title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-061 - mAdbID:65384

description: mAdb experiment ID: 65384

source_name: 03-061B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-456 - mAdbID:65223

status: Public on Oct 25 2007

type: RNA

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 65223

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: not provided

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

molecule: total RNA

organism: Homo sapiens

label_protocol: Cy5 Sample Labeling Protocol - generic

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

tag: Tissue

value: liver

tag: Disease state

value: HBV positive Hepatocellular Carcinoma (HCC)

tag: Individual

tag: Genotype/Genetic variation

value: EpCAM negative

source_name: 03-456B - Control

label_protocol: Cy3 Sample Labeling Protocol - generic

value: HBV-infected with chirrhosis


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-350 - mAdbID:65189

description: mAdb experiment ID: 65189

source_name: 03-350B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma AN - mAdbID:65197

description: mAdb experiment ID: 65197

source_name: ANA

tag: Individual:

source_name: ANB - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-435 - mAdbID:65165

description: mAdb experiment ID: 65165

source_name: 03-435B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-365 - mAdbID:65163

description: mAdb experiment ID: 65163

value: EpCAM positive

source_name: 03-365B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-182 - mAdbID:65217

description: mAdb experiment ID: 65217

source_name: 03-182B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-398 - mAdbID:65154

description: mAdb experiment ID: 65154

source_name: 03-398B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-199 - mAdbID:65150

description: mAdb experiment ID: 65150

source_name: 03-199B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-149 - mAdbID:65192

description: mAdb experiment ID: 65192

source_name: 03-149B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-291 - mAdbID:65221

description: mAdb experiment ID: 65221

source_name: 02-291B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-023 - mAdbID:65383

description: mAdb experiment ID: 65383

source_name: 03-023B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-452 - mAdbID:65196

description: mAdb experiment ID: 65196

source_name: 03-452B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-192 - mAdbID:65160

description: mAdb experiment ID: 65160

source_name: 03-192B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-295 - mAdbID:65159

description: mAdb experiment ID: 65159

source_name: 02-295B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma (HCC) 03-210 - mAdbID:65218

description: mAdb experiment ID: 65218

source_name: 03-210B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-024 - mAdbID:65220

description: mAdb experiment ID: 65220

source_name: 03-024B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-220 - mAdbID:65162

description: mAdb experiment ID: 65162

source_name: 03-220B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-335 - mAdbID:65194

description: mAdb experiment ID: 65194

source_name: 03-335B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-292 - mAdbID:65151

description: mAdb experiment ID: 65151

source_name: 03-292B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-366 - mAdbID:65166

description: mAdb experiment ID: 65166

source_name: 02-366B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-464 - mAdbID:65224

description: mAdb experiment ID: 65224

source_name: 03-464B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-384 - mAdbID:65164

description: mAdb experiment ID: 65164

source_name: 03-384B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-363 - mAdbID:65379

description: mAdb experiment ID: 65379

source_name: 02-363B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-346 - mAdbID:65191

description: mAdb experiment ID: 65191

source_name: 02-346B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-148 - mAdbID:65222

description: mAdb experiment ID: 65222

source_name: 03-148B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-197 - mAdbID:65161

description: mAdb experiment ID: 65161

source_name: 03-197B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-468 - mAdbID:65225

description: mAdb experiment ID: 65225

source_name: 03-468B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-356 - mAdbID:65152

description: mAdb experiment ID: 65152

source_name: 03-356B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-165 - mAdbID:65193

description: mAdb experiment ID: 65193

source_name: 03-165B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-445 - mAdbID:65149

description: mAdb experiment ID: 65149

source_name: 02-445B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-387 - mAdbID:65029

description: mAdb experiment ID: 65029

source_name: 02-387B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-303 - mAdbID:65035

description: mAdb experiment ID: 65035

source_name: 03-303B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-112 - mAdbID:65015

description: mAdb experiment ID: 65015

source_name: 03-112B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-318 - mAdbID:65147

description: mAdb experiment ID: 65147

source_name: 02-318B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-241 - mAdbID:65017

description: mAdb experiment ID: 65017

source_name: 03-241B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-274 - mAdbID:65034

