: Abdominal pain
Presenting Symptoms: Bloating
Pathological T: X
Pathological N: X
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Primary Site: Peritoneum
Histology: Adenocarcinoma

source_name: Peritoneum


title: Kidney - 45127

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 40
Pathological T: 3b
Pathological N: 0
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Colon - 4333

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-80
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: 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: Colon


title: Breast - 4450

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 12
Mammogram: Yes
Number of years in which a mammogram was obtained?: 36-40
Pathological T: 1c
Pathological N: 0(i-)
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological ER: Positive
Pathological PR: Positive
Pathological HER/2 Neu: Negative
Primary Site: Breast
Histology: Lobular Carcinoma

source_name: Breast


title: Kidney - 38213

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 40
Clinical T: 1b
Clinical N: 0
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Corpus Uteri - 3759

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Pathological T: 2b
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Peritoneum
Pathological Stage: 4B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Corpus Uteri
Histology: Serous adenocarcinoma (papillary serous)

source_name: Corpus Uteri


title: Lung - 45125

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Workplace or household smokers?: No
Pathological T: 2
Pathological N: 0
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Kidney - 36328

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-80
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 3b
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 2
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Colon - 36327

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 16
Presenting Symptoms: Bright red stools
Presenting Symptoms: Diarrhea
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma


title: Lung - 36318

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Pulmonary
Retreatment Stage: 4
Retreatment Grade: 2
Primary Site: Colon
Histology: Metastatic Adenocarcinoma


title: Ovary - 4191

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 80-90
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Abdominal mass
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Ovary
Histology: Papillary Serous Carcinoma

source_name: Ovary


title: Rectum - 36320

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-60
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: Corpus Uteri - 7230

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical Question: Histology
Clinical Value: High Grade Sarcoma with focal heterologous elements
Clinical Question: Stage
Clinical Value: No AJCC Staging Scheme
Primary Site: Myometrium


title: Lung - 36311

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-60
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 6-10
Retreatment T: X
Retreatment N: X
Retreatment M: 1b
Retreatment Metastatic Sites: Pulmonary
Retreatment Stage: 4
Primary Site: Melanoma of Skin
Histology: Metastatic Spindle cell melanoma


title: Colon - 36314

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 80-90
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 30
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: 0
Pathological Stage: 2A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: B
Primary Site: Colon
Histology: Adenocarcinoma


title: Kidney - 33798

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-70
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
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

source_name: Kidney