title: Atelp2_8hr_rep1

source_name: Atelp2, infected, 8hr, replicate 1


title: TBCF10839 - late exp. - replicate 1

status: Public on Jun 30 2012

type: RNA

city: Hannover

first: Jens

last: Klockgether

address: Carl-Neuberg-Str. 1

department: Ped. Pneumology

country: Germany

institute: Hannover Medical School

description: gene expression late exp. growth phase phase

hyb_protocol: Labelled cDNA was hybridized onto GeneChip P. aeruginosa Genome Arrays by incubating at 50°C for 16 h at 60 rpm (Affymetrix GeneChip Hybridization Oven 640)

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Operation Software Version 1.4 (Affymetrix GeneChip Scanner GCS 30) and data were processed using Agilent Scan Control and Feature Extraction Software

data_processing: Data were analyzed with the Affymetrix Microarray Suite software 5.0 using default parameters. The average microarray hybridization signal intensity was scaled to 150.

label: biotin

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: TBCF10839 late exp.

label_protocol: Terminal labeling was performed following the Affymetrix standard protocol (GeneChip DNA Labeling Reagent, P/N900542)

growth_protocol: Preliminary cultures of the respective P. aeruginosa strains were inoculated from a -80°C stock culture and incubated at 37°C at 250 rpm in LB medium to an optical density (600 nm) of about 2.0. Aliquot of 0.2 mL were then added to 20 mL fresh LB medium in 100 mL flasks (three per strain)  and incubated at 37°C. When reaching the required optical densities. 10 m Lsamples were taken from the cultures and used for cell harvest and subsequent parallel extraction of total RNA

extract_protocol: Total RNA extraction was performed according the manufacturer's protocol provided by Qiagen for bacteria.

tag: strain

tag: growth phase

value: late exponential

tag: source

value: cystic fibrosis patient airways


title: Acute leukemia remission 1015_Xba

type: genomic

city: Monza

first: Antonella

last: Lettieri

address: via Pergolesi 33

country: Italy

institute: Tettamanti Research Center

description: Hybridized to 50K_Xba

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The SNP arrays raw data were acquired by the Affymetrix GCOS software (version 1.4) and SNP calls were generated by the GTYPE software (version 4.0). The recommended QC and SNP call rate thresholds were used (BRLMM algorithm). Paired copy number analysis was performed using three different algorithms: PartekGS, CRMA and CNAG. The aberration segments provided by Partek Genomics Suite 6.08 software were generated using the genomic segmentation algorithm at a p-value of 0.001 and a signal to noise ratio of 0.3 and a minimum of ten genomic markers. The segmentation data were then filtered for p-value ≤ 0.01. Copy-number values obtained by Robust Multichip Analysis (CRMAv.2) were generated by normalizing each tumor’s probe set intensity to that of its paired normal reference. Raw copy number was estimated by using the CRMA algorithm (Bengtsson et al., 2008). Copy number segmentation of log2 ratios was performed in R using the DNA copy number package v1.16.0 which applies CBS (Circular Binary Segmentation) (Venkatraman and Olshen, 2007). Genomic copy numbers were also calculated using the CNAG v2.0 software package which relies on the Hidden Markov Model (HMM) analysis (Nannya et al., 2005). Copy number values ≤ 1.7 and ≥ 2.3 were considered losses and gains, respectively.[Combined_Hind_Xba_matrix provided as supplementary file on Series records]
primary data description : Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Acute leukemia remission

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Normal and tumor genomic DNA of T-ALL patients was extracted from freshly isolated BM-MNC by a commercial procedure (Puregene Blood kit, Gentra Systems, Minneapolis, MN), and genomic DNA from T-LBL patients was obtained from nucleated cells isolated by differential lysis using the QIAamp tissue kit (Qiagen, Hilden, Germany)

tag: disease type

value: T-ALL

tag: sample type

value: remission

tag: tissue

value: diagnostic bone marrow aspirates or tumor tissue


title: Atelp2_8hr_rep2

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

country: USA

institute: University of Florida

description: Gene expression 8 hr after Pst DC3000/avrRpt2 infection

hyb_protocol: For each array, 1.65 μg of Cy 3 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr.  Samples were hybridized to Arabidopsis 4 × 44k arrays (Agilent Technologies).  The arrays were washed according to the manufacturer’s protocol.

scan_protocol: The arrays were scanned on a G2505B scanner (Agilent Technologies).

data_processing:
Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies).
Data (individual signal intensity values) obtained from the 36 microarray probes were log transformed (using 2 as the base) and normalized between individual samples by scaling the individual log-transformed signal intensities so that all datasets had comparable lower quartile, median and upper quartile values. Normalized, log2 signals generated using MATLAB.

organism: Arabidopsis thaliana

source_name: Atelp2, infected, 8hr, replicate 2

label_protocol: cDNA was synthesized from 200 ng of total RNA and used as a template for in vitro transcription in the presence of T7 RNA Polymerase and cyanine labeled CTP’s using the Quick Amp Labeling kit (Agilent Technologies) according the manufacturer’s protocol.  The amplified, labeled complementary RNA (cRNA) was purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

growth_protocol: Arabidopsis seeds were sown on autoclaved soil (Metro-Mix 200, Grace-Sierra, Malpitas, CA) and vernalized at 4°C for 3 days.  Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.

extract_protocol: About 100 mg leaf tissues were ground into a fine powder in liquid nitrgen and resuspended in 500 μL 80°C water-saturated phenol and 500 μL 80°C extraction buffer (100 mM LiCl, 100 mM Tris pH 8.0, 10 mM EDTA, 1% SDS).  After brief vortexing and centrifugation at 14,000 rpm for 5 min, the aqueous phase was transferred to another cold tube containing 500 μL of 24:1 chloroform:isoamyl alcohol.  After vortexing and centrifugation, the aqueous phase was transferred to a DEPC-treated tube with 1/10 volume of 3 M NaOAc and 2 volume of 100% ethanol.  The tube was inverted to mix and placed at -80°C for 30 min and then spun at 14,000 rpm for 15 min.  After removing the supernatant, the pellet was washed with 80% ethanol, dried briefly, and resuspended in DEPC-treated water.

treatment_protocol: Leaves of 4-week-old plats were inoculated with a 1 mL needless syringe by pressure-infiltration and leaf tissues were collected at the indicated time points.

tag: genotype/variation

tag: infection

value: avirulent bacterial pathogen Pst DC3000/avrRpt2

tag: time point

value: 8 hr

value: leaf


title: Acute leukemia remission 757_Xba

description: Hybridized to 50K_Xba


title: Lymphoblastic lymphoma diagnosis 13BP_Xba

description: Hybridized to 50K_Xba

source_name: Lymphoblastic lymphoma diagnosis

value: T-LBL

value: diagnosis


title: Atelp2_4hr_rep3

description: Gene expression 4 hr after Pst DC3000/avrRpt2 infection

source_name: Atelp2, infected, 4hr, replicate 3

value: 4 hr


title: Lymphoblastic lymphoma diagnosis 10SA_Xba

description: Hybridized to 50K_Xba


title: ROH12 13 #1 Liver

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory

description: Gene expression at age 44-45d in liver

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: polyA RNA

organism: Mus musculus

source_name: Liver, male 44-45d

label_protocol: Muscle and liver cDNA samples were hybridized on a Mouse GE 4x44k Microarray (Agilent Technologies, Inc., Waldbronn, Germany) according to manufacturer’s recommendations. Three technical replicate each was done on pooled cDNA samples from each mouse line.

growth_protocol: Mice from each line were fed ad libitum with standard laboratory conditions

extract_protocol: Mouse tissue samples (muscle and liver) were collected from 44 and 45 days old males from each of the nine out of thirteen lines (5 High lines: BEHi, DUHi, EDHi, MUHi, ROHi and 4 Control lines: BELi, EDLi, MULi and ROLi; n=23 total) at the University of Edinburgh. Frozen tissue samples were stored at -80ºC until use. Tissues were dissociated using TissueLyser II with steel beads (both Qiagen) following manufacturers’ instructions. mRNA was extracted and purified using TRIzol Reagent and the PureLink RNA Mini Kit (Life Technologies GmbH, Darmstadt, Germany). cDNA was synthesized using Maxima First Strand cDNA synthesis kit (Thermo Fisher Scientific, St. Leon-Rot, Germany).

tag: phenotype

value: high body weight

tag: genetic background

value: mixed

tag: weight

value: Liver

tag: age

tag: gender

value: male

tag: line

value: ROHi


title: Atelp2_4hr_rep2

source_name: Atelp2, infected, 4hr, replicate 2


title: Lymphoblastic lymphoma diagnosis 11AS_Xba

description: Hybridized to 50K_Xba


title: TBCF121838 - early exp. - replicate 2

description: gene expression early exp. growth phase phase

source_name: TBCF121838 early exp.

value: early exponential


title: Atelp2_0hr_rep3

description: Gene expression 0 hr after Pst DC3000/avrRpt2 infection

source_name: Atelp2, infected, 0hr, replicate 3

value: 0 hr


title: Lymphoblastic lymphoma diagnosis 9AM_Xba

description: Hybridized to 50K_Xba


title: MUL9 10 #1 Liver

description: Gene expression at age 44-45d in liver

value: low body weight

value: MULi


title: TBCF121838 - early exp. - replicate 1

value: cystic fibrosis patient airways


title: Atelp2_0hr_rep2

source_name: Atelp2, infected, 0hr, replicate 2


title: TBCF10839 - early exp. - replicate 2

source_name: TBCF10839 early exp.


title: Atelp2_0hr_rep1

source_name: Atelp2, infected, 0hr, replicate 1


title: Lymphoblastic lymphoma diagnosis 6TA_Xba

description: Hybridized to 50K_Xba

value: diagnostic bone marrow aspirates or tumor tissue


title: BEL4 5#2 Liver

description: Gene expression at age 44-45d in liver

value: BELi


title: MUL9 10 #2 Liver

description: Gene expression at age 44-45d in liver


title: MUH7 8#3 Liver

description: Gene expression at age 44-45d in liver

value: MUHi


title: Lymphoblastic lymphoma diagnosis 5NL_Xba

description: Hybridized to 50K_Xba


title: Lymphoblastic lymphoma diagnosis 1BD_Xba

description: Hybridized to 50K_Xba


title: Atelp2_4hr_rep1

source_name: Atelp2, infected, 4hr, replicate 1

value: avirulent bacterial pathogen Pst DC3000/avrRpt2

value: leaf


title: Acute leukemia diagnosis 2422_Xba

description: Hybridized to 50K_Xba

source_name: Acute leukemia diagnosis

value: T-ALL

value: diagnosis


title: MUH7 8#1 Liver

description: Gene expression at age 44-45d in liver

value: high body weight


title: MUL9 10 #3 Liver

description: Gene expression at age 44-45d in liver

value: mixed


title: Lymphoblastic lymphoma diagnosis 2NP_Xba

description: Hybridized to 50K_Xba

value: T-LBL


title: MUH7 8#2 Liver

description: Gene expression at age 44-45d in liver

value: Liver

value: male


title: HTM at 40% O2, with E. coli, rep 2

city: Durham

first: Paloma

last: Liton

state: NC

address: PO Box 3802

department: Ophthalmology

institute: Duke University

hyb_protocol: standard Affymetrix hyb and scan protocol for 1 cycle IVT.

