title: Porcine alveolar macrophages, control, biological rep1

status: Public on Jul 15 2011

city: Wuhan

first: Tao

middle: Wen

last: Li

state: Hubei

address: No.1, Shizi_shan street, Hongshan district

department: Division of Animal Infectious Disease

institute: Huazhong agricultural university, State Key Laboratory of Agricultural Microbiology

description:
control 1
Gene expression data from porcine alveolar macrophages isolated from control pigs at 7 d.p.i.

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

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.

organism: Sus scrofa

source_name: Porcine alveolar macrophages isolated from control pigs, 7 dpi

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

growth_protocol: Six 28-day-old healthy pigs were obtained. Three pigs were inoculated intranasally with 2 ml of 4.84×10^6 colony-forming units of SS2 strain SC19, and the other three pigs were intranasally challenged with 2 ml PBS as a control. All pigs were slaughtered at 7 dpi.

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

treatment_protocol: Bronchoalveolar lavage of the lungs was performed with 100mL aliquots of sterile PBS containing genamicin at 70 μg/mL(Sigma). Lavage fluids were centrifuged at 230 ×g for 15 min, and cells were washed twice with Dulbecco’s Modified Eagle’s Medium (DMEM) containing gentamicin (50μg/mL).

tag: breed

value: Large White

value: lung

tag: cell type

value: alveolar macrophages

tag: disease state

value: healthy

tag: age

value: 35 days

value: PBS control

tag: treatment duration

value: 7 dpi


title: Be_DNA4

status: Public on Jul 27 2011

type: genomic

city: Münster

first: Fei

last: He

address: Hüfferstr. 1

department: Münster University

country: Germany

institute: Institute for Evolution and Biodiversity

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G

data_processing:
GeneChip Operating Software Version 1.4 (GCOS)
primary_data_description: raw intensity was read from .CEL file, log transformed, background corrected, quantile normalzied, then convert back to normal scale

label: Biotin

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: seedling

label_protocol: Biotin, Invitrogen Bioprime random labeling

growth_protocol: stratifying for 7 days at 4°C and growing in the greenhouse under 16h cool white light supplemented with red light at 20°C

extract_protocol: Qiagen DNeasy Plant Mini Kit

treatment_protocol: 3 four-weeks-old leaves, 3-4 open flowers and 3-4 flower buds

tag: ecotype

tag: tissue

value: seedling


title: Porcine alveolar macrophages, control, biological rep2

type: RNA

country: China

description:
control 2
Gene expression data from porcine alveolar macrophages isolated from control pigs at 7 d.p.i.

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

label: biotin

molecule: total RNA

tag: treatment


title: Porcine alveolar macrophages, SS2 infection, biological rep3

description:
infection 3
Gene expression data from porcine alveolar macrophages isolated from SS2-infected pigs at 7 d.p.i.

source_name: Porcine alveolar macrophages isolated from SS2-infected pigs, 7 dpi

value: infection with Streptococcus suis serotype 2 (SS2) strain SC19


title: Porcine alveolar macrophages, control, biological rep3

description:
control 3
Gene expression data from porcine alveolar macrophages isolated from control pigs at 7 d.p.i.


title: hybrid_FlowerBud_RNA4

organism: Arabidopsis thaliana x Arabidopsis lyrata

source_name: flower bud

extract_protocol: Qiagen RNeasy Plant Mini Kit

value: Be-0 x LF10

value: flower bud


title: LF10_DNA2

organism: Arabidopsis lyrata


title: NIH3T3 K-ras at T72, grown 1mM glucose, biological rep1

status: Public on Jul 14 2011

city: Milan

first: Ferdinando

last: Chiaradonna

address: Piazza della scienza, 2

department: Biotechnology and Biosciences

country: Italy

institute: University of Milano-Bicocca

hyb_protocol: The biotinylated cRNA was hybridized to the Mouse Genome 430 2.0 Array, containing over 39000 transcripts from Mus musculus Genome databases GenBank, dbEST, and RefSeq.

scan_protocol: Chips were washed and scanned on the Affymetrix Complete GeneChip Instrument System, generating digitized image data files.

data_processing: GeneSpring GX11.5, RMA, normalized to baseline to median of all samples.

organism: Mus musculus

source_name: NIH3T3 K-ras, 1mM, T72h

label_protocol: cRNA was generated by using the Affymetrix One-Cycle Target Labeling and Control Reagent kit (Affymetrix Inc., Santa Clara, CA) following the protocol of the manufacturer.

growth_protocol: NIH3T3 and NIH3T3 K-ras cell lines were routinely grown in Dulbecco's modified Eagle's medium, (DMEM) (Invitrogen) containing 10% newborn calf serum (Invitrogen), 4 mM glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin (normal growth medium), at 37 °C in a humidified atmosphere of 5% CO2. Cells were maintained in culture for 18 h before any experimental manipulation.

extract_protocol: Total RNA by Trizol and further purified by the RNeasy minikit (Qiagen).

treatment_protocol: The cells were grown in a medium with 4 mM glutamine and two different glucose concentrations (25 and 1 mM).

tag: cell line

value: NIH3T3 K-ras

tag: glucose availability

value: 1mM glucose

tag: time

value: 72 hours


title: NIH3T3 K-ras at T24, grown 1mM glucose, biological rep1

source_name: NIH3T3 K-ras, 1mM, T24h

value: 24 hours


title: Control (28 WPI), 1

status: Public on Jul 21 2011

city: NEW YORK

first: TAMAS

middle: A

last: GONDA

state: NY

address: 161 FT WASHINGTON

department: MEDICINE

country: USA

institute: COLUMBIA UNIVERSITY

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

source_name: stomach, control, 28 WPI

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: background strain

value: FVB

tag: genotype

value: INS-GAS transgenic

tag: phenotype

value: hypergastrinemic

value: stomach

tag: infection

value: Helicobacter felis

tag: dysplasia score

value: normal folate diet


title: NIH3T3 K-ras at T72, grown 25mM glucose, biological rep2

source_name: NIH3T3 K-ras, 25mM, T72h

value: 25mM glucose


title: NIH3T3 K-ras at T48, grown 1mM glucose, biological rep2

source_name: NIH3T3 K-ras, 1mM, T48h

value: 48 hours


title: NIH3T3 K-ras at T72, grown 1mM glucose, biological rep2


title: NIH3T3 K-ras at T72, grown 25mM glucose, biological rep1


title: Porcine alveolar macrophages, SS2 infection, biological rep2

description:
infection 2
Gene expression data from porcine alveolar macrophages isolated from SS2-infected pigs at 7 d.p.i.

value: Large White

value: lung

value: alveolar macrophages

value: healthy

value: 35 days

value: 7 dpi


title: Control vs. Burkholderia pseudomallei infected cells

city: Taoyuan County

first: Ssu Ching

last: Chen

address: 300 Jhongda Rd., Jhongli City

country: Tajikistan

institute: National Central University

hyb_protocol: Agilent two-color microarry-based gene expression analysis v6.

scan_protocol: standard Agilent protocol

data_processing: Agilent Feature Extraction Software (10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Mouse macrophage cells

label_protocol: Agilent low input quick amp labeling kit

growth_protocol: The extraction of RNA, cDNA synthesis, and PCR amplification were used for control cells vs infected cells

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Infected cells with Burkeholderia pseudomallei for 6h.

value: macrophage

value: uninfected

source_name: Total RNA from pooled  mouse cells, labeled with Cyanine-3 (green).

value: Burkeholderia pseudomallei


title: NIH3T3 K-ras at T48, grown 1mM glucose, biological rep1

value: NIH3T3 K-ras

value: 1mM glucose


title: NIH3T3 K-ras at T24, grown 25mM glucose, biological rep2

source_name: NIH3T3 K-ras, 25mM, T24h

value: 24 hours


title: NIH3T3 K-ras at T0, grown 25mM glucose, biological rep2

source_name: NIH3T3 K-ras, 25mM, T0h

value: 0 hours


title: NIH3T3 K-ras at T24, grown 1mM glucose, biological rep2


title: NIH3T3 K-ras at T48, grown 25mM glucose, biological rep2

source_name: NIH3T3 K-ras, 25mM, T48h


title: NIH3T3 K-ras at T24, grown 25mM glucose, biological rep1


title: Porcine alveolar macrophages, SS2 infection, biological rep1

description:
infection 1
Gene expression data from porcine alveolar macrophages isolated from SS2-infected pigs at 7 d.p.i.

value: infection with Streptococcus suis serotype 2 (SS2) strain SC19


title: NIH3T3 K-ras at T48, grown 25mM glucose, biological rep1


title: NIH3T3 at T24, grown 1mM glucose, biological rep2

source_name: NIH3T3, 1mM, T24h


title: NIH3T3 at T72, grown 25mM glucose, biological rep2

source_name: NIH3T3, 25mM, T72h

value: 72 hours


title: NIH3T3 at T24, grown 1mM glucose, biological rep1


title: NIH3T3 at T48, grown 25mM glucose, biological rep2

source_name: NIH3T3, 25mM, T48h

value: 25mM glucose


title: Folate - 8 wks, 2

source_name: stomach, folate, 8 wks

value: FVB

value: INS-GAS transgenic

value: hypergastrinemic

value: stomach

value: Helicobacter felis

value: folate-supplemented diet

tag: time of treatment

value: 8 wks after H. felis infection


title: NIH3T3 at T48, grown 25mM glucose, biological rep1

value: 48 hours


title: NIH3T3 at T24, grown 25mM glucose, biological rep2

source_name: NIH3T3, 25mM, T24h


title: NIH3T3 at T48, grown 1mM glucose, biological rep2

source_name: NIH3T3, 1mM, T48h


title: NIH3T3 K-ras at T0, grown 25mM glucose, biological rep1


title: NIH3T3 at T72, grown 1mM glucose, biological rep1

source_name: NIH3T3, 1mM, T72h


title: NIH3T3 at T72, grown 25mM glucose, biological rep1


title: P3C #3

status: Public on Jun 23 2011

city: San Francisco

first: Kevin

last: Wilhelmsen

state: CA

address: 513 Parnassus Ave.

department: Anesthesia

institute: University of California, San Francisco

description:
confluent monolayer in EGM-2 media treated 3hr with 10 ug/mL Pam3Cys
test

data_processing:
For the normalization it uses the average of two housekeeping genes: HPRT1 , GUSB
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold-change calculations were caluculated using 2^-deltadeltaCt, where deltadeltaCt=(average deltaCt_test - average deltaCt control)
Fold Change worksheet reports test/control (i.e., Pam3Cys-treated OR Pam3Cys-treated after TLR2 knockdown/untreated) ratios.

label: FAM Taqman

organism: Homo sapiens

source_name: HUVEC

label_protocol: PCR assays were performed using the human immune array PCR array (Applied Biosystems) following the Manufacturer’s instructions. Reverse transcription was performed from 2000 ng total RNA using the  High Capacity RNA-to-cDNA Kit from Applied Biosystems). 2.5 ng cDNA used per well. Quantitative real-time PCR were performed (ABI Prism 7000 Sequence Detection System; Applied Biosystems) at 95°C for 20 sec was followed by 40 cycles of 1 sec at 95C and 20 sec at 60C.

