title: 1634_MMF


title: ATL14

status: Public on Feb 01 2009

type: RNA

city: Bethesda

first: John

last: Brady

state: MD

country: USA

institute: NCI

hyb_protocol: cRNA samples were hybridized for 16 hours at 45C.  The arrays were processed using the GeneChip Hybridization Wash and Stain kit.  The wash protocol used was Midi_euk2v3.

scan_protocol: Arrays were scanned with GeneChip Scanner 3000.

data_processing: All data were processed using GeneChip Operating System MAS5.0.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBL, ATL

label_protocol: Biotin labeled cRNA was prepared using the Affymetrix protocol with GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagent.

growth_protocol: ATL peripheral blood lymphocytes (PBLs) were purified from apheresis samples.  Control CD4+ lymphocytes were purified by positive or negative selection (Dynal, Oslo, Norway).

extract_protocol: Total RNA was isolated from lymphocytes using RNA-Bee reagent (Tel-Test, TX), followed by purification using Rneasy Mini-columns (Qiagen, Inc., CA).

treatment_protocol: RNA was isolated from non-cultured lymphocytes.

tag: acute leukemia


title: 1571_MMF

city: Amsterdam

first: Oscar

middle: Leonard

last: Volger

state: Noor Holland

address: Meibergdreef 15

department: Cardiology

country: Netherlands

institute: Academic Medical Center

description: All hybridizations were performed according to the manufacturer's specifications.

hyb_protocol: 750ng of biotinylated cRNA was hybridized onto the HumanRef-8 Expression BeadChips according to the Manufacturer.

scan_protocol: According to the Manufacturer, performed by ServiceXS http://www.servicexs.com).

data_processing: Gene expression analysis was performed by using Illumina's Beadstudio v3 software, followed by a quantile inter-array normalization (R, Bioconductor).

label: Biotin

source_name: Carotid Endarterectomy, MMF-treated

label_protocol: The Illumina® TotalPrep™ RNA Amplification Kit (Ambion) was used for the linear amplification of mRNA molecules into antisense biotinylated cRNAs.

extract_protocol: Total RNA molecules were isolated from N=5 consecutive 6 micron thick frozen cross-sections of the endarterectomy sample by using Trizol reagent (Invitrogen), followed by column purification with DNase-I treatment, RNeasy Micro kit (Qiagen).

treatment_protocol: The patient was randomly assigned to treatment with 1000 mg mycophenolate mofetil (MMF), 2 weeks before carotid endarterectomy surgery.

tag: Tissue

value: human carotid endarterectomy from patient with a carotid artertery stenosis (>70% diameter stenosis on angiography) as defined by the North American Symptomatic Carotid Endarterectomy Trial (NACET).


title: Normalchoroidplexus_LMD_patient6

city: Münster

first: Martin

last: Hasselblatt

address: Domagkstraße 19

department: Institute of Neuropathology

country: Germany

institute: University Hospital Münster

description: Cryosections (10 µm) from tissue obtained at autopsy were prepared on a cryostat and mounted on foil slides (P.A.L.M. Microlaser Technologies GmbH, Martinsried, Germany). Sections were cresyl violet stained and air-dried. Laser microdissection was performed using a Zeiss system equipped with an UVA-laser. A total of 10,000 cells were microdissected from each sample and collected in microcentrifuge tubes containing Buffer RLT (RNeasy Micro Kit; Qiagen, Hilden, Germany).

hyb_protocol: Following fragmentation, cRNA was hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

scan_protocol: Fluorescence was scanned on a GeneChip Scanner 3000 (Affymetrix)

data_processing: Fluorescence gradient correction using Expressionist Pro Refiner followed by normalization using Expressionist Analyst (Stratagene; Arithmetic Mean; Target Value: Fixed Value; Reference Value: 1000). Only Affymetrix probe intensities with a 'P' call were considered (p-value < 0.04). Intensities with 'A' or 'M' calls were set to null.

label: biotin-labeling

source_name: Epithelial cells lasermicrodissected from normal choroid plexus

label_protocol: RNA was amplified using the GeneChip® Two-Cycle cDNA Synthesis Kit (Affymetrix, Wooburn Green, UK) and subsequently in vitro transcribed to complementary RNA using the GeneChip® IVT Labeling Kit (Affymetrix).

extract_protocol: Total RNA from the sample was extracted using the RNeasy Micro Kit (Qiagen).

tag: Patient identifyier

tag: Type

value: Autopsy tissue

tag: Location

value: Lateral ventricle


title: Normalchoroidplexus_LMD_patient8


title: Normalchoroidplexus_LMD_patient9


title: Normalchoroidplexus_LMD_patient3


title: Tiling array analysis for Streptococcus pneumoniae_replicate2

status: Public on Feb 10 2009

city: starkville

first: Ranjit

last: Kumar

state: MS

address: 240 Wise Center Drive,PO Box 6100

department: Dept of Basic Science

institute: MSU

description: Nimblegen provided the raw intensity data after scan.

hyb_protocol: Hibridization was performed by Nimblegen Systems, Inc. www.nimblegen.com

scan_protocol: Scan was performed by Nimblegen Systems, Inc.

data_processing: Array spatial effects were removed by using NMPP package(specifc for Nimblegen arrays), the data was log transformed.The data was normalized using quantile normalization through the Affy package(present in  htp://www.bioconductor.org  and  http://pbil.univ-lyon1.fr/library/affy/html/normalize.quantiles.html).

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae TIGR4_mid log phase(OD600 nm, 0.4–0.6)

label_protocol: One microgram of total RNA was used by Nimblegen systems for labeling and hybridization. Samples were labeled by Nimblegen Systems, Inc.

growth_protocol: S. pneumoniae strain TIGR4 (ref) was grown in THYmedium, Todd-Hewitt broth supplemented with 0.5% yeast extract.

extract_protocol: Cells were harvested from duplicate cultures from mid-log phase (OD600 nm, 0.4–0.6) of growth by centrifugation.The harvested pellets were washed twice in sterile PBS (pH 7.0) and stored at -80°C. RNA was purified from frozen bacterial pellets using Qiagen RNeasy kit by following the manufacturer’s protocol. Isolated RNA was treated with DNase to remove genomic DNA contamination, and purity was checked by performing a one-step RT-PCR using primers specific for 16S rRNA in presence or absence of reverse transcriptase. RNA concentration and quality were determined by using Agilent Bioanalyzer. Purified RNA was stored in nuclease free water at -80°C.


