title: Scrambled BMEL 1

description: BMEL gene expression data


title: Scrambled BMEL 3

status: Public on Dec 31 2008

type: RNA

city: Philadelphia

first: Joshua

last: Friedman

state: PA

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

country: USA

institute: University of Pennsylvania School of Medicine

description: BMEL gene expression data

hyb_protocol: The hybridization was performed according to the Affymatrix manual using a Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: Slides were scanned by a ScanArray 4000 XL scanner (Packard Biochip Technologies, USA)

data_processing: Image analysis was carried out using the ImaGene 6.1.0 software (BioDiscovery, Inc., USA)

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: BMELs, transfected with LNA oligo

label_protocol: 100ng of total RNA per sample was amplified and biotinylated using the MessageAmp Premier kit (Ambion)

growth_protocol: Grown under growth conditions as described in PMID: 12297826

extract_protocol: mirVana™ miRNA Isolation Kit (Ambion)

treatment_protocol: Oligofectamine transfection

tag: Cell line derived from fetal mouse liver

tag: BMELs grown under growth conditions


title: Scrambled BMEL 4

description: BMEL gene expression data


title: ASO-30a BMEL 4

description: BMEL gene expression data


title: Oct4-MO injected, rep1-2

city: Stanford

first: Bokyung

last: Choi

state: CA

address: 318 Campus Drive

department: Applied physics

institute: Stanford University

description: 1-cell stage mouse embryos (see treatment protocol below) were injected with 0.6 mM of antisense morpholino oligonucleotide which was designed to specifically target the translational start site of Oct4.

hyb_protocol: Fragmented, labeled, ssDNA samples were submitted to Stanford University PAN Core Facility for hybridization to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix), and laser scanning.

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with dChip 2007 with the default setting. The mask file for normalization control was used.

label: biotin

source_name: Oct4-MO injected, rep1-2

label_protocol: Direct biotin labeling and fragmentation were performed (FL-Ovation cDNA Biotin Module (Nugen).

extract_protocol: Samples containing 20 pooled injected or control mouse embryos were washed through 3 drops of PBS/PVP and collected for total RNA extraction and isolation (Picopure Total RNA Isolation Kit, Molecular Devices Corp.), to yield 10 μL of total RNA.  5 μL of total RNA, or the equivalent of 10 mouse embryos, was subjected to two rounds of amplification (WT-Ovation Pico system, Nugen) according to manufacturer’s instructions.   The quality of ssDNA resulting from the second round amplification was tested on the Bioanalyzer 2100 (Agilent), and a typical yield of 5-8 μg per sample was quantitated by the ND-1000 UV spectrophotometer (Nanodrop Technologies).

treatment_protocol: 3-5 week old wild type F1 (C57BL6xDBA/2) females (Charles River) were superovulated by intraperitonial injections of 5 IU of pregnant mare’s serum gonadotropin (Sigma) followed by 5 IU of human chorionic gonadotropin (Sigma) 48 hours later, and mated overnight with wild type males. Mice were sacrificed by cervical dislocation 17 hours after hCG injection, and 1-cell embryos were released from oviducts. Cumulus cells were removed by hyaluronidase (Sigma) treatment and pipetting. Pre-implantation embryos at the two pronuclei stage were recovered, pooled from 3-6 females in M2 media (Chemicon International), followed by immediate cytoplasmic microinjection of gene-specific antisense morpholino oligonucleotides and culture in Human Tubal Fluid with 10% serum supplement (In-Vitro Fertilization, Inc.) microdrops under mineral oil (Sigma) in mixed gas (90% nitrogen, 5% oxygen, 5% carbon dioxide; Praxair) at 37°C, and cultured at ten embryos per 20 μL drop. Uninjected control embryos derived from the same embryo pool, and were placed in identical conditions in parallel, except that they were not injected.

tag: Embryos were collected at the mid-2-cell stage at 43 hours post-human chorionic gonadotropin injection.


title: FoxO3 RNAi in C2C12 cells

city: Berkeley

first: Ping

last: Hu

address: Hearst & Oxford

department: MCB

institute: University of California, Berkeley

description: C2C12 cells grown in DMEM transfected with FoxO3 shRNA.

hyb_protocol: Follow the protocol from Affymetrix.

scan_protocol: Follow the protocol from Affymetrix.

data_processing: Using Affymetrix GeneChip GCOS expression analysis software to process.

source_name: C2C12 cells

label_protocol: Follow the protocol from Affymetrix.

growth_protocol: C2C12 cells were grown in DMEM with puromycine. All serums used were tested for cytotoxicity.

extract_protocol: Qiagen RNeasy kit was used to extract total RNA.

treatment_protocol: C2C12 cells were transfected with shRNA against FoxO3. Different colonies were screened for the best depletion of FoxO3.  .


title: ASO-30a BMEL 2

description: BMEL gene expression data


title: Oct4-MO injected, rep1-1

source_name: Oct4-MO injected, rep1-1


title: FoxO1 RNAi in C2C12 cells

description: C2C12 cells grown in DMEM transfected with FoxO1 shRNA.

treatment_protocol: C2C12 cells were transfected with shRNA against FoxO1. Different colonies were screened for the best depletion of FoxO1.


title: FoxO4 RNAi in C2C12 cells

description: C2C12 cells grown in DMEM transfected with FoxO4 shRNA.

treatment_protocol: C2C12 cells were transfected with shRNA against FoxO4. Different colonies were screened for the best depletion of FoxO4.


title: No injection, rep1-3

description: Uninjected control embryos processed and cultured in parallel with embryos from Sample 5.

source_name: No injection, rep1-3


title: ASO-30a BMEL 1

description: BMEL gene expression data


title: Tail-SpretusxFVB-3

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description: Gene expression data from tail epidermis taken at time of sacrifice

hyb_protocol: 200 microliters of hybridization sample were incubated in the Affymetrix Hybridization Oven 640 instrument for 16 hours at 45C with 60 rpm rotation.  Arrays were processed with the Affymetrix Fluidics Station 450 instrument, using the FS450_0001 fluidics script and GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: The Affymetrix GCS3000 7G instrument was used to acquire the microarray image data.

data_processing: CEL files were background corrected and normalized with RMA using RMAExpress software and log2 transformed

organism: Mus musculus x Mus spretus

source_name: Total RNA from untreated FVB/N x Spretus/Ei F1 tail epidermis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Trizol followed by Qiagen RNEasy clean-up

treatment_protocol:
No treatment
Backcross mice were treated as noted; parental and F1 strains were untreated.


title: Tail-SpretusxFVB-4

tag: untreated FVB/N x Spretus/Ei F1 tail epidermis


title: Tail-FVBBX-71

source_name: Total RNA from (SPRET/Ei X FVB/N) X FVB/N tail epidermis

treatment_protocol:
Tumors were initiated on dorsal back skin with a single dose of DMBA (25 µg per mouse in 200 µl acetone). Starting one week after the initiation tumors were promoted with TPA (200 µl of 10-4 M solution in acetone)  twice weekly for 20 weeks.
Backcross mice were treated as noted; parental and F1 strains were untreated.