description: mAdb experiment ID: 65034

source_name: 03-274B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-099 - mAdbID:65031

description: mAdb experiment ID: 65031

source_name: 03-099B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-108 - mAdbID:65037

description: mAdb experiment ID: 65037

source_name: 03-108B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-427 - mAdbID:65070

description: mAdb experiment ID: 65070

source_name: 03-427B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-404 - mAdbID:64981

description: mAdb experiment ID: 64981

source_name: 03-404B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-427 - mAdbID:65030

description: mAdb experiment ID: 65030

source_name: 02-427B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-316 - mAdbID:65026

description: mAdb experiment ID: 65026

source_name: 03-316B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-462 - mAdbID:64975

description: mAdb experiment ID: 64975

source_name: 02-462B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-012 - mAdbID:65064

description: mAdb experiment ID: 65064

source_name: 03-012B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-188 - mAdbID:64979

description: mAdb experiment ID: 64979

source_name: 03-188B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-467 - mAdbID:65027

description: mAdb experiment ID: 65027

source_name: 03-467B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-359 - mAdbID:64972

description: mAdb experiment ID: 64972

source_name: 02-359B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-131 - mAdbID:64977

description: mAdb experiment ID: 64977

source_name: 03-131B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-380 - mAdbID:64974

description: mAdb experiment ID: 64974

source_name: 02-380B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-424 - mAdbID:65020

description: mAdb experiment ID: 65020

source_name: 03-424B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-459 - mAdbID:65014

description: mAdb experiment ID: 65014

source_name: 02-459B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-298 - mAdbID:65012

description: mAdb experiment ID: 65012

source_name: 02-298B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-248 - mAdbID:64978

description: mAdb experiment ID: 64978

source_name: 03-248B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 02-347 - mAdbID:64954

description: mAdb experiment ID: 64954

source_name: 02-347B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-307 - mAdbID:65013

description: mAdb experiment ID: 65013

source_name: 02-307B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-218 - mAdbID:64963

description: mAdb experiment ID: 64963

source_name: 03-218B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-255 - mAdbID:64967

description: mAdb experiment ID: 64967

source_name: 03-255B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-243 - mAdbID:64965

description: mAdb experiment ID: 64965

source_name: 03-243B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-455 - mAdbID:64956

description: mAdb experiment ID: 64956

source_name: 02-455B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-059 - mAdbID:64958

description: mAdb experiment ID: 64958

source_name: 03-059B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-282 - mAdbID:64830

description: mAdb experiment ID: 64830

source_name: 03-282B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-428 - mAdbID:64833

description: mAdb experiment ID: 64833

source_name: 02-428B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-363 - mAdbID:64650

description: mAdb experiment ID: 64650

source_name: 03-363B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-282 - mAdbID:64832

description: mAdb experiment ID: 64832

source_name: 02-282B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-101 - mAdbID:64826

description: mAdb experiment ID: 64826

source_name: 03-101B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-346 - mAdbID:64647

description: mAdb experiment ID: 64647

source_name: 03-346B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-437 - mAdbID:64605

description: mAdb experiment ID: 64605

source_name: 02-437B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-212 - mAdbID:64649

description: mAdb experiment ID: 64649

source_name: 03-212B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-141 - mAdbID:64827

description: mAdb experiment ID: 64827

source_name: 03-141B - Control


title: EpCAM positive HBV positive Hepatocellular Carcinoma 03-222 - mAdbID:64635

description: mAdb experiment ID: 64635

source_name: 03-222B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-370 - mAdbID:64726

description: mAdb experiment ID: 64726

source_name: 03-370B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-453 - mAdbID:64831

description: mAdb experiment ID: 64831

source_name: 03-453B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-276 - mAdbID:64455

description: mAdb experiment ID: 64455

source_name: 02-276B - Control


title: MCF7_E2_replicate1

status: Public on Oct 19 2007

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: Standard hybridization to Affymetrix U133A 2.0 microarray.

scan_protocol: Standard scanning protocol

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling.

label: Biotin

source_name: MCF7 cells, treated for 3 hours with EtOH or 17beta-estradiol (E2)

label_protocol: Seven μg of total RNA were subjected to One-Cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray.

extract_protocol: Total RNA was prepared using Trizol Reagent according to the manufacturer’s instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen).

tag: MCF-7 cells were grown as described above and treated with ethanol or 100 nM E2 for 3h.