growth_protocol: EGM-2 media (2% FBS) (Clonetics Corp; Walkersville, MD)

extract_protocol: Total RNA was extracted with High Capacity RNA-to-cDNA Kit from AB (4387406)

treatment_protocol: Pam3Cys-SKKKK (EMC Microcollections; Tubingen, Germany) at 10 ug/mL for 3 hours

value: primary endothelial cell


title: P3C #2

extract_protocol: Total RNA was extracted with Trizol (Invitrogen)


title: untreated #2

description:
confluent monolayer in EGM-2 media
control

value: untreated


title: P3C #1


title: untreated #3


title: P3C con siRNA #1

description:
control siRNA (L-005120-01-0005; Dharmafect 4 reagent; Thermo Scientific (Rockford, IL)) transfected HUVEC (lysed 48-hour post transfection) confluent monolayer in EGM-2 media treated 3hr with 10 ug/mL Pam3Cys
test

tag: knockdown

value: control


title: P3C TLR2 siRNA #3

description:
TLR2 siRNA (D-001810-10-05; Dharmafect 4 reagent; Thermo Scientific (Rockford, IL)) transfected HUVEC (lysed 48-hour post transfection) confluent monolayer in EGM-2 media treated 3hr with 10 ug/mL Pam3Cys
test

tag: cell type


title: untreated #1


title: NIH3T3 at T48, grown 1mM glucose, biological rep1

value: 1mM glucose


title: NIH3T3 at T0, grown 25mM glucose, biological rep2

source_name: NIH3T3, 25mM, T0h


title: NIH3T3 at T0, grown 25mM glucose, biological rep1

source_name: NIH3T3, 25mM,T0h


title: P3C TLR2 siRNA #1


title: P3C TLR2 siRNA #2


title: Fibroblasts - Fibronectin vs. Plastic

status: Public on Jun 22 2011

type: protein

city: Toronto

first: Benjamin

last: Alman

state: Ontario

address: TMDT, 101 College Street

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

description: Tissue from TCF Reporter Mice (Cheon et al. 2002 PNAS 99:6973-6978 (PMID 11983872)).

hyb_protocol: Kinexus Bioinformatics Corp. (Vancouver, BC) (www.kinexus.ca).

data_processing: The analysis for each target includes the following parameters: Flag (indication of spot's quality), Signal Median (measurement of spot intensity), Background median, signal/noise ratio, net signal median, Normalized Net Signal Median, Control average, Control % range, Treated Average, Treated % Range, Treated Average/Control (Fold change), % CFC, Log2(Treated Average/Control Average), confidence.  (References Kinexus Bioinformatics Literature: Customer Information Package Version 8JN18 and Kinex Reference page).  Data processing/analysis was performed by Kinexus Bioinformatics Corp.

label: fluorescent dye (maximum excitation wavelength at 550 nm)

molecule: protein

source_name: dermal fibroblasts, plastic

label_protocol: Control and treatment lysate samples are labeled with the same dye; they are analyzed separately, but on the same chip (www.kinexus.ca).

growth_protocol: Cells were seeded at 35,000 cells per 10 cm2 on plastic or fibronectin and harvested after 48 hours.

extract_protocol: Cells were rinsed with cold PBS and detached with trypsin.  Cell pellets were collected by centrifugation and rinsed with cold PBS.  Cells were lysed in lysis buffer and sonicated to rupture cells and shear nuclear DNA.  Homogenate was centrifuged, and the supernatant fraction was collected and assayed for protein concentration.

value: skin (dermis)

value: primary fibroblasts

tag: growth condition

value: plastic

tag: sample type

source_name: dermal fibroblasts, fibronectin

treatment_protocol: Concentration of fibronectin on fibronectin-coated plates was 2 μg/cm2.

value: fibronectin

value: treated


title: NIH3T3 at T24, grown 25mM glucose, biological rep1

value: 25mM glucose

value: 24 hours


title: NT09/336 Tumor_Colon (1699538180_H)

status: Public on May 29 2011

city: Singapore

first: Sherry

last: Wang

address: 21 Lower Kent Ridge Road

department: Biochemistry

country: Singapore

institute: National University of Singapore

description:
primary culture from patient sample not used in this study
1699538180_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanner used: Illumina BeadArray Reader Scanning protocol: Scan factor of 1, PMT525,550 Software: Illumina Beadscan version 3.0

data_processing:
Data is extracted using Illumina Genomestudio version 2010.2, Expression Module version 1.7.0
Data were analyzed using Partek GS6.4 Ver 6.09.0922.
Normalization algorithm: RMA
Analysis was performed using ANOVA.

source_name: Colon Tissue

label_protocol: Standard Illumina label protocol

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (HIFBS) (Gibco, Invitrogen), 2mM L-glutamine (Gibco, Invitrogen) and 100U/ml penicillin and streptomycin (Gibco, Invitrogen).

extract_protocol: Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen) with modifications. Cells were first washed with PBS twice and then lysed in TRIzol (Invitrogen) before purification using RNA extraction columns and buffers provided in the kit. The RNA concentration was quantified using Nanodrop (Thermo Scientific). 500ng total RNA was used for cRNA amplification using Illumina TotalPrep RNA Amplification kit (Ambion). Steps were carried out by following the instructional manual in the kit.

value: primary cell culture

tag: tumor/normal status

value: tumor

tag: gender

value: male


title: NT09/468 Tumor_Colon (1699538180_E)

description:
primary culture
1699538180_E

value: female


title: NT09/446 Tumor_Colon (1699538180_G)

description:
primary culture
1699538180_G


title: NT09/323 Normal_Colon (1699538179_B)

description:
patient sample not used in this study
1699538179_B

value: primary tissue

value: normal


title: NT09/453 Normal_Colon (1699538180_F)

description:
primary culture
1699538180_F


title: NT09/323 Tumor_Colon (1699538179_E)

description:
patient sample not used in this study
1699538179_E


title: NIH3T3 at T72, grown 1mM glucose, biological rep2

value: 72 hours


title: NT09/446 Normal_Colon (1699538180_C)

description:
primary culture
1699538180_C


title: NT09/468 Normal_Colon (1699538180_B)

description:
primary culture
1699538180_B


title: NT09/350 Normal_Colon (1699538179_G)

description:
tissue sample
1699538179_G


title: NT09/453 Tumor_Colon (1699538180_A)

description:
primary culture
1699538180_A


title: NT09/340 Normal_Colon (1699538179_H)

description:
tissue sample
1699538179_H


title: NT09/340 Tumor_Colon (1699538179_D)

description:
tissue sample
1699538179_D


title: NT09/350 Tumor_Colon (1699538179_C)

description:
tissue sample
1699538179_C


title: 22/73_96PV_bio2_tech3

status: Public on Apr 28 2011

city: S. Michele a/Adige

first: Giulia

last: Malacarne

state: Trento

address: Via Edmund Mach,1

department: Genomics and Biology of Fruit Crops Department

institute: Edmund Mach Foundation

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C.  Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS).  Hybridization washings were performed as following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).

scan_protocol: The arrays were scanned with a ScanArray4000XL (Perkin Elmer, USA) and TIF images were exported to MicroArray Imager 5.8 (Combimatrix, USA) for densometric analysis.

data_processing: Raw data was extracted using Microarray Imager 5.8.0 software (Combimatrix). Spot flagging and visual inspection of the images was carried out in order to exclude bad spots (based on spot saturation and heterogeneity). The raw signals were analyzed and negatively flagged spots were excluded from further analysis by assigning them a zero weight. Only probes with a signal intensity of at least 500 fluorescence units (Galbraith, 2003) for all biological replicates were considered for further analysis. A scaling normalization was further performed using Actin and Ufgt (UDP-glucose:flavonoid 3-O-glucosyltransferase) as reference genes. A mean expression value from normalized values of technical replicates for each probe was calculated.

organism: Vitis vinifera

source_name: F1 22/73_infected_96h

label_protocol: Total RNA (1 microgram) was amplified using the Amino Allyl MessageAmpII aRNA Amplification kit (Ambion, USA) and the resulted amminoallyl-aRNA was conjugated to a fluorescent label (Cy-5). The purified labeled aaRNA was quantified by spectrophotometry (ATI Unicam) and 2 micrograms were hybridized to the custom Combimatrix array according to the manufacters directions.

growth_protocol: F1 individuals from Merzling x Teroldego cross were replicated annually by grafting wood cuttings onto rootstock KOBER 5BB. The plants were kept in a growth chamber in 1L pots filled with soil:sand:peat:vermiculite (3:1:3:3, v/v) in greenhouse at 25°C/20°C day/night temperature, 16 h photoperiod and a relative humidity (RH) of 70 ± 10%.

extract_protocol: Total RNA was extracted from frozen leaves according to Moser et al., 2004

treatment_protocol: Sporangiophores of P. viticola (Berk. and Curt) Berl. et De Toni were collected from infected leaves of V. vinifera cv Pinot Gris plants by brushing the white mould present on the underside of the leaves in cold bidistilled water. Fully expanded leaves of 8 to 10 week old grafted plants were inoculated by spraying a conidial suspension of 10^4/10^5 spores/ml onto the abaxial leaf surface and were kept overnight in the dark in a growth chamber at 24°C with 80% RH . The infected plants were then transferred to the greenhouse and kept in the same conditions as described above. Mock-inoculated plants were obtained by spraying distilled water in the greenhouse. Leaves for the analysis (the second and third from the apex) were collected from two biological replicates each of F1 21/66, F1 22/73 and Teroldego at 12 and 96 hours post infection (hpi)  and at 0 hours post mock-inoculation (hpmi), immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: F1 22/73  (Merzling x Teroldego cross)

tag: tissue

value: leaf

value: Plasmopara viticola

tag: time point


title: 22/73_96PV_bio2_tech2


title: control triceps, biological rep4

status: Public on May 18 2011

city: Berlin

first: Mateusz

last: Kolanczyk

address: Ihnestr 73

institute: Max Planck Institute

description: Gene expression data from 3-month-old triceps muscle.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MouseGene1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Data were processed using RMA (Affymetrix Expression Console software).

source_name: triceps, control mouse

growth_protocol: 3-month-old mice fed with standard chow.

extract_protocol: RNA was isolated from the triceps muscles using peqGOLD TriFast (PeqLab Biotechnologie GmbH) according to the supplied protocol.  The cRNA synthesis and microarray hybridizaton was done according to standard protocols applied in the Laboratory of Functional Genome Research Charité - Core Facility. A total of 8 high-density oligonucleotide mouse GENE 1.0 ST arrays (Affymetrix) were used in this study. Samples from each animal (4 Nf1, and 4 wild-type) were applied individually to each array.

treatment_protocol: Triceps muscle was isolated and directly homogenized in TriFast solution.