title: Normalchoroidplexus_LMD_patient7


title: 1443_Placebo

source_name: Carotid Endarterectomy, Placebo

treatment_protocol: The patient was randomly assigned to Placebo treatment 2 weeks before carotid endarterectomy surgery.


title: Normalchoroidplexus_LMD_patient4


title: 1648_Placebo


title: Normalchoroidplexus_LMD_patient1


title: 1568_Placebo


title: ATL3


title: 1594_MMF


title: 1559_Placebo


title: 1671_Placebo


title: 1635_Placebo


title: Normalchoroidplexus_LMD_patient5


title: Choroidplexuspapilloma_LMD_patient4

description: Cryosections (10 µm) from tissue obtained at surgery were prepared on a cryostat and mounted on foil slides (P.A.L.M. Microlaser Technologies GmbH, Martinsried, Germany). Sections were cresyl violet stained and air-dried. Laser microdissection was performed using a Zeiss system equipped with an UVA-laser. A total of 10,000 cells were microdissected from each sample and collected in microcentrifuge tubes containing Buffer RLT (RNeasy Micro Kit; Qiagen, Hilden, Germany).

source_name: Tumor cells lasermicrodissected from choroid plexus papilloma (Grade I WHO)

value: GM

tag: Sex

value: female

tag: Age of patient

value: 0 years


title: 1403_Placebo


title: 917_Placebo


title: 1404_Placebo


title: Choroidplexuspapilloma_LMD_patient2

value: CH

value: 45 years


title: Choroidplexuspapilloma_LMD_patient6

value: WHO

value: male


title: 1297_Placebo


title: Choroidplexuspapilloma_LMD_patient1

value: KP


title: Choroidplexuspapilloma_LMD_patient7

value: FA

value: 32 years


title: 860_Placebo


title: Choroidplexuspapilloma_LMD_patient5

value: WC

value: 22 years


title: Sample 5134 - Tumor

status: Public on Jan 31 2009

type: genomic

city: Chicago

first: Samuel

last: Volchenboum

state: IL

address: 5640 S. Ellis RI405

institute: University of Chicago

hyb_protocol: The labeled DNA was hybridized to the 100K SNP chips, washed, incubated with streptavidin, and stained with biotinylated antistreptavidin antibody and a streptavidin R-phycoerythrin conjugate.

scan_protocol: The chips were scanned with an HP scanner (Hewlett-Packard, Palo Alto, CA) according to the manufacturer's recommendations.

data_processing:
Affymetrix genotyping software (Affymetrix GeneChip 5.0) was used to examine the SNP hybridization patterns and to make SNP calls of all loci in each of the tumor samples and their corresponding matched controls.
Analysis_of_LOH: The resulting data were analyzed with the dChip software package, freely available from http://www.dchip.org. At each locus, an LOH call was assigned through the following rules: LOH (AB in blood, A or B in tumor/cell line; blue), ROH or retention of heterozygosity (AB in both blood and tumor/cell line; yellow)]; non-informative (A or B in blood; gray); no call (SNP no call in either blood or tumor/cell line; white), or conflict A or B in blood, B or A or AB in tumor/cell line; red). Larger areas of LOH were obtained by using hidden Markov models to infer the LOH status at non-informative SNPs.
Measurement_of_DNA_Copy_Number_Change: Copy number changes were calculated by comparing the normal and tumor samples, using the dChip software as previously described. The patient blood samples were averaged for use as normal for copy number comparison. As in our previous work, copy number gain was defined as between 2.8 and 5 copies. Amplification was defined as more than 5 copies, and copy number loss was defined as less than 1.2 copies.
Data_Analysis: LOH data and inferred copy number data were exported from dChip for subsequent analysis. Further data manipulation was performed using Python scripts (http://www.python.org). A custom suite of Python scripts was developed to manipulate and analyze dChip-exported SNP and LOH data. Furthermore, visualization tools were created that facilitated the display of copy number changes and LOH events throughout the genome.

molecule: genomic DNA

source_name: Human neuroblastoma tumor

label_protocol: The Affymetrix 100K SNP array was used for all experiments, according to the methods described by the manufacturer (http://www.affymetrix.com). Briefly, 250 ng of tumor, cell line and control DNA were each digested with the appropriate restriction enzyme (Hind III/Xba1) and ligated to an adaptor sequence (Xba/Hind). For each sample, the ligated DNA was PCR amplified under recommended conditions, using primers complementary to the adapters. Purified PCR products were fragmented and end-labeled with biotinylated ddATP, using terminal deoxynucleotidyl transferase.

extract_protocol: DNA was extracted from tumor tissue, cell lines, and blood samples using the Qiagen method. Cryopreserved cell lines which had been established at the time of initial diagnosis as previously described, passaged not more than 4-5 times, were thawed and grown in culture for at most two passages in RPMI media with 10% FBS. When 80 to 90% confluent, cells were collected by trypsinization, and pelleted by centrifugation at 3500 rpm for 3 minutes. DNA was extracted using the Qiagen kit

tag: Phenotype

value: High-risk neuroblastoma


title: Sample 5134 - Blood

source_name: Human blood


title: Sample 4903.2 - Cell line

source_name: Human neuroblastoma derived cell line


title: Sample 4793 - Tumor


title: Sample 5134 - Cell line


title: NFI-1_Pre-immune_N2_Mixedstage_ChIP6

city: Chapel Hill

first: Christina

middle: M

last: Whittle

state: NC

address: 406 Fordham Hall, CB#3280

department: Biology

institute: University of North Carolina-Chapel Hill

hyb_protocol: Samples were hybridized using standard Agilent protocols.

scan_protocol: Images were scanned using an Axon 4000B scanner with 5uM scan resolution, 2 line averaging, and captured using Genepix Pro 6.

data_processing: Low quality probes were flagged and removed using Genepix (Axon) software. Repetitive probes were removed from analysis. Raw intensities for each ChIP were normalized by median centering the log2(ChIP/Input), converting to standard z-scores, and combined by taking the median of replicates.

organism: Caenorhabditis elegans

source_name: NFI-1 pre-immune ChIP DNA

label_protocol: Samples were direct labeled using the Bioprime klenow labeling kit (Invitrogen).

extract_protocol: Rabbit polyclonal antiserum was raised against recombinant NFI-1-GST fusion protein. Cross-linked pellets (120-150 mg) were resuspended in 1 ml of ChIP lysis buffer (Upstate) and sonicated using a Branson Sonifier 250 (output 30 and DutyCycle 30% setting) with 15 rounds of 10 one second pulses on ice. ChIP was performed using the ChIP assay kit (Upstate) with either 5ul anti-NFI immune serum or preimmune serum with 5% of the set aside as the input sample. Samples were amplified using an adapted Whole Genome Amplification (Sigma) protocol previously described (PMID: 17140114).