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-386 - mAdbID:64425

description: mAdb experiment ID: 64425

source_name: 02-386B - Control


title: EpCAM negative HBV positive Hepatocellular Carcinoma 03-121 - mAdbID:64604

description: mAdb experiment ID: 64604

source_name: 03-121B - Control


title: MCF7_EtOH_replicate1


title: Uterus - 341548

status: Public on Jun 25 2007

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 2.0
Patient Age: 40-50
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Pathological T: 2b
Pathological N: 0
Pathological M: 0
Pathological Stage: 2B
Pathological Grade: 3
Primary Site: Endometrium
Histology: Endometrioid carcinoma

source_name: Uterus


title: EpCAM negative HBV positive Hepatocellular Carcinoma 02-402 - mAdbID:64426

description: mAdb experiment ID: 64426

source_name: 02-402B - Control


title: aa_NY79

status: Public on Jun 21 2007

city: New York

first: Elisa

last: Wurmbach

state: NY

address: 1 Gustave L. Levy Place

department: Hematology/Oncology

institute: Mount Sinai School of Medicine

description: very advanced HCC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix.

scan_protocol: Affymetrix standard procedure

data_processing: MAS probe set signal intensity

label: biotin

source_name: human liver; very advanced HCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

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

tag: very advanced HCC


title: e_NY44

description: early HCC

source_name: human liver; early HCC

tag: early HCC


title: a_B35B

description: advanced HCC

source_name: human liver; advanced HCC

tag: advanced HCC


title: aa_NY82

description: very advanced HCC


title: a_NY70

description: advanced HCC


title: aa_NY216

description: very advanced HCC


title: aa_NY224

description: very advanced HCC


title: e_M43B

description: early HCC


title: e_B13

description: early HCC


title: aa_NY39

description: very advanced HCC


title: e_NY2

description: early HCC


title: a_NY18

description: advanced HCC


title: a_NY36

description: advanced HCC


title: e_NY16

description: early HCC


title: a_NY34

description: advanced HCC


title: e_NY204

description: early HCC


title: aa_NY226

description: very advanced HCC


title: a_NY7

description: advanced HCC


title: ve_NY6

description: very early HCC

source_name: human liver; very early HCC

tag: very early HCC


title: ve_NY26

description: very early HCC


title: 11_0020_Control_Day1_37

status: Public on Jun 14 2007

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

description: 1) Control day 1; 2) Septic shock day 1; 3) Septic shock day 3 (same patient cohort as Septic shock day 1).

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

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

data_processing:
The image file was captured on an Affymetrix GeneChip Scanner 3000 and initially processed with Microarray suite 5.0 (Affymetrix).
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
Each array was normalized the same. Global scaling is used by adjusting the average intensity or signal value of each probe array to the same Target Intensity Value (TGV) of 1500. Genechip Operating Software 1v4 (Affymetrix) was then used to generate CEL files from each experiment, which were then imported into GeneSpring for all further data analysis.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

source_name: Whole blood from normal children and children with septic shock.

label_protocol: Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to manufacturer's instructions.

extract_protocol:
Total RNA was extracted from whole blood using the PaxGene system.
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Samples were not manipulated.


title: ve_NY41

description: very early HCC


title: 11_0014_Control_Day1_46


title: 15_0003_Control_Day1_19


title: 11_0011_Control_Day1_49


title: 11_0008_Control_Day1_52


title: 11_0027_Control_Day1_31


title: Non-BLC (T161)

status: Public on May 30 2007

city: Boston

first: Andrea

last: Richardson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description:
no additional info
none

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

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

data_processing: The data were analyzed with dchip with default normalization settings.