data_processing: MAS5 normalized with Affymetrix Expression Console

source_name: trabecular meshwork cells

label_protocol: Microarrays were hibridized in Duke Microarray Facility using Affymetrix 1 cycle IVT

growth_protocol: Physiological condiitons: 5% oxygen, 5.2% Co2, 37 degrees ; Oxidative stress: 40% Oxygen, 5.2% Co2, 37 degrees

extract_protocol: Total RNA, Rneasy with in column DNA digestion

treatment_protocol: 1E6 particles/ mL

tag: cell type

value: trabecular meshwork cells

tag: ligand

value: E. coli

tag: oxygen stress


title: BEL4 5#3 Liver

description: Gene expression at age 44-45d in liver

value: low body weight


title: HTM at 40% O2, with pigment, rep 1

scan_protocol: standard Affymetrix hyb and scan protocol for 1 cycle IVT.

value: Pigment


title: HTM at 40% O2, with E. coli, rep 1


title: TBCF10839 - early exp. - replicate 1

tag: strain

tag: growth phase

value: early exponential

value: cystic fibrosis patient airways


title: Lymphoblastic lymphoma diagnosis 3MM_Xba

description: Hybridized to 50K_Xba

tag: disease type

value: diagnostic bone marrow aspirates or tumor tissue


title: HTM at 40% O2, control, rep 2


title: HTM at 40% O2, with pigment, rep 2


title: Acute leukemia diagnosis 1928_Xba

description: Hybridized to 50K_Xba

tag: sample type


title: Acute leukemia diagnosis 1870_Xba

description: Hybridized to 50K_Xba

tag: tissue


title: BEH2 3#2 Liver

description: Gene expression at age 44-45d in liver

value: BEHi


title: Acute leukemia diagnosis 1847_Xba

description: Hybridized to 50K_Xba


title: BEH2 3#3 Liver

description: Gene expression at age 44-45d in liver


title: Acute leukemia diagnosis 1520_Xba

description: Hybridized to 50K_Xba


title: BEH2 3#1 Liver

description: Gene expression at age 44-45d in liver


title: BEL4 5#1 Liver

description: Gene expression at age 44-45d in liver

value: BELi


title: Acute leukemia diagnosis 757_Xba

description: Hybridized to 50K_Xba


title: HTM at 5% O2, with E. coli, rep 2


title: HTM at 5% O2, with pigment, rep 1


title: Acute leukemia diagnosis 1433_Xba

description: Hybridized to 50K_Xba


title: Ada3FL/FL MEF, Cre, biological replicate 2

city: Omaha

first: Vimla

last: Band

state: NE

address: Room 6011, DRC, 985805 Nebraska Medical Center

department: Genetics, Cell Biology and Anatomy

institute: University of Nebraska Medical Center

description: Gene expression data of asynchronous cells after 3 days of Cre adenovirus infection

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console using Robust Multi-chip Averaging (RMA) background correction as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 50.

source_name: Ada3FL/FL MEFs_Cre adenovirus

label_protocol: Biotinylated cRNA was prepared using Ambion Expression Kit according to the manufacturer's instructions from 200 ng total RNA.

growth_protocol: Ada3FL/FL MEFs were grown in DMEM medium supplemented with 10% FCS

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

treatment_protocol: Exponetially growing MEFs were infected with control or Cre adenovirus and total RNA was extracted from cells after 3 days of infection

tag: strain background

value: 129/B6 mixed

value: Ada3FL/FL MEF, immortalized

tag: infected with

value: Cre adenovirus


title: Acute leukemia diagnosis 1238_Xba

description: Hybridized to 50K_Xba

value: T-ALL

value: diagnosis


title: HTM at 5% O2, control, rep 1


title: Ada3FL/FL MEF, control, biological replicate 2

description: Gene expression data of asynchronous cells after 3 days of control adenovirus infection

source_name: Ada3FL/FL MEFs_control adenovirus

value: control adenovirus


title: HTM at 5% O2, with E. coli, rep 1


title: HTM at 5% O2, with pigment, rep 2


title: A15 vs WT2

status: Public on Jun 29 2012

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: A15 vs WT2

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2011-01-13 Scan Time : 16:47:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

growth_protocol: OD : midlog

extract_protocol:
Extracted molecule : Total RNA
Extraction method : acid phenol prep http://dunham.gs.washington.edu/MDyeastRNA.pdf

tag: strain name

value: wt


title: Ada3FL/FL MEF, control, biological replicate 1


title: Acute leukemia diagnosis 1015_Xba

description: Hybridized to 50K_Xba


title: A13 vs WT2

description: A13 vs WT2

label_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf


title: A10 vs WT2

description: A10 vs WT2


title: WT1 vs WT2

description: WT1 vs WT2


title: A9 vs WT2

description: A9 vs WT2


title: A14 vs WT2

description: A14 vs WT2


title: Ada3FL/FL MEF, Cre, biological replicate 1


title: HTM at 40% O2, control, rep 1


title: A3 vs WT2

description: A3 vs WT2


title: HTM at 5% O2, control, rep 2


title: A2 vs WT2

description: A2 vs WT2


title: L3 stage worm AS_Control, biological replicate 1

city: Laurel

first: Jada

last: Lewis

state: MD

address: 8301 Muirkirk Road

institute: FDA

hyb_protocol: cRNA was synthesized from 10 μg of total RNA, and samples were hybridized to the C. elegans GeneChip (Affymetrix, Santa Clara, CA)

scan_protocol: Gene Chips were scanned using the Gene Array Scanner

data_processing:
The data was processed using PARTEK Genomics Suite, version 6.4 Partek
MAS5.0-generated CHP files have been linked as supplementary files.

organism: Caenorhabditis elegans

source_name: C.elegans L3 Stage

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

growth_protocol: Nematodes were bleached (0.5M NaOH, 1% Hypochlorite) to collect eggs which were incubated in M9 media for 24 hours to bring them to synchronized L3 stage and then transferred to C. elegans habitation media (CeHM)

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen)

treatment_protocol: Animals were collected by spinning at 800rpm for 5 minutes and transferred to Sodium arsenite containing (0.03% and 0.003% w/v) CeHM media and incubated at 22 °C for 6 hours

tag: developmental stage

tag: agent

value: control

tag: dose


title: L3 stage worm AS_Control, biological replicate 2


title: L3 stage worm AS_.03, biological replicate 2

value: arsenic


title: L3 stage worm AS_.03, biological replicate 3


title: L3 stage worm AS_Control, biological replicate 3


title: L3 stage worm AS_.03, biological replicate 1


title: L3 stage worm AS_.003, biological replicate 3


title: L3 stage worm AS_.003, biological replicate 2


title: Recombinant LCN2 protein treated mouse primary astrocytes

city: Daegu

first: Kyoungho

last: Suk

address: 101 Dong-In, Joong-gu

department: Department of Pharmacology

country: South Korea

institute: Kyungpook National University School of Medicine

description: LCN2-treated primary astrocytes, harvested.

hyb_protocol: The labeled cDNA mixture was then concentrated using ethanol precipitation method.  The concentrated Cy3 and Cy5 labeled cDNAs were resuspended in 10 ml of hybridization solution (GenoCheck, Korea).  After two labeled cDNAs were mixed, placed on Agilent Mouse Whole Oligo chip (G4122A, Agilent technologies, CA) and covered by a hybridization chamber.  The hybridized slides were washed in 2 x SSC, 0.1% SDS for 2 min, 1 x SSC for 3 min, and then 0.2 x SSC for 2 min at room temperature.  The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: Scanned on an Axon Instruments GenePix 4000B scanner.

data_processing: Images were quantified using software program GenePix Pro 5.1 (Axon, CA) and GeneSpring 7.2 (Sillicongenetics, CA).

source_name: pooled whole mouse brain primary astrocytes

label_protocol: Each total RNA sample (30 micro gram) was labeled with Cyanine (Cy3) or Cyanine (Cy5) conjugated dCTP (Amersharm, Piscataway, NJ) by a reverse transcription reaction using reverse transcriptase, SuperScrip ll (Invitrogen, Carlsbad, CA).

growth_protocol: Primary astrocytes were grown at DMEM with 10% FBS, 100 U/ml penicillin and 100 micro gram/ml streptomycin.

extract_protocol: Total RNA extracted using Trizol (Invitrogen, Calsbad, CA) following manufacturer's instructions

treatment_protocol: Primary astrocytes were treated with recombinant LCN2 protein (10 micro gram/ml) for 8 hr.

value: ICR

tag: age

value: day 3

value: astrocytes

source_name: Recombinant LCN2 protein treated mouse brain primary astrocytes

value: ICR mice


title: L3 stage worm AS_.003, biological replicate 1


title: hESCs expressing T121, biological rep 1

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

description: LSJ2 hESCs expressing T121

hyb_protocol: Following fragmentation, labelled cRNA were hyb using GeneChip Hybridization Oven 640 for 16h. GeneChips were washed and stained in the Genechip Fluidics Station 450

scan_protocol: The arrays were scanned by Affymetrix GeneChip Scanner 3000 7G and the software used was Affymetrix GeneChip Command Console

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and quantile as normalization method.

source_name: human embryonic stem cells expressing T121

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express kit protocol.

growth_protocol: hESCs were maintained on irradiated feeders as described previously ((E.Chiao et al. Stem Cells 26, 2032 (Aug, 2008).

treatment_protocol: hESCs were plated in duplicate overnight before doxycycline was added to the media to half of the wells to induce expression of either RB7LP or T121. Three days after doxycycline treatment began, cells were trypsinized, washed, pelleted and snap frozen before RNA extraction.

value: human embryonic stem cells

tag: cell line

value: LSJ2 line


title: hESCs control for T121, biological rep 2

description: H9 hESCs control for T121

source_name: human embryonic stem cells

value: H9 line


title: hESCs control for T121, biological rep 1

description: LSJ2 hESCs control for T121


title: hESCs control for RB7LP, biological rep 1

description: H9 hESCs control for RB7LP


title: hESCs expressing RB7LP for 3d, biological rep 2

description: H9 hESCs expressing RB7LP for 3d

source_name: human embryonic stem cells expressing RB7LP


title: 4 hours no drug, 3

city: Vancouver

first: Victoria

last: Svinti

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

hyb_protocol: Samples were hybridized on Illumina HumanHT-12 v3 BeadChips following the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331).

scan_protocol: BeadChips were imaged and quantified with the Illumina iScan scanner.

data_processing: Data was processed with Illumina BeadStudio v3.3.8, which included averaging signal intensities for each unique Beadtype.  The microarray profiling was performed at the Vancouver Prostate Centre Laboratory for Advanced Genome Analysis.

source_name: Huh7 cells

label_protocol: An input of 200 ng of total RNA was used to generate biotin-labeled cRNA following the Illumina® TotalPrep RNA Amplification Kit (Ambion, Inc.).