value: wild type

value: triceps muscle

tag: age

value: 3 months


title: mutant triceps, biological rep1

source_name: triceps, mutant mouse


title: control triceps, biological rep3


title: control triceps, biological rep1


title: mutant triceps, biological rep3


title: mutant triceps, biological rep2


title: control triceps, biological rep2


title: 22/73_96PV_bio2_tech1


title: 22/73_96PV_bio1_tech3


title: mutant triceps, biological rep4


title: 22/73_12PV_bio1_tech3

source_name: F1 22/73_infected_12h


title: 22/73_12PV_bio2_tech3


title: 22/73_12PV_bio2_tech1


title: 22/73_96PV_bio1_tech1


title: 22/73_12PV_bio2_tech2


title: 22/73_96PV_bio1_tech2


title: Lower #1, L3N530.gpr

status: Public on May 19 2011

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
lower vs normal stem #1
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: true

hyb_protocol: Prehybridization of slides, application of the probe to the microarray slides, hybridisation, and subsequent washing steps were performed according to manufacturer's instructions (Corning Microarray Technology).

scan_protocol: Microarrays were scanned with a GenePix TM4000A laser scanner (Axon Instruments, Inc, Foster City, CA). Spot intensities from scanned slides were quantified using GenePix Pro 3.0 software. Grids were predefined and manually adjusted to ensure optimal spot recognition. Spots with dust or locally high background were discarded. After opening the scanned image, loading GenePix setting file and GenePix array list file, the analysis was performed using the Analyze option of 1 GenePix Pro3.0, resulting in a GPR file of gene expression.

data_processing: Normalization Method: Limma PrintTipLoess Normalisation within arrays, Limma Quantile Normalisation between arrays. Ref: Smyth, G.K. 2004. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology. Vol. 3: Iss. 1, Article 3.

organism: Eucalyptus nitens

source_name: vertical CY5

label_protocol: Glass slides were processed according to the TeleChem protocols. Cy3-and Cy5-labeled (Amersham Pharmacia) cDNA probes were generated using the two-step labelling method described by Schenk et al. (2000). Application of the probe to microarray slides, hybridization, and subsequent washes of the slides were performed according to Schenk et al. (2000).

extract_protocol: Two nine-year-old Eucalyptus nitens trees, tree 347 and tree Tall6, growing in Canberra, Australia, were used as a source of biological material. RNA was isolated from xylem from the vertical main stem and from the upper and lower quarter of branches oriented at approximately 45° from vertical. A bark window approximately 400 x 60 mm was removed from the stem using a hammer and chisel and young xylem tissue scraped from the exposed wood. A nine-year-old E. grandis tree growing in the same orchard was used as a source of xylem tissue for RNA isolation and cDNA library construction. Tissues were placed on ice after harvesting and then frozen in liquid nitrogen and stored at -80ºC. For each tree, slides were hybridized with probes synthesized from vertical xylem and one or other of upper or lower branch xylem.

tag: Age

value: 9 years

source_name: lower CY3


title: Lower#2, L5N323.gpr

description:
lower vs normal stem #2
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: false

source_name: lower CY5

source_name: vertical CY3


title: 22/73_12PV_bio1_tech2


title: 22/73_12PV_bio1_tech1


title: Upper#2, u3N524.gpr

description:
upper wood vs normal wood #2
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

source_name: upper CY3


title: Upper#2, u3n59.gpr

description:
upper wood vs normal wood #2
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: 22/73_C_bio2_tech3

source_name: F1 22/73_control_0h

value: water


title: Lower #1, L3N514.gpr

description:
lower vs normal stem #1
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true


title: 22/73_C_bio2_tech1


title: Upper #1, u5N334.gpr

description:
upper vs normal stem #1
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false

source_name: upper CY5


title: Lower#2, L5N310.gpr

description:
lower vs normal stem #2
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: false


title: Upper #1, u5n321.gpr

description:
upper vs normal stem #1
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: Teroldego_96PV_bio1_tech2

value: Teroldego


title: 22/73_C_bio1_tech1


title: 22/73_C_bio1_tech2


title: Teroldego_96PV_bio2_tech1


title: 22/73_C_bio1_tech3


title: Teroldego_96PV_bio2_tech2


title: Teroldego_96PV_bio2_tech3


title: Teroldego_96PV_bio1_tech1


title: Teroldego_12PV_bio2_tech3


title: 22/73_C_bio2_tech2


title: Teroldego_12PV_bio2_tech2


title: Teroldego_12PV_bio2_tech1


title: Teroldego_12PV_bio1_tech3


title: Teroldego_C_bio2_tech3


title: Teroldego_12PV_bio1_tech1


title: Teroldego_12PV_bio1_tech2


title: Teroldego_C_bio2_tech1


title: Teroldego_C_bio2_tech2


title: Teroldego_96PV_bio1_tech3


title: Teroldego_C_bio1_tech3


title: Teroldego_C_bio1_tech2


title: Teroldego_C_bio1_tech1


title: 21/66_96PV_bio2_tech3

source_name: F1 21/66_infected_96h

value: F1 21/66 (Merzling x Teroldego cross)


title: 21/66_96PV_bio2_tech1


title: 21/66_96PV_bio2_tech2


title: 21/66_96PV_bio1_tech3


title: 21/66_96PV_bio1_tech1


title: 21/66_96PV_bio1_tech2


title: 21/66_12PV_bio2_tech3

source_name: F1 21/66_infected_12h


title: 21/66_12PV_bio2_tech1


title: 21/66_12PV_bio2_tech2


title: 21/66_12PV_bio1_tech2


title: 21/66_C_bio2_tech3

source_name: F1 21/66_control_0h


title: 21/66_12PV_bio1_tech1


title: 21/66_12PV_bio1_tech3


title: 21/66_C_bio1_tech2


title: 21/66_C_bio2_tech2


title: 21/66_C_bio1_tech3


title: 21/66_C_bio2_tech1


title: 21/66_C_bio1_tech1


title: Liver control 4 versus Liver highfat 8

status: Public on Apr 02 2011

city: Leiden

first: Anja

last: Schiel

address: Einthovenweg 20

department: Human Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: comparison of control versus high fat fed

hyb_protocol: Hybridization was performed as described in 't Hoen, Peter A C;de Kort, Floor;van Ommen, G J B;den Dunnen, Johan T,  Fluorescent labelling of cRNA for microarray applications, Nucleic Acids Res, 31, 2003

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were background corrected in GenePix (version 5.0) with the default background subtraction method and then normalized with the Bioconductor packages “limma” and “vsn”

source_name: Total RNA from liver, amino-allyl-labelled amplified aRNA

label_protocol: To allow dye swaps a total of 3.75 microgram of amino-allyl labelled aRNA was labelled with monofunctional cyanine-3 and cyanine-5 dyes (Amersham Biosiences) as described in 't Hoen, Peter A C;de Kort, Floor;van Ommen, G J B;den Dunnen, Johan T,  Fluorescent labelling of cRNA for microarray applications, Nucleic Acids Res, 31, 2003

growth_protocol: mice were 12-16 weeks of age

extract_protocol: Total RNA was isolated with the Machery-Nagel NuceloSpin-RNA II kit (#740955) according to the manufacturers protocol.

treatment_protocol: mice were fed a high fat diet for two weeks, chow for two weeks or fed chow for two weeks and the fasted for 16 hrs prior to sacrifice

tag: control

tag: Strain

tag: high fat fed for 2 weeks


title: Liver highfat 9 versus Liver control 2


title: Liver control 3 versus Liver highfat 10


title: Liver fasted 12 versus Liver highfat 6

description: direct comparison of high fat fed versus fasted

tag: fasted for 16 hrs


title: Liver highfat 6 versus Liver control 1


title: Liver fasted 15 versus Liver control 2

description: comparison of control versus fasted


title: Liver highfat 10 versus Liver control 3


title: Liver fasted 14 versus Liver highfat 7


title: Liver control 5 versus Liver highfat 7


title: Liver control 2 versus Liver highfat 9


title: Liver control 2 versus Liver fasted 15

description: comparison of control versus fasted


title: Liver highfat 7 versus Liver control 5


title: Liver highfat 7 versus Liver fasted 14


title: Liver fasted 11 versus Liver control 4

description: comparison of control versus fasted


title: Liver control 1 versus Liver highfat 6


title: Liver highfat 8 versus Liver fasted 13

source_name: Total RNA from liver, amino-allyl-labelled amplified aRNA, amino-allyl-labelled amplified aRNA


title: Liver highfat 9 versus Liver fasted 11


title: Liver fasted 13 versus Liver highfat 8


title: Liver highfat 8 versus Liver control 4


title: Liver control 3 versus Liver fasted 14

description: comparison of control versus fasted


title: Liver fasted 11 versus Liver highfat 9


title: Liver control 5 versus Liver fasted 13

description: comparison of control versus fasted


title: Liver highfat 10 versus Liver fasted 15


title: Liver fasted 15 versus Liver highfat 10


title: Liver highfat 6 versus Liver fasted 12


title: Liver fasted 14 versus Liver control 3

description: comparison of control versus fasted


status: Public on Apr 01 2011

city: Boston

first: Jong-Min

last: Lee

state: MA

address: 185 Cambridge Street

department: Center for Human Genetic Reseaarch

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: gcRMA log2 scale

source_name: HdhQ111/HdhQ111 cerebellum at 3~10 weeks biological rep 6s

label_protocol: Affymetrix protocol

extract_protocol: Trizol extraction and Qiagen mini coulmn clean-up

tag: hdh genotype

value: cerebellum

value: 3~10 weeks


title: Liver control 4 versus Liver fasted 11

description: comparison of control versus fasted


title: HdhQ111/HdhQ111 cerebellum at 3~10 weeks biological rep 5


title: Liver fasted 13 versus Liver control 5

description: comparison of control versus fasted


title: Hdh+/Hdh+ cerebellum at 3~10 weeks biological rep 6

description: Hdh+/Hdh+ cerebellum at 3~10 weeks


title: HdhQ111/HdhQ111 striatum at 3~10 weeks biological rep 6

description: HdhQ111/HdhQ111 striatum at 3~10 weeks

value: striatum


title: HdhQ111/HdhQ111 striatum at 3~10 weeks biological rep 4

description: HdhQ111/HdhQ111 striatum at 3~10 weeks


title: HdhQ111/HdhQ111 striatum at 3~10 weeks biological rep 5

description: HdhQ111/HdhQ111 striatum at 3~10 weeks


title: Hdh+/Hdh+ cerebellum at 3~10 weeks biological rep 5

description: Hdh+/Hdh+ cerebellum at 3~10 weeks


title: Th1

status: Public on Mar 31 2011

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

description: Gene expression data from wild type CD4+ T cells cultured for 5 days in Th1 condition

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values were determined using GeneChip Operating Software (GCOS) v1.2 software.

source_name: primary CD4 T cells from spleen

label_protocol: Total RNA was extracted using the IVT Labeling kit from Affymetrix

growth_protocol: Splenic CD4 T cells were prepared using a magnetic cell sorter (AutoMACS; Miltenyi Biotec) yielding a purity of >98%. Where indicated, cells from C57BL/6 mice were stimulated with immobilized anti-TCR mAb (H57−597; 3 mg/ml) and anti-CD28 mAb under Th1- or Th2-culture conditions for 2days in vitro.  Th1 conditions; 25 U/ml IL-2, 10 U/ml IL-12, and antiﾐIL-4 mAb.  Th2 conditions; 25 U/ml IL-2, 100 U/ml IL-4. pMX-IRES-NGFR retrovirus were added to the Th1 and Th2 cell differentiation cultures on day 2. After culturing for 3 more days, the cells were harvested.