tag: Purified and amplified DNA from Chromatin Immuoprecipitation of NFI-1 pre-immune serum in wildtype (N2) mixed stage C. elegans.

source_name: Input gDNA

tag: Purified and amplified DNA from wildtype (N2) mixed stage C. elegans.


title: Sample 4903.2 - Tumor


title: Sample 4903.2 - Blood


title: NFI-1_Pre-immune_N2_Mixedstage_ChIP2


title: Sample 5463 - Tumor


title: Sample 4793 - Blood


title: Sample 1038 - Cell line


title: Sample 1355 - Blood


title: Sample 4793 - Cell line


title: Sample 5463 - Blood


title: NFI-1_N2_Mixedstage_ChIP6

source_name: NFI-1 ChIP DNA

tag: Purified and amplified DNA from Chromatin Immuoprecipitation of NFI-1 in wildtype (N2) mixed stage C. elegans.


title: Untreated at 10 h, biol. rep2 in Exp2

city: Geneva

first: Marc

last: Lamarine

state: Geneva

address: 9 Chemin des Mines

country: Switzerland

institute: Merck Serono S.A. · Geneva

description: Oli-neu after 10 h  Untreated in Experiment 2

hyb_protocol: In our study, 3 μg of total RNA isolated were first reverse tanscribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets were then cleaned up, an aliquot of 20 μg was fragmented, and finally 15 μg were hybridized to GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, P/N 900495, 900496, 900497). Chips were washed andlabeled in the fluidics station, using protocol EuKGE-WS2v_45 After scanning.

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G

data_processing: Intensity Profile pipeline from Rosetta© was used to create an intensity (expression) profile for each sample. Intensity Profile pipeline applies the actual error model to estimate error in the measurements for the reporters and derive the P-values for significance of expression. The estimated error of the hybridization intensity is the larger of the actual measurement error, computed as propagated from the errors of the probe cells, and the modeled error. Three terms are included in the error model: an additive term related to background noise, a term related to binding site randomness (a Poisson process), and multiplicative term related to fractional error of the intensity- Intensities are not log transformed.

organism: Mus musculus

source_name: Oli-neu after 10 h  Untreated

label_protocol: The One-Cycle Eukaryotic Target Labeling Assay (One-Cycle Target Labeling and Control Reagents,Affymetrix, P/N 900493) was used to produce fragmented biotinylated cRNA from total RNA as described in the standard Affymetrix protocol (P/N 701021 Rev. 5).

growth_protocol: Oli-Neu cell line were maintained in DMEMF12 (Invitrogen # 21331) supplemented with 50μg/ml apo-1 Transferrin (Sigma T-1147), 5ng/ml sodium selenite (Sigma S-9133), 5μg/ml Insulin (Sigma I-0516),100μM Putrescine (Sigma P-7505), 22nM Progesterone (Sigma P-7556), 0.5 nM T3 (Sigma T-6397), 1% HS (Invitrogen 26050), 1% nicillin/Streptomycin (Invitrogen 15070), 2mM glutamine Invitrogen 25030), 0.1% Sodium bicarbonate (Invitrogen 25080) and 15mM Hepes Invitrogen 15630)

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

treatment_protocol: Differentiation medium, DMEM,F12 supplemented with 50μg/ml apo-Transferrin, 5ng/ml sodium selenite, 100μM Putrescine, 130nM Progesterone, 200 nM T3, 1% HS, 1% Pennicilin/Streptomycin, 2mM glutamine, 0.1% Sodium bicarbonate and 15mM Hepes. Chemical treatments for micro-array analysis

tag: differentiation medium

value: DFEM supplemented with 50μg/ml apo-Transferrin, 5ng/ml sodium selenite,100μM Putrescine, 130nM Progesterone, 200 nM T3, 1% HS, 1% Pennicilin/Streptomycin, 2mM, glutamine, 0.1% Sodium bicarbonate and 15mM Hepes


title: Sample 1355 - Tumor


title: Sample 1038 - Blood


title: Sample 4030.2 - Tumor


title: Sample 5463 - Cell line


title: Sample 4030.2 - Blood


title: Sample 1355 - Cell line


title: Sample 1038 - Tumor


title: Sample 400 - Cell line


title: NFI-1_N2_Mixedstage_ChIP7


title: NFI-1_N2_Mixedstage_ChIP3

label_protocol: Samples were incorporated with amino-allyl UTP during amplification and post-labeled using reactive dye packs (Amerisham).

extract_protocol: Rabbit polyclonal antiserum was raised against recombinant NFI-1-GST fusion protein. Cross-linked pellets (120-150 mg) were resuspended in 1 ml of ChIP lysis buffer (Upstate) and sonicated using a Branson Sonifier 250 (output 30 and DutyCycle 30% setting) with 15 rounds of 10 one second pulses on ice. ChIP was performed using the ChIP assay kit (Upstate) with either 5ul anti-NFI immune serum or preimmune serum with 5% of the set aside as the input sample. Samples were amplified using ligation-mediated PCR as previously described (PMID: 17293863).

extract_protocol: Rabbit polyclonal antiserum was raised against recombinant NFI-1-GST fusion protein. Cross-linked pellets (120-150 mg) were resuspended in 1 ml of ChIP lysis buffer (Upstate) and sonicated using a Branson Sonifier 250 (output 30 and DutyCycle 30% setting) with 15 rounds of 10 one second pulses on ice. ChIP was performed using the ChIP assay kit (Upstate) with either 5ul anti-NFI immune serum or preimmune serum with 5% of the set aside as the input sample.Samples were amplified using ligation-mediated PCR as previously described (PMID: 17293863).


title: Sample 4030.2 - Cell line


title: NFI-1_N2_Mixedstage_ChIP2

hyb_protocol: Samples were hybridized using standard agilent protocols.

source_name: gDNA Input

tag: Purified and amplified genomic DNA from wildtype (N2) mixed stage C. elegans.