growth_protocol: Huh-7 cells were grown in Dulbecco’s modified Eagle medium (DMEM) (Sigma) with 10% fetal bovine serum (v/v) (Hiclone), 2 mM L-glutamine (Invitrogen), and 50 µg/mL penicillin/streptomycin (Invitrogen).

extract_protocol: Trizol extraction.

treatment_protocol: Huh-7 cells were pretreated with DMSO (control) or 10 µM GENK for 1 and 4 hours and performed in triplicate.

tag: treatment

value: DMSO for 4 hour


title: hESCs expressing T121, biological rep 2

description: H9 hESCs expressing T121

tag: cell type


title: 4 hours drug treatment, 2

value: 10 µM GENK for 4 hour


title: hESCs control for RB7LP, biological rep 2

description: H9 hESCs control for RB7LP


title: 4 hours drug treatment, 3


title: hESCs expressing RB7LP for 3d, biological rep 1

description: H9 hESCs expressing RB7LP for 3d


title: 4 hours no drug, 2


title: hESCs control for T121, biological rep 3

description: H9 hESCs control for T121


title: hESCs expressing T121, biological rep 3

description: H9 hESCs expressing T121


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 KO/KO, biological rep4

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: Gene expression data from murine pancreatic ductal adenocarcinomas

hyb_protocol: As recommended by manufacturer

scan_protocol: GeneChip Scanner 3000 7G was used for scanning.  Affymetrix GeneChip Command Console software (AGCC 3.2) was used for image processing

data_processing: Data was normalized by GCRMA (Bioconductor v.2.8/ R v.2.13).

source_name: Murine Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 KO/KO pancreas

label_protocol: As recommended by manufacturer

extract_protocol: Roche's MagNA Pure Compact Nucleic Acid Purification System was used for automated RNA isolation.

value: mixed  C57/BL/6,129/BALB/c

tag: genotype/variation

value: loss of Pten (Pten +/-) and K-ras activation (K-rasG12D) with COX-2 knockout (Cox-2 KO)

value: older than 8 weeks

value: pancreatic tumor


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 KO/KO, biological rep3


title: siNT mock infected replicate 2

city: Winston-Salem

first: Jeff

last: Chou

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

hyb_protocol: RNA hybridization was conducted with GeneAtlas Hybridization, Wash, and Stain Kit for 3' IVT Arrays (Affymetrix, USA) using the GeneAtlas System.

scan_protocol: Arrays were scanned by the GeneAtlas Imaging Station incorporated on the GeneAtlas System.

data_processing: Data was generated by the GeneAtlas Instrument Control Software.  The raw intensity data were normalized using Systematic Variation Normalization.

source_name: siNT mock infected replicate 2

label_protocol: RNA was labeled with the 3'-IVT Labeling Kit (Affymetrix) according to manufacturer's instructions.

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium containing 7% fetal bovine serum and 2 mM glutamine.

treatment_protocol: Cells were transfected with Rae1 siRNA or NT siRNA using  Hiperfect transfection reagent (Qiagen Corporation). At 72 hours post transfection with Rae1 siRNA or NT siRNA, cells were mock-infected or infected with rwt virus at MOI= 30. At 6 h postinfection total RNA was extracted

value: HeLa


title: siNT rwt infected replicate 2

source_name: siNT rwt infected replicate 2


title: 4 hours no drug, 1


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 KO/KO, biological rep2


title: 1 hour no drug, 2

value: DMSO for 1 hour


title: 1 hour drug treatment, 3

value: 10 µM GENK for 1 hour


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 COE/W, biological rep3

source_name: Murine Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 COE/W pancreas

value: loss of Pten (Pten +/-) and K-ras activation (K-rasG12D) with COX-2 over-expression (Cox-2 COE)


title: 4 hours drug treatment, 1


title: 1 hour no drug, 3


title: siRae1 mock infected replicate 2

source_name: siRae1 mock infected replicate 2


title: siNT rwt infected replicate 1

source_name: siNT rwt infected replicate 1


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 COE/W, biological rep4


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 COE/W, biological rep1


title: siRae1 mock infected replicate 1

source_name: siRae1 mock infected replicate 1


title: untagged alpha cell control

city: San Francisco

first: Lauren

middle: N

last: Booth

address: 600 16th Street, N374

department: Micobiology and Immunology

institute: University of California, San Francisco

hyb_protocol: See Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133; PMID 19529758.

data_processing: LOWESS normalization of the data was conducted in GeneSpring GX version 7.3 (Agilent Technologies). For additional details, see Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133; PMID 19529758.

organism: Lachancea kluyveri

source_name: ChIP of WT alpha cells

growth_protocol: YEPD, 30 degrees, to OD600=0.6.

value: alpha

tag: tag

tag: chip antibody

value: anti-myc

tag: antibody vendor

value: Biosource

tag: antibody catalog #

source_name: Input of WT alpha cells


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 KO/KO, biological rep1


title: Pdx1-Cre+;PtenL/W;K-rasG12D/W, Cox-2 COE/W, biological rep2


title: 1 hour drug treatment, 2


title: siRae1 rwt infected replicate 2

source_name: siRae1 rwt infected replicate 2


title: siNT mock infected replicate 1

source_name: siNT mock infected replicate 1


title: 1 hour no drug, 1


title: alpha2, rep2

scan_protocol: See Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133; PMID 19529758.

source_name: ChIP of myc-tagged-alpha2 alpha cells

growth_protocol: YEPD, 30 degrees, to OD600=0.5.

value: myc-tagged alpha2

source_name: Input of myc-tagged-alpha2 alpha cells


title: siRae1 rwt infected replicate 1

source_name: siRae1 rwt infected replicate 1


title: a2, rep1

source_name: ChIP of myc-tagged-a2 a cells

label_protocol: See Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133; PMID 19529758.

value: a

value: myc-tagged a2

source_name: Input of myc-tagged-a2 a cells


title: 1 hour drug treatment, 1

source_name: Huh7 cells


title: alpha2, rep1

growth_protocol: YEPD, 30 degrees, to OD600=0.4.

extract_protocol: See Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133; PMID 19529758.


title: a2, rep2


title: untagged a cell control

source_name: ChIP of WT a cells

source_name: Input of WT a cells


title: IP methylated DNA from non-tumor-associated prostate tissue 151_2

status: Public on Jun 28 2012

city: Madison

first: Bing

last: Yang

state: WI

address: 1111 Highland Ave

department: Urology

institute: UW-Madison

description:
DNA was isolated from OCT blocks of prostate tissue from men without any evidence of prostate tumor
IP/Input non-tumor associated methylation

hyb_protocol: The labeled IP and Input DNA were co-hybridized to the Encode HG 18 DNA methylation array in Maui hybridization stations for 16-18 h at 42oC, and then washed in 42oC 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. The hybridization was performed by Nimbelgen.

scan_protocol: Arrays were scanned on an Axon 4000B scanner by Nimbelgen.

data_processing: Array images are used for data extraction as pair files with NimbleScan 2.4 extraction software. Genomic feature formate (GFF) files are then produced for visulization of Scaled log2-ratio data. The intensity ratio of IP to Input is plotted versus genomic position to identifiy regions where increased signal (methylated DNA fragment enrichment) is observed relative to the control samples.

source_name: immunoprecipitated methylated DNA from non-tumor-associated prostate tissue

label_protocol: 1 µg immunoprecipitate methylated DNA was directly labeled by Klenow (New England Biolabs) fragment-catalyzed primer extension using Cy5 nonamers (IP DNA isolated from prostate tissue) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). And 1 µg input DNA was directly labeled by Klenowfragment-catalyzed primer extension using Cy3 nonamers.

extract_protocol: Genomic DNA was isolated from prostate tissue using the DNeasy Blood & Tissue kit (Qiagen). Up to 6 µg of high-quality genomic DNA was digested with MseI (New England Biolabs, Ipswich, MA) to produce 200-1,000 bp fragments (keeping CpG islands intact) and then heat denatured to a single strand.  Methylated DNA fragments were immunoprecipitated (IP) with 1µg of antibody against 5-methylcytidine (Abcam) and captured with agarose beads. The DNA:antibody:bead mixture was digested with Proteinase K, then purified with phenol-chloroform. Methylated immunoprecipitation DNA was validated with PCR primers H19ICR specific for methylated and FLJ25439 specific for unmethylated regions as described. Enriched DNA was amplified with the WGA2 Kit (Promega).

value: Non-tumor-associated prostate tissue

tag: antibody

value: Anti-5-methyl cytidine

source_name: total genomic DNA from non-tumor-associated prostate tissue

value: Input DNA


title: IP methylated DNA from tumor-associated prostate tissue 440_2

description:
DNA was isolated from histologically normal tissue from OCT blocks of prostate from men with prostate cancer
IP/Input tumor associated methylation

source_name: immunoprecipitated methylated DNA from tumor-associated prostate tissue

tag: tissue

value: Tumor-associated prostate tissue

source_name: total genomic DNA from tumor-associated prostate tissue


title: HGCIN8

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridisation buffer as supplied by the manufacturer was added to the mixture and this was hybridised for 20 hours at 55 degrees at a rotation speed of 20 rpm.

scan_protocol: scanning was performed using a G2505B scanner (Agilent) using the protocol designed for the used platform by the manufacturer (Agilent).

data_processing: The obtained single-channel microarray data were log-transformed and normalised using quantile normalisation. Probes with intensities below 64 in more than 90% of the samples were discarded as it was assumed that hybridisation for this probe was inefficient (n=44). For the 428 remaining probes (representing 213 miRNAs) the intensity values were averaged per probe for further analyses.

source_name: cervical intraepithelial neoplasia, grade 2-3

label_protocol: Labelling was performed according to the manufacturers’ instructions. In short, miRNAs were dephoshorylated using Calfs Intestine Phosphatase (CIP) and a Cy3 labelled dCTP was ligated to the miRNA.

extract_protocol: 10 micrometer frozen sections of all tissue samples were first subjected to laser capture microdissection using a Leica ASLMD microscope (Leica, Heidelberg, Germany) to enrich for neoplastic, dysplastic or normal epithelial cells as described previously (Wilting et al, Genes, Chromosomes Cancer 2008). Total RNA was isolated from microdissected tissue samples using TRIzol Reagent according to the manufacturers’ instructions. To ensure comparable RNA integrity between specimens analysed by array, RNA pico chips were performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: hpv

value: high-risk HPV positive


title: HGCIN12


title: CxSCC27

source_name: cervical squamous cell carcinoma


title: HGCIN10


title: HGCIN15


title: HGCIN17


title: CxSCC2


title: HGCIN9


title: CxAdCA12

source_name: cervical adenocarcinoma


title: CxAdCA11


title: HGCIN19


title: HGCIN4


title: HGCIN18


title: HGCIN1


title: HGCIN7


title: CxSCC15


title: CxSCC12


title: HGCIN5


title: Normal01265

source_name: normal cervical squamous epithelium


title: CxSCC4


title: IP methylated DNA from tumor-associated prostate tissue 507_2


title: IP methylated DNA from tumor-associated prostate tissue 504


title: IP methylated DNA from non-tumor-associated prostate tissue 262


title: CxAdCA9


title: Normal02218


title: Normal02371


title: Normal02449

value: HPV negative


title: IP methylated DNA from non-tumor-associated prostate tissue F395


title: Normal0196


title: Normal01194


title: CxAdCA10


title: CxSCC39


title: Normal04441


title: CxSCC38


title: CxAdCA5


title: CxAdCA2


title: CxAdCA1


title: Normal03764


title: Normal01306


title: Normal02400


title: CxSCC36


title: IP methylated DNA from non-tumor-associated prostate tissue 339


title: CxSCC28


title: IP methylated DNA from non-tumor-associated prostate tissue PR261


title: CxAdCA15


title: CxAdCA14


title: CxSCC32


title: HGCIN39


title: HGCIN33


title: HGCIN21


title: HGCIN32


title: HGCIN24


title: HGCIN25


title: Glom_LD_482

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from the glomerular compartment of human pre-transplant living donor control kidney