tag: papillomas


title: Tail-FVBBX-68


title: Tail-FVBBX-66


title: Tail-FVB-1

source_name: Total RNA from untreated FVB/N tail epidermis

tag: untreated FVB/N tail epidermis


title: Tail-FVBBX-70


title: Tail-Spretus-3

organism: Mus spretus

source_name: Total RNA from untreated Spretus/Ei tail epidermis

tag: untreated Spretus/Ei tail epidermis


title: Tail-FVBBX-65


title: Tail-FVBBX-69


title: Tail-FVB-4


title: Tail-FVB-3


title: Tail-FVBBX-73


title: Tail-Spretus-1


title: Tail-FVBBX-72


title: Tail-SpretusxFVB-2


title: Tail-FVBBX-59


title: Tail-FVB-2


title: Tail-Spretus-4


title: Tail-FVBBX-55


title: Tail-FVBBX-61


title: Tail-Spretus-2


title: Tail-FVBBX-60


title: Tail-SpretusxFVB-1


title: Tail-FVBBX-62


title: Tail-FVBBX-64


title: Tail-FVBBX-58


title: Tail-FVBBX-63


title: Tail-FVBBX-56


title: Tail-FVBBX-46


title: Tail-FVBBX-49


title: Tail-FVBBX-53


title: Tail-FVBBX-36


title: Tail-FVBBX-50


title: Tail-FVBBX-51


title: Tail-FVBBX-54


title: Tail-FVBBX-44


title: Tail-FVBBX-39


title: Tail-FVBBX-43


title: Tail-FVBBX-67


title: Tail-FVBBX-45


title: Tail-FVBBX-52


title: Tail-FVBBX-37


title: Tail-FVBBX-40


title: Tail-FVBBX-42


title: Tail-FVBBX-32


title: Tail-FVBBX-41


title: Tail-FVBBX-29


title: Tail-FVBBX-38


title: Tail-FVBBX-47


title: Tail-FVBBX-25


title: Tail-FVBBX-28


title: Tail-FVBBX-27


title: Tail-FVBBX-31


title: Tail-FVBBX-26


title: Tail-FVBBX-34


title: Tail-FVBBX-35


title: Tail-FVBBX-30


title: Tail-FVBBX-33


title: Tail-FVBBX-18


title: Tail-FVBBX-24


title: Tail-FVBBX-23


title: Tail-FVBBX-15


title: Tail-FVBBX-21


title: Tail-FVBBX-3


title: Tail-FVBBX-13


title: Tail-FVBBX-19


title: Tail-FVBBX-7


title: Tail-FVBBX-8


title: Tail-FVBBX-6


title: Tail-FVBBX-10


title: Tail-FVBBX-14


title: Tail-FVBBX-20


title: Tail-FVBBX-17


title: Tail-FVBBX-1


title: Tail-FVBBX-22


title: Tail-FVBBX-11


title: Tail-FVBBX-2


title: Tail-FVBBX-12


title: Tail-FVBBX-16


title: Tail-FVBBX-5


title: Tail-FVBBX-9


title: Tail-FVBBX-4


title: R1 embryonic stem cells 4

city: Seoul

first: heebal

last: kim

address: San 56-1 Sillim-dong Gwanak-gu

country: South Korea

institute: Seoul National University

description: Crossing two 129 substrains (129S1/SvImJ and 129X1/SvJ)

hyb_protocol: The biotin-labeled IVT-RNA was then fragmented. Fragmented cRNA was hybridized to the Mouse Genome 430 2.0 Array at 45°C for 16 h according to the manufacturer's instructions.

scan_protocol: After hybridization, the arrays were washed in a GeneChip® Fluidics Station 450 with a non-stringent wash buffer at 25°C followed by a stringent wash buffer at 50°C. After washing, the arrays were stained with a streptavidin–phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner, which was controlled by GeneChip® Operating Software (GCOS; Affymetrix).

data_processing: All arrays were processed for background correction and normalization using the robust multi-array averaging of the R package Affy. The expression values were computed from the raw CEL files by applying the RMA model of probe-specific correction for perfect-match probes. The corrected probe values were then quantile normalized, and a median polish was applied to compute one expression measure from all probe values. The resulting RMA expression values were log2-transformed.

source_name: R1 embryonic stem cells

label_protocol: After cleanup with a Sample Cleanup Module (Affymetrix), ds-cDNA was used for in vitro transcription (IVT). cDNA was transcribed using the Affymetrix GeneChip® IVT Labeling Kit in the presence of biotin-labeled CTP and UTP.

extract_protocol: Total RNA from the sample was extracted using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. cDNA was synthesized using the One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA). Single-stranded cDNA was synthesized using Superscript II reverse transcriptase and T7-oligo (dT) primers at 42°C for 1 h. Double-stranded cDNA was obtained using DNA ligase, DNA polymerase I, and RNase H at 16°C for 2 h, followed by T4 DNA polymerase at 16°C for 5 min.

tag: Pluripotency, self-renewal


title: embryonic stem cells derived from parthenogenetic blastocyst of B6D2F1 hybrid mouse 4

description: B6D2F1 = female C57BL6 and male DBA2

source_name: Parthenogenetic embryonic stem cells


title: R1 embryonic stem cells 3


title: embryonic stem cells derived from normal fertilization of female C57BL6 and male DBA2 mice 4

description: B6D2F1 = female C57BL6 and male DBA2

source_name: Embryonic stem cells


title: embryonic stem cells derived from normal fertilization of female C57BL6 and male DBA2 mice 3

description: B6D2F1 = female C57BL6 and male DBA2


title: Control_liver_5

description: Hepatic gene expression data

source_name: Liver

growth_protocol: Standard housing, feeding, and water. Fasted for 5 hours prior to euthanasia.

tag: Strain

value: mixed

tag: Tissue

value: liver

tag: Age

value: 28 days


title: Mutant_liver_3

description: Hepatic gene expression data


title: Mutant_liver_5

description: Hepatic gene expression data


title: embryonic stem cells derived from parthenogenetic blastocyst of B6D2F1 hybrid mouse 5

description: B6D2F1 = female C57BL6 and male DBA2


title: AtT-20_siNT_Rpt2

city: Stoke on Trent

first: Kevin

middle: John

last: Dudley

state: Staffordshire

address: Thornburrow Drive

department: Institute of Science and Technology in Medicine

country: United Kingdom

institute: University of Keele

description: Non targeting control replicate 2

hyb_protocol: According to manufacturers instructions

scan_protocol: According to manufacturers instructions

data_processing: GCOS

label_protocol: According to manufacturers instructions

growth_protocol: Recommended conditions

extract_protocol: Guanidinium-thiocyanate

treatment_protocol: Eight-day treatment with 20 nM siNT

tag: AtT-20/D16v-F2 pituitary adenoma cell line


title: embryonic stem cells derived from parthenogenetic blastocyst of B6D2F1 hybrid mouse

description: B6D2F1 = female C57BL6 and male DBA2


title: AtT-20_siNT_Rpt3

description: Non-targeting control replicate 3


title: Mutant_liver_1

description: Hepatic gene expression data


title: Mutant_liver_2

description: Hepatic gene expression data


title: Control_liver_2

description: Hepatic gene expression data


title: Control_liver_1

description: Hepatic gene expression data


title: embryonic stem cells derived from preantral follicle culture and oocyte parthenogenesis of B6D2F1 hybrid mouse 2

description: B6D2F1 = female C57BL6 and male DBA2

source_name: Follicle-derived parthenogenetic embryonic stem cells


title: embryonic stem cells derived from preantral follicle culture and oocyte parthenogenesis of B6D2F1 hybrid mouse 1

description: B6D2F1 = female C57BL6 and male DBA2


title: Mutant_liver_4

description: Hepatic gene expression data


title: Control_liver_4

description: Hepatic gene expression data


title: AtT-20_siNT_Rpt1

description: Non targeting control replicate 1


title: embryonic stem cells derived from preantral follicle culture and oocyte parthenogenesis of B6D2F1 hybrid mouse 3

description: B6D2F1 = female C57BL6 and male DBA2


title: embryonic stem cells derived from preantral follicle culture and oocyte parthenogenesis of B6CBAF1 hybrid mouse

description: B6CBAF1 = female C57BL6 and male CBA/ca

data_processing: All arrays were processed for background correction and normalization using the robust multi-array averaging of the R package Affy [66]. The expression values were computed from the raw CEL files by applying the RMA model of probe-specific correction for perfect-match probes. The corrected probe values were then quantile normalized, and a median polish was applied to compute one expression measure from all probe values. The resulting RMA expression values were log2-transformed.


title: embryonic stem cells derived from normal fertilization of female C57BL6 and male DBA2 mice 2

description: B6D2F1 = female C57BL6 and male DBA2


title: embryonic stem cells derived from preantral follicle culture and oocyte parthenogenesis of B6CBAF1 hybrid mouse 1

description: B6CBAF1 = female C57BL6 and male CBA/ca


title: AtT-20_siDNMT1_Rpt2

description: Dnmt1 knockdown replicate 2

treatment_protocol: Eight-day treatment with 20 nM siDNMT1


title: R1 embryonic stem cells 5


title: AtT-20_siDNMT1_Rpt3

description: Dnmt1 knockdown replicate 3


title: embryonic stem cells derived from preantral follicle culture and oocyte parthenogenesis of B6CBAF1 hybrid mouse 3

description: B6CBAF1 = female C57BL6 and male CBA/ca


title: Control_liver_3

description: Hepatic gene expression data


title: AtT-20_siDNMT1_Rpt1

description: Dnmt1 knockdown replicate 1


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-6)

city: Boston

first: BIDMC

last: GENOMICS

state: MA

address: 4 BlackFan Circle

department: Genomics Center

institute: Beth Israel Deaconess Medical Center

description: TRAMP Tumors

hyb_protocol: As described by Affymetrix. Standard protocol.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 and GeneChip Operating Software acquired raw fluorescence data.