title: Sample 298 - Blood


title: Sample 298 - Cell line


title: Sample 298 - Tumor


title: Sample 5134 - Cell line


title: Sample 5463 - Blood


title: Sample 5463 - Tumor


title: Insulin at 24 h, biol. rep2 in Exp2

description: Oli-neu after 24 h treated with Insulin in Experiment 2

source_name: Oli-neu after 24 h treated with Insulin

tag: Insulin 10μg/ml,


title: Sample 5134 - Blood


title: Sample 5134 - Tumor


title: Sample 4793 - Blood


title: Sample 4793 - Cell line


title: Sample 4793 - Tumor


title: Sample 1355 - Cell line


title: Sample 4903.2 - Tumor


title: Sample 1355 - Blood


title: Sample 400 - Blood


title: Sample 4903.2 - Blood


title: Sample 4903.2 - Cell line


title: Sample 1355 - Tumor


title: Serotype 7 field strain 881 vs 5bL20 strain, replicate 3

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

country: Canada

institute: Université de Montréal - Faculté de Médecine Vétérinaire

description: Technical replicate 3

hyb_protocol: The hybridization profile for each strain was obtained by co-hybridizing labeled DNA from the tester strain with labeled DNA from the A. pleuropneumoniae serovar 5b (L20) control strain to the microarray. DNA from tester strains was labeled with Cy3 and DNA from the control strain with Cy5. Dye swaps were performed on selected strains to test for any dye-incorporation bias. Labeled samples were normalized by selecting tester/control sample pairs with similar dye incorporation efficiencies. Equivalent amounts (2 μg) of labeled tester and control samples were pooled, lyophilized, and then re-suspended in 42 μl of hybridization buffer [1 × DIGEasy hybridization solution (Roche Applied Science); 0.5 μg/μl of Torulla yeast tRNA (Invitrogen); 0.5 μg/μl of salmon sperm genomic DNA (Invitrogen)]. Labeled gDNA was denatured at 65°C for 5 min and applied to the microarray. Hybridizations were performed overnight at 37°C under 22 × 40-mm glass cover slips in a high-humidity chamber.

scan_protocol: Scanned with a Perkin-Elmer ScanArray Express scanner according to the manufacturer's recommendations. Image and data analysis were performed using TM4 suite of softwares. Raw data were generated using Spotfinder v.3.1.1.

data_processing: The integrated intensities of each spot, equivalent to the sum of unsaturated pixels in a spot were quantified and the integrated intensity of the local background was subtracted for each spot. The same operation was performed with the median spot intensities. Data were normalized with the MIDAS software tool using cross-channel Loess normalization. Spots with median intensities lower than 1000 were removed from the normalized data set. Intensities for duplicate spot were merged to generate the final normalized data set.

organism: Actinobacillus pleuropneumoniae

source_name: App 881

label_protocol: Isolated genomic DNA was fragmented by nebulization. One hundred μg of DNA in H2O and 35% glycerol (v/v) was placed in an AeroMist Nebulizer chamber (IPI Medical Products, Chicago, IL), and sheared by passing nitrogen gas through the chamber at 15 psi for 1 min. The DNA was precipitated with ethanol and suspended in 100 μl of ddH2O. Typically, the DNA was fragmented to a range of 0.4 to 12 kb in size. Five μg of fragmented DNA were fluorescently labeled using direct chemical coupling with the Label-IT (Mirus Corp., Madison, WI) cyanine dyes Cy3 and Cy5 as recommended by the manufacturer. Probes were purified from unincorporated dyes by passing samples through Qiaquick columns (Qiagen, Mississauga, ON).

growth_protocol: Growth on BHI agar supplemented with 15 mg/ml NAD at 37C for 16-18h.

extract_protocol: A. pleuropneumoniae strains were harvested after growth on agar plates for 16-18 h, resuspended in H2O, and treated with lysozyme (Roche, Laval, QC) and RNase A (Qiagen, Mississauga, ON) for 10 min at room temperature. The cell suspensions were then digested with proteinase K (MBI Fermentas, Burlington, ON) for 1 h at 37°C, and complete lysis was obtained by addition of sodium dodecyl sulfate to a final concentration of 0.1% (wt/vol). Genomic DNA, extracted from the cell lysates by two extractions with phenol-chloroform-isoamyl alcohol (25:24:1) and two extractions with chloroform, was precipitated in ethanol.

tag: Serotype 7 field strain 881, Ontario

source_name: App L20

tag: Serotype 5b reference strain L20


title: Sample 1038 - Cell line


title: Serotype 7 reference strain WF83 vs 5bL20 strain, replicate 2

description: Technical replicate 2

source_name: App WF83

tag: Serotype 7 reference strain WF83


title: Sample 400 - Tumor


title: Serotype 7 field strain 881 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Insulin at 10 h, biol. rep2 in Exp2

description: Oli-neu after 10 h treated with Insulin in Experiment 2

source_name: Oli-neu after 10 h treated with Insulin


title: Serotype 7 field strain 881 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 7 reference strain WF83 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: Sample 1038 - Tumor


title: Serotype 7 reference strain WF83 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Sample 4030.2 - Tumor


title: Serotype 7 field strain 05-3695 vs 5bL20 strain, replicate 2

description: Technical replicate 2

tag: Serotype 7 field strain 05-3695, Québec


title: Serotype 7 field strain 05-3695 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: Sample 4030.2 - Cell line


title: Serotype 7 field strain 05-3695 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Sample 298 - Tumor


title: Sample 4030.2 - Blood


title: Sample 1038 - Blood


title: Kidney_1K_SBH4 (female)

city: Ashkelon

first: Yoram

last: Yagil

address: Hahistadrut

country: Israel

institute: Ben-Gurion University, Barzilai Medical Center Campus

description: Expression data from female rat kidney

hyb_protocol: Following fragmentation, we hybridized cRNA overnight at 450C on GeneChip 230 2.0 Array. We washed the GeneChips and stained them in an Affymetrix Fluidics Station.

scan_protocol: We scanned the GeneChips using the GenChip Scanner 3000Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with the GeneChip Operating Software (GCOS); the arrays were normalized by the log scale Robust Multiarray Analysis (RMA)

organism: Rattus norvegicus

label_protocol: We used the Genechip Affymetrix labeling kit and the standard protocol recommended by Affymetrix

growth_protocol: We fed the animals standard rat chow and provided water ad libitum

extract_protocol: We extracted total RNA using the RNeasy mini-kit from QIAGEN (Cat #74104)

tag: Strain:SBH/y after right uninephrectomy Gender:Female Age:5 months Diet:Regular rat chow


title: Sample 298 - Blood


title: Kidney_1K_SBH7 (female)

description: Expression data from female rat kidney

source_name: Strain:SBH/y after right uninephrectomy Gender:Female


title: Sample 400 - Blood


title: Sample 298 - Cell line


title: Sample 400 - Cell line


title: Serotype 7 field strain 1951 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 7 field strain 1951, Ontario


title: Kidney_1K_SBH6 (female)

description: Expression data from female rat kidney


title: Serotype 7 field strain 06-3060 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 7 field strain 06-3060, Québec