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

growth_protocol: RNA extration, cRNA synthesis and hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64 (2004), pp. 64-71

extract_protocol: RNA extration, cRNA synthesis and hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64 (2004), pp. 64-73

treatment_protocol: RNA extration, cRNA synthesis and hyb performed according to J. Clin. Invest. 110(2002), pp. 633-641 and Cancer Res. 64 (2004), pp. 64-72

tag: non-BLC


title: Non-BLC (T44)

description:
no additional info
none


title: 11_0013_Control_Day1_47


title: 11_0012_Control_Day1_48


title: 11_0037_Control_Day1_25


title: 11_0018_Control_Day1_39


title: 11_0009_Control_Day1_51


title: 11_0019_Control_Day1_38


title: Non-BLC (T41)

description:
no additional info
none


title: Normal breast (B69)

description:
no additional info
none

tag: NB


title: 15_0005_Control_Day1_16


title: Normal breast (B87)

description:
no additional info
none


title: Normal breast (B58)

description:
no additional info
none


title: Normal breast (B64)

description:
no additional info
none


title: Normal breast (B83)

description:
no additional info
none


title: Non-BLC (T73)

description:
no additional info
none


title: Normal breast (B60)

description:
no additional info
none


title: Non-BLC (T92)

description:
no additional info
none


title: 15_0002_Control_Day1_20


title: 15_0001_Control_Day1_21


title: Normal breast (B42)

description:
no additional info
none


title: Non-BLC (T4)

description:
no additional info
none


title: Non-BLC (T50)

description:
no additional info
none


title: Non-BLC (T30)

description:
no additional info
none


title: Non-BLC (T81)

description:
no additional info
none


title: aa_NY218

description: very advanced HCC


title: Non-BLC (T37)

description:
no additional info
none


title: Non-BLC (T115)

description:
no additional info
none


title: Non-BLC (T84)

description:
no additional info
none


title: Non-BLC (T188)

description:
no additional info
none


title: Non-BLC (T74)

description:
no additional info
none


title: Non-BLC (T119)

description:
no additional info
none


title: BRCA1 (T911)

description:
no additional info
none


title: Non-BLC (T145)

description:
no additional info
none


title: Non-BLC (T162)

description:
no additional info
none


title: Non-BLC (T178)

description:
no additional info
none


title: Non-BLC (T117)

description:
no additional info
none


title: BRCA1 (T636)

description:
no additional info
none


title: Non-BLC (T175)

description:
no additional info
none


title: BRCA1 (T152)

description:
no additional info
none


title: Basal (T116)

description:
no additional info
none

tag: Basal


title: Basal (T143)

description:
no additional info
none


title: Non-BLC (T183)

description:
no additional info
none


title: Basal (T123)

description:
no additional info
none


title: Basal (T133)

description:
no additional info
none


title: Basal (T137)

description:
no additional info
none


title: BRCA1 (T151)

description:
no additional info
none


title: Basal (T134)

description:
no additional info
none


title: Basal (T130)

description:
no additional info
none


title: Basal (T38)

description:
no additional info
none


title: Basal (T146)

description:
no additional info
none


title: Basal (T56)

description:
no additional info
none


title: Basal (T141)

description:
no additional info
none


title: Basal (T118)

description:
no additional info
none


title: Basal (T147)

description:
no additional info
none


title: Basal (T144)

description:
no additional info
none


title: Basal (T140)

description:
no additional info
none


title: Basal (T129)

description:
no additional info
none


title: Basal (T21)

description:
no additional info
none


title: Basal (T149)

description:
no additional info
none


title: C178

status: Public on May 26 2007

first: James

middle: Dirk

last: Iglehart

address: 44 Binney St.

department: Cancer Biology

institute: Dana Farber Cancer Institute

description: Gene expression data from breast cancer tumor tissue.

hyb_protocol: standard Affymetrix protocol.

scan_protocol: standard Affymetrix protocol.

data_processing: Raw gene expression values were obtained using Affymetrix GeneChip software and further analyzed using the DNA-Chip Analyzer (dChip).

source_name: breast cancer tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA extracted from frozen tissue was used to generate biotinylated cRNA target.

treatment_protocol: The frozen bulk tumor samples were confirmed to contain at least 70% viable tumor by area on histologic thin sections.