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

label_protocol: Affymetrix standard protocol.

extract_protocol: Trizol

tag: TRAMP Tumors


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-8)

description: TRAMP Tumors


title: Normal prostates (NORP-8)

description: ventral and dorsolateral lobes of normal prostates

source_name: normal prostates


title: Normal prostates (NORP-6)

tag: ventral and dorsolateral lobes of normal prostates


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-7)

description: TRAMP Tumors


title: Normal prostates (NORP-5)


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-5)

description: TRAMP Tumors


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-3)

description: TRAMP Tumors


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-2)

description: TRAMP Tumors


title: Normal prostates (NORP-3)


title: Normal prostates (NORP-1)


title: Fat from NOD mice with blood glucose level of >300mg/dl for 3 consecutive days_DIA1

first: Terry

middle: B

last: Strom

address: 77 Avenue Louis Pasteur

description: Fat from NOD mice with blood glucose level of >300mg/dl for 3 consecutive days.

scan_protocol: Affymetrix GeneChip® Operating Software (GCOS) automates the control of GeneChip® Fluidics Stations and Scanners. In addition, GCOS acquires data, manages sample and experimental information, and performs gene expression data analysis.

source_name: fat tissue

label_protocol: Affymetrix single cycle protocol.


title: Normal prostates (NORP-7)


title: Normal prostates (NORP-2)


title: Normal prostates (NORP-9)


title: Fat from 10 weeks normal Glycemic NOD female mice_NOR2


title: Fat from AAT (Alpha-1-antitrypsin) treated NOD mice with stable reversion and insulin independence_AAT1


title: Fat from 10 weeks normal Glycemic NOD female mice_NOR1


title: Fat from AAT (Alpha-1-antitrypsin) treated NOD mice with stable reversion and insulin independence_AAT2


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-4)

description: TRAMP Tumors


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-1)

description: TRAMP Tumors


title: Fat from NOD mice with blood glucose level of >300mg/dl for 3 consecutive days_DIA2

tag: Fat from NOD mice with blood glucose level of >300mg/dl for 3 consecutive days.


title: Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) tumor (TRAMP-9)

description: TRAMP Tumors


title: Spleen of 15-week garlic-fed mouse, biological rep3

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

description: Gene expression data from spleen of mice fed on raw garlic powder for 15 weekds

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with EukGE_2v5-450 protocol.

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) using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: 8-week old male C57BL/6J mouse fed on garlic diet for 15 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: 8-week old mice were divided into two groups and maintained in the SPF facility of Institute of Biomedical Sciences, Taipei, Taiwan, ROC.

extract_protocol: Total RNA was isolated from the frozen spleen tissues using Qiagen RNeasy Midi Kit according to the manufacturer's instructions.

treatment_protocol: Garlic bulbs (husk free) were homogenized with a food processor, lyophilized, ground into dry powder in a mortar with pestle and stored at -20 C until use. Mice were fed (ad libitum) a diet containing 20/ vitamin free casein, 10% sucrose, 53.95% cornstarch, 7% soybean oil, 3.5% AIN93 regular mineal mix, 1% AIN93G vitamin mix, 0.25% choline bitartrate (41.1% choline), 0.3% L-cysteine with the adition of 4% cellulose (Control diet) or 4% lyophilized raw garlic powder (Garlic diet). At the end of the 15-week treatment period, mice were sacrifificed by cervical dislocation to collect spleens, which were snap-frozen in liquid nitrogen for storage at -80C until use.

tag: Starting age

value: 8-week old; Gender male; Strain:C57BL/6J; Organ:Spleen

tag: Diet

value: 4% lyophilized raw garlic powder in a special diet (Yeh and Yeh, 1994)


title: Spleen of 15-week cellulose-fed mouse, biological rep3

description: Gene expression data from spleen of mice fed on cellulose for 15 weekds

source_name: 8-week old male C57BL/6J mouse fed on cellulose diet for 15 weeks

value: 4% cellulose in a special diet (Yeh and Yeh, 1994)


title: Spleen of 15-week garlic-fed mouse, biological rep1


title: Spleen of 15-week cellulose-fed mouse, biological rep1


title: Spleen of 15-week cellulose-fed mouse, biological rep2


title: Mouse_Klf5 KO_ES_clone 2

city: Tsukuba

first: Kazuhiko

last: Uchida

state: Ibaraki

address: 1-1-1 Tennnoudai

department: Institute of Basic Medical Sciences

country: Japan

institute: University of Tsukuba

description:
Affymetrix
GeneChip Expression Analysis
Technical manual
Rev 3

source_name: Mouse_Klf5 KO_ES_clone 2

growth_protocol: ES medium + 15% FBS　＋LIF

extract_protocol: RNeasy mini Kit

tag: Mouse_E14 ES cell_Undifferentialted


title: Mouse_Klf5 KO_ES_clone 1

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical manual Rev 3

source_name: Mouse_Klf5 KO_ES_clone 1


title: Mouse_WT_ES_clone 1

scan_protocol: Affymetrix GeneChip Expression Analysis Technical manual Rev 3

source_name: Mouse_WT_ES_clone 1


title: Healthy control saliva-4

city: Los Angeles

first: Lei

last: Zhang

address: 10833 Le Conte Ave., CHS 73-029

institute: UCLA Dental Research Institute

description: no additional information

hyb_protocol: Standard Affymetrix protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

data_processing: The CEL files from all datasets (array data from 12 pancreatic cancer saliva samples and 12 healthy saliva samples) were imported into Affymetrix® Expression Console™ Software. The analysis was performed as follows: the PLIER expression measures were computed after background correction and quantile normalization for each microarray dataset. Probeset-level quantile normalization was performed across all samples to make the effect sizes similar among all datasets.

organism: Homo sapiens

source_name: saliva

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)

extract_protocol:
Twelve pancreatic cancer samples and 12 matched control samples were used for salivary transcriptome profiling. RNA was isolated from 330 mL of saliva supernatant using the MagMAX Viral RNA Isolation Kit (Ambion). This process was automated using KingFisher mL technology (Thermo Fisher Scientific Inc.), followed by TURBO™ DNase treatment (Ambion). Eluted 10 mL RNA was reserved for subsequent quantitative real-time polymerase chain reaction (qPCR) validation. The remaining RNA (90 mL) was concentrated to 11 mL and then linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA).
After purification, cDNA was in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA).

tag: healthy control


title: Healthy control saliva-10

description: no additional information

scan_protocol: Standard Affymetrix protocols via UCLA Microarray Core (http://microarray.genetics.ucla.edu/)


title: pancreatic cancer saliva-9

description: no additional information

tag: early pancreatic cancer


title: pancreatic cancer saliva-12

description: no additional information


title: pancreatic cancer saliva-11

description: no additional information


title: Mouse_WT_ES_clone 2

data_processing:
Affymetrix
GeneChip Expression Analysis
Technical manual
Rev 3

source_name: Mouse_WT_ES_clone 2


title: Healthy control saliva-9

description: no additional information


title: Healthy control saliva-11

description: no additional information


title: pancreatic cancer saliva-10

description: no additional information


title: pancreatic cancer saliva-6

description: no additional information


title: Healthy control saliva-1

description: no additional information


title: Healthy control saliva-12

description: no additional information


title: Healthy control saliva-2

description: no additional information


title: Healthy control saliva-8

description: no additional information


title: pancreatic cancer saliva-5

description: no additional information


title: Healthy control saliva-6

description: no additional information


title: pancreatic cancer saliva-7

description: no additional information


title: Healthy control saliva-7

description: no additional information


title: Healthy control saliva-3

description: no additional information


title: pancreatic cancer saliva-8

description: no additional information


title: Healthy control saliva-5

description: no additional information


title: Normal prostates (NORP-4)


title: pancreatic cancer saliva-1

description: no additional information


title: pancreatic cancer saliva-2

description: no additional information


title: pancreatic cancer saliva-3

description: no additional information


title: Prostate - 486153

city: Phoenix

first: Erin

last: Curley

state: AZ

address: 445 N. 5th Street

institute: IGC

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 42
PSA: Elevated
# of years PSA Tested?: 11-15
Cancer discovered by digital exam?: Yes
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Uterus - 486154