title: Serotype 7 field strain 1951 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 7 field strain 05-14401 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 7 field strain 05-14401, Saskatchewan


title: Serotype 7 field strain 06-3060 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 7 field strain 06-3060 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Forskolin at 10 h, biol. rep1 in Exp2

description: Oli-neu after 10 h treated with Forskolin in Experiment 2

tag: Forskolin (Sigma F6886) 10μM,


title: Serotype 7 field strain 1951 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Kidney_1K_SBH3 (female)

description: Expression data from female rat kidney


title: Serotype 7 field strain 04-13054 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 7 field strain 04-13054, Saskatchewan


title: Serotype 7 field strain 04-13054 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 7 field strain 05-14401 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 5b field strain 03-22383 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 5b field strain 03-22383 Saskatchewan


title: Serotype 7 field strain 04-13054 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Kidney_1K_SBH5 (female)

description: Expression data from female rat kidney


title: Serotype 5b reference strain L20 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 5b reference strain L20 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Kidney_1K_SBH1 (female)

description: Expression data from female rat kidney


title: Kidney_1K_SBH2 (female)

description: Expression data from female rat kidney


title: Serotype 5b field strain 03-22383 vs 5bL20 strain, replicate 4

description: Technical replicate 4


title: Serotype 5b field strain 03-22382 vs 5bL20 strain, replicate 1

description: Technical replicate 1

tag: Serotype 5b field strain 03-22382, Saskatchewan


title: Kidney_2K_SBH7 (female)

description: Expression data from female rat kidney

tag: Strain:SBH/y with 2 indwelling kidneys Gender:Female Age:5 months Diet:Regular rat chow


title: Serotype 5b field strain 03-22383 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 5b field strain 03-22382 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Kidney_2K_SBH5 (female)

description: Expression data from female rat kidney

source_name: Strain:SBH/y with 2 indwelling kidneys Gender:Female


title: Serotype 5b field strain 03-22382 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: Serotype 5b field strain 03-22383 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Kidney_2K_SBH6 (female)

description: Expression data from female rat kidney


title: Kidney_2K_SBH4 (female)

description: Expression data from female rat kidney


title: Serotype 5b field strain 04-17496 vs 5bL20 strain, replicate 1

description: Technical replicate 1

tag: Serotype 5b field strain 04-17496, Saskatchewan


title: Serotype 5a reference strain K17 vs 5bL20 strain, replicate 2

description: Technical replicate 2

source_name: App K17

tag: Serotype 5a reference strain K17


title: Serotype 5b field strain 04-17496 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: Kidney_2K_SBH3 (female)

description: Expression data from female rat kidney


title: Serotype 5b field strain 04-17496 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Kidney_2K_SBH1 (female)

description: Expression data from female rat kidney


title: Serotype 5a reference strain K17 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 15 field strain 05-20080 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 15 field strain 05-20080, Saskatchewan


title: Kidney_2K_SBH2 (female)

description: Expression data from female rat kidney


title: Serotype 5a field strain 04-37943 vs 5bL20 strain, replicate 1

description: Technical replicate 1

tag: Serotype 5a field strain 04-37943, Saskatchewan


title: Serotype 5a field strain 04-3128 vs 5bL20 strain, replicate 1

description: Technical replicate 1

tag: Serotype 5a field strain 04-3128, Saskatchewan


title: Serotype 5a field strain 04-3128 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 5b reference strain L20


title: Serotype 5a field strain 05-508 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 5a field strain 05-508, Saskatchewan


title: Serotype 15 field strain 05-20080 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Kidney_1K_SBN7 (female)

description: Expression data from female rat kidney

tag: Strain:SBN/y after right uninephrectomy Gender:Female Age:5 months Diet:Regular rat chow


title: Kidney_1K_SBN6 (female)

description: Expression data from female rat kidney

source_name: Strain:SBN/y after right uninephrectomy Gender:Female


title: Kidney_1K_SBN3 (female)

description: Expression data from female rat kidney


title: Kidney_1K_SBN4 (female)

description: Expression data from female rat kidney


title: Serotype 5a field strain 04-37943 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: Kidney_1K_SBN5 (female)

description: Expression data from female rat kidney


title: Serotype 7 field strain 05-14401 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 5a field strain 04-37943 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 5a field strain 05-508 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Non-typeable strain 05-15225 vs 5bL20 strain, replicate 2

description: Technical replicate 2

tag: Non-typeable strain 05-15225, Saskatchewan


title: Kidney_2K_SBN7 (female)

description: Expression data from female rat kidney

tag: Strain:SBN/y with 2 indwelling kidneys Gender:Female Age:5 months Diet:Regular rat chow


title: Serotype 15 field strain 05-20080 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 5a field strain 04-3128 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 15 field strain 05-14657 vs 5bL20 strain, replicate 2

description: Technical replicate 2

tag: Serotype 15 field strain 05-14657, Saskatchewan


title: Serotype 15 field strain 05-14657 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Non-typeable strain 05-15225 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 15 reference strain HS143 vs 5bL20 strain, replicate 3

description: Technical replicate 3

source_name: App HS143

tag: Serotype 15 reference strain HS143


title: Kidney_1K_SBN2 (female)

description: Expression data from female rat kidney


title: Kidney_1K_SBN1 (female)

description: Expression data from female rat kidney


title: Kidney_2K_SBN4 (female)

description: Expression data from female rat kidney

source_name: Strain:SBN/y with 2 indwelling kidneys Gender:Female


title: Kidney_2K_SBN5 (female)

description: Expression data from female rat kidney


title: Kidney_2K_SBN1 (female)

description: Expression data from female rat kidney


title: Serotype 15 field strain 05-14657 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: Kidney_2K_SBN6 (female)

description: Expression data from female rat kidney


title: Serotype 15 reference strain HS143 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 15 reference strain HS143 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 15 field strain 05-13146 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 15 field strain 05-13146, Saskatchewan


title: Kidney_2K_SBN3 (female)

description: Expression data from female rat kidney


title: Serotype 15 field strain 05-13146 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Serotype 1 field strain 05-7431 vs 5bL20 strain, replicate 2

description: Technical replicate 2

tag: Serotype 1 field strain 05-7431, Saskatchewan


title: Serotype 15 field strain 05-13146 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 5a field strain 05-508 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Non-typeable strain 05-15225 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: Kidney_2K_SBN2 (female)

description: Expression data from female rat kidney


title: rAAVintA-rep3

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: MRC-5 cells transduced with rAAV vector only

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: fibroblasts-MRC-5 cells transduced with recombinant DNA, Vector only