treatment_protocol: Th1 and Th2 culture cells were collected and resuspendet in the Trizol solution (GibcoBRL).

tag: strain

value: spleen

value: CD4 T cell

tag: culture conditions


title: Hdh+/Hdh+ cerebellum at 3~10 weeks biological rep 4

description: Hdh+/Hdh+ cerebellum at 3~10 weeks


title: Hdh+/Hdh+ striatum at 3~10 weeks biological rep 4

description: Hdh+/Hdh+ striatum at 3~10 weeks


title: Hdh+/Hdh+ striatum at 3~10 weeks biological rep 6

description: Hdh+/Hdh+ striatum at 3~10 weeks


title: Th2

description: Gene expression data from wild type CD4+ T cells cultured for 5 days in Th2 condition


title: Hdh+/Hdh+ striatum at 3~10 weeks biological rep 5

description: Hdh+/Hdh+ striatum at 3~10 weeks


title: HdhQ111/HdhQ111 cerebellum at 3~10 weeks biological rep 4


title: HdhQ111/Hdh+ striatum at 5 months

description: HdhQ111/Hdh+ striatum at 5 months

source_name: HdhQ111/Hdh+ striatum at 5 months

tag: Hdh genotype

tag: Tissue

value: 5 months


title: HdhQ111/Hdh+ cerebellum at 5 months

description: HdhQ111/Hdh+ cerebellum at 5 months

source_name: HdhQ111/Hdh+ cerebellum at 5 months


title: Local Prostate Cancer 1

status: Public on Mar 30 2011

city: Detroit

first: Laila

middle: M

last: Poisson

state: MI

address: 1 Ford Place

department: Biostatistics and Research Epidemiology

institute: Henry Ford Health Systems

description: Localized prostate tumor, Gleason sum: 4+3

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 1x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization. Samples M5a and M5b were isolated from the same patient and normalized values were averaged before data analysis.

source_name: Benign prostate pool

label_protocol: One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol: Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.

tag: Clontech, Mountain View, CA, catalog 636550

source_name: Local Prostate Cancer 1

tag: Localized prostate tumor, Gleason sum


title: Local Prostate Cancer 6

source_name: Local Prostate Cancer 6


title: Benign Prostate  16

description: Benign prostate tissue

source_name: Benign Prostate  16

tag: Benign prostate tissue


title: Benign Prostate  15

description: Benign prostate tissue

source_name: Benign Prostate  15


title: Local Prostate Cancer 12

description: Localized prostate tumor, Gleason sum: 3+4

source_name: Local Prostate Cancer 12


title: Local Prostate Cancer 10

source_name: Local Prostate Cancer 10


title: Benign Prostate  13

description: Benign prostate tissue

source_name: Benign Prostate  13


title: Local Prostate Cancer 3

description: Localized prostate tumor, Gleason sum: 3+3

source_name: Local Prostate Cancer 3


title: Local Prostate Cancer 4

source_name: Local Prostate Cancer 4


title: Local Prostate Cancer 11

source_name: Local Prostate Cancer 11


title: Local Prostate Cancer 2

source_name: Local Prostate Cancer 2


title: Local Prostate Cancer 9

description: Localized prostate tumor, Gleason sum: 4+4

source_name: Local Prostate Cancer 9


title: Local Prostate Cancer 7

source_name: Local Prostate Cancer 7


title: Local Prostate Cancer 8

source_name: Local Prostate Cancer 8


title: Benign Prostate  14

description: Benign prostate tissue

source_name: Benign Prostate  14


title: Local Prostate Cancer 5

source_name: Local Prostate Cancer 5


title: Benign Prostate  12

description: Benign prostate tissue

source_name: Benign prostate pool

source_name: Benign Prostate  12


title: Benign Prostate  7

description: Benign prostate tissue

source_name: Benign Prostate  7


title: Benign Prostate  10

description: Benign prostate tissue

source_name: Benign Prostate  10


title: Benign Prostate  9

description: Benign prostate tissue

source_name: Benign Prostate  9


title: Benign Prostate  11

description: Benign prostate tissue

source_name: Benign Prostate  11


title: Benign Prostate  8

description: Benign prostate tissue

source_name: Benign Prostate  8


title: Benign Prostate  5

description: Benign prostate tissue

source_name: Benign Prostate  5


title: Benign Prostate  2

description: Benign prostate tissue

source_name: Benign Prostate  2


title: Metastatic Prostate Cancer  12

description: Metatstatic tissue from the liver, collected by warm autopsy

source_name: Metastatic Prostate Cancer  12


title: Benign Prostate  4

description: Benign prostate tissue

source_name: Benign Prostate  4


title: Benign Prostate  3

description: Benign prostate tissue

source_name: Benign Prostate  3


title: Benign Prostate  6

description: Benign prostate tissue

source_name: Benign Prostate  6


title: Metastatic Prostate Cancer  11

source_name: Metastatic Prostate Cancer  11

tag: Metatstatic tissue from the liver, collected by warm autopsy


title: Benign Prostate  1

description: Benign prostate tissue

source_name: Benign Prostate  1


title: Metastatic Prostate Cancer  10

description: Metastatic tissue from soft tissue, collected by warm autopsy

source_name: Metastatic Prostate Cancer  10


title: Metastatic Prostate Cancer  8

source_name: Metastatic Prostate Cancer  8


title: Metastatic Prostate Cancer  5b

description:
Metastatic tissue collected by warm autopsy
isolated from the same patient as M5a

source_name: Benign prostate pool

source_name: Metastatic Prostate Cancer  5b


title: Metastatic Prostate Cancer  9

source_name: Metastatic Prostate Cancer  9


title: detached-A.thaliana-leaf_12hpi_rep4

status: Public on Mar 01 2011

city: Cape Town

first: Joseph

middle: Mary Kusasira

last: Mulema

state: Western Cape

address: Private Bag, Rondebosch

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

hyb_protocol: Microarray slides were prepared based on Manufacturers instructions (Galbraith Laboratory, Arizona, USA) Labeled probes were concetrated, quantified and mixed in equal concentrations of labeled cDNA. Hybridization solution ( 20 μL of 20X SSC, 12 μL of 10% (v/v) BSA, 8 μL of SDS) was added and the volume made to 200 μL with Milli-Q water. The labeled probe was denatured by placing in boiling water for 2 min and transferred immediately to ice. The microarray slide was placed on a 65 oC heating block (label-side-up); the labeled probe was applied and covered with a coverslip avoiding trapping any air bubbles. The slide was incubated in a sealed chamber in a 55 oC water bath for 8-12 hrs. Slides were washed in 2X SSC, 0.5% (v/v) SDS for 5 min at 55 oC followed by 0.5X SSC for 5 min and 0.05X SSC for 5 min at room temperature.

scan_protocol: Slided were scanned on a GenePix scanner 4200A (Axon Instruments, Union City, CA). Images were analyzed with Genepix (Version 5.1) (Axon Instruments, Union City, CA) to generate fluorescent and background intensity values for each spot in both the Cy3 (green) and Cy5 (red) channels.

data_processing:
Print-tip LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.
Following normalization, spot replication within each slide were merged based on average

source_name: Control A. thaliana leaves harvested after 12 hr

label_protocol:
25 µg of total RNA were reversed transcribed at 46°C overnight for in the presence of 200 U SuperScript II RTase (Invitrogen), 10 mM aminoallyl-dUTP, 15 mM dTTP and 25 mM each of dATP, dCTP, dGTP.
Synthesized cDNA was prurified using the RNeasy mini columns (Qiagen, Valencia, CA) based on manufacturer’s instructions and its concentration determined with a NanoDrop.
Purified cDNA was dried under vacuum and resuspended in 0.1 M NaHCO3 and labeled with 5 µL of cyanine 3 (Cy3) and cyanine 5 (Cy5) (Amersham Pharmacia, UK) for 1 hr in the dark mixing every 15 min.
cDNA from mock-treated and infected leaves was labelled with Cy5 and Cy3 in the first replicate (dye-swap) respectively. In the last four replicates (rep 2-5), cDNA from mock treated and infected leaves was labelled with Cy3 and Cy5 respectively.

growth_protocol: Arabidopsis thalaina plants (Col-0 ecotype) were grown in a mixture of soil composed of peat plugs and vermiculite (1:1 ratio) in a controlled environment room at 22°C under fluorescent light (80-100 μmol photon/sec/m2) with a 16 hr light and 8 hr dark cycle.

extract_protocol: Total RNA extracted using Phenol-Lithium chloride method

treatment_protocol:
Control leaves were inoculated with half-stregnth commercial grape juice with no spores.
Leaves were harvested 12 aand 24 hpurs after inoculation

tag: ecotype

tag: tissue

value: leaves

source_name: B. cinerea-treated A. thaliana leaves harvested after 12 hr

treatment_protocol:
Four-week Arabidopsis thaliana plants were inoculated with Botrytis cinerea (Pepper isolate) at a concentration of 500,000 spores ml-1 prepared in half strength commercial grape juice. The detarched leaf method was used in which 8-10 drops of 10 μl spore suspension depending on the size of the leaf were placed on top of each leaf.
Leaves were harvested 12 aand 24 hpurs after inoculation


title: Metastatic Prostate Cancer  3

description: Metastatic tissue from rib, collected by warm autopsy

source_name: Metastatic Prostate Cancer  3


title: Metastatic Prostate Cancer  7

source_name: Metastatic Prostate Cancer  7

tag: Metastatic tissue from soft tissue, collected by warm autopsy


title: Metastatic Prostate Cancer  1

source_name: Metastatic Prostate Cancer  1


title: detached-A.thaliana-leaf_12hpi_rep5


title: Metastatic Prostate Cancer  2

description: Metastatic tissue from the liver, collected by warm autopsy

source_name: Metastatic Prostate Cancer  2


title: Metastatic Prostate Cancer  4

source_name: Metastatic Prostate Cancer  4


title: Metastatic Prostate Cancer  6

source_name: Metastatic Prostate Cancer  6

tag: Metastatic tissue from the liver, collected by warm autopsy


title: Human liver_1 week posttransplantation

status: Public on Mar 02 2011

city: Gothenburg

first: Madeleine

last: Ingelsten

address: Bruna Straket 16

department: Renal Center

country: Sweden

institute: Gothenburg university

description: Human liver 1 week posttransplantation in combined liver-kidney transplantation.

hyb_protocol: Fifteen μg of DIG-labelled cRNA was hybridised to the Applied Biosystems Human Genome Survey Microarray v.2.0 according to the manufacturer’s instructions.

scan_protocol: The chemiluminescent signal detection, image acquisition and image analysis of the microarrays were performed on the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer.