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 were used for the normalization.

source_name: Glomeruli from control living donor

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

extract_protocol: Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.

tag: patient number

tag: disease status

value: control

value: Glomeruli from kidney biopsy


title: IP methylated DNA from tumor-associated prostate tissue 601


title: IP methylated DNA from tumor-associated prostate tissue 440


title: IP methylated DNA from tumor-associated prostate tissue 507


title: Glom_LD_481


title: IP methylated DNA from non-tumor-associated prostate tissue 151


title: Sham OB2

city: Bronx

first: Weiping

last: Qin

state: NY

address: 130 West Kingsbridge Road, Room 1E-02

department: Center of SCI

institute: James J. Peters Veterans Affairs Medical Center

description:
sample original  ID: 1372 OB d10
571367007_J
Gene expression profile from osteoblasts drived from bone marrows of sham spinal cord injuried rats

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw expression values were normalized using the Rank-invariant normalization function of the lumi module of Bioconductor after background subtraction.  Because background subtraction may yield negative expression values, expression values less than 0.1 will be arbitrarily set to 0.1, a level we consider to represent absent expression.

organism: Rattus norvegicus

source_name: Osteoblasts drived from bone marrows of sham spinal cord injuried rats

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

growth_protocol: The animal studies were reviewed and approved by the Institutional Animal Care and Use Committee of the James J. Peters VA Medical Center.

extract_protocol: Microarray analysis was performed for total RNA from sham, SCI and FES+SCI rats. Total RNA was extracted from osteoblasts and osteoclasts derived from cultured bone marrow cells. Specifically, RNA was extracted using phenol-chloroform , then further enriched using RNAeasy minicolumns (Qiagen, Valencia, CA). Total RNAs from 3-4 animals of each group were pooled. The resulting pooled RNA of each group was subjected to microarray analysis for duplicate.   Verification of RNA integrity and microarray analysis was performed by the Microarray Core Facility at the Children's National Medical Center. Samples selected for microarray analysis yielded RNA integrities greater than 8.0 using an Agilent Bioanalyzer.

treatment_protocol: Implantation of the FES microstimulators was performed 14 weeks after SCI.  The FES was begun during the 16th week following spinal cord transection.  Stimulation was provided for 60 minutes on each training day and consisted of brief periods of contraction (2 seconds) at 40 Hz at 1.5 V with longer periods of rest (18 seconds).   Animals received FES on 7 consecutive days; collection of blood and tissues occurred at day at after initiating FES, as described below. The SCI-Sham FES animals received the implant surgery and gastrocnemius ablation during the 14th week after the spinal cord transection, but did not have a stimulator unit inserted; samples were collected from these animals at week 17.

tag: strain

value: Wistar-Hannover

tag: gender

value: Male

value: bone marrows

tag: protocol

value: sham spinal cord injury

value: Osteoblast


title: Sham OC2

description:
sample original  ID: 1372 OC d3
571367007_L
Gene expression profile from osteoclasts drived from bone marrows of sham spinal cord injuried rats

source_name: Osteoclasts drived from bone marrows of sham spinal cord injuried rats

value: Osteoclast


title: SCI OC2

description:
sample original  ID: 1302R OC
571367007_G
Gene expression profile from osteoclasts drived from bone marrows of spinal cord injuried rats

source_name: Osteoclasts drived from bone marrows of spinal cord injuried rats

value: spinal cord injury


title: Glom_LD_478


title: Glom_LD_479


title: SCI+FES OC2

description:
sample original  ID: 1302L OC d3
571367007_I
Gene expression profile from osteoclasts drived from bone marrows of spinal cord injuried rats with FES

source_name: Osteoclasts drived from bone marrows of spinal cord injuried rats with FES

value: spinal cord injury and FES


title: SCI OB2

description:
sample original  ID: 1314 OB d10
571367007_H
Gene expression profile from osteoblasts drived from bone marrows of spinal cord injuried rats

source_name: Osteoblasts drived from bone marrows of spinal cord injuried rats


title: SCI+FES OB2

description:
sample original  ID: 1302 OB d10
571367007_K
Gene expression profile from osteoblasts drived from bone marrows of spinal cord injuried rats with FES

source_name: Osteoblasts drived from bone marrows of spinal cord injuried rats with FES


title: Glom_LD_480


title: Sham OC

description:
sample original  ID: 1372 OC d3
571367007_F
Gene expression profile from osteoclasts drived from bone marrows of sham spinal cord injuried rats


title: Glom_LD_476


title: MCR40 gingival fibroblast

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

institute: East-West Medical Research Institute, Kyung Hee University

description: Gene expression data from LPS- and MCR40-treated human gingival fibroblast

hyb_protocol: Following labeling, each cDNA was hybridized for 17 hr at 45℃ at 60 rpm on Affymetrix HumanGene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0007.

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

data_processing: The quality control was estimated by confirming the order of the signal intensities of the Poly-A controls and Hybridization controls using Expression Console Software (Affymetrix, USA). The microarray data was analyzed using a GenPlex V3.0 (ISTECH, Korea). The data were analyzed with Robust Multichip Analysis (RMA) quantification method as a probe set summarization algorithm for log transformation with base 2 (log2) and Quantile normalization method as a normalization method in the Preprocessing module of GenPlex V3.0. The signal intensities of all genes (33,297 probes (28,869 genes) in a platform) were obtained from one chip of each experimental group.

label_protocol: Fragmented and biotinylated cDNA were prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual from 300 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual, Affymetrix).

growth_protocol: 5-passaged human gingival fibroblasts were cultured.

extract_protocol: The total RNA in the human gingival fibroblast of each group was extracted using an RNeasy Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

treatment_protocol: Human gingival fibroblasts were divided into three experimental groups: CTL (no treatment control), LPS (LPS treatment only), and MCR40 (LPS and MCR40 extract treatments). The cells were stimulated with 1 µg/ml of LPS (from Escherichia coli serotype 0111:B4) in DMEM (low glucose and serum free) for 24 hr. The MCR extract (40 µg/ml) was treated at 1 hr before the LPS stimulation.

value: gingival fibroblast

tag: passage

value: passage 5

tag: developmental stage

value: Adult

value: LPS and Moutan Cortex Radicis


title: Glom_LD_473


title: Glom_LD_475


title: SCI+FES OC

description:
sample original  ID: 1302L OC d3
571367007_C
Gene expression profile from osteoclasts drived from bone marrows of spinal cord injuried rats with FES


title: Control gingival fibroblast

description: Gene expression data from normal human gingival fibroblast

source_name: Control human gingival fibroblast

tag: treatment


title: LPS gingival fibroblast

description: Gene expression data from LPS-stimulated human gingival fibroblast

source_name: LPS-treated human gingival fibroblast

tag: cell type

value: LPS


title: Sham OB

description:
sample original  ID: 1372 OB d10
571367007_D
Gene expression profile from osteoblasts drived from bone marrows of sham spinal cord injuried rats


title: Glom_LD_472


title: Glom_LD_474


title: SCI+FES OB

description:
sample original  ID: 1302 OB d10
571367007_E
Gene expression profile from osteoblasts drived from bone marrows of spinal cord injuried rats with FES


title: SCI OB

description:
sample original  ID: 1314 OB d10
571367007_B
Gene expression profile from osteoblasts drived from bone marrows of spinal cord injuried rats


title: neuron infected 3 month rep1

city: Philadelphia

first: Emily

middle: Ann

last: Gomme

state: PA

address: 233 S. 10th Street, Room 531

department: Microbology & Immunology

institute: Thomas Jefferson University

hyb_protocol: Affymetrix gene chips, Mouse gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 ug) in 110 ul of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Background correction and normalization were done using Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 2-fold (p-value<0.05) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

source_name: Brain neuron infected

label_protocol: 2.5 ug ST-cDNAs were fragmented and chemically labeled with biotin to generate biotinylated ST-cDNA using FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

growth_protocol: Neurons isolated from mouse brains were dissociated and purified as described by Huettner and Baughman (1986).

extract_protocol: RNA was isolated from purified brain neurons as per the RNAeasy Mini Kit (Qiagen) manufacturer’s protocol.

tag: infection

value: rabies virus

value: Neuron


title: Glom_LD_471

value: control


title: neuron uninfected 3 month rep1

source_name: Brain neuron uninfected

treatment_protocol: Neurons isolated from mouse brains were dissociated and purified as described by Huettner and Baughman (1986).

value: uninfected


title: neuron uninfected 3 month rep2


title: Glom_LN_464

description: Gene expression data from the glomerular compartment of human LN kidney

source_name: Glomeruli from LN patient

value: LN patient

value: Glomeruli from kidney biopsy


title: Glom_LD_469


title: Glom_LD_470


title: Glom_LN_454


title: Glom_LN_450


title: Glom_LN_448


title: Glom_LN_465


title: Glom_LN_467


title: Glom_LD_468


title: Glom_LN_466


title: neuron infected 3 month rep2


title: Glom_LN_445


title: Glom_LN_442


title: neuron_infected_3month_rep2

first: Sankar

last: Addya

address: 233 South 10th Street

department: Kimmel Cancer Center

institute: Thomas Jefferson University Hospital

value: Cre

value: Neurons

value: EGFP+ infected cells from the brains


title: neuron_uninfected_3month_rep2

value: tdTomato+ uninfected cells


title: Glom_LN_444


title: Glom_LN_463


title: neuron_uninfected_3month_rep1


title: neuron_infected_3month_rep1


title: Glom_LN_462


title: Glom_LN_438


title: Glom_LN_451


title: Glom_LN_430


title: SCI OC

description:
sample original  ID: 1302R OC
571367007_A
Gene expression profile from osteoclast  drived from bone marrows of spinal cord injuried rats

value: Wistar-Hannover

value: Male

value: bone marrows

value: spinal cord injury

value: Osteoclast


title: Glom_LN_419


title: Glom_LN_440


title: Glom_LN_410


title: Glom_LN_411


title: Glom_LN_423


title: Glom_LN_414


title: Glom_LN_409


title: Glom_LN_404


title: Glom_LN_408


title: Glom_LN_405


title: Glom_LN_406


title: Glom_LN_402


title: Tub_LD_375

description: Gene expression data from the tubulointerstitial compartment of human pre-transplant living donor control kidney

source_name: Tubulointerstitium from control living donor

value: Tubulointerstitium from kidney biopsy


title: Tub_LD_377


title: Glom_LN_418


title: Tub_LD_378


title: Tub_LD_376


title: Glom_LN_401


title: Tub_LD_373


title: Tub_LD_374


title: Tub_LD_369


title: Tub_LD_368


title: Glom_LN_407


title: Tub_LD_365


title: Tub_LD_370


title: Tub_LD_371


title: Tub_LD_366


title: Tub_LD_364


title: Tub_LD_363


title: Tub_LN_362

description: Gene expression data from the tubulointerstitial compartment of human LN kidney

source_name: Tubulointerstitium from LN patient


title: Tub_LN_361


title: Tub_LN_360


title: Tub_LD_367


title: Tub_LN_359


title: Tub_LN_358


title: Tub_LN_346


title: Glom_LN_413


title: Tub_LN_338


title: Tub_LN_349


title: Tub_LN_340


title: Tub_LN_352


title: Tub_LN_342


title: Tub_LN_357


title: Tub_LN_329


title: Tub_LN_336


title: Tub_LN_319


title: Tub_LN_323


title: Tub_LN_348


title: Tub_LN_343


title: Tub_LN_311


title: Tub_LN_312


title: Tub_LN_313


title: Tub_LN_318


title: Tub_LN_310


title: Tub_LN_314


title: NHBE

city: Taichung

first: YAWEN

last: CHENG

address: No. 110, Sec. 1, Jianguo N. Rd.