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

growth_protocol: The MRC-5 cells were grown in Dulbecco’s modified Eagle’s medium with low glucose (DMEM low) supplemented with 10% fetal bovine serum ( FBS) ( Hyclone, Utah), 2mM L-glutamine(G ), 100units/ml penicillin and 100μg/ml streptomycin ( P/S)

extract_protocol: Total RNA was purified with RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. ).  After ribosomal RNA reduction (Invitrogen, Carlsbad, CA) to remove most of the 18S and 28S rRNAs, the GeneChip WT (whole transcript) cDNA Synthesis Kit, WT cDNA Amplification Kit, and WT Terminal Labeling Kit (Affymetrix, Inc., Santa Clara, CA) were used for target preparation. Ten µg of cRNA (antisense RNA) were added to the second-cycle cDNA reaction followed by fragmentation and Terminal Labeling process.

treatment_protocol: The MRC-5 cells were transduced in triplicate, with rAAVintA,  rAAVpp65N, rAAVpp65NLSKO and incubated for 48hrs at 37C.

tag: Vector only


title: rAAVpp65N-rep3

description: MRC-5 cells transduced with rAAV wide type CMV PP65

source_name: fibroblasts-MRC-5 cells transduced with recombinant DNA, WT PP65

tag: WT PP65


title: rAAVpp65mIINLSKO-rep3

description: MRC-5 cells transduced with rAAV mutated CMV PP65

source_name: fibroblasts-MRC-5 cells transduced with recombinant DNA, mutated PP65

tag: mutated PP65


title: Serotype 1 field strain 719 vs 5bL20 strain, replicate 2

description: Technical replicate 2

source_name: App 719

tag: Serotype 1 field strain 719, Ontario


title: Serotype 1 field strain 2521 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 1 field strain 2521, Ontario


title: rAAVintA-rep2


title: Serotype 1 field strain 05-7431 vs 5bL20 strain, replicate 3

description: Technical replicate 3


title: rAAVpp65N-rep2


title: rAAVpp65mIINLSKO-rep2


title: Serotype 1 field strain 05-7431 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: rAAVpp65N-rep1


title: Monocytes_CD14_uninfected2

city: Chestnut Hill

first: K

middle: C

last: Williams

state: MA

address: 140 Commonwealth Avenue

institute: Boston College

description: The transcriptional profile in the CD14+ monocyte subset of a rhesus monkey was examined using the Affymetrix GeneChip Rhesus Macaque Genome Array containing a total of 47,000 Macaca mulatta transcripts

hyb_protocol: Standard Affymetrix protocol, processed at Pathologica, LLC

data_processing: Expression data was obtained using an Affymetrix GSC3000 scanner and processed by GCOS software (Affymetrix). Partek Genomic Suite System was used for downstream analysis of GCOS processed data.

organism: Macaca mulatta

source_name: FACS sorted CD14+ monocytes

extract_protocol: FACS-isolated monocytes were spun down and lysed in Trizol reagents (Invitrogen), and total RNA was prepared using PureLink Micro-to-Midi Total RNA Purification system (Invitrogen). Quality of RNA was determined by 2100 Bioanalyzer RNA LabChip (Agilent Technologies).

treatment_protocol: normal animal

tag: Country of origin

value: India,

tag: Internal identifier number

tag: SIV status

value: negative,

tag: Tissue

value: peripheral blood.


title: Xoo PXO99A raxR knockout VS RaxR constitutively express in PSB media replicate2

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

description: Biological replicate2 of 3

hyb_protocol: Probes were resuspended in 28 ul of preheated 1X hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42°C. To block non-specific hybridization, add 2 ul salmon sperm DNA (10 ug/ul) into the solution. Labeled probes were denatured by heating mixture at 95 °C for 3 mins and snap cool on ice for 30 seconds. Probed were applied into injector to hybridize with printed slides. Samples were hybridized for 16 hours (42°C in humidified water bath), sequentially washed with 42°C preheated low stringency wash buffer (2x SSC and 0.1% SDS) 5 minutes, then washed with high stringency wash buffer (0.1x SSC and 0.1% SDS) 5 minutes. Slides were transferred to 0.1x SSC buffer and agitated for 5 mins (2times) and dried under N2 (5 min, 30C). Slides were kept under N2 until scanning.

scan_protocol: Hybridized microarray slides were imaged using a GenePix 4000B dual laser microarray scanner (Axon Instruments, USA) at 5 µm resolution. Slides were imaged using 100% laser power for both lasers (532 and 635 nm) and scanned twice using a high and low power of the scanner photomultiplicator settings (PMT). All images were processed using GenePix software (Axon Instruments, USA) for element identification and quantitation. The metadata associated with the hybridizations, along with the “raw” intensities obtained from the GenePix quantitation.

data_processing: LMgene packages and Bioconductor packages for R languages wereused to extract and normalize data from the GPR files. The reference for LMgene is Rocke DM: Design and analysis of experiments with high throughput biological assay data. Semin Cell Dev Biol 2004, 15(6):703-713.

organism: Xanthomonas oryzae pv. oryzae PXO99A

source_name: Xoo raxR knockout mutant

label_protocol: cDNA was generated by using SuperScriptTM III First-Strand kit and following the manufacturer’s protocol (Invitrogen, Carlsbad, CA, U.S.A.).  Twenty micrograms of high quality RNA was mixed with random hexamers that were used as primers for cDNA generation and the mixture then preheated at 70°C for 15 mins. Primers were annealed to total RNA and extended with a labeling mixture consisting of 6.0 ul of 5X buffer, 2.0 ul of  0.1M DTT, 1.0 ul of RNasin, 2.0 ul of superscript III reverse transcriptase, 2.0 ul of 25X dNTP-allyl-amino (aa) dUTP mixture (final concentration 0.5 mM each of dATP, cCTP, and dGTP, 0.35 mM aa-dUTP, 0.15 mM dTTP) at 25deg. C  for 10min followed by 2 h at 42deg. C. The RNA template was hydrolyzed using 3 μl of 2.5 N NaOH (37deg. C, 15 min) followed by neutralization with 15 μl of 2M HEPES. Unincorporated primers and nucleotides were removed using the Zymo research kit according to the manufacturer’s protocol (Zymo research, Genetix, UK) and the purified amino allyl-modified cDNA was resuspended in 60 μl of 50 mM sodium bicarbonate (pH 9.0). The amino allyl-modified cDNA was used to resuspend lyophilized Cy3 or Cy5 and incubated for 1 hr at room temperature in the dark. The reaction was quenched by adding 15 μl of 4 M hydroxylamine (15 min, room temperature in the dark). The dye-coupled cDNA was then purified by using the Zymo research kit (Zymo research, Genetix, UK) and then proceed to hybrization experiment.