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software.

label: DIG-dUTP

source_name: Human liver, 1 week posttransplantation

label_protocol: 500ng of total RNA from each sample was reversely transcribed, amplified and DIG-labelled (DIG-dUTP; Roche, Germany), using the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit.

extract_protocol: Qiagen RNeasy Mini kit for total RNA purification according to manufacturers instructions.

tag: Female, 64 years, in combined liver-kidney transplantation


title: Human liver_pretransplantation

description: Human transplanted liver 5 min pre-perfusion of liver in combined liver-kidney transplantation.

source_name: Human transplanted liver, 5 min pre-perfusion

tag: Female, 64 years, combined liver-kidney transplantation


title: T196

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description: Primary breast tumor

hyb_protocol: see Affymetrix standard protocols (www.affymetrix.com)

data_processing: RMA using a quantile normalization (R package affy, v 1.20.0)

source_name: human breast cancer tumors

extract_protocol: Guanidinium isothiocyanate and centrifugation over a cesium chloride gradient.

value: negative


title: Human liver_1h postperfusion of transplanted liver

description: Human transplanted liver 1 h postperfusion of liver in combined liver-kidney transplantation.

source_name: Human transplanted liver, 1 hour after reperfusion


title: detached-A.thaliana-leaf_24hpi_rep4

source_name: Control A. thaliana leaves harvested after 24 hr

source_name: B. cinerea-treated A. thaliana leaves harvested after 24 hr


title: detached-A.thaliana-leaf_24hpi_rep5


title: Human native liver_1 week posttransplantation of auxiliary liver

description: Human native liver 1 week posttransplantation of auxiliary liver.

source_name: Human native liver, 1 week posttransplantation of auxiliary liver


title: Human kidney_1 week posttransplantation

description: Human kidney 1 week posttransplantation in combined liver-kidney transplantation.

tag: Female, 64 years, in combined liver-kidney transplantation.


title: T190

description: Primary breast tumor

scan_protocol: see Affymetrix standard protocols (www.affymetrix.com)


title: Human native liver_1h postperfusion of auxiliary liver.

description: Human native liver 1 h postperfusion of auxiliary liver in combined liver-kidney transplantation.

source_name: Human native liver, 1 h postperfusion of auxiliary liver.


title: T194

description: Primary breast tumor

label_protocol: see Affymetrix standard protocols (www.affymetrix.com)


title: T193

description: Primary breast tumor

value: positive


title: Human kidney_posttransplantation_1h

description: Human kidney 1 h postperfusion of kidney in combined liver-kidney transplantation.

source_name: Human kidney, 1h posttransplantation

tag: Female 64 years, 1 h postperfusion in combined liver-kidney transplantation.


title: Human liver_native liver_2 h pre-perfusion of auxiliary liver.

description: Human native liver 2 h preperfusion of auxiliary liver in combined liver-kidney transplantation.

source_name: Human native liver, 2 hours pre-perfusion of auxiliary liver.

tag: Female, 64 years, native liver in combined liver-kidney transplantation.


title: Human liver_posttransplantation_4h

description: Human liver 4 hours postperfusion of combined liver-kidney transplantation.

source_name: Human liver 4 h posttransplantation

tag: Female, 64 years, combined liver-kidney transplantation.


title: Human kidney_preperfusion_5min

description: Human kidney 5 min pre-perfusion of kidney in combined liver-kidney transplantation.

source_name: Human kidney pretransplantation


title: T185

description: Primary breast tumor


title: T177

description: Primary breast tumor


title: T183

description: Primary breast tumor


title: T172

description: Primary breast tumor


title: T186

description: Primary breast tumor


title: T178

description: Primary breast tumor


title: T162

description: Primary breast tumor


title: T161

description: Primary breast tumor


title: T189

description: Primary breast tumor


title: T135

description: Primary breast tumor


title: T184

description: Primary breast tumor


title: T152

description: Primary breast tumor


title: T146

description: Primary breast tumor


title: T173

description: Primary breast tumor


title: T155

description: Primary breast tumor


title: T129

description: Primary breast tumor


title: T160

description: Primary breast tumor


title: T149

description: Primary breast tumor


title: T134

description: Primary breast tumor


title: T131

description: Primary breast tumor


title: T128

description: Primary breast tumor


title: T123

description: Primary breast tumor


title: T150

description: Primary breast tumor


title: T130

description: Primary breast tumor


title: T113

description: Primary breast tumor


title: T117

description: Primary breast tumor


title: T108

description: Primary breast tumor


title: T107

description: Primary breast tumor


title: T120

description: Primary breast tumor


title: T98

description: Primary breast tumor


title: T71

description: Primary breast tumor


title: T105

description: Primary breast tumor


title: T109

description: Primary breast tumor


title: T79

description: Primary breast tumor


title: T106

description: Primary breast tumor


title: T95

description: Primary breast tumor


title: T100

description: Primary breast tumor


title: T94

description: Primary breast tumor


title: T72

description: Primary breast tumor


title: T68

description: Primary breast tumor


title: T104

description: Primary breast tumor


title: T70

description: Primary breast tumor


title: T77

description: Primary breast tumor


title: T63

description: Primary breast tumor


title: T54

description: Primary breast tumor


title: T59

description: Primary breast tumor


title: T76

description: Primary breast tumor


title: T57

description: Primary breast tumor


title: T73

description: Primary breast tumor


title: T45

description: Primary breast tumor


title: T49

description: Primary breast tumor


title: T44

description: Primary breast tumor


title: Metastatic Prostate Cancer  5a

description:
Metastatic tissue from the diaphragm, collected by warm autopsy
isolated from the same patient as M5b

source_name: Benign prostate pool

source_name: Metastatic Prostate Cancer  5a


title: T40

description: Primary breast tumor


title: T41

description: Primary breast tumor


title: [CD4+ T-Cells]_[Control]_[1]

status: Public on Feb 14 2011

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

description: Mouse CD4 T cells were cultured in vitro to obtain RNA for the assay

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled forHigh-Resolution Scanning.  The instruments were controlled using GCOS version1.4 software.

data_processing: The data were condensed with MAS 5.0 using the GeneChip Operation Software.

label: Biotin  (as a biotinylated nucleotide)

source_name: Mouse Spleen, peripheral lymph nodes, mesenteric lymph nodes

label_protocol:
Biotinylated cRNA were prepared from 2 ug total RNA according to the
Single Round RNA Amplification and Biotin Labeling System  (Enzo Life Sciences Intl.  Plymouth Meeting, PA)

extract_protocol:
Trizol
Qiagen Total RNA isolation kit

value: Spleen + Lymph Nodes

tag: cell type

value: CD4+ T cells


title: [CD4+ T-Cells]_[Control]_[2]

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System  (Enzo Life Sciences Intl.  Plymouth Meeting, PA)

treatment_protocol: hIL-2(100U/ml), hTGF-b1(5ng/ml), mIL-6(20ng/ml), mIL-1b(10ng/ml), mIL-23(10ng/ml), mIL-21(10ng/ml), mTNF-a(20ng/ml), anti-mIL-4(clone 11B11, 10ng/ml) and anti-mIFN-gamma(clone XMG2.4, 10ug/ml) cultured for 5 days.


title: SHR AP 5

status: Public on Jan 22 2011

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the area postrema from 5 SHR animals

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: MessageAmpII aRNA Amplification kit (Ambion)

organism: Rattus norvegicus

source_name: SHR Area postrema

label_protocol: Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

tag: strain

value: SHR

tag: gender

value: Male

tag: age

value: 10-13 weeks

value: Area postrema


title: WKY AP 3

description: Sample represents the area postrema from 5 WKY animals

source_name: WKY Area postrema

value: WKY


title: WKY AP 4


title: 4447846203H

status: Public on Jan 20 2011

city: Cambridge

first: Bin

last: Zheng

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

scan_protocol: Standard Illumina scan protocol.

data_processing:
The data were normalized using average normalization implemented in GenomeStudio.

Non-normalized data is available in 'GSE20159_non-normalized.txt', which is linked to the Series GSE20159 record as a supplementary file.

source_name: SN, ILB

label_protocol: Illumina Ambion kit.

growth_protocol: Substantia nigras were snap frozen.

extract_protocol: Trizol (Scherzer et al., Proc Natl Acad Sci 105, 2008).

treatment_protocol: None.

value: substantia nigra

tag: diagnosis

value: incidental Lewy body disease

value: F


title: 4447846203D

value: M


title: T48

description: Primary breast tumor


title: 4447846203B


title: 4447846203I

source_name: SN, control

value: normal

tag: sample type

value: control


title: WKY AP


title: SHR AP 2


title: 4447846205L


title: SHR AP 3


title: 4447846203C


title: WKY AP 2


title: WKY AP 5


title: 4447846203F


title: 4447846203G


title: 4447846203E


title: 4447846205J


title: 4447846203A


title: 4447846205K


title: SHR AP 4


title: 4447846205H


title: 4447846205I


title: SHR AP


title: 4447846205F


title: 4447846205G


title: 4447846205E


title: 4447846205D


title: 4447846205B


title: 4447846205C


title: 4493594358L


title: 677U133A

hyb_protocol: standard Affy protocols

scan_protocol: standard Affy protocols

data_processing: The data were processed and scaled to a target intensity of 100 for all probe sets by MAS5 in Biocondutor affy package.

source_name: Human Cbm

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

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

value: cerebellum

tag: disease status

value: healthy control


title: HS911

hyb_protocol: Standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocols.

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

growth_protocol: None.


title: 4493594358J

hyb_protocol: Standard Illumina hybridization protocol.


title: 4447846205A


title: 4493594358K


title: 650U133A

value: parkinson's disease


title: HS81A

source_name: SN, PD

value: Parkinson's disease


title: 4493594358C


title: HS258


title: 4493594358E


title: 868U133A


title: 4493594358I


title: 628U133A


title: 936U133


title: 4493594358D


title: 4493594358F


title: 4493594358A


title: 4493594358G


title: HS185


title: HS872


title: 731U133A


title: 758U133A


title: 4493594358H


title: 4493594358B


title: 755U133A


title: HS154


title: HS673


title: HS543B


title: HS214


title: HS1037


title: HS1035


title: BRCA1 - B158

status: Public on Dec 02 2010

city: Hamburg

first: Simon

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.

label_protocol: According to the manufacturer's instructions (Kreatech Biotechnology, Amsterdam).

extract_protocol: DNA is extracted as described in: Joosse et al. (submitted)

tag: organ

value: mammary gland; breast

tag: disease

value: infiltrating ductal carcinoma

tag: mutation

value: BRCA1 gene

source_name: Women reference pool

value: A pool of DNA from peripheral blood lymphocytes, from 7 apparently healthy women.


title: BRCA1 - B164

scan_protocol: As described in: Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.


title: BRCA1 - B146

data_processing:
As described in:
Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer. 2007 Mar 7;7:43.


title: BRCA1 - B165


title: BRCA1 - B156


title: BRCA1 - B162


title: BRCA1 - B171


title: BRCA1 - B152


title: BRCA1 - B160


title: BRCA1 - B125


title: BRCA1 - B153


title: BRCA1 - B137


title: BRCA1 - B150


title: Lymph node-naive-TB-tnf 3

status: Public on Dec 07 2010

city: Frederick

first: Sergei

middle: I

last: Grivennikov

state: MD

address: P.O. Box B

institute: National Cancer Institute

description: TB

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

source_name: TB

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: Pooled Lymph nodes were immediately frozen in luquid N2  and RNA was prepared using Tri-reagent according to manufacturer recommendations. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in DEPC dH2O. After that RNA was precipitated by LiCL and dissolved in DEPC water. 2 microgram of total RNA were taken for microarray analysis.