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 1c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Mixed Cell Adenocarcinoma

source_name: Uterus


title: Sigmoid Colon - 486145

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-69
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 37
Presenting Symptoms: Bright red stools
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: D
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Sigmoid Colon


title: Rectosigmoid - 465785

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 46-50
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 70
Prior Therapy: Chemotherapy
Prior Therapy: Radiation
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: Yes
Pathological Dukes Stage: C
Primary Site: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid


title: Right Colon - 486150

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
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: 1
Pathological M: 1
Pathological Metastatic Sites: Hepatic
Pathological Stage: 4
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Right Colon


title: Rectosigmoid - 465789

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 40-49
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
Presenting Symptoms: Bright red stools
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Rectosigmoid
Histology: Adenocarcinoma


title: Cecum - 487435

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Presenting Symptoms: Black tarry 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: Colon
Histology: Adenocarcinoma

source_name: Cecum


title: Kidney - 470080

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Pipe
Alcohol Consumption?: Yes
Family History of Cancer?: No
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Clear Cell Renal Carcinoma

source_name: Kidney


title: Breast - 470077

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Mammogram: Yes
Number of years in which a mammogram was obtained?: 11-15
Oral contraceptives?: No
Oophorectomy?: No
Fibrocystic disease?: No
Mammogram calcifications?: No
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Breast
Histology: Invasive Ductal Carcinoma

source_name: Breast


title: Endometrium - 472796

description:
Quality metric = 28S to 18S: 2.2
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma

source_name: Endometrium


title: Sigmoid Colon - 465787

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 4
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma


title: Uterus - 487457

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Pathological T: 1c
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: Corpus Uteri
Histology: Carcinosarcoma


title: Kidney - 470078

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Kidney - 470085

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
Gender: Female
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 4
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Papillary renal cell carcinoma


title: Uterus - 486148

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 21-25
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma


title: Sigmoid Colon - 486147

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Bright red stools
Presenting Symptoms: Constipation
Presenting Symptoms: Diarrhea
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 - 486151

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 15
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma

source_name: Colon


title: Lung - 486139

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 45
Presenting Symptoms: Hemoptysis
Workplace or household smokers?: Yes
Pathological T: 3
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: Lung
Histology: Squamous cell carcinoma

source_name: Lung


title: Pelvic Soft Tissue - 465786

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
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 T: 3c
Retreatment N: X
Retreatment M: 0
Retreatment Metastatic Sites: Other
Retreatment Stage: 3C
Retreatment Grade: 3
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Ovary
Histology: Carcinoma, NOS

source_name: Pelvic Soft Tissue


title: Uterus - 486146

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma


title: Kidney - 470086

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Clinical T: 1b
Clinical N: X
Clinical M: X
Clinical Stage: Unknown
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Clear Cell Renal Carcinoma


title: Cecum - 465780

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 7
Presenting Symptoms: Abdominal Pain
Presenting Symptoms: Bright red stools
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Mucinous Adenocarcinoma


title: Kidney - 470083

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 30-39
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 1
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Clear Cell Renal Carcinoma


title: Thyroid - 470075

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Clinical T: 3
Clinical N: 0
Clinical M: 0
Clinical Stage: 3
Clinical Multiple Tumours: No
Clinical Staged During or Following Multimodality Therapy: No
Primary Site: Thyroid
Histology: Hurthle cell adenocarcinoma

source_name: Thyroid


title: Uterus - 465783

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-79
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: 45
Pathological T: 1c
Pathological N: 1
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid Adenocarcinoma


title: Axillary Lymph Node - 465788

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 40-49
Gender: Male
Ethnic Background: African-American
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Presenting Symptoms: Lymphadenopathy
Clinical Stage: 3
Clinical Symptoms: A
Primary Site: Lymph Nodes (Nodal Lymphoma)
Histology: Classic Hodgkin's Disease, Nodular Sclerosing Type

source_name: Axillary Lymph Node


title: Kidney - 465778

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 21
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Prostate - 465779

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 120
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Uterus - 465776

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 70-79
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?: No
Days from Patient Diagnosis to Excision: 51
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: pancreatic cancer saliva-4

description: no additional information


title: Prostate - 465769

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 6-10
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 90
PSA: Elevated
# of years PSA Tested?: 6-10
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Prostate - 441133

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 8-10
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Lung - 465774

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 180
Workplace or household smokers?: No
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Bronchioloalveolar carcinoma


title: Sigmoid Colon - 443046

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 60
Presenting Symptoms: Bright red stools
Diagnosis made by: Colonoscopy
Pathological T: 2
Pathological N: 2
Pathological M: 0
Pathological Stage: 3C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma arising in a villous adenoma


title: Colon - 433125

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Clinical T: 2
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Dukes Stage: A
Primary Site: Colon
Histology: Adenocarcinoma


title: Uterus - 433119

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 11-15
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 28
Pathological T: 1a
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Endometrioid carcinoma


title: Kidney - 465770

description:
Quality metric = 28S to 18S: 1.1
Patient Age: 50-59
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?: Yes
Days from Patient Diagnosis to Excision: 77
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Lung - 465775

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 21
Workplace or household smokers?: No
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Large cell carcinoma


title: Uterus - 465761

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 26-30
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 30
Clinical T: 3a
Clinical N: 0
Clinical M: 0
Clinical Stage: 3A
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Mixed endometrioid and serous adenocarcinoma


title: Uterus - 465768

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 0-5
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 28
Pathological T: 1c
Pathological N: 0
Pathological M: 0
Pathological Stage: 1C
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Undifferentiated Carcinoma


title: Rectosigmoid Colon - 443042

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 0
Pathological M: X
Pathological Stage: Unknown
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Rectosigmoid
Histology: Adenocarcinoma

source_name: Rectosigmoid Colon


title: Uterus - 443031

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 11
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1B
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Endometrium
Histology: Malignant mixed Mullerian tumor


title: Lung - 465762

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-89
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
Pathological T: 1
Pathological N: 0
Pathological M: 0
Pathological Stage: 1A
Pathological Grade: 1
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Bronchioloalveolar carcinoma


title: Lung - 441147

description:
Quality metric = 28S to 18S: 1.9
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 36-40
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Retreatment T: X
Retreatment N: X
Retreatment M: 1
Retreatment Metastatic Sites: Pulmonary
Retreatment Stage: 4
Retreatment Grade: X
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: Yes
Primary Site: Colon
Histology: Metastatic Adenocarcinoma


title: Kidney - 443040

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-59
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?: No
Days from Patient Diagnosis to Excision: 14
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Conventional (clear cell) renal carcinoma


title: Kidney - 443041

description:
Quality metric = 28S to 18S: 1.0
Patient Age: 50-59
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: 120
Clinical T: 1a
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 4
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Clear Cell Renal Carcinoma


title: Colon - 443034

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Weight loss
Have you ever had chemotherapy for any previous cancer prior to your current diagnosis?: No
Clinical Question: Stage
Clinical Value: I E
Clinical Question: Stage During or Following Multimodality Therapy
Clinical Value: No
Primary Site: Colon (Extralymphatic Lymphoma)
Clinical Question: Histology
Clinical Value: Mantle Cell Lymphoma


title: Kidney - 443039

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 57
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: Clear Cell Renal Carcinoma


title: Colon - 443035

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 41-45
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 5
Presenting Symptoms: Bright red stools
Screening studies performed?: No
Diagnosis made by: Colonoscopy
Pathological T: X
Pathological N: X
Pathological M: 0
Pathological Stage: Unknown
Pathological Grade: 1
Pathological Multiple Tumors: Yes
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Colon
Histology: Adenocarcinoma


title: Parotid Lymph Node - 433113

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 40-49
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Prior Therapy: Surgical
Relapse Since Primary Treatment: Yes
Number of Years Until Relapse: 0-5
Retreatment T: X
Retreatment N: 2b
Retreatment M: 0
Retreatment Stage: 3B
Retreatment Multiple Tumors: No
Retreatment Stage During or Following Multimodality Therapy: No
Primary Site: Melanoma of Skin
Histology: Malignant melanoma, NOS

source_name: Parotid Lymph Node


title: Prostate - 443033

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 60-69
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 70
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: Yes
Clinical T: 2c
Clinical N: 0
Clinical M: 0
Clinical Stage: 2
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Cecum - 441145

description:
Quality metric = 28S to 18S: 1.8
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: No
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: Prostate - 441135