growth_protocol: Cells were grown at 28deg. C with shaking at 200 rpm, in nutrient-rich PSB media containing 10 g of peptone, 10 g of sucrose, 1 g of L-glutamic acid (monosodium salt). Bacterial cells were cultured in PSB media until OD600 is 0.5. Cells were washed one time and harvested. Three separated cultures were used for each microarray studies

extract_protocol: A bacterial 1010-cells culture was harvested in a centrifuge tube and cell pellets were frozen in -80deg. C immediately until RNA isolation. RNA was isolated using Trizol reagent (Invitrogen Corp.) and protocol is described in manufacturer manual. The RNA samples were treated with DNaseI (10 units, Promega Corp., Madison, WI, U.S.A.) for 30 mins at 37deg. C, followed by column purification using RNeasy mini kit (Qiagen, Germantown, MD, U.S.A.). The quality of RNA was determined by gel electrophoresis on a 1% agarose gel and verified visually on a Nanodrop, or by Agilent 2100 Bioanalyzer (Agilent Technologies). The quantity of total RNA and mRNA were determined by measuring the absorbance at 260nm and 280nm. In addition, the level of protein contamination in the RNA was measured by using A260/A280 ratio.

tag: Xanthomonas oryzae pv. oryzae PXO99A

source_name: Xoo RaxR constitutively express mutant


title: Serotype 1 field strain 2521 vs 5bL20 strain, replicate 2

description: Technical replicate 2

tag: Serotype 5b reference strain L20


title: Xoo PXO99A raxR knockout VS RaxR constitutively express in PSB media replicate2, counter dye swap

description: Biological replicate2 of 3


title: Monocytes_CD14_CD16_uninfected2

description: The transcriptional profile in the CD14+CD16+ monocyte subset of a rhesus monkey was examined using the Affymetrix GeneChip Rhesus Macaque Genome Array containing a total of 47,000 Macaca mulatta transcripts

scan_protocol: Standard Affymetrix protocol, processed at Pathologica, LLC

source_name: FACS sorted CD14+CD16+ monocytes


title: rAAVpp65mIINLSKO-rep1


title: Monocytes_CD16_uninfected1

description: The transcriptional profile in the CD16+ monocyte subset of a rhesus monkey was examined using the Affymetrix GeneChip Rhesus Macaque Genome Array containing a total of 47,000 Macaca mulatta transcripts

source_name: FACS sorted CD16+ monocytes

label_protocol: Standard Affymetrix protocol, processed at Pathologica, LLC


title: Monocytes_CD14_uninfected1


title: Serotype 1 field strain 719 vs 5bL20 strain, replicate 1

description: Technical replicate 1

source_name: App L20


title: Serotype 1 field strain 05-7430 vs 5bL20 strain, replicate 2

description: Technical replicate 2

tag: Serotype 1 field strain 05-7430, Saskatchewan


title: Xoo PXO99A raxR knockout VS RaxR constitutively express in PSB media replicate1, counter dye swap

description: Biological replicate1 of 3


title: Serotype 1 field strain 2398 vs 5bL20 strain, replicate 3

description: Technical replicate 3

tag: Serotype 1 field strain 2398, Ontario


title: Xoo PXO99A raxR knockout VS RaxR constitutively express in PSB media replicate3, counter dye swap

description: Biological replicate3 of 3


title: Monocytes_CD16_uninfected2


title: Serotype 1 field strain 2521 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 1 field strain 05-7430 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 1 ref strains vs 5bL20 strain, replicate 2

description: Technical replicate 2

source_name: App S4074

tag: Serotype 1 reference strain


title: Xoo PXO99A RaxR constitutively express VS wildtype in PSB media replicate2, counter dye swap

description: Biological replicate2 of 3

source_name: Xoo PXO99A


title: Xoo PXO99A RaxR constitutively express VS wildtype in PSB media replicate2

description: Biological replicate2 of 3


title: rAAVintA-rep1


title: Xoo PXO99A raxR knockout VS RaxR constitutively express in PSB media replicate3

description: Biological replicate3 of 3


title: Monocytes_CD14_CD16_uninfected1


title: Xoo PXO99A raxR knockout VS wildtype in PSB media replicate1, counter dye swap

description: Biological replicate1 of 3


title: Xoo PXO99A raxR knockout VS RaxR constitutively express in PSB media replicate1

description: Biological replicate1 of 3


title: Xoo PXO99A raxR knockout VS wildtype in PSB media replicate3

description: Biological replicate3 of 3


title: Serotype 1 field strain 2398 vs 5bL20 strain, replicate 2

description: Technical replicate 2


title: Xoo PXO99A raxR knockout VS wildtype in PSB media replicate3, counter dye swap

description: Biological replicate3 of 3


title: Xoo PXO99A raxR knockout VS wildtype in PSB media replicate2, counter dye swap

description: Biological replicate2 of 3


title: Yeast_pap1-1_25°C_Crodycepin_Rep3

status: Public on Jan 30 2009

city: Zürich

first: Bernahrd

last: Dichtl

address: Winterthurer Strasse 190

department: Institute of Molecular Biology

institute: University of Zürich

hyb_protocol: The concentrated labelled DNA was mixed with MWG formamide buffer (Ocimun Biosolutions) and poly(A) RNA was added to a final concentration of 0.5 mg/ml. The mix was incubated at 80°C for 10 minutes, loaded on Nexterion slides (carrying 70-mer oligo probes for 10,944 features) and hybridised overnight at 42°C. Following washes in 2x SSC, 0.2% SDS and 2x SSC and 0.2x SSC the arrays were immersed in 100% ethanol to fix the cDNA, dried by centrifugation

scan_protocol: Scanning was done with Axon instruments scanner 4000 (Foster City, California, United States). Scanning parameters were adjusted to similar fluorescent intensities in both channels and data were collected with GENEPIX 3.0 (Axon Instruments)

data_processing: Spots with abnormal morphology were identified by eye and excluded from further analysis. Arrays were normalized by the Stanford Microarray Database (SMD) (Gollub et al., 2003). The calculated log2 ratios were imported into Acuity 4.0 (Axon Instruments) and filtered for regression correlation of greater than 0.5 (filters for large variations in the ratios of pixels within each spot) and a signal to noise ratio of greater than 2.5 (signal over background).