tag: Strain

value: TB-TNF KO double

tag: Gender

value: male

tag: Development stage

value: adult

tag: Genetic modification

value: gene knock out

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: BRCA1 - B141


title: Lymph node-naive-TB-tnf 2

description: TB

value: female


title: BRCA1 - B135


title: BRCA1 - B127


title: BRCA1 - B126


title: BRCA1 - B145


title: BRCA1 - B124


title: BRCA1 - B149


title: BRCA1 - B161


title: Lymph node-naive-B-tnf 1

description: EO-B

source_name: EO-B

value: B-TNF KO


title: Lymph node-naive-TB-tnf 1

description: TB


title: Lymph node-naive-B-tnf 3

description: EO-B


title: BRCA1 - B122


title: BRCA1 - B119


title: BRCA1 - B118


title: Lymph node-naive-B-tnf 2

description: EO-B


title: BRCA1 - B107


title: BRCA1 - B108


title: BRCA1 - B109


title: BRCA1 - B116


title: Whole heart; wild type; SHAM (G34 Control)

status: Public on Nov 17 2010

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

institute: Saint Michaels Hospital

description: G34 Control

hyb_protocol: As per Center for Applied Genomics at the University of Toronto

scan_protocol: Affymetrix GeneChip Scanner 300 Scaling target signals: 150

data_processing:
.Cel files were processed in MeV
Probe based analysis was performed and Quantile Normalization (per chip and per gene) was performed.

source_name: Whole heart; wild type; SHAM

label_protocol: IVT ID, EuKGE-WS2v4

growth_protocol: Animals were kept as per specified protocols for the vivarium at the University of Toronto

extract_protocol: Snap frozen hearts, stored at -80C were powdered using a pestel and mortar. 1ml Trizol reagent was used to extract total RNA. Protocol for RNA extraction was performed as per manufacturers specifications. Total RNA was further purified using Qiagen kit as per specifications.

treatment_protocol: SHAM Protocol: Mice were anaesthetised (0.1-0.5% inhaled isoflurane in 100% oxygen). The peritoneal cavity opened via a 7mm midline incision. The caecum was identified and mobilized. The caecum was returned to the abdomen, and the abdomen was closed. Buprenorphine 1g (0.05-0.1 mg/kg) in 0.5ml sterile 0.9% saline was administered subcutaneously at the end of the procedure. Mice were returned to their cages with free access to food and water and 0.5 ml 0.9% saline was administered subcutaneously in the scruff of the neck every 8 hours. At the completion of the experiment 48hrs. Animals were sacrificed and 48 hours after surgery, mice were anaesthetised (intraperitoneal 100 mg/kg ketamine and 10 mg/kg xylazine). The right common carotid artery was cannulated and invasive measurements of cardiac contractility were obtained and hearts were removed, snap frozen and Total RNA was extracted using Trizol procedure as per manufacturers specifications.

tag: tissue

value: whole heart

tag: strain/genotype

value: C57/BL6 (wild type)


title: Whole heart; wild type; CLP (G52 Max Dep)

description: G52 Max Dep

source_name: Whole heart; wild type; CLP

treatment_protocol: CLP Protocol: Mice were anaesthetised (0.1-0.5% inhaled isoflurane in 100% oxygen). The peritoneal cavity opened via a 7mm midline incision. The caecum was identified, ligated at its midpoint, and punctured twice using a 22G needle. A small amount of fecal material was expressed using forceps. The caecum was returned to the abdomen, and the abdomen was closed. Buprenorphine 1mcg (0.05-0.1 mg/kg) in 0.5ml sterile 0.9% saline was administered subcutaneously at the end of the procedure. Mice were returned to their cages with free access to food and water and 0.5 ml 0.9% saline was administered subcutaneously in the scruff of the neck every 8 hours. At the completion of the experiment 48hrs. Animals were sacrificed and 48 hours after surgery, mice were anaesthetised (intraperitoneal 100 mg/kg ketamine and 10 mg/kg xylazine). The right common carotid artery was cannulated and invasive measurements of cardiac contractility were obtained and hearts were removed, snap frozen and Total RNA was extracted using Trizol procedure as per manufacturers specifications.


title: Whole Heart; iNOS KO; CLP (G81 CLP)

description: G81 CLP

source_name: Whole Heart; iNOS KO; CLP

value: congenic B6.129P2-Nos2tm1Lau/J (iNOS KO)


title: Sporadic basal-like - C049

status: Public on Oct 26 2010

tag: sample

tag: cell type

value: peripheral blood lymphocytes

value: healthy appearing


title: Hela-Taf6d1

status: Public on Nov 27 2010

city: Bures-sur-Yvette

first: Arndt

last: Benecke

address: 35 route des Chartres

department: Integrative Biology

institute: Institut des Hautes Etudes Scientifiques & I.R.I.-CNRS

description: TAF6 orchestrates transcription programs and apoptosis in the absence of p53.

hyb_protocol: Array hybridization was performed for 16 hrs at 55 oC. Pre-Hybridization, Hybridization, antibody binding and Chemiluminescence reaction were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) following the manufacturer’s protocol (P/N 4339627).

scan_protocol: Image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer 1.1.1 (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v1.1.1 (P/N 4336391). Median normalization and Probabilty for a gene to be expressed(A) were calculated with proprietary software.

label: DIG-UTP

source_name: Hela cell line

label_protocol: Digoxigenin-UTP labeled cRNA was generated and amplified from 2 μg of total RNA from each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturer’s protocol(P/N 4365710).

extract_protocol: RNA was extracted from the cell lines using RNeasy Midi Kit (Quiagen) according to the instructions provided by the manufacturer

tag: Hela cells + Taf6d-exon 2 antisense RNA oligo


title: Whole Heart; iNOS KO; SHAM (G95 Control)

description: G95 Control

source_name: Whole Heart; iNOS KO; SHAM

treatment_protocol: Sham Protocol: Mice were anaesthetised (0.1-0.5% inhaled isoflurane in 100% oxygen). The peritoneal cavity opened via a 7mm midline incision. The caecum was identified, mobilized and returned to the abdomen. Buprenorphine 1mcg (0.05-0.1 mg/kg) in 0.5ml sterile 0.9% saline was administered subcutaneously at the end of the procedure. Mice were returned to their cages with free access to food and water and 0.5 ml 0.9% saline was administered subcutaneously in the scruff of the neck every 8 hours. Animals were sacrificed and 48 hours after surgery, mice were anaesthetised (intraperitoneal 100 mg/kg ketamine and 10 mg/kg xylazine). The right common carotid artery was cannulated and invasive measurements of cardiac contractility were obtained and hearts were removed, snap frozen and Total RNA was extracted using Trizol procedure as per manufacturers specifications.


title: Whole Heart; iNOS KO; SHAM (H5 Control)

description: H5 Control


title: Whole heart; wild type; CLP (G16 Max Dep)

description: G16 Max Dep


title: Whole Heart; iNOS KO; CLP (G83 CLP)

description: G83 CLP


title: Whole Heart; iNOS KO; SHAM (G97 Control)

description: G97 Control


title: Whole heart; wild type; CLP (G53 Max Dep)

description: G53 Max Dep


title: Sporadic - C048


title: Whole Heart; iNOS KO; CLP (G80 CLP)

description: G80 CLP


title: Whole heart; wild type; CLP (G61 Min Dep)

description: G61 Min Dep


title: Sporadic basal-like - C056


title: Sporadic - C051


title: Hela-Taf6d3


title: Sporadic - C068


title: Whole heart; wild type; CLP (G50 Min Dep)

description: G50 Min Dep


title: Hela-Taf6d2


title: Sporadic basal-like - C047


title: Whole heart; wild type; SHAM (G35 Control)

description: G35 Control


title: Sporadic - C067


title: Sporadic basal-like - C053


title: Whole heart; wild type; CLP (G51 Min Dep)

description: G51 Min Dep


title: Whole heart; wild type; SHAM (G32 Control)

description: G32 Control


title: Sporadic - C065


title: Sporadic - C035


title: Sporadic - C046


title: Sporadic basal-like - C033


title: Sporadic - C043


title: Sporadic - C002

hyb_protocol: As described in: Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. Joosse SA, et al. BMC Cancer. 2007 Mar 7;7:43.

extract_protocol:
As decribed in:
Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH.
Joosse SA, et al.
Breast Cancer Res Treat. 2008 Aug 14

value: mammary gland

tag: type

value: sporadic breast tumor


title: Sporadic basal-like - C018

scan_protocol: As described in: Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. Joosse SA, et al. BMC Cancer. 2007 Mar 7;7:43.


title: Sporadic - C013

data_processing:
As described in:
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.
Joosse SA, et al.
BMC Cancer. 2007 Mar 7;7:43.


title: Sporadic - C020

label_protocol:
As described in:
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.
Joosse SA, et al.
BMC Cancer. 2007 Mar 7;7:43.

extract_protocol:
Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH.
Joosse SA, et al.
Breast Cancer Res Treat. 2008 Aug 14


title: Sporadic - C016


title: Sporadic - C006


title: FG cell line_normoxic growth_replicate 2

status: Public on Sep 30 2010

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

hyb_protocol: fragmented cRNA was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays and washed and stained with Affymetrix Wash&Stain Kit on an Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: RMA Normalization

source_name: Pancreatic cancer cell line FG

label_protocol: total RNA was transcribed and labeled with Ambion Kit MessageAmp II Biotin Enhanced according to the manufacturers protocol

growth_protocol: Two human pancreatic carcinoma cell lines: FG, L3.6pl (Bruns et al., 1999) were used in this study. Both cell lines were cultivated in Dulbecco's Modified Eagle Medium (Gibco/Invitrogen) supplemented with 10% foetal bovine serum (Biochrom, Lot No.: 923 FF), 1x Glutamax-1 (Gibco/Invitrogen), 2x MEM vitamin solution (PAN Biotech, Aidenbach Germany), 2x MEM NEAA (PAN Biotech, Aidenbach Germany), 1x Penicillin/streptomycin (100 U/ml Penicillin + 0,1 mg/ml streptomycin) (PAN Biotech, Aidenbach Germany). Cells were cultivated at 37°C and 5% CO2 starting from frozen stock without further passaging. 500000 frozen cells were plated into 175cm2 Nunclon Δ-treated flask with filter cap (Nunc Roskilde Denmark) containing 25 ml medium and cultivated until an apparent confluence of 80% was reached (typically 9 days). Medium was changed every second day. The last 24 hours cells were treated by hypoxia where air was replaced by nitrogen to reach an oxygen concentration of 1% or left untreated respectively.

extract_protocol: Total RNA was extracted from cultured cells with the Trizol method according to the manufacturers protocol

tag: low metastatic potential; growth under normal oxygen


title: a849sh_136914

status: Public on Sep 13 2010

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

description: Sham

hyb_protocol: labeled targets were hybridized to Affymetrix(Santa Clara, CA) Mouse Genome 430 2.0 Array GeneChip™ microarrays for 16 hours at 45° C. The arrays were washed and scanned according to Affymetrix standard protocols

scan_protocol: Scanned in an Affymetrix scanner according to Affymetrix standard protocols.