country: Taiwan

institute: Chung Shan Medical University

description: The Applied Biosystems Human Genome Survey Microarray V2.0 contains 32,878 probes for the interrogation of 29,098 genes. Most of the probes, which are 60-mers, are found within 1,500 bases of the 3' end of the source transcript.

hyb_protocol: Labeled cRNA from each RT-IVT reaction was hybridized onto Applied Biosystems Human Genome Survey Microarrays following the manufacturer’s recommendations

scan_protocol: Microarrays were analyzed using the AB1700 Chemiluminescent Microarray Analyzer

data_processing: Applied Biosystems Expression System software was used to extract Assays Signal, and Assay Signal to Noise ratio values from the microarray images.

label: DIG

source_name: primary lung bronchial epithelial cell line

label_protocol: One ug of total RNA was used to synthesize DIG-labeled cRNA as described by the Applied Biosystems Chemiluminescent RT-IVT Labeling protocol (Applied Biosystems)

growth_protocol: PBLs (1×105) with high HPV DNA copy numbers (>10000 HPV DNA copies/μg) were co-cultured with 5×103 human lung cancer cells (A549 and TL-4) or NHBE cells in a culture medium containing 2% FBS, using a tissue culture insert (NUNC Brand Products, Rochester site, MN, USA) with a 0.2-μm Anopore membrane.

extract_protocol: Total RNA from the  cell lines (1×105 cells) was extracted by homogenization in 1 ml TRIzol reagent followed by chloroform re-extraction and isopropanol precipitation.

value: epithelial cells

tag: cell line

value: NHBE


title: WT-saline 5543266022_H

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Labeled cRNA was used to probe MouseRef-8 Expression BeadChips.  Hybridization, washing, and scanning of the Illumina arrays were carried out according to the manufacturer’s instructions.  Briefly, cRNA/hybridization buffer mixtures were incubated at 65°C for 5 minutes, followed by brief centrifugation to collect.  The mixtures were added to BeadChips and then BeadChips inserted into hybridization chambers, and hybridization was carried out at 58°C for 16-18 hours at rocking speed set to 5.

scan_protocol: BeadChips were washed and stained in the following steps:  1) 55°C for 10 minutes static in HighTemp Wash Buffer in a Hybex waterbath, 2) ambient temperature shaking for 5 minutes in E1BC wash buffer, 3) ambient temperature shaking for 10 minutes in ethanol, 4) ambient temperature shaking for 2 minutes in E1BC buffer, 5) ambient temperature for 10 minutes rocking in Block E1 buffer, 6) ambient temperature for 10 minutes rocking in Block E1 buffer containing 1ug/ml Cy3-streptavidin, and 7) ambient temperature shaking for 5 minutes in E1BC buffer.  BeadArrays were dried in a centrifuge for 4 minutes and scanned using an Illumina BeadArray Reader.  Illumina BeadScan software was used to produce .idat, .xml, and .tif files for each array on a slide and .sdf files for each barcode on a slide of 8 arrays.  Raw data were extracted using Illumina BeadStudio software v3.  Following quality assessment, data from the replicate beads on each array were summarized into raw intensity values with and without background subtraction in an Excel report.

data_processing: Background subtracted data were quantile normalized with the bioconductor affy package. If the minimum value in a row was less than 2, a constant was added to all values in that row such that the minimum was increased to 2.

source_name: quadriceps muscle

label_protocol: Samples for mRNA profiling studies were processed by Asuragen, Inc., according to the company’s standard operating procedures.  The purity and quantity of total RNA samples were determined by absorbance readings at 260 and 280 nm using a NanoDrop ND-1000 UV spectrophotometer.  The integrity of total RNA was qualified by Agilent Bioanalyzer 2100 capillary electrophoresis.  Total RNA (100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using Illumina’s TotalPrep Kit (Ambion Inc., Austin, TX) and one round of amplification.  The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.

extract_protocol: Quadriceps muscles were homogenized with a Polytron homogenizer in Trizol reagent according to the manufacturer's recommendations.

treatment_protocol: Subcutaneous saline or oligo injections were administered to adult mice biweekly for 4 weeks.

value: saline

tag: genotype

value: WT

tag: genetic background

value: FVB/n

value: quadriceps muscle


title: NHBE-V

treatment_protocol: PBLs (1×105) with high HPV DNA copy numbers (>10000 HPV DNA copies/μg) were co-cultured with 5×103 human lung cancer cells (A549 and TL-4) or NHBE cells in a culture medium containing 2% FBS, using a tissue culture insert (NUNC Brand Products, Rochester site, MN, USA) with a 0.2-μm Anopore membrane.

value: Adenocarcinoma with HPV infection


title: WT-saline 5543266022_G


title: HSALR-ASO190401 5543266022_E

value: HSALR transgenic


title: HSALR-ASO190401 5543266022_C


title: SiHa

source_name: Cervical cancer cell line

value: SiHa


title: Tub_LN_308

value: LN patient


title: WT-saline 5543266022_F


title: HSALR-ASO190401 5543266022_D


title: Tub_LN_307


title: Tub_LN_306


title: Tub_LN_309


title: HSALR-saline 5543266006_F


title: HSALR-ASO445236 5543266006_H


title: WT-saline 5543266022_A


title: Tub_LN_304


title: HSALR-ASO190401 5543266022_B


title: HSALR-ASO445236 5543266006_G


title: Tub_LN_305


title: Tub_LN_301


title: HSALR-saline 5543266006_D


title: Liver_Brain Dead_rep5

first: Jamie

middle: M.

last: Sperger

address: 1111 Highland Ave.

department: Dept. of Surgery

institute: University of Wisconsin - Madison

hyb_protocol: aRNA (10µg) was applied to the Genechip® Rhesus macaque Genome Array (Affymetrix, Santa Clara, CA)  and hybridized for 16 hours at 45°C according to manufacturer’s instructions.  Genechips were processed on the Affymetrix Fluidics450 Station and data extracted from GC3000 G7 scanned image using the Affymetrix command console.

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: Macaca mulatta

source_name: liver from donor after 6 hours brain death

label_protocol: RNA (1 µg) was labeled and fragmented using the MessageAmp™ Biotin II-Enhanced IVT kit following manufacturer’s instructions.

growth_protocol: Living donors were sedated, anesthetized and mechanically ventilated for a period of 1 hour prior to Livers were recovered after in situ abdominal organ flush with UW organ preservation solution. and organ recovery.  Organs from both experimental groups were immediately transferred to the laboratory for processing.

extract_protocol: Liver was homogenized in Trizol (Invitrogen, Carlsbad, CA) and RNA extracted.  RNA purification was performed by Qiagen RNeasy column (Qiagen, Germantown, MD) including the on-column DNase digestion step.  RNA concentration was measured using a NanoDrop® ND-1000 UV-Vis spectrophotometer and integrity confirmed using the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Brain dearh was induced by drilling a burr hole  in the right fronto-parietal region of the skull using a Dremel Minimite 750 rotary tool (Dremel, Mt. Prospect, IL). A 16F Foley catheter was inserted 3-5cm in the extradural space with an antero-superior orientation of the tip. The catheter balloon was then inflated gradually with a 10ml syringe containing a mixture of 50% water / 50% contrast medium at a rate of 1 cc/min until hemodynamic signs of BD were documented. The balloon was kept inflated and hemodynamic parameters were recorded every 5 minutes throughout the duration of the experiment.  During the 6 hour BD period a target mean arterial pressure (MAP) of 50-70mmHg was maintained using IV lactated Ringer’s. Approximately 30 minutes after induction arginine-vasopressin (AVP) [0.1 – 6 units/hour] and/or dopamine [0.5 – 10 µg/kg/min] were given to stabilize blood pressure.  Living donors were sedated, anesthetized and mechanically ventilated for a period of 1 hour prior to organ recovery.

value: liver

tag: age

value: 7 y

value: male

tag: condition

value: 6 hours brain death


title: HSALR-saline 5543266006_B

tag: tissue


title: Liver_Brain Dead-rep4

scan_protocol: Genechips were processed on the Affymetrix Fluidics450 Station and data extracted from GC3000 G7 scanned image using the Affymetrix command console.


title: Liver_Brain Dead_rep2

value: female


title: Tub_LN_302


title: Liver_Brain Dead_rep1


title: Liver_Brain Dead_rep3


title: Liver_Control_rep5

source_name: liver from control living donor

value: control


title: HSALR-ASO445236 5543266006_A


title: Liver_Control_rep3

value: 4 y


title: HSALR-saline 5543266006_C


title: Liver_Control_rep2


title: MC3T3-E1 cell-Day 28-Replicate 2

city: Charleston

first: Louis

middle: M

last: Luttrell

address: 173 Ashley Ave

institute: MUSC

description: Commercially available mouse total RNA preparation

hyb_protocol: After baking and crosslinking, slides were prehybridized 1 h in coplin jars in a water bath at 42°C using preheated prehybridization solution (5X SSC, 0.1% SDS, and 0.5% BSA; filtered by 0.45 micron filter). Slides were rinsed twice for 1 min in deionized water with agitation, then centrifuged for 2-3 min at 1500 rpm and stored in a dessicator until hybridization. Labeled samples were resuspended in 80µl hybridization solution (50% formamide, 5X SSC, and 0.1% SDS); 1.85 µl of mouse COT1 DNA (20 µg/µl) and 1.9 µL of Poly(A)-DNA (20 µg/µl) were added, samples were heated denatured 2 min at 95°C, and then spun briefly (30 s) in a microfuge. Slides were heated at 80°C for 2 min, and then denatured samples were added to the slides and coverslips applied. Samples were hybridized overnight at 42°C.  Slides were washed as follows: 1xSSC, 0.2%SDS at 42C for 2-3 minutes; 1xSSC, 0.2%SDS at 42C for 1 minute; 0.2xSSC, 0.01%SDS at room temperature for 1 minute; 0.2xSSC at room temperature for 2 minutes; 0.05xSSC at room temperature for 1 minute. Slides were spun dry for 2 minutes at 1200rpm.