organism: Saccharomyces cerevisiae

source_name: wild-type 25°C

label_protocol: Ten microgram total RNA was used for reverse transcription using superscript II (Invitrogen) with oligo(dT) and pdN9 primers and Ambion spike control. Following RNA hydrolysis and neutralization DNA was concentrated to 9 μl using the Microcon-30 concentrator (Amicon). NHS-Cy3 and NHS-Cy5 dyes (Amersham) were coupled to the DNA and purified using the Qia-quick PCR purification kit (Qiagen). The Cy3- and Cy5-labelled cDNA samples were mixed and concentrated in Microcon-30 concentrators (Amicon) to a final volume of 10.5 μl and labelling efficiency was measured by NanoDrop using the microarray application

growth_protocol: Yeast cells were grown in 50 ml synthetic minimal complete medium at 25°C, to an OD600nm of 0.3 to 0.4

extract_protocol: hot phenol extraction and further purification with RNA micro-kit (Qiagen)

treatment_protocol: samples labelled with 'cordycepin' where treated by addition of 20 mg/ml cordycepin for 1 hour

tag: Strain S288C Mat alpha

source_name: pap1-1 25°C, 20 mg/ml 1hour

tag: pap1-1 Mat alpha


title: Xoo PXO99A RaxR constitutively express VS wildtype in PSB media replicate3, counter dye swap

description: Biological replicate3 of 3


title: Serotype 1 field strain 2398 vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Serotype 1 ref strains vs 5bL20 strain, replicate 1

description: Technical replicate 1


title: Xoo PXO99A RaxR constitutively express VS wildtype in PSB media replicate3

description: Biological replicate3 of 3


title: Xoo PXO99A RaxR constitutively express VS wildtype in PSB media replicate1, counter dye swap

description: Biological replicate1 of 3


title: Xoo PXO99A raxR knockout VS wildtype in PSB media replicate2

description: Biological replicate2 of 3


title: Xoo PXO99A RaxR constitutively express VS wildtype in PSB media replicate1

description: Biological replicate1 of 3


title: Yeast_pap1-1_25°C_Rep2

source_name: pap1-1 25°C


title: Ctr9_ChIP

city: Dresden

first: Li

last: Ding

address: Pfotenhauerstr. 108

institute: MPI-CBG

description: Ctr9 ChIP, Technical Rep. 1-3, Promoter

hyb_protocol: ChIP samples were hybridized to Mouse promoter 1.0R arrays (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing:
Data was processed with Partek Genomic Suite.The following steps were applied to the raw intensities: probe sequences adjustment, RMA background correction and quantile normalization. Each probe intensity was reduced by a baseline intensity, which was defined as an average of three control replicates.

Ctr9_binding_mm8.bed contains a list of Ctr9 binding sites identified by the data processing algorithm. Each row of the file contains three columns: the name of the chromosome, the starting position and the ending position of a binding site. Positions are based on the mm8 mouse genome assembly.

source_name: GFP ChIP DNA from BAC-transgenic mouse ESCs

label_protocol: ChIPed DNA were amplified using random primer / adaptor mediated PCR (Affymetrix), fragmented, and labeled using GeneChip WT Double-stranded DNA terminal Labeling Kit (Affymetrix).

growth_protocol: LAP-tagged Ctr9 BAC-transgenic ES cells were cultured on gelatin-coated plates in Glasgow Minimum Essential Medium (Sigma) supplemented with 10% FBS (Pan biotech), 2.2 mM L-Glutamine, 1 mM Sodium Pyruvate, 50 μM 2-mercaptoethanol, 1x NEAA (Invitrogen), and LIF (generated in house). ES cells were trypsinized and splitted every 2 days, and the medium was changed daily.

extract_protocol: Chromatin extracts containing DNA fragments were immunoprecipitated using a polyclonal goat anti-GFP antibody (MPI-CBG, protein facility).mmunoprecipiated protein-DNA complexes were elutated from protein G sepharose (Fastflow GE healthcare) using 200 μl elution buffer (1% SDS, 0.1M NaHCO3), and incubated at 65 °C overnight to reverse the 5 crosslinks. Elutions were treated with RNase A and proteinase K, and purified with a PCR DNA purification kit (Qiagen).

treatment_protocol: 1X107  Lap-tagged Ctr9 BAC-transgenic ES cells were crosslinked with 1% (v/v) formaldehyde for 10 min at room temperature. Formaldehyde was then inactivated by the addition of 125 mM glycine. Cell extracts were sonicated into approximately 500-nt chromatin fragments using a Branson 450-D sonicator.

tag: Amplification method

tag: Antibody

value: GFP goat polyclonal

source_name: Input DNA from BAC-transgenic mouse ESCs

tag: Input DNA


title: Xoo PXO99A raxR knockout VS wildtype in PSB media replicate1

description: Biological replicate1 of 3


title: Yeast_pap1-1_25°C_Rep3


title: Yeast_pap1-1_25°C_Crodycepin_Rep1


title: Yeast_pap1-1_25°C_Crodycepin_Rep2


title: Yeast_Wildtype_Cordycepin_Rep2

source_name: wild-type 25°C, 20 mg/ml 1hour


title: Yeast_Wildtype_Cordycepin_Rep3


title: FL sample number 1910; diagnostic sample

city: London

first: derville

last: o'shea

address: Charterhouse Square

country: United Kingdom

institute: Medical Oncology

description: SNP genotype data from FL patient at diagnosis

hyb_protocol: Affymetrix 10K 2.0 mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000-7G

data_processing: GCOS, GTYPE. Genotype calling algorithm MPAM

source_name: FL lymph node

extract_protocol: DNA was prepared using standard proteinase K digestion and phenol/chloroform extraction

tag: FL lymph node


title: FL sample number 1913; diagnostic sample

label_protocol: Affymetrix 10K 2.0 mapping assay protocol


title: Yeast_Wildtype_Cordycepin_Rep1


title: FL sample number 1906; diagnostic sample


title: FL sample number 1916; diagnostic sample


title: Yeast_pap1-1_25°C_Rep1


title: FL sample number 1919; diagnostic sample


title: FL sample number 1918; diagnostic sample


title: FL sample number 1898; diagnostic sample


title: FL sample number 1912; diagnostic sample


title: FL sample number 1903; diagnostic sample


title: FL sample number 1894; diagnostic sample


title: FL sample number 1907; diagnostic sample


title: FL sample number 1900; diagnostic sample


title: FL sample number 1888; diagnostic sample


title: FL sample number 1897; diagnostic sample


title: FL sample number 1904; diagnostic sample


title: FL sample number 1885; diagnostic sample


title: FL sample number 1862; diagnostic sample


title: FL sample number 1854; diagnostic sample


title: FL sample number 1882; diagnostic sample


title: FL sample number