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: No
Clinical T: 2c
Clinical N: X
Clinical M: X
Clinical Stage: Unknown
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 5-6
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Kidney - 433123

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 16-20
Type of Tobacco Use: Cigarettes
Type of Tobacco Use: Pipe
Alcohol Consumption?: No
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 14
Clinical T: 1b
Clinical N: 0
Clinical M: 0
Clinical Stage: 1
Clinical Grade: 2
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Kidney
Histology: Clear Cell Renal Carcinoma


title: Prostate - 441134

description:
Quality metric = 28S to 18S: 1.7
Patient Age: 70-79
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
PSA: Elevated
Pathological T: 3a
Pathological N: 0
Pathological M: 0
Pathological Stage: 3
Pathological Grade: 2
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Prostate - 433129

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 60-69
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?: Yes
Days from Patient Diagnosis to Excision: 60
PSA: Elevated
# of years PSA Tested?: 0-5
Cancer discovered by digital exam?: Yes
Clinical T: 2c
Clinical N: X
Clinical M: X
Clinical Stage: Unknown
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Colon - 441141

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 50-59
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
Screening studies performed?: Yes
Pathological T: X
Pathological N: 0
Pathological M: 1
Pathological Metastatic Sites: Other
Pathological Stage: 4
Pathological Grade: X
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Primary Site: Appendix
Histology: Metastatic Mucinous Adenocarcinoma


title: Omentum - 433112

description:
Quality metric = 28S to 18S: 1.2
Patient Age: 60-69
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: Yes
Family History of Cancer?: Yes
Days from Patient Diagnosis to Excision: 90
Prior Therapy: Chemotherapy
Pathological Question: T
Pathological Value: 3c
Pathological Question: N
Pathological Value: 1
Pathological Question: M
Pathological Value: 0
Pathological Question: Stage
Pathological Value: 3c
Pathological Question: Grade
Pathological Value: 3
Pathological Question: Multiple Tumors
Pathological Value: No
Pathological Question: Stage During or Following Multimodality Therapy
Pathological Value: Yes
Primary Site: Primary Peritoneum
Pathological Question: Histology
Pathological Value: Serous Adenocarcinoma

source_name: Omentum


title: Lung - 433110

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 51-55
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 42
Presenting Symptoms: SOB
Workplace or household smokers?: No
Clinical T: 1
Clinical N: 0
Clinical M: 0
Clinical Stage: 1A
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Primary Site: Lung
Histology: Adenocarcinoma, NOS


title: Prostate - 423091

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 50-59
Gender: Male
Ethnic Background: African-American
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
PSA: Elevated
Cancer discovered by digital exam?: No
Clinical T: 2c
Clinical N: X
Clinical M: X
Clinical Stage: Unknown
Clinical Grade: 3
Clinical Multiple Tumors: No
Clinical Stage During or Following Multimodality Therapy: No
Clinical Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS

source_name: Prostate


title: Prostate - 403717

description:
Quality metric = 28S to 18S: 1.4
Patient Age: 70-79
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: Yes
PSA: Elevated
Pathological T: 2c
Pathological N: 0
Pathological M: 0
Pathological Stage: 2
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Gleason Score: 7
Primary Site: Prostate
Histology: Adenocarcinoma, NOS


title: Colon - 403721

description:
Quality metric = 28S to 18S: 1.5
Patient Age: 70-79
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: X
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Adenocarcinoma


title: Cecum - 345979

description:
Quality metric = 28S to 18S: 1.3
Patient Age: 80-89
Gender: Female
Ethnic Background: Caucasian
Tobacco Use : No
Alcohol Consumption?: No
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Screening studies performed?: Yes
Diagnosis made by: Colonoscopy
Pathological T: 3
Pathological N: 1
Pathological M: 0
Pathological Stage: 3B
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: C
Primary Site: Colon
Histology: Mucinous Adenocarcinoma


title: Control 30 h culture, biological rep2

city: Zurich

first: Michael

last: Zaugg

address: Raemistrasse 100

department: Anesthesiology

country: Switzerland

institute: Anesthesiology, University Hospital Zurich

description: Gene expression data from control cultures (30h, vehicle)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® U_133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Normalization and computation of expression values was performed using the Robust Multichip Average (RMA) algorithm

source_name: human aortic smooth muscle cells (HASMCs)

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

growth_protocol: HASMCs were grown to subconfluence and growth arrested for 24 hrs

extract_protocol: Total RNA was extracted using RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: The cultures were treated with 0.0 (vehicle) or 1.0 uM 2-ME in the presence of 2.5% fetal calf serum (to stimulate proliferation) for 4 hours (acute phase response/early gene induction) and for 30 hrs (late phase).

tag: control


title: U251_Rep1

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

description: The control for hybridization and labeling were from Affymetrix.

hyb_protocol: Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Human Genome HG-U133_Plus_2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.

scan_protocol: Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software

data_processing: Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition

label: phycoerythrin

source_name: ATCC

label_protocol: One ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)

growth_protocol:
Growth Medium: Dulbecco's Modified Eagle Medium and the following growth supplements: Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated

extract_protocol: Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer

tag: Cell strain

value: Normal Human Astrocytes (NHA)

tag: Passage

tag: Growth Medium

value: Dulbecco's Modified Eagle Medium and the following growth supplements:Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.

tag: Untreated


title: Normal Human Astrocyte_Rep2

source_name: Normal Human Astrocytes from Lonza

growth_protocol:
Growth Medium: Astrocyte Basal Medium (ABM™) and the following growth supplements: rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated

value: Astrocyte Basal Medium (ABM™) and the following growth supplements:rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.


title: Control 4h culture, biological rep3

description: Gene expression data from control cultures (4h, vehicle)


title: ME-treated 4h culture, biological rep3

description: Gene expression data from control cultures (4h, 2-ME)


title: ME-treated 30 h culture, biological rep4

description: Gene expression data from control cultures (30h, 2-ME)


title: Rectum - 465777

description:
Quality metric = 28S to 18S: 1.6
Patient Age: 50-59
Gender: Male
Ethnic Background: Caucasian
Tobacco Use : Yes
Years of Tobacco Use: 31-35
Type of Tobacco Use: Cigarettes
Alcohol Consumption?: Yes
Family History of Cancer?: No
Days from Patient Diagnosis to Excision: 14
Presenting Symptoms: Bright red stools
Pathological T: 2
Pathological N: 0
Pathological M: 0
Pathological Stage: 1
Pathological Grade: 3
Pathological Multiple Tumors: No
Pathological Stage During or Following Multimodality Therapy: No
Pathological Dukes Stage: A
Primary Site: Rectum
Histology: Adenocarcinoma

source_name: Rectum


title: ME-treated 30 h culture, biological rep3


title: Normal Human Astrocyte_Rep1

tag: Grown at 37C in 5%CO2, seeded at 5000 cells/cm2


title: Control 4h culture, biological rep1


title: U251_Rep2


title: ME-treated 4h culture, biological rep2


title: U251_Rep3


title: Control 30 h culture, biological rep3


title: Normal Human Astrocyte_Rep3


title: ME-treated 30 h culture, biological rep2


title: Control 30 h culture, biological rep1


title: ME-treated 4h culture, biological rep1


title: G001 VM

city: Madison

first: Hyun-Jung

last: Kim

state: WI

address: 1500 Highland ave.

department: Waisman center

institute: UW-Madison

hyb_protocol: followed affymetrix kit instruction

scan_protocol: Scan was done at UW-Madison, core facility.