scan_protocol: Scanning was performed using an Axon GenePix 4000B scanner at wavelengths 635 and 532 without normalization and with the Local Feature background subtraction setting. Other scanner settings: PMTGain=570 and 520; ScanPower=100 and 100; LaserPower=3.69335 and 3.52; LaserOnTime=29868 and 29845.

data_processing: Pre-processing and normalization were conducted on GenePix scan results files (i.e., gpr files) using the Bioconductor limmaGUI package 1.28.0 run with R 2.13.0 software (G.K. Smyth and T. Speed, 2003; PMID: 14597310). Briefly, gpr files were specified as input, background correction was performed using normexp method with offset of 16, and spot quality weighting was applied as follows: 1 for Good (100) or Unflagged (0); 0.1 for Bad (-100), Not Found (-50) and Absent (-75) flags. Print-tip group loess normalization was applied for normalization within arrays. Review of box plots of normalized M values indicated that normalization between arrays was not warranted. Normalized M values were exported and the values multiplied by -1 so that the values appropriately represented the log2Green (experimental) minus log2Red (reference) relationship.

source_name: MC3T3-E1 cell

label_protocol: cDNA was synthesized from total RNA samples using Superscript III with either Cy3 or Cy5 in 13µl reaction volumes using standard methodology. After cDNA synthesis, reactions were incubated at 95°C for 5 min and then 4°C for 5 min. NaOH was added to reactions (6.25µl of 1M), and reactions were incubated at 37°C for 10 min followed by addition of Tris-HCl (6.25µl of 1M) and HCl (6.25µl of 1M). Reactions were purified by Qiaquick PCR Purification Kit and the sample collected by two column elutions with 30µl; both eluates were combined. Samples were then dried in a Speed Vac for approximately 38 min.

growth_protocol: MC3T3-E1 cells were maintained in alpha-minimum essential medium (MEM) supplemented with 10% v/v fetal bovine serum, penicillin (100 units/mL) and streptomycin (100 pg/mL) in a humidified 10% CO2 atmosphere at 37 ˚C.  To induce osteoblastic differentiation, cells were plated at an initial density of 1 x 10^5 cells/dish in 10 cm dishes in alpha-MEM supplemented with 10% v/v fetal bovine serum, 5 mM 8-glycerol phosphate and 25 pg/mL ascorbic acid.  Medium was replaced every 3 days.  Total RNA was isolated from cultures after 2, 5, 10 or 28 days in culture.

extract_protocol: Total RNA was prepared by the Trizol extraction method following manufacturer recommendations.

value: 8-glycerol phosphate and ascorbic acid

tag: time

value: Day 28

value: mature osteoblast

source_name: Mouse reference RNA (Stratagene)

tag: sample type

value: Mouse reference RNA (Stratagene)


title: Rice_3

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

description: Gene expression of a Rice model.

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C. After hybridization, the microarrays were washed according to the manufacturer’s protocol.

scan_protocol: The microarrays were scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).

data_processing: The resulting images were processed, and raw data were collected using Agilent's Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 12 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.

source_name: cerebral cortex, Rice

label_protocol: Five hundred ng of the RNA sample was transcribed using oligo(dT)-based T7 promoter primer and MMLV-RT in the first- and second-strand cDNA synthesis reactions. The double-stranded cDNAs were used as templates in the preparation of fluorescent complementary RNAs (cRNAs) in the presence of T7 RNA polymerase and cyanine 3-CTP dye in an in vitro transcription reaction.

extract_protocol: Total RNA was extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase I (Qiagen) and cleaned using the RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed by ultraviolet spectrophotometry and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2, and a 28S:18S ratio of >1.6; the RNA integrity number (RIN) was >9.0.

value: Wistar

value: hypoxic-ischemic (HI) brain insult

value: cerebral cortex

value: 8 weeks


title: MC3T3-E1 cell-Day 28-Replicate 1


title: Liver_Control_rep4


title: MC3T3-E1 cell-Day 28-Replicate 3


title: HSALR-ASO445236 5543266006_E

value: HSALR transgenic

value: FVB/n

value: quadriceps muscle


title: Rice_2

description: Gene expression of a Rice model.


title: Hyppocampi from transgenic 3xTG 12 months old mice vs. hyppocampi from WT 12 months old mice exp2

city: Chieti

first: Valentina

last: Gatta

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

institute: G. d’Annunzio University Foundation Chieti

description:
Raw data file:
GSM862435_Res_V90_Cy3_4_3xTG_12MvsCy5_25_WT_12M.gpr

hyb_protocol: 2.5 µg of aRNA fragmented and respectively Cy3-Cy5 labeled from each sample was hybridized on Phalanx Mouse OneArray™ by 1.5X OneArray hybridization Buffer at 42°C in oven for 14-16 hrs

scan_protocol: After hybridization, Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner "ScanArray Express" (Packard BioScience) and analysed using the software "ScanArray Express - MicroArray Analysis System" version 3.0 (Perkin Elmer)

data_processing: The values of the median signal intensity from each spot were subtracted from the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for row data normalization to evaluate signal to noise ratio and generate log ratios of sample vs. reference signal. A gene was considered to be differentially expressed when showing an absolute value of log-ratio higher or equal to 0.5, an index that translates to a fold-change of 1.4 in transcript quantity

source_name: Transgenic 3xTG 12 months old mouse 4 [SAMPLE]

label_protocol: Extracted RNA was linearly amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA). Five to ten ug of amplified aRNA were fluorescently labelled with Cy3

extract_protocol: Total RNA was extracted from one hyppocampi of the WT mouse 12 months old using the SVtotal RNA Izolation System kit (Promega, Madison, WI, USA) after homogenization of the sample

value: B6;129Psen1tm1Mpm Tg (APPSwe,tauP201L) 1Lfa

value: 12 months old

value: one hyppocampi

source_name: WT 12 months old mouse 25 [REFERENCE]

label_protocol: Extracted RNA was linearly amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA). Five to ten ug of amplified aRNA were fluorescently labelled with Cy5

extract_protocol: Total RNA was extracted from one hyppocampi of the WT mouse 3 months old using the SVtotal RNA Izolation System kit (Promega, Madison, WI, USA) after homogenization of the sample

value: 129SV with C57BL6

value: WT


title: MC3T3-E1 cell-Day 10-Replicate 3

value: Day 10

value: differentiating osteoblast


title: MC3T3-E1 cell-Day 10-Replicate 2

value: 8-glycerol phosphate and ascorbic acid


title: MC3T3-E1 cell-Day 10-Replicate 1


title: Control_4

description: Gene expression of a control animal.

source_name: cerebral cortex, control


title: Rice_4

description: Gene expression of a Rice model.


title: Hyppocampi from transgenic 3xTG 12 months old mice vs. hyppocampi from WT 12 months old mice exp3

description:
Raw data file:
GSM862436_Res_V91_Cy5_7_3xTG_12MvsCy3_24_WT_12M.gpr

source_name: Transgenic 3xTG 12 months old mouse 7 [SAMPLE]

value: female

source_name: WT 12 months old mouse 24 [REFERENCE]


title: MC3T3-E1 cell-Day 5-Replicate 2

value: Day 5

value: growth arrest

value: Mouse reference RNA (Stratagene)


title: MC3T3-E1 cell-Day 5-Replicate 1


title: Hyppocampi from transgenic 3xTG 3 months old mice vs. hyppocampi from WT 3 months old mice exp2

description:
Raw data file:
GSM862408_Res_V86_Cy3_22_3xTG_3MvsCy5_15_WT_3M.gpr

source_name: Transgenic 3xTG 3 months old mouse 22 [SAMPLE]

value: 3 months old

source_name: WT 3 months old mouse 15 [REFERENCE]


title: Rice_1

description: Gene expression of a Rice model.

value: Wistar

value: hypoxic-ischemic (HI) brain insult

value: cerebral cortex

value: 8 weeks


title: MC3T3-E1 cell-Day 2-Replicate 3

value: Day 2

value: log phase growth


title: Control_1

description: Gene expression of a control animal.


title: Hyppocampi from transgenic 3xTG 3 months old mice vs. hyppocampi from WT 3 months old mice exp3

description:
Raw data file:
GSM862409_Res_V87_Cy5_22_3xTG_3MvsCy3_16_WT_3M.gpr

value: B6;129Psen1tm1Mpm Tg (APPSwe,tauP201L) 1Lfa

value: one hyppocampi

source_name: WT 3 months old mouse 16 [REFERENCE]


title: Hyppocampi from transgenic 3xTG 12 months old mice vs. hyppocampi from WT 12 months old mice exp1

description:
Raw data file:
GSM862410_Res_V66_Cy3_4_3xTG_12MvsCy5_24_WT_12M.gpr

value: 12 months old

value: 129SV with C57BL6

value: WT


title: Liver_Control_rep1

value: liver

value: control


title: Control_2

description: Gene expression of a control animal.


title: MC3T3-E1 cell-Day 5-Replicate 3

value: 8-glycerol phosphate and ascorbic acid

value: Day 5


title: MC3T3-E1 cell-Day 2-Replicate 2

value: Mouse reference RNA (Stratagene)


title: Control_3

description: Gene expression of a control animal.


title: Glom_LN_412

source_name: Glomeruli from LN patient

tag: patient number

tag: disease status

value: LN patient

value: Glomeruli from kidney biopsy


title: Hyppocampi from transgenic 3xTG 3 months old mice vs. hyppocampi from WT 3 months old mice exp1

description:
Raw data file:
GSM862407_Res_V65_Cy3_23_3xTG_3MvsCy5_15_WT_3M.gpr

source_name: Transgenic 3xTG 3 months old mouse 23 [SAMPLE]

tag: strain

tag: gender

value: female

value: 3 months old


title: PAX8_vs_scramble_4

city: Madrid

first: Pilar

last: Santisteban

state: Madrid

address: Arturo Duperier 4

department: Physiopathology of the Endocrine and Nervous System

country: Spain

institute: Biomedical Research Institute-CSIC

description: Biological Replicate

hyb_protocol: All procedures of hybridization, slide and image processing were carried out according to the manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis protocol). In each experiment, 825 ng of contrasting cRNA samples were fragmented at 60°C for 30 min and hybridized at 65ºC for 17 h.

scan_protocol: Agilent G2565BA Microarray Scanner Signal quantification was carried out with Feature Extraction 9.1 software

data_processing: Limma package for R was used for background subtraction and LOWESS and QUANTILE normalization.