tag: ER

value: neg

value: pos

tag: B-R grade

value: III

tag: node status

tag: LVI

tag: tumor type

value: Ductal

tag: tumor size


title: C161

value: II


title: C173


title: C154


title: B97

value: I

value: Mixed


title: C162


title: B93


title: B50


title: B94

value: Lobular


title: C163


title: C171


title: B91


title: B89


title: C175


title: B96


title: C156


title: B86


title: B84


title: B95


title: B81


title: B88


title: B75


title: B78


title: B72


title: B79


title: B90


title: B74


title: B77


title: B85


title: B73


title: B71


title: B76


title: B63


title: B57


title: B67


title: B35


title: B47


title: B43


title: B38


title: B41


title: B55


title: B52


title: B65


title: B54


title: B39


title: B32


title: B44


title: B37


title: B53


title: B45


title: B34


title: B31


title: B33


title: B30


title: B22


title: B25


title: B23


title: B26


title: B17


title: B21


title: B24


title: B18


title: B14


title: B7


title: B15


title: B3


title: B8


title: B12


title: B4


title: B11


title: B1


title: C147


title: C146


title: B13


title: B10


title: C144


title: B2


title: C149


title: C140


title: C141


title: C136


title: C148


title: B5


title: C132


title: C138


title: C145


title: C139


title: C131


title: C134


title: C130


title: C142


title: C133


title: C143


title: C125


title: C121


title: C119


title: C122


title: C128


title: C120


title: C123


title: C115


title: C135


title: C116


title: C114


title: C118

value: n


title: C113


title: Endometrium/Ovary 14 Disease

status: Public on Apr 09 2007

city: San Diego

first: Richard

middle: B

last: Roth

state: CA

address: 12790 El Camino Real

department: Molecular Medicine

institute: Neurocrine Biosciences, Inc.

description: Disease

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing.

source_name: Male/Female; Normal/Diseased

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

treatment_protocol: Not treated

tag: Tissue/Cell Line [C]

value: endometrium/ovary

tag: Disease/Normal or Treatment [C]

value: disease

tag: Gender

value: F

tag: Disease type

value: Endometriosis


title: Endometrium 11 Normal

description: Normal

value: endometrium

value: normal

value: Normal


title: Endometrium 20 Normal

description: Normal


title: Endometrium 23 Normal

description: Normal


title: Endometrium/Ovary 10 Disease

description: Disease


title: Endometrium/Ovary 11 Disease

description: Disease


title: Endometrium/Ovary 9 Disease

description: Disease


title: Endometrium/Ovary 8 Disease

description: Disease


title: Endometrium/Ovary 13 Disease

description: Disease


title: Endometrium 22 Normal

description: Normal


title: Endometrium 4 Normal

description: Normal


title: Endometrium/Ovary 4 Disease

description: Disease


title: Endometrium 12 Normal

description: Normal


title: Endometrium/Ovary 7 Disease

description: Disease


title: Endometrium/Ovary 5 Disease

description: Disease


title: Endometrium 6 Normal

description: Normal


title: Tumorigenic (PE15TG)

status: Public on Mar 10 2007

city: Redwood City

first: Xinhao

address: 800 Chesapeake

institute: OncoMed Pharmaceuticals Inc

description: Tumorigenic population (ESA+ CD44+ CD24-/low Lin-) of a breast tumor isolated using fluorescence activated cell sorting. Sample consists of three replicates.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the manufacturer's instructions.

data_processing: To obtain an expression measure for a given probeset, the mismatch hybridization values were subtracted from the perfect match values, and the average of the middle 50% of these differences was used as the expression measure for the probe set. A quantile normalization procedure was then applied to adjust for differences in the probe intensity distribution across different chips. Specifically, we applied a monotone linear spline to each chip that mapped quantiles 0.01 up to 0.99 (in increments of 0.01) exactly to the corresponding quantiles of a standard chip. The transform log2 [200 + max(X;0)] was then applied.

source_name: breast tumor (ESA+ CD44+ CD24-/low Lin-)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

tag: tumorigenic population (ESA+ CD44+ CD24-/low Lin-)


title: Endometrium/Ovary 12 Disease

description: Disease


title: Melanoma cell line SKMEL5

status: Public on Mar 31 2007

city: Herston

first: Leisl

last: Packer

state: QLD

address: 300 Herston Rd

department: Cancer and Cell Biology

country: Australia

institute: Queensland Institute of Medical Research

description: For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.