data_processing: Gene expression values were ex-tracted and normalized for all 24 chips simultaneously using Dchip.

source_name: murine splenocytes

label_protocol: 20 ng of total RNA was used to make single-stranded antisense cDNA using the NuGEN Technologies (San Carlo, CA) Ovation™ Biotin System in accordance with the manufacturer’s directions.  This was compared with using 1-2 ug of total RNA following the Affymetrix standard protocol.

extract_protocol: Isolation of RNA was then performed using the Qiagen (Valencia, CA) recommendated protocol for the RNeasy method with DNase treatment.

treatment_protocol: Splenocyte isolation from macerated spleen followed by RBC lysis with proprietary buffer, followed by a wash in Dulbeco's PBS followed by RLT suspension process.

tag: C57BL/6J 8 weeks


title: a854tr_136919

description: Trauma/Hemorrhage


title: L3.6pl cell line_normoxic growth_replicate 2

source_name: Pancreatic cancer cell line L3.6pl

treatment_protocol: Two human pancreatic carcinoma cell lines: FG, L3.6pl (Bruns et al., 1999) were used in this study. Both cell lines were cultivated in Dulbecco's Modified Eagle Medium (Gibco/Invitrogen) supplemented with 10% foetal bovine serum (Biochrom, Lot No.: 923 FF), 1x Glutamax-1 (Gibco/Invitrogen), 2x MEM vitamin solution (PAN Biotech, Aidenbach Germany), 2x MEM NEAA (PAN Biotech, Aidenbach Germany), 1x Penicillin/streptomycin (100 U/ml Penicillin + 0,1 mg/ml streptomycin) (PAN Biotech, Aidenbach Germany). Cells were cultivated at 37°C and 5% CO2 starting from frozen stock without further passaging. 500000 frozen cells were plated into 175cm2 Nunclon Δ-treated flask with filter cap (Nunc Roskilde Denmark) containing 25 ml medium and cultivated until an apparent confluence of 80% was reached (typically 9 days). Medium was changed every second day. The last 24 hours cells were treated by hypoxia where air was replaced by nitrogen to reach an oxygen concentration of 1% or left untreated respectively.

tag: high metastatic potential; growth under normal oxygen


title: FG cell line_normoxic growth_replicate 3


title: a853tr_136918

description: Trauma/Hemorrhage


title: a844sh_136910

description: Sham


title: a852tr_136917

description: Trauma/Hemorrhage


title: a851tr_136916

description: Trauma/Hemorrhage


title: L3.6pl cell line_normoxic growth_replicate 1


title: a846sh_136911

description: Sham


title: L3.6pl cell line_hypoxic growth_replicate 3

tag: high metastatic potential; growth under reduced oxygen


title: a855tr_136920

description: Trauma/Hemorrhage


title: a850tr_136915

description: Trauma/Hemorrhage


title: FG cell line_hypoxic growth_replicate 1

tag: low metastatic potential; growth under reduced oxygen


title: a848sh_136913

description: Sham


title: L3.6pl cell line_normoxic growth_replicate 3


title: n855tr_135926

description: Trauma/Hemorrhage


title: a845sh_136909

description: Sham


title: L3.6pl cell line_hypoxic growth_replicate 1


title: FG cell line_hypoxic growth_replicate 3


title: FG cell line_hypoxic growth_replicate 2


title: FG cell line_normoxic growth_replicate 1


title: a847sh_136912

description: Sham


title: n853tr_135924

description: Trauma/Hemorrhage


title: L3.6pl cell line_hypoxic growth_replicate 2


title: n851tr_135922

description: Trauma/Hemorrhage


title: n852tr_135923

description: Trauma/Hemorrhage


title: n849sh_135920

description: Sham


title: n845sh_135916

description: Sham


title: n846sh_135917

description: Sham


title: n850tr_135921

description: Trauma/Hemorrhage


title: n848sh_135919

description: Sham


title: SAEC-nutlin-12h-rep4

status: Public on Aug 30 2010

city: La Jolla

first: Conrado

middle: T

last: Soria

address: 10010 North Torrey Pines Rd

department: MCBL-O

institute: The Salk Institute for Biological Studies

hyb_protocol: Samples were hybridized using the Affymetrix hybridization, wash and stain kit materials as per manufacturer standard procedure.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G.

data_processing:
Affymetrix GeneChip Operating Software v. 1.3 was used to produce .CEL intensity files. Partek Analysis software was used to perform a pre-background adjustment for GC content followed by Robust Multi-Array Analysis (RMA) background correction, quantile normalization and mean probeset summarization.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: small airway epithelial cells, nutlin-3 treated 12hrs

label_protocol: Samples were fragmented and biotinylated using the GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Small airway epithelial cells (Lonza) were grown in small airway basal media with standard media Singlequot supplements (Lonza), except for gentamicin/amphotericin-B. Cells were fed every 2-3 days, and were rendered quiescent by allowing cells to remain 100% confluent for 10 days.

extract_protocol: Total RNA was extracted and purified using Trizol and the Micro-to-Midi RNA purification kit (Invitrogen).  cDNA synthesis was performed using the Ambion WT Expression kit.

treatment_protocol: Quiescent cells were infected with purified adenovirus at a multiplicity of infection (M.O.I.) of 10 for 36 hours. Cells treated with nutlin (Sigma) was used at a final concentration of 10uM for 12 hours.

value: quiescent small airway epithelial cells

tag: infection/treatment

value: nutlin-3 treated

tag: technical replicate

value: experimental 2 replicate


title: n844sh_135915

description: Sham


title: SAEC-nutlin-12h-rep3


title: SAEC-d55kdORF3-36hpi-rep3

source_name: small airway epithelial cells, d55kdORF3 infected 36hrs

value: dE1B-55k/dE4-ORF3 infected


title: SAEC-nutlin-12h-rep1

value: experimental 1 replicate


title: SAEC-d55kdORF3-36hpi-rep4


title: SAEC-d55kdORF3-36hpi-rep1


title: SAEC-nutlin-12h-rep2


title: SAEC-d55kdORF3-36hpi-rep2


title: n847sh_135918

description: Sham


title: SAEC-d55k-36hpi-rep5

source_name: small airway epithelial cells, d55k infected 36hrs

value: dE1B-55k infected


title: n854tr_135925

description: Trauma/Hemorrhage


title: SAEC-d55k-36hpi-rep2


title: SAEC-mock-36hpi-rep3

source_name: small airway epithelial cells, mock infected 36hrs

value: mock infected


title: SAEC-mock-36hpi-rep2


title: SAEC-d55k-36hpi-rep3


title: SAEC-mock-36hpi-rep4


title: Strain LR113 (three biological replicates)

status: Public on Aug 14 2010

city: Seattle

first: Lakshmi

last: Rajagopal

state: WA

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

description: Catalog design for Streptococcus agalactiae A909 (Taxonomy Id: 205921) covering NC_007432. Probes selected for 1996/1996 sequences. Median number of probes/sequence is 18 with an average of 18.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.

hyb_protocol: Hybridization was performed by NimbleGen Inc.

scan_protocol: Each chip was scanned in 5 technical replicates by NimbleGen Inc., with the average scan values reported here.

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities by NimbleGen Inc.

organism: Streptococcus agalactiae

label_protocol: Labeling was performed by NimbleGen Inc. using Cy3.

extract_protocol: Total prokaryotic RNA was extracted from late log-phase (OD600=0.6) cultures of GBS grown in TSB at 37C and 5% CO2. Three biological replicates were used, on three separate chips, with average values reported here.

tag: stk1 deletion mutant


title: SAEC-d55k-36hpi-rep4


title: SAEC-mock-36hpi-rep1


title: 1352FFPE_T1B

status: Public on Aug 03 2010

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

description: FFPE HNSCC from 2001 surgical resection at time of original diagnosis, biorep 2

hyb_protocol: manufacturer specifications

scan_protocol: manufacturer specifications

data_processing: GC-RMA processing performed in R v2.4.0 using the gcrma package

label_protocol: NuGen protocol

extract_protocol: manufacturer specifications

tag: FFPE

tag: HNSCC

tag: no treatment


title: 1352FFPE_T2A

description: FFPE HNSCC from 2004 surgical resection at time of recurrence after radiation therapy and before chemotherapy, biorep 1

tag: post radiation


title: SAEC-d55k-36hpi-rep1


title: 2007-01-22-Pre-1352frozen_T3A

description: Frozen HNSCC from 2007 post-cetuximab and pre-AMG 479, biorep 1

tag: Frozen

tag: post radiation / post cetuximab


title: 1352FFPE_T2B

description: FFPE HNSCC from 2004 surgical resection at time of recurrence after radiation therapy and before chemotherapy, biorep 2


title: 1352FFPE_NL1

description: FFPE normal adjacent epithelia from 2001 surgical resection at time of original diagnosis

tag: normal adjacent


title: 2007-01-22-Pre-1352frozen_T3B

description: Frozen HNSCC from 2007 post-cetuximab and pre-AMG 479, biorep 2


title: 1352FFPE_NL2

description: FFPE normal adjacent epithelia from 2004 surgical resection at time of recurrence after radiation therapy and before chemotherapy, biorep 1


title: 2007-03-06-Post-1352frozen_T4A

description: Frozen HNSCC from 2007 post-cetuximab and post-AMG 479, biorep 1

tag: post radiation / post cetuximab / post AMG 479


title: 2007-03-06-Post-1352frozen_T4B

description: Frozen HNSCC from 2007 post-cetuximab and post-AMG 479, biorep 2


title: Co-hybridization of E. coli Oslo stx positive strain mRNA vs. genomic DNA #2

status: Public on Sep 01 2010

type: mixed

city: Kgs. Lyngby

first: Hanni

last: Willenbrock

address: Kemikalievej, bygning 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: DTU

description: co-hybridization of mRNA with genomic DNA from an E. coli Stx positive strain

hyb_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

data_processing: raw data

organism: Escherichia coli

source_name: E. coli stx positive strain

label_protocol: NimbleGen standard protocols for expression arrays (prepared and hybridized by NimbleGen)

growth_protocol: Grown in LB broth at 37oC with continuous agitation, and samples for RNA extraction were taken in log phase

extract_protocol: mRNA isolation with RNeasy Midi kit (Qiagen)

tag: mRNA (cDNA) from shiga toxin positive E. coli strain

growth_protocol: Grown overnight in Luria-Bertani (LB) broth at 37oC with continuous agitation.