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de).

source_name: neural progenitor cells (hNPC) from ventral midbrain (VM)

label_protocol: followed affymetrix kit instruction

extract_protocol: Qiagen column

tag: tissue

value: human brain (G001)

tag: dev stage

value: 8-10 wk gestation embryo

tag: cell type


title: G002 CTX

source_name: neural progenitor cells (hNPC) from developing cortex (CTX)

value: human brain (G002)


title: G002 VM

value: neural progenitor cells (hNPC) from ventral midbrain (VM)


title: G001 CTX

value: neural progenitor cells (hNPC) from developing cortex (CTX)


title: Control 4h culture, biological rep2


title: Donor 2, M-CSF + IFN-gamma + Pam3Cys

city: New York

first: Janice

last: Chen

state: NY

address: 535 East 70th St, 4th floor Research

department: Research

institute: Hospital for Special Surgery

description: Donor 2, M-CSF + IFN-gamma + Pam3Cys

hyb_protocol: Samples were hybridized to Affymetrix HG U133 Plus 2.0 GeneChip using Affymetrix fluidics station according to the instructions of the manufacturer.

scan_protocol: Affymetrix Gene-Array Scanner

data_processing: Data was processed using the Affymetrix Microarray Suite. Further data analysis was performed using GeneSpring software.

source_name: Donor 2, M-CSF + IFN-gamma + Pam3Cys

label_protocol: Labeled cRNA was prepared with the Affymetrix GeneChip IVT Labeling Kit.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen), followed by clean-up with the RNeasy Mini Kit (Qiagen).

treatment_protocol: CD14+ human monocytes were cultured in RPMI 1640 supplemented with 10% FBS and 10 ng/mL M-CSF + 100 U/mL IFN-gamma for 24 h, then stimulated with 10 ng/mL Pam3Cys for an additional 6 h.

tag: Peripheral blood from healthy human donor


title: Donor 2, M-CSF

description: Donor 2, M-CSF

source_name: Donor 2, M-CSF

treatment_protocol: CD14+ human monocytes were cultured in RPMI 1640 supplemented with 10% FBS and 10 ng/mL M-CSF for 30 h.


title: Donor 1, M-CSF + IFN-gamma + Pam3Cys

description: Donor 1, M-CSF + IFN-gamma + Pam3Cys

source_name: Donor 1, M-CSF + IFN-gamma + Pam3Cys


title: Donor 1, M-CSF + Pam3Cys

description: Donor 1, M-CSF + Pam3Cys

source_name: Donor 1, M-CSF + Pam3Cys

treatment_protocol: CD14+ human monocytes were cultured in RPMI 1640 supplemented with 10% FBS and 10 ng/mL M-CSF for 24 h, then stimulated with 10 ng/mL Pam3Cys for an additional 6 h.


title: Donor 1, M-CSF + IFN-gamma

description: Donor 1, M-CSF + IFN-gamma

source_name: Donor 1, M-CSF + IFN-gamma

treatment_protocol: CD14+ human monocytes were cultured in RPMI 1640 supplemented with 10% FBS and 10 ng/mL M-CSF + 100 U/mL IFN-gamma for 30 h.


title: retina_nasal_rep4

status: Public on Dec 30 2008

city: Canberra

first: Peter

last: Kozulin

state: ACT

address: Building 46, Sullivan's Creek Road

department: Research School of Biological Sciences

country: Australia

institute: ANU

description: biological replicate: Macula4_human, Nasal4_human, Surround4_human

hyb_protocol: The target cRNAs were fragmented, combined with poly-A sense RNA labeling controls and cRNA hybridisation controls, then hybridized to the HG-U133 Plus 2.0 GeneChip microarrays for 16 hr at 45 deg C according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.). GeneChips were washed and stained with streptavidin phycoerythrin conjugate in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned with an Affymetrix GeneChip Scanner 3000 using a 570 nm excitation wavelength laser.

data_processing: Probe-level data was analyzed with GC-RMA (robust multi-array average (RMA) analysis adjusted for probe sequence and GC content). GC-RMA adjusts for background noise on each array using only perfect match probe intensities. Subsequent data normalisation was performed across all arrays using quantile normalization. The background-adjusted, normalized PM values were then compiled, or summarised, within each probe set using the median polish technique, to generate a single measure of expression. These expression measures were then log transformed, base 2.

source_name: 19-20 weeks' gestation human retina, nasal biopsy

label_protocol: Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 2003, Affymetrix, Inc.).

extract_protocol: Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.

treatment_protocol: Retinal tissue was not subjected to any pre-treatment prior to RNA extraction which commenced 90-120 minutes after surgery to terminate pregnancy.

tag: Gestational age

value: 19-20 weeks' gestation

tag: Tissue

value: retina


title: retina_surround_rep4

source_name: 19-20 weeks' gestation human retina, surround biopsy (remaining retina after macula and nasal biopsies)


title: retina_nasal_rep3

description: biological replicate: Macula3_human, Nasal3_human, Surround3_human


title: Donor 2, M-CSF + IFN-gamma

description: Donor 2, M-CSF + IFN-gamma

source_name: Donor 2, M-CSF + IFN-gamma


title: retina_macula_rep4

source_name: 19-20 weeks' gestation human retina, macula biopsy


title: retina_surround_rep1

description: biological replicate: Macula1_human, Nasal1_human, Surround1_human


title: retina_macula_rep1


title: Donor 1, M-CSF

description: Donor 1, M-CSF

source_name: Donor 1, M-CSF


title: retina_surround_rep3


title: Sxlfp7BO male head replicate 2

first: Sha

last: Sun

address: 16 Barker Hall

department: Molecular and Cell Biology

description:
Sxlfp7BO is a small deletion that removes the entire Sxl locus. The mutant Sxlfp7BO males were backcrossed to the wild-type Oregon-R flies for more than six generations to homogenize the genetic background. Two flanking phenotypic markers, cm and ct, on the proximal and distal sides of Sxlfp7BO, were used to trace the mutant allele during the backcross. cm Sxlfp7BO ct and WT males were brothers from a single-pair cross: cm Sxlfp7BO ct/+ X cm Sxlfp7BO ct/Y.
Three biological replicates were performed for each male type.

hyb_protocol: Array hybridization was processed by UC Berkeley Functional Genomic Laboratory/Affymetrix Gene Chip Core Facility.

scan_protocol: Array scan and data extraction were processed by UC Berkeley Functional Genomic Laboratory/Affymetrix Gene Chip Core Facility.

data_processing: Analysis of array data was performed using the GeneTraffic UNO software package made by Iobion Informatics and provided by UC Berkeley Functional Genomic Laboratory

organism: Drosophila melanogaster

source_name: Male head, 2-5 day adult

label_protocol: cDNA synthesis, labeling, and cRNA preparation were performed according to the Affymetrix "Expression Analysis Technical Manual".

growth_protocol: Flies were raised at 25°C in uncrowded conditions on a regular medium containing 6.5% cornmeal, 2.7% yeast, 1.6% sucrose, 8.2% Molasses, 0.7% agar, 0.75% Na Tartrate (4 hydrate), 0.06% CaCl2 (2 hydrate), 0.5% Propionic Acid, 0.09% Tegosept and 0.7% Ethanol.

extract_protocol: RNA extraction was performed according to the Affymetrix "Expression Analysis Technical Manual".

treatment_protocol: Male flies of 2-5 day old were decapitated on an ice pack; the heads were transferred directly into TRIzol before RNA extraction.

tag: Strain

value: cm Sxlfp7BO ct;

tag: Gender

value: Male;

tag: Age

value: 2-5 day after eclosion;

value: Head.


title: Donor 2, M-CSF + Pam3Cys

description: Donor 2, M-CSF + Pam3Cys

source_name: Donor 2, M-CSF + Pam3Cys


title: retina_surround_rep2

description: biological replicate: Macula2_human, Nasal2_human, Surround2_human


title: retina_nasal_rep1


title: Sxlfp7BO male head replicate 3

source_name: Male head, 2-5 day old

value: Head


title: retina_macula_rep2


title: Sxlfp7BO male head replicate 1


title: Wildtype male head replicate 3

value: Wildtype Oregon-R;


title: Wildtype male head replicate 2


title: Mouse Testis Thy1 Positive Fraction Rep1

city: University Park

first: Jon

last: Oatley

address: 324 Henning

department: Dairy and Animal Science

institute: Pennsylvania State University

description: Affymetrix microarray suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. The number of probe pairs meeting the default discrimination threshold (t = 0.015) was used to assign a call of absent, present, or marginal for each assayed gene, and a P value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated by using the One-step Tukey’s Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene signals across multiple microarrays: After exclusion of the highest and lowest 2%, the average total chip signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All signal values from one microarray were then multiplied by the appropriate scaling factor.

hyb_protocol: In vitro transcription was conducted, followed by fragmentation of the cRNA and hybridization to Mouse Genome 430 2.0 arrays (Affymetrix). Each sample was hybridized to individual arrays, and each treatment contained three samples. Microarrays were then washed and stained with streptavidin-phycoerythrin.