source_name: PCCL3 PAX silenced

label_protocol: Labelling was performed by using the Low RNA Input Linear Amplification Kit, PLUS, Two-Color (Agilent Technologies, Palo Alto, CA). Briefly, for each sample 2 μg of total RNA input were amplified in two rounds of amplification by following manufacturer’s instructions. The first strand cDNA synthesis and amplification reactions were carried out by using random and T7 primers, respectively. During the 2 hour in vitro transcription, Cy3- or Cy5-labeled CTP was incorporated on each amplified RNA (cRNA). Products of the reaction were then purified using RNAeasy mini spin column.

growth_protocol: PCCl3 thyroid cells were grown were grown in Coon’s modified Ham’s F-12 medium supplemented with 5% donor calf serum and a six-hormone mixture [1 nM TSH, 10  g/ml insulin, 10 ng/ml somatostatin, 5  g/ml transferrin, 10 nM hydrocortisone, and 10 ng/ml glycyl-L-histidyl-L-lysine acetate]

extract_protocol: Total RNA isolation was performed using TRIzol reagent (Invitrogen, Carlsbad, CA), following the manufacturer’s recommended protocol

treatment_protocol: PCCl3 cells transient transfections were performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) both for scramble and PAX8 siRNAs conditions (10 ng siRNA /ml) (Dharmacon, Denver, USA).

value: PCCl3 thyroid cells


title: Hyppocampi from WT 12 months old mice vs. hyppocampi from WT 3 months old mice exp2

description:
Raw data file:
GSM862405_Res_V58_Cy3_24_WT_12MvsCy5_16_WT_3M.gpr

source_name: WT 12 months old mouse 24 [SAMPLE]


title: PAX8_vs_scramble_3

description: Biological Replicate


title: PAX8_vs_scramble_2

description: Biological Replicate


title: MC3T3-E1 cell-Day 2-Replicate 1

value: Day 2


title: Hyppocampi from WT 12 months old mice vs. hyppocampi from WT 3 months old mice exp3

description:
Raw data file:
GSM862406_Res_V65_Cy3_25_WT_12MvsCy5_16_WT_3M.gpr

source_name: WT 12 months old mouse 25 [SAMPLE]


title: Hyppocampi from WT 12 months old mice vs. hyppocampi from WT 3 months old mice exp1

description:
Raw data file:
GSM862396_Res_V57_Cy5_25_WT_12MvsCy3_15_WT_3M.gpr


title: PAX8_vs_scramble_1

description: Biological Replicate


title: r-hLH (r-hFSH+r-hLH)-treated COCs vs r-hFSH-treated COCs exp4

hyb_protocol: 3 µg of aRNA fragmented and respectively Cy3-Cy5 labeled from each sample was hybridized on Phalanx Human OneArray™ by 1.5X OneArray hybridization Buffer at 42°C in oven for 14-16 hrs

source_name: r-hLH-treated COCs P10AC

extract_protocol: Total RNA was extracted from a pool of 4 COCs obtained by the patient using the PICOPURE RNA isolation kit (Arcturus, MDS Analytical Technologies, Sunnyvale CA, USA)

tag: protocol

value: COCs obtained from a woman treated with r-hLH stimulation protocol

value: COC

tag: agent

value: r-hLH

value: 33 years old

tag: infertility

value: male causes

tag: r-hlh dosage

value: 1fL/die - tot 12 fL

source_name: r-hFSH-treated COCs GF2

extract_protocol: Total RNA was extracted from a pool of 3 COCs obtained by the patient using the PICOPURE RNA isolation kit (Arcturus, MDS Analytical Technologies, Sunnyvale CA, USA)

value: COCs obtained from a woman treated with r-hFSH stimulation protocol

value: 39 years old

value: tubaric

tag: r-hfsh dosage

value: 300 ui/die - tot 2950 ui


title: r-hLH (r-hFSH+r-hLH)-treated COCs vs r-hFSH-treated COCs exp3

tag: cell type

source_name: r-hFSH-treated COCs GF1

value: 32 years old

value: 200 ui/die - tot 2200 ui


title: r-hLH (r-hFSH+r-hLH)-treated COCs vs r-hFSH-treated COCs exp2

source_name: r-hFSH-treated COCs P9AC

value: 34 years old


title: Scramble_vs_PAX8_2

description: Biological Replicate


title: Scramble_vs_PAX8_4

description: Biological Replicate


title: r-hLH (r-hFSH+r-hLH)-treated COCs vs r-hFSH-treated COCs exp1

value: female


title: PAX8_vs_WT_2

description: Biological Replicate

source_name: PCCL3 Wild type


title: PAX8_vs_WT_3

description: Biological Replicate


title: Scramble_vs_PAX8_3

description: Biological Replicate


title: WT_vs_PAX8_4

description: Biological Replicate


title: Scramble_vs_PAX8_1

description: Biological Replicate


title: WT_vs_PAX8_1

description: Biological Replicate


title: WJ-MSC 12vs4 exp6

hyb_protocol: 2 µg of aRNA fragmented and respectively Cy3-Cy5 labeled from each sample was hybridized on Phalanx Human OneArray™ by 1.5X OneArray hybridization Buffer at 42°C in oven for 14-16 hrs

source_name: WJ-MSC 12th cycle

extract_protocol: Total RNA was extracted from two WJCs pools at 12th in vitro cycle expansion using a total of 1000000 cells using the SVtotal RNA Izolation System kit (Promega, Madison, WI, USA)

value: WJ-MSC obtained from human umbilical cord at 12th cycle of expansion in vitro

tag: cell pool

value: UCA

source_name: WJ-MSC 4th cycle

extract_protocol: Total RNA was extracted from two WJCs pools at 4th in vitro cycle expansion using a total of 1000000 cells using the SVtotal RNA Izolation System kit (Promega, Madison, WI, USA)

value: WJ-MSC obtained from human umbilical cord at 4th cycle of expansion in vitro


title: WT_vs_PAX8_3

description: Biological Replicate

value: PCCl3 thyroid cells


title: WJ-MSC 12vs4 exp3


title: WT_vs_PAX8_2

description: Biological Replicate


title: WJ-MSC 12vs4 exp5

value: UCB


title: PAX8_vs_WT_4

description: Biological Replicate


title: WJ-MSC 12vs4 exp4


title: hCG (hMG-HP)-treated COCs vs r-hFSH-treated COCs exp2

source_name: hCG-treated COCs P11AC

value: COCs obtained from a woman treated with hCG stimulation protocol

value: COC

value: hCG

tag: hcg dosage


title: hCG (hMG-HP)-treated COCs vs r-hFSH-treated COCs exp1

tag: age

value: 33 years old


title: Disc Cells in 3D IL-1 (107)

status: Public on Jun 27 2012

city: Charlotte

first: Helen

last: Gruber

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

hyb_protocol: Fragmented cRNA was hybridized to the  X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned once via the Affymetrix 3000G scanner.

data_processing: The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).

source_name: Disc Cells in 3D IL-1

label_protocol: Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.

growth_protocol: Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 102 pM IL-1beta. Cells were allowed to grow an additional 5 days without changing the media.

extract_protocol: Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent

value: annulus disc cells

tag: tissue grade

value: IV

tag: feed media


title: Disc Cells in 3D IL-1 (154)

treatment_protocol: They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 102 pM IL-1beta. Cells were allowed to grow an additional 5 days without changing the media.


title: Disc Cells in 3D IL-1 (95)


title: Disc Cells in 3D Control (107)

source_name: Disc Cells in 3D Control


title: TAX577397

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Microarrays were hybridized as described (PMID: 17334996)

scan_protocol: Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <1 signal units. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Prior to normalization only oligonucleotide probes without cross-hybridization to other genomic regions or transcripts were selected. Normalization was performed using block (print tip) based lowess. After normalization, a probe presence filter was applied to select only probes with suffcient presence, followed by imputation of missing values using weighted nearest-neighbor imputation (WENNI). Probes were subsequently merged on probe identifier and row-centered across the entire data set.

source_name: Breast tumor

label_protocol: Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions from 5ug of total RNA using the Corning Pronto Plus System 6 kit as described (PMID:17334996)

extract_protocol: Total RNA from fresh frozen breast tumor tissue was extracted using Trizol reagent (Invitrogen) followed by the RNeasy Midi Purification kit (Qiagen). RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.

tag: tissue

value: Breast tumor

tag: hu subtype

value: Basal

tag: familial status

tag: er

tag: osbin

tag: os

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

tag: pam50 correlation

tag: brca1 methylation status

value: negative

source_name: Stratagene Universal reference RNA

tag: reference

value: Stratagene Universal reference RNA


title: TAX577445

value: LumA

value: familial

value: brcax


title: TAX577401


title: TAX577402

value: sporadic

value: positive


title: TAX577451

value: LumB


title: TAX577398


title: Disc Cells in 3D IL-1 (126)

tag: cell type

value: III


title: TAX577400


title: PAX8_vs_WT_1

description: Biological Replicate

value: PCCl3 thyroid cells


title: TAX577405


title: WJ-MSC 12vs4 exp2

value: WJ-MSC obtained from human umbilical cord at 12th cycle of expansion in vitro

tag: cell pool

value: UCB

value: WJ-MSC obtained from human umbilical cord at 4th cycle of expansion in vitro


title: TAX577418


title: TAX577434


title: TAX577428


title: TAX577415

value: other


title: TAX577389


title: TAX577431


title: TAX577419


title: TAX577437


title: TAX577410


title: TAX577440


title: TAX577384


title: TAX577414


title: TAX577391


title: TAX577385


title: TAX577416


title: TAX577383


title: TAX577392


title: TAX577382


title: WJ-MSC 12vs4 exp1

value: UCA


title: TAX577373

value: Breast tumor


title: TAX577349

value: Basal


title: TAX577356


title: TAX577355


title: TAX577344

value: negative


title: TAX577374

value: Stratagene Universal reference RNA


title: TAX577342


title: TAX577348


title: TAX577381


title: TAX577366


title: TAX577363


title: TAX577341


title: TAX577318

value: Normal

value: LumA


title: TAX577333


title: TAX577301


title: TAX577312


title: TAX577299


title: TAX577336


title: TAX577340

value: familial

value: brcax


title: TAX577308


title: TAX577317

value: sporadic


title: TAX577309


title: TAX577296


title: TAX577310


title: TAX577326


title: TAX577311


title: TAX577328


title: TAX577315


title: TAX577321


title: TAX577319


title: TAX577280


title: TAX577283


title: TAX577291


title: TAX577292


title: TAX577295


title: TAX577288


title: COPD [261361_miRNA]

city: Seattle

first: Ji-Hoon

last: Cho

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: COPD

hyb_protocol: The labelled miRNA probes were hybridized to the miRCURY LNA arrays v11.0 for 16h at 56ºC

scan_protocol: Hybridized slides were washed and scanned with ScanArray Express (Perkin Elmer)

data_processing: miRNA expression data was consolidated by taking median value across replicated probes. Then, it was normalized by quantile method, and transformed in log2-scale

source_name: Lung tissue from smoker with COPD

label_protocol: miRNAs were labeled according to the manufacturer's instruction (Exiqon, Woburn, Massachusetts, USA)

extract_protocol: Total RNA was isolated from frozen tissue samples using a freeze fracture protocol, followed by Trizol extraction and precipitation at  -20ºC overnight to increase the yield of small RNAs. RNA integrity was determined by capillary electrophoresis on an Agilent 2100 Bioanalyzer. Only RNA with an integrity number $7 was used in the profiling studies.