extract_protocol: Genomic DNA isolation according to Grimberg et al. Nucleic acids research 1989, 17(21):8893

tag: genomic DNA from shiga toxin positive E. coli strain


title: 1352FFPE_T1A

description: FFPE HNSCC from 2001 surgical resection at time of original diagnosis, biorep 1


title: Co-hybridization of E. coli Oslo stx negative strain mRNA vs. genomic DNA #1

scan_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

source_name: E. coli stx negative strain

tag: mRNA (cDNA) from shiga toxin negative E. coli outbreak strain

tag: genomic DNA from shiga toxin negative E. coli outbreak strain


title: NPC_SA01_3

status: Public on Jul 21 2010

city: EVRY

first: DENIS

middle: Alexandre

last: Jérôme

address: 5 rue Henri Desbruères

institute: INSERM/UEVE UMR 861, I-STEM, AFM

description: gene expression data for SA01 hES cells line-derived NPC

hyb_protocol: Hybridisation, washing and staining procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

scan_protocol: Scanning procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

data_processing: Hybridizing data were exploited using Array Assist 4.2 software (Stratagene). First, the software allowed validating quality controls. Next, experiment grouping was performed and GC-RMA statistical algorithm procedure was used to normalize hybridization intensity values. After this step, we used one way-ANOVA test on transformed logarithm basis 2 data to retain only values were not changing significantly (α<0,05) among triplicate sample. Next, we compared on the one hand NCAM-NPC to ES and on the other hand CD73-MPC to ES using Student parametric statistical test adjusted by FDR Benjamini-Hodgberg correction. At last, we retained as significant modulated genes those that at last one probesets vary to up to 2 folds (Fold Change, FC >2)  with a corrected p-value, αc<0,05. The final gene lists was established by removing doubling datas (several probesets measured the same gene) to retain the most modulated one.  At last, we also performed the correlation plot between the 18 arrays of the experiment using this software.

source_name: Neural precursor cells derived from hES cell line SA01, biological replicate 3

label_protocol: 100 ng of total RNA was used to generate biotinylated cRNA using the GeneChip® Two-Cycle Target Labeling and Control Reagents from Affymetrix according to the manufactures protocol

growth_protocol:
GROWTH PROTOCOL (hES): hES cells were maintained and propagated on a feeder layer of STO (SIM mice Thioguanine and Ouabaine resistant) murine embryonic fibroblast cell line inactivated by Mitomycin C (Sigma Aldrich, 2.5 μg per mL overnight at 37°C). Cells were cultured within a humidified 10% CO2 incubator setted at 37°C  in a serum replacement medium (DMEM, 20 % Knock-out Serum Remplacement (KSR), 1% Glutamax 1mM, 1% Non Essential Amino Acid (NEAA), 0.1% Beta-Mercaptoethanol (BM) 0.1% and 1% Penicillin/streptomycin (P/S), all from GIBCO) supplemented with 8ng/mL of bFGF (Invitrogen).
DIFFERENTIATION PROTOCOL (NPC): The protocol for the differentiation of hES towards neurectodermal rosettes was adapted from (Perrier at al). Briefly, hES cells were dissociated from STO by manual dissociation and plated in a density of approximately 103 cells per cm² on a confluent layer of mitotically inactivated murine stromal feeder (MS5). The cells were cultured in KSR medium (Knock-out Serum Replacement, 15 % SR; 1% Glutamax; 1% NEAA and 0.1% BM, all from GIBCO) for 14-16 DIV (Days in Vitro), replaced by Neurobasal medium, N2 (DMEM-F12 + Glutamax, 1% N2 supplement and 1% P/S) until DIV21. Cells were harvested at DIV21 using TrypLE Express (GIBCO) and about 5.106 cells were suspended in PBS -2% Fetal Calf Serum containing 1% of 7-amino-actinomycin D (7AAD) (Sigma) and then incubated with IgG1κ Direct conjugated Phyco-erythrin (PE) monoclonal anti human Neural Cell Adhesion Molecules (hNCAM) antibody diluted 1/10 provided by BD Biosciences Pharmingen™. This antibody recognizes an extracellular immunoglobulin-like domain common to three molecular weight forms –Mr 120, 140 and 180 kilodaltons –of the NCAM protein. The cell sorting was performed by MoFlow Cell Sorter Cytometer from Cytomation and alived positive and negative fractions were collected in 1mL of N2 medium with 1% P/S.
DIFFERENTIATION PROTOCOL (MSC): Mesodermal differentiation was obtained based on a protocol described by Barberi et al  Briefly, differentiation was induced by plating 2.104 ES cells/cm2 on 0.1% gelatin coated dishes in the presence of KO-DMEM medium supplemented with 20% of Fetal Bovine Serum (FBS, Invitrogen), 1mM L-glutamine, 1% non-essential amino-acid, 1% penicillin-streptomycin and 0.1mM β-mercaptoethanol. Medium was changed every other day. Confluent cells were passed with trypsin/EDTA 1X (Invitrogen) in new gelatin coated dishes.

extract_protocol: Total RNA was extracted from the cells using the RNeasy Mini kit (Qiagen) according to the manufacturer protocol

tag: Differentiation of hES cells line SA01 towards neural rosettes

tag: Neural precursor phenotype


title: MSC_SA01_3

description: gene expression data for SA01 hES cell line-derived MPC

source_name: Mesodermal Precursor Cells derived from hES cell line SA01, biological replicate 3

tag: Differentiation of hES cells line SA01 towards MPC-like cells

tag: Mesenchymal stem cells phenotype


title: MSC_VUB01_1

description: gene expression data for VUB01 hES cell line-derived MPC

source_name: Mesodermal Precursor Cells derived from hES cell line VUB01, biological replicate 1

tag: Differentiation of hES cells line VUB01 towards MPC-like cells


title: MSC_SA01_1

source_name: Mesodermal Precursor Cells derived from hES cell line SA01, biological replicate 1


title: MSC_VUB01_2

source_name: Mesodermal Precursor Cells derived from hES cell line VUB01, biological replicate 2


title: NPC_SA01_2

source_name: Neural precursor cells derived from hES cell line SA01, biological replicate 2


title: Co-hybridization of E. coli control strain O157:H7 EDL933 mRNA vs. genomic DNA #1

description: control co-hybridization of mRNA with genomic DNA from E. coli O157:H7 EDL933

source_name: E. coli O157:H7 EDL933

tag: control strain mRNA (cDNA)

label_protocol: NimbleGen standard protocols for CGH (prepared and hybridized by NimbleGen)

tag: control strain genomic DNA


title: NPC_VUB01_2

description: gene expression data for VUB01 hES cells line-derived NPC

source_name: Neural precursor cells derived from hES cell line VUB01, biological replicate 2

tag: Differentiation of hES cells line VUB01 towards neural rosettes


title: hES_SA01_3

description: gene expression data from undifferentiated hES cells line SA01

source_name: human embryonic stem (hES) cell line SA01, biological replicate 3

tag: human ES cells line from Cellartis, Sweden  commercial line derived from normal embryos

tag: Karyotype

value: X,Y


title: hES_SA01_2

source_name: human embryonic stem (hES) cell line SA01, biological replicate 2


title: NPC_SA01_1

source_name: Neural precursor cells derived from hES cell line SA01, biological replicate 1


title: Co-hybridization of E. coli Oslo stx positive strain mRNA vs. genomic DNA - acidic conditions #3

tag: mRNA (cDNA) from shiga toxin positive E. coli strain grown under acidic conditions


title: NPC_VUB01_3

source_name: Neural precursor cells derived from hES cell line VUB01, biological replicate 3


title: MSC_SA01_2

source_name: Mesodermal Precursor Cells derived from hES cell line SA01, biological replicate 2


title: Co-hybridization of E. coli Oslo stx positive strain mRNA vs. genomic DNA #3

tag: mRNA from shiga toxin positive E. coli strain (cDNA)


title: Co-hybridization of E. coli Oslo stx positive strain mRNA vs. genomic DNA - acidic conditions #1


title: hES_VUB01_3

description: gene expression data from undifferentiated hES cells line VUB01

source_name: human embryonic stem (hES) cell line VUB01, biological replicate 3

tag: human ES cells line from AZ-VUB laboratory, Belgium  derived from normal embryos


title: NPC_VUB01_1

source_name: Neural precursor cells derived from hES cell line VUB01, biological replicate 1


title: hES_SA01_1

source_name: human embryonic stem (hES) cell line SA01, biological replicate 1


title: Co-hybridization of E. coli Oslo stx positive strain mRNA vs. genomic DNA - acidic conditions #2

source_name: E. coli stx positive strain


title: Co-hybridization of E. coli Oslo stx negative strain mRNA vs. genomic DNA #3

source_name: E. coli stx negative strain


title: Co-hybridization of E. coli control strain O157:H7 EDL933 mRNA vs. genomic DNA #2


title: Co-hybridization of E. coli Oslo stx negative strain mRNA vs. genomic DNA #2


title: Sporadic - C069

status: Public on Jul 05 2010

tag: organ

tag: disease

value: infiltrating ductal carcinoma

tag: type

source_name: Women reference pool

tag: sample

value: A pool of DNA from peripheral blood lymphocytes, from 7 apparently healthy women.

tag: cell type


title: Sporadic - C063

value: mammary gland; breast


title: Co-hybridization of E. coli control strain O157:H7 EDL933 mRNA vs. genomic DNA #3


title: Sporadic - C061


title: hES_VUB01_1

source_name: human embryonic stem (hES) cell line VUB01, biological replicate 1


title: hES_VUB01_2

source_name: human embryonic stem (hES) cell line VUB01, biological replicate 2


title: Sporadic - C037


title: Sporadic - C052


title: Sporadic - C044


title: Sporadic - C060


title: Sporadic - C057


title: Sporadic - C058


title: Sporadic - C042


title: Sporadic - C034


title: Sporadic - C036


title: Sporadic - C031


title: MSC_VUB01_3

source_name: Mesodermal Precursor Cells derived from hES cell line VUB01, biological replicate 3


title: Sporadic - C029


title: Sporadic - C030


title: Sporadic - C039


title: Sporadic - C023


title: Sporadic - C025


title: Sporadic - C028


title: Sporadic - C026


title: Sporadic - C027


title: Sporadic - C022


title: Sporadic - C019


title: Sporadic - C010


title: Sporadic - C004


title: Sporadic - C015


title: Sporadic - C001


title: Co-hybridization of E. coli Oslo stx positive strain mRNA vs. genomic DNA #1

tag: mRNA (cDNA) from shiga toxin positive E. coli strain

tag: genomic DNA from shiga toxin positive E. coli strain


title: shdj103 | normal karyotype

status: Public on Jul 11 2010

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33568.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene common reference

extract_protocol: not provided

tag: reference

value: Stratagene common reference

source_name: AML 94

label_protocol: RNA from AML specimens was labeled with Cy5-dUTP using an anchored poly(dT) primer during first strand reverse transcription (Superscript II).  A universal reference RNA (pooled from 11 cell lines) was labeled identically but with Cy3-dUTP

extract_protocol: Normal karyotype acute myeloid leukemia (NK-AML) specimens comprise Ficoll gradient purified mononuclear cells (>80% blasts) from diagnostic peripheral blood or bone marrow.  Total RNA was isolated from stored, frozen mononuclear AML-cell pellets using Trizol reagent, and RNA quality assessed by gel electrophoresis.; Protocol Type = Extract preparation

tag: source

value: AML 94

tag: age

tag: overall survival time

value: 2198 days

tag: overall survival status

value: alive

tag: genotype

value: normal karyotype

tag: npm1 mutation status

value: mutated

tag: gender

value: female

tag: runx1 mutation