scan_protocol: A confocal scanner was used to collect the fluorescence signals, and the average signal from two sequential scans was calculated for each microarray.

data_processing: Affymetrix CEL files for each genechip were imported into Stratagene Array Assist Lite software version 3.4 to calculate normalized GC Robust Microarray Analysis (GCRMA) expression levels for each probe set on each array. Data (CHP files from GCRMA calculations) were then imported into GeneSpring 7.2 software (Agilent Biotechnology; Santa Clara, CA USA) to visualize expression patterns and data were normalized to the median. Filter flags were then applied including a Present call in 3 out of 6 samples and differential expression in Thy1+ vs. Thy1-depleted samples. These parameters resulted in the filtering out of 26,927 genes from the 45,101 genes present on the genechips. The GCRMA raw values for these filtered genes were then exported into Excel for statistical analysis. A 2-class paired test using Statistical Analysis of Microarray version 2.23A tool which included a 3% false discovery rate with P-value <0.05 was used to identify genes with differential expression at the 10-fold level between Thy1+ and Thy1-depleted cell fractions.

source_name: Mouse Testis

label_protocol: Total RNA reverse transcribed using Superscript II reverse transcriptase primed by a biotynalated poly(T) oligomer that incorporated the T7 promoter

extract_protocol: Trizol + RNeasy Column

tag: 6 Days Old C57BL/6 Donor Mouse, MACS Isolated Thy1 Positive Fraction, 1st Replicate Sample


title: Mouse Testis Thy1 Positive Fraction Rep2

tag: 6 Days Old C57BL/6 Donor Mouse, MACS Isolated Thy1 Positive Fraction, 2nd Replicate Sample


title: Mouse Testis Thy1 Positive Fraction Rep3

tag: 6 Days Old C57BL/6 Donor Mouse, MACS Isolated Thy1 Positive Fraction, 3rd Replicate Sample


title: Wildtype male head replicate 1


title: retina_macula_rep3


title: Mouse Testis Thy1 Negative Fraction Rep 2

tag: 6 Days Old C57BL/6 Donor Mouse, MACS Isolated Thy1 Negative Fraction, 2nd Replicate Sample


title: SL2 expression sample 2

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

description: wild type SL2 expression

hyb_protocol: Recommended Affymetrix protocol

scan_protocol: Recommended Affymetrix protocol

data_processing: Data from CEL files were imported in R, scaled and normalized using the rma from  the affy package (Gautier et al., 2004, Bioinfomatics).

source_name: wild-type Scheider cells SL2

label_protocol: GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix)

growth_protocol: Exponentiaolly growing SL2 cells in Schneider's media supplemented with 10% FBS

extract_protocol: Quiagen RNAeasy kit with Qiashreder following manufacturer protocol (Qiagen)

treatment_protocol: No treatment

tag: Cell culture


title: SL2 expression sample 1

description: wild type SL2 expression


title: Mouse Testis Thy1 Negative Fraction Rep 3

tag: 6 Days Old C57BL/6 Donor Mouse, MACS Isolated Thy1 Negative Fraction, 3rd Replicate Sample


title: Primary T-ALL cells isolated from patient 5; second of two replicates.

status: Public on Dec 27 2008

city: Cincinnati

first: Gerlinde

last: Layh-Schmitt

state: OH

address: 3333 Burnet Ave

department: Experimental Hematology

institute: Cincinnati Children's Hospital Research Foundation

description: Gene expression data from primary patient 5 T-ALL cells; second of two replicates

hyb_protocol: All hybridization, staining and washing steps were carried out as specified by the Affymetrix technical manual.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G with GeneChip Operating Software Version 1.4.0.036 (Affymetrix)

data_processing: Data were pre-processed with RMA

source_name: Primary human T-ALL cells from patient 5; T-ALL developed after gene therapy for SCID due to insertional mutagenesis of the LMO2 locus; second of two replicates.

label_protocol: For cDNA generation, and cRNA labeling we used the ‘One-cycle target labeling’ protocol as described by the respective Affymetrix technical manual.

extract_protocol: total RNA from cells was extracted using TRIZOL

tag: Primary human T-ALL cells derived from patient 5  which developed leukemia  3 years after gene therapy for SCID due to insertional activation of LMO2; T-ALL cells were  passaged in NOD/SCID mouse;  second of two replicates


title: CD8 cells isolated from mixed normal donors; second of two replicates.

description: Gene expression data from CD8 cells of mixed normal donors; second of two replicates

source_name: CD8 cells isolated from normal donor blood, second of two replicates.

tag: Normal donor CD8 cells; second of two replicates


title: Primary T-ALL cells isolated from patient 5; first of two replicates.

description: Gene expression data from primary patient 5 T-ALL cells; first of two replicates

source_name: Primary human T-ALL cells from patient 5; T-ALL developed after gene therapy for SCID due to insertional mutagenesis of the LMO2 locus;first of two replicates.

tag: Primary human T-ALL cells derived from patient 5  which developed leukemia 3 years after gene therapy for SCID due to insertional activation of LMO2; first of two replicates


title: CD8 cells isolated from mixed normal donors; first of two replicates.

description: Gene expression data from CD8 cells of mixed normal donors; first of two replicates

source_name: CD8 cells isolated from normal donor blood, first of two replicates.

tag: Normal donor CD8 cells; first of two replicates


title: Mouse Testis Thy1 Negative Fraction Rep 1

tag: 6 Days Old C57BL/6 Donor Mouse, MACS Isolated Thy1 Negative Fraction, 1st Replicate Sample


title: Patient 5 T-ALL cells propagated in NOD/SCID mice and harvested from bone marrow; second of two replicates.

description: Gene expression data from primary T-ALL cells of patient 5 propagated in NOD/SCID mice and isolated from bone marrow;second of two replicates

source_name: Human T-ALL cells from patient 5 propagated in NOD/SCID mice; T-ALL developed after gene therapy for SCID due to insertional mutagenesis of the LMO2 locus;second of two replicates.


title: 3 weeks old transgenic plants (inducible overexpression ANAC092), biological rep2

status: Public on Dec 23 2008

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

description:
Gene expression data from ANAC092 inducible overexpression
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

hyb_protocol: Affymetrix protocol, performed by Atlas Biolabs

data_processing: The data were analyzed with Robust Multi-array Average (Irizarry et al., 2003).

organism: Arabidopsis thaliana

source_name: 3 weeks old transgenic plants (inducible overexpression ANAC092), WT_col0

label_protocol: Labling procedure performed using MessageAmpTM II-Biotin Enhanced Kit

growth_protocol: Seeds were surface sterilized and sown in half-strength MS medium supplemented with 1% sucrose and solidified with 0.7% phytoagar and appropriate antibiotic. After inbibition, the seeds were strafied at 4C° for 3 days. The seeds were germinated at 22 C° under a 16-h day (140µmol m2- s1-) / 8-h night regime. The three weeks old Arabidopsis seedlings were removed carefully and subjected to the treatment. T-DNA insertion lines were grown in soil and germinated under controlled condition in a growth chamber with a 16-h day lenght provided by fluorescent light at 80 or 120 µmol m2- s1- and a days/night temperature of 20/16 C° and relative humidity 60/75%.

extract_protocol: RNA extraction performed using Rneasy Plant MiniKit (Qiagene)

treatment_protocol: Three weeks old Arabidopsis seedlings were treated with 10µM estradiole for 5 hourse and then shoots were carefully harvested.. The leaf no.11 of wt and ANAC059 and ANAC092 T-DNA insertion lines were carefully harvested.

tag: 5hr estradiole treated shoot


title: Patient 5 T-ALL cells propagated in NOD/SCID mice and harvested from bone marrow; first of two replicates.

description: Gene expression data from primary T-ALL cells of patient 5 propagated in NOD/SCID mice and isolated from bone marrow; first of two replicates

source_name: Human T-ALL cells from patient 5 propagated in NOD/SCID mice; T-ALL developed after gene therapy for SCID due to insertional mutagenesis of the LMO2 locus; first of two replicates.