source_name: Melanoma cell line SKMEL5

growth_protocol: Melanoma cell lines were cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

extract_protocol: RNA extractions were performed using Qiagen RNeasy Midi-kits as per the manufacturer’s instructions. RNA quality and concentration were assessed using a 2100 BioAnalyser (Agilent Technologies).

tag: Melanoma cell line established from metastatic melanoma


title: Non-tumorigenic (PE15NTG)

description: Non-tumorigenic population of a breast tumor isolated using fluorescence activated cell sorting. Sample consists of three replicates.

source_name: non-tumorigenic breast tumor

tag: non-tumorigenic breast tumor


title: Endometrium 5 Normal

description: Normal


title: Endometrium 7 Normal

description: Normal


title: Non-tumorigenic (PE13NTG)

description: Non-tumorigenic population of a breast tumor isolated using fluorescence activated cell sorting


title: HeLa_RNA_rep 3 - HG-U133Plus2

status: Public on Oct 11 2006

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

description: RNA samples were isolated from HeLa S3 cells and purified with trizol (Invitrogen) and RNeasy (Qiagen). RNA was amplified and hybridized to Affymetrix U133 Plus 2 arrays using standard methods.

data_processing: Three biological replicates were quantile normalized. Gene expression was indicated by the median of PM-MM values over all probes. The hypothesis of difference in gene expression between groups of genes, based on median PM-MM, was tested using the Wilcoxon rank sum statistic.

source_name: HeLa_RNA_rep 3

tag: HeLa_RNA_rep 3


title: HeLa_RNA_rep 1 - HG-U133Plus2

source_name: HeLa_RNA_rep 1

tag: HeLa_RNA_rep 1


title: HeLa_RNA_rep 2 - HG-U133Plus2

source_name: HeLa_RNA_rep 2

tag: HeLa_RNA_rep 2


title: cpxR__U_N0075_r1

status: Public on Jan 22 2007

first: Timothy

middle: S

last: Gardner

address: 44 Cummington St.

department: Biomedical Engineering

institute: Boston University

description: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Escherichia coli

source_name: Escherichia coli

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix E. coli protocol

extract_protocol: RNAEasy with RNAProtect(Qiagen)

tag: cpxR upregulation, 0.075 ug/ml norfloxacin


title: S5-0

status: Public on Dec 12 2006

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

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

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

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

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

source_name: Time: Day 0; Smoking status: smoker

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

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

tag: Time

value: Day 0

tag: Smoking status

value: smoker

tag: Pack-years

tag: Age

tag: Sex

tag: Ethnic group

value: black


title: bcp___U_N0075_r3

scan_protocol: GeneChips were washed and stained with an FS450 fluidics machine and scanned using a GeneChip Scanner 3000

tag: bcp upregulation, 0.075 ug/ml norfloxacin


title: NS2-0

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

source_name: Time: Day 0; Smoking status: non-smoker

value: non-smoker

value: M

value: white


title: NS3-0


title: S3R-0


title: S2-0


title: S1-0


title: S4-0


title: NS1-0


title: adipose_tissue_subcutaneous_4

status: Public on Mar 30 2006

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA

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

extract_protocol: Total RNA extracted using standard Trizol protocol, followed by Qiagen RNeasy column clean-up

tag: Normal tissue


title: NS4-0


title: medulla_2

source_name: medulla


title: bronchus_4

source_name: bronchus


title: tongue_main_corpus_1


title: putamen_3

source_name: putamen


title: saphenous_vein_2


title: adipose_tissue_4


title: trachea_4

source_name: trachea


title: lung_4

source_name: lung


title: pharyngeal_mucosa_4


title: tongue_main_corpus_4


title: tonsil_2

source_name: tonsil


title: frontal_lobe_2


title: medulla_4


title: tongue_main_corpus_2


title: B-ALL-32-0h

status: Public on Nov 14 2005

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 3.7 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.

source_name: Patient 32, peripheral blood


title: T-ALL-25-6h

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 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.

source_name: Patient 25, peripheral blood


title: pharyngeal_mucosa_1