tag: diagnosis

value: COPD

tag: fvc-group

tag: gold stage

tag: age

tag: gender (1=male, 2=female)

tag: pkyrs


title: COPD [271100_miRNA]

description: COPD


title: TAX577278

tag: tissue

tag: hu subtype

tag: familial status

tag: er

tag: osbin

tag: os


title: TAX577282

tag: pgr

tag: primary

tag: grade

tag: brca status

tag: pam50 classification

tag: pam50 correlation


title: TAX577272

value: non malignant

tag: brca1 methylation status

tag: reference


title: TAX577273


title: TAX577293


title: COPD [260111_miRNA]

description: COPD

tag: diagnosis

tag: fvc-group

tag: gold stage

tag: age


title: COPD [206010_miRNA]

description: COPD

tag: gender (1=male, 2=female)

tag: pkyrs


title: COPD [20278_miRNA]

description: COPD


title: TAX577266

tag: tissue

tag: hu subtype

tag: familial status

tag: er


title: TAX577267

tag: osbin

tag: os

tag: pgr

tag: primary


title: TAX577294

tag: grade

tag: brca status

tag: pam50 classification

tag: pam50 correlation


title: COPD [158231_miRNA]

description: COPD

tag: diagnosis

tag: fvc-group


title: TAX577264

tag: brca1 methylation status

tag: reference


title: COPD [119716_miRNA]

description: COPD

tag: gold stage

tag: age

tag: gender (1=male, 2=female)

tag: pkyrs


title: COPD [220968_miRNA]

description: COPD


title: COPD [271851_miRNA]

description: COPD


title: TAX577262

tag: tissue

tag: hu subtype

tag: familial status

tag: er


title: TAX577269

tag: osbin

tag: os

tag: pgr

tag: primary


title: TAX577270

tag: grade

tag: brca status

tag: pam50 classification

tag: pam50 correlation


title: TAX577271

tag: brca1 methylation status

tag: reference


title: TAX577258


title: TAX577255


title: COPD [234573_miRNA]

description: COPD

tag: diagnosis

tag: fvc-group

tag: gold stage

tag: age


title: COPD [219183_miRNA]

description: COPD

tag: gender (1=male, 2=female)

tag: pkyrs


title: COPD [275177_miRNA]

description: COPD


title: TAX577251

tag: tissue

tag: hu subtype

tag: familial status

tag: er

value: Unclassified


title: COPD [294945_miRNA]

description: COPD


title: COPD [192361_miRNA]

description: COPD


title: COPD [270854_miRNA]

description: COPD


title: COPD [295167_miRNA]

description: COPD


title: TAX577254

value: nonClassified

tag: osbin

tag: os

tag: pgr

tag: primary


title: COPD [122541_miRNA]

description: COPD


title: COPD [132625_miRNA]

description: COPD


title: Normal/Smoker [290677_miRNA]

description: Normal

source_name: Lung tissue from smoker with no evidence of obstructive lung disease


title: Normal/Smoker [218081_miRNA]

description: Normal


title: TAX577248

tag: grade

tag: brca status

tag: pam50 classification

value: LumB

tag: pam50 correlation


title: TAX577246

tag: brca1 methylation status

tag: reference


title: TAX577245


title: TAX577247


title: TAX577239


title: TAX577232


title: TAX577241


title: TAX577244


title: TAX577238


title: Normal/Smoker [188486_miRNA]

description: Normal

tag: diagnosis


title: Normal/Smoker [290165_miRNA]

description: Normal


title: Normal/Smoker [162039_miRNA]

description: Normal


title: TAX577217


title: TAX577229


title: TAX577250


title: COPD [59320_miRNA]

description: COPD

tag: fvc-group

tag: gold stage

tag: age

tag: gender (1=male, 2=female)


title: TAX577213

tag: tissue

tag: hu subtype

tag: familial status


title: Normal/Smoker [231005_miRNA]

description: Normal


title: Normal/Smoker [80343_miRNA]

description: Normal


title: Normal/Smoker [224671_miRNA]

description: Normal


title: TAX577206

tag: er

tag: osbin

tag: os


title: TAX577202

tag: pgr

tag: primary

tag: grade


title: TAX577185

tag: brca status

tag: pam50 classification

tag: pam50 correlation


title: TAX577169

tag: brca1 methylation status

tag: reference


title: TAX577176


title: TAX577157


title: TAX577160


title: TAX577177


title: DSS + L-Arg colon tissue, biological rep3

city: Nashville

first: Keith

last: Wilson

address: 2215B Garland Ave.

institute: Vanderbilt University School of Medicine

description: colon

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. A total of 2 μg of fragmented, labeled target was hybridized to the array. The cartridge array was washed and stained per standard Affymetrix Protocols using Affymetrix Hybridization Wash and Stain kit reagents on the Affymetrix Fluidics Station 450, using script FS450_0007

scan_protocol: Affymetrix 7G plus scanner using AGCC v. 1.1

data_processing:
Data were processed using the Affymetrix Expression Console v. 1.1 using an RMA normalization algorithm producing log base 2 results
probe group file: MoEx-1_0-st-v1.r2.pgf
probe group file: MoEx-1_0-st-v1.r2.dt1.mm9.mps

label_protocol: Samples were enzymatically fragmented and biotinylated using the Whole Transcript Terminal Labeling Kit (Affymetrix)

growth_protocol: 7-week-old male wild-type C57BL/6 mice were used in our experiment. Animals were maintained on a 12 h light/12 h dark cycle under biosafety level 2 conditions. The mice had ad libitum access to a standard diet and water until reaching the desired age for experiments.

extract_protocol: At the time sacrifice (day 10 of protocol), a piece of the colon was obtained, cleaned, and placed in RNALater. The following day, the RNALater was removed and the RNA was isolated from the tissue using a Qiagen Rneasy kit per manufacturer's protocol. The samples were submitted to the Vanderbilt Genomic Sciences Resource for first strand cDNA synthesis, 2nd strand cDNA synthesis and IVT-cRNA synthesis. Reactions were performed with Ambion's WT-Expression target preparation kit .

treatment_protocol: The mice were exposed to 4% dextran sulfate sodium (DSS) in the drinking water for 6 days followed by 4 days of water or 1% L-arginine in the drinking water (10-day protocol). The mice were assigned to one of the following groups: Control (Ctrl), Ctrl + L-Arg, DSS, or DSS + L-Arg

tag: genotype

value: wild-type

tag: strain

tag: gender

value: male

value: 8 weeks, 3 days

value: colon


title: TAX577154

tag: tissue

value: Breast tumor


title: TAX577156

tag: hu subtype


title: TAX577168

tag: familial status


title: TAX577180

tag: er


title: TAX577165

tag: osbin


title: DSS colon tissue, biological rep3

description: colon

source_name: DSS colon tissue, biological rep3

tag: age


title: TAX577144

tag: os

tag: pgr


title: DSS + L-Arg colon tissue, biological rep2

description: colon


title: TAX577167

tag: primary

tag: grade

value: negative


title: TAX577146

tag: brca status

tag: pam50 classification

value: Stratagene Universal reference RNA


title: DSS colon tissue, biological rep1

description: colon

source_name: DSS colon tissue, biological rep1


title: DSS + L-Arg colon tissue, biological rep1

description: colon


title: DSS colon tissue, biological rep2

description: colon

source_name: DSS colon tissue, biological rep2


title: control colon tissue, biological rep2

description: colon

source_name: control colon tissue, biological rep2


title: control + L-Arg colon tissue, biological rep2

description: colon


title: control colon tissue, biological rep3

description: colon

source_name: control colon tissue, biological rep3


title: control + L-Arg colon tissue, biological rep3

description: colon


title: control colon tissue, biological rep1

description: colon

source_name: control colon tissue, biological rep1


title: TAX577140

value: Normal

tag: pam50 correlation

tag: brca1 methylation status


title: control + L-Arg colon tissue, biological rep1

description: colon

tag: genotype


title: WP9C209NO

city: Maastricht

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

institute: Maastricht University

description: female neonate

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.

source_name: pooled control for WP9C209NO

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

extract_protocol: Total RNA was isolated from the RNAlater-preserved whole blood samples using the RiboPure-Blood system (Ambion) according to the manufacturer’s instructions. RNA yield and purity was measured by means of Nanodrop equipment (Wilmington, DE, USA) and integrity was verified by automated gel electrophoresis (2100 BioAnalyzer, Agilent Technologies, Amstelveen, the Netherlands).

value: Human cord blood

value: female

value: neonate


title: TAX577142

value: LumA

value: sporadic

tag: reference


title: WP9C210NO

description: male neonate

source_name: pooled control for WP9C210NO

tag: gender


title: TAX577126

tag: tissue

value: familial

value: brcax


title: TAX577127

tag: hu subtype


title: TAX577130

tag: familial status


title: TAX577132

tag: er


title: WP9C203NO

description: female neonate

source_name: pooled control for WP9C203NO


title: TAX577131

tag: osbin


title: TAX577141


title: TAX577121


title: WP9C208NO

description: male neonate

source_name: pooled control for WP9C208NO

tag: age


title: WP9C205NO

description: male neonate

source_name: pooled control for WP9C205NO


title: TAX577138

tag: os


title: WP9C198NO

description: male neonate

source_name: pooled control for WP9C198NO


title: WP9C202NO

description: female neonate

source_name: pooled control for WP9C202NO


title: TAX577118

source_name: Breast tumor

tag: pgr


title: WP9C193NO

description: male neonate

source_name: pooled control for WP9C193NO


title: WP9C192NO

description: female neonate

source_name: pooled control for WP9C192NO


title: WP9C197NO

description: female neonate

source_name: pooled control for WP9C197NO


title: TAX577123

tag: primary

source_name: Stratagene Universal reference RNA


title: WP9C204NO

description: male neonate

source_name: pooled control for WP9C204NO


title: TAX577120

tag: grade


title: WP9C191NO

description: male neonate

source_name: pooled control for WP9C191NO


title: WP9C196NO

description: male neonate

source_name: pooled control for WP9C196NO


title: TAX577109

tag: brca status


title: TAX577110

tag: pam50 classification


title: TAX577115

tag: pam50 correlation


title: TAX577100

tag: brca1 methylation status


title: TAX577106


title: TAX577102


title: WP9C185NO

description: female neonate

source_name: pooled control for WP9C185NO


title: TAX577103


title: WP9C178NO

description: female neonate

source_name: pooled control for WP9C178NO


title: TAX577101


title: TAX577099


title: WP9C189NO

description: male neonate

source_name: pooled control for WP9C189NO


title: TAX577105


title: WP9C173NO

description: male neonate

source_name: pooled control for WP9C173NO


title: TAX577094


title: TAX577096


title: WP9C168NO

description: male neonate

source_name: pooled control for WP9C168NO


title: TAX577092


title: WP9C188NO

description: male neonate

source_name: pooled control for WP9C188NO


title: TAX577090