tag: Primary human T-ALL cells derived from patient 5  which developed leukemia  3 years after gene therapy for SCID due to insertional activation of LMO2; T-ALL cells were  passaged in NOD/SCID mouse; first of two replicates


title: leaves of 38 days old plants, T-DNA insertion line of ANAC092, biological rep1

description:
Gene expression data from ANAC092 T-DNA insertion line
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

scan_protocol: Affymetrix protocol, performed by Atlas Biolabs

tag: leaf no.11, 38 days old plants


title: leaves of 38 days old plants, Col-0 wild-type, biological rep1

description:
Gene expression data from wild-type Col-0
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

source_name: leaves of 38 days old plants, Col-0 wild-type, WT_col0


title: leaves of 38 days old plants, T-DNA insertion line of ANAC059, biological rep1

description:
Gene expression data from ANAC059 T-DNA insertion line
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.


title: 3 weeks old transgenic plants (inducible overexpression ANAC092), biological rep1

description:
Gene expression data from ANAC092 inducible overexpression!
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.


title: 3 weeks old transgenic plants (inducible overexpression ANAC092), biological rep3


title: 3 weeks old transgenic plants (inducible overexpression ANAC059), biological rep2

description:
Gene expression data from ANAC059 inducible overexpression
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

source_name: 3 weeks old transgenic plants (inducible overexpression ANAC059), WT_col0


title: 3 weeks old transgenic plants (inducible overexpression ANAC059), biological rep1


title: 3 weeks old transgenic plants (empty vector; inducible system), biological rep3

description:
Gene expression data from empty inducible vector
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

source_name: 3 weeks old transgenic plants (empty vector; inducible system), WT_col0


title: H295R _2OHBDE85_rep1

status: Public on Dec 25 2008

city: Leicester

first: George

middle: DD

last: Jones

address: Biocentre, University Road

department: Cancer Studies & Molecular Medicine

institute: University of Leicester

hyb_protocol: Fragmented, labelled cRNA (15 µg) was added to 15 µl of 2× hybridisation buffer (final 1× concentration is 100 mM 2-Morpholinoethanesulfonic acid (MES), 1 M [Na+], 20 mM EDTA, 0.01% Tween 20), 3 µl of 10 mg/ml herring sperm DNA (Promega, Southampton, UK), 3 µl of 50 mg/ml acetylated bovine serum albumin (BSA) (Invitrogen, Paisley, UK) and 30 µl of DMSO. The hybridisation buffer was spiked with 5 µl of 3nM control oligonucleotide B2 and 15 µl of the 20× eukaryotic cRNA controls bioB, bioC, bioD and cre (final concentration is 1.5, 5, 25 and 100 pM, respectively), all controls were from the GeneChip Eukaryotic Hybridisation Control Kit (Affymetrix, Santa Clara, California, USA). The hybridisation mixture was heated to 99 °C for 5 minutes, cooled to 45 °C for 5 minutes and centrifuged at 14,000 × g for 5 minutes to remove any insoluble material from the hybridisation mixture. Each hybridisation mixture containing 10 µg of fragmented biotin-labelled cRNA (200 µl) was hybridised to a pre-wetted (with hybridisation buffer) GeneChip Human U133 Plus 2.0 array (Affymetrix, Santa Clara, California, USA) for 16 hours at 45 °C with permanent rotation at 60 rpm in a Hybridisation Oven 640 (Affymetrix, Santa Clara, California, USA). Probe array washing and staining were performed according to EukGE-WS2v5 Gene Chip protocol (Affymetrix, Santa Clara, California, USA) in the Fluidics Station 400 (Affymetrix, Santa Clara, California, USA). Briefly, arrays were washed in a non-stringent wash buffer containing 6× SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA) (Cambrex, Berkshire, UK) and 0.01% Tween-20 at 25 °C, then with a stringent buffer containing 100 mM MES, 0.1 M [Na+], 0.01% Tween-20 at 50 °C. Following this wash, the probe arrays were stained with a solution containing 10 µg/ml of streptavidin-phycoerythrin (SAPE) conjugate (Invitrogen, Paisley, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK) dissolved in a buffer containing 100 mM MES, 1 M [Na+], 0.05% Tween 20. Following staining, the probe arrays were exposed to 3 µg/ml goat biotinylated anti-streptavidin antibody (Vector laboratories, Peterborough, UK) in a buffer as above containing 0.1 mg/ml normal goat IgG (Sigma, Poole, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK). Finally, the probe arrays were re-stained with SAPE as described above.

scan_protocol: Probe arrays were scanned once at 570 nm using an Affymetrix GeneChip scanner (Affymetrix, Santa Clara, California, USA) and the fluorescence intensity of the scanned image registered in CEL intensity files.

data_processing: DNA-Chip Analyser (dChip) software (Li and Wong 2001 PNAS, 98:31) was used to automatically select probes, detect outliers/artefacts, normalise the fluorescence intensity over multiple arrays and calculate model-based expression values from CEL intensity files using the PM/MM values.

source_name: H295R adrenocortical carcinoma cells, 2-OH-BDE85-treated

label_protocol:
The One-cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, California, USA) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 6 g of T-RNA, 2 µl of diluted poly-A RNA controls, 2 µl of 50 µM T7-oligo (dT) primer and RNase-free water to a final volume of 12 µl. This mixture was incubated at 70 °C for 10 minutes and chilled at 4 °C for 5 minutes, after which the following reagents were added: 4 µl of first strand reaction mix, 2 µl of 100 mM dithiothreitol (DTT) and 1 µl of 10 mM dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (1µl) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 3 µl of 10mM dNTP, 1 µl of E. coli DNA ligase, 4 µl of E. coli DNA polymerase I, 1 µl of E. coli RNase H, 30 µl of second strand reaction buffer and 91 µl of RNase-free water. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 2 µl of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 10 µl of 0.5 M EDTA. The resulting ds-cDNA was cleaned up using the Sample Cleanup Module (Affymetrix, Santa Clara, California, USA), according to the manufacturer’s instructions.
Synthesis of biotin labelled cRNA was performed by in vitro transcription using the IVT labelling kit (Affymetrix, Santa Clara, California, USA). Briefly, the ds-cDNA synthesised above (12 µl) was used as template, and added to 4 µl of 10× IVT labelling buffer, 12 µl of Labeling NTP mix, 4 µl of IVT Labeling Enzyme mix and 8 µl of RNase-free water. The reaction was incubated at 37 °C for 16 hours. This step was followed by cRNA cleanup with the Affymetrix Sample Cleanup Module, according to the manufacturer’s specifications. Quantification of cRNA was performed in a spectrophotometer by measuring the absorbance at 260 nm and the adjusted cRNA yield calculated taking into account the carryover of unlabelled T-RNA by the following formula: adjusted cRNA yield = RNAm – (T-RNAi)(y), where RNAm is the amount of cRNA measured after the IVT reaction, T-RNAi is the starting amount of T-RNA and y is the fraction of cDNA used in the IVT reaction. Size distribution of the labelled transcripts was investigated in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA). The appropriate amount of cRNA (20 µg) was fragmented by adding 8 µl of the fragmentation buffer provided in the Sample Cleanup Module and RNase-free water to a final volume of 40 µl, and incubating at 94 °C for 35 minutes. Fragmentation efficiency was confirmed by analysing the size distribution of the fragmented, labelled transcripts in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA).

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with Ham’s nutrient mixture F-12 with 1% ITS+Premix and 2.5% Nu-Serum at 37°C in a 5% CO2 atmosphere.

extract_protocol: After treatment, T-RNA was extracted using QIAGEN RNeasy Mini kit according to the manufacturer’s instructions. T-RNA concentration was determined by measuring the absorbance of a 1:100 diluted solution at 260 nm in a GeneQuant II RNA/DNA calculator spectrophotometer (Pharmacia Biotech, Cambridge, UK), assuming that if A260 = 1, the content equals 40 µg/ml of RNA. T-RNA integrity was investigated in the Agilent 2100 Bioanalyzer, by assessing size distribution of the T-RNA using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA), according to the manufacturer’s specifications.

treatment_protocol: Cells were exposed to 10 µM of 2-OH-BDE85 dissolved in 0.1% dimethyl sulfoxide (DMSO) for 24 hours.

tag: H295R adrenocortical carcinoma cell line


title: 3 weeks old transgenic plants (empty vector; inducible system), biological rep2, normalized w/ANAC059

data_processing: The data were analyzed with Robust Multi-array Average (Irizarry et al., 2003). GSM353590 raw files (CEL and CHP) are identical to GSM353585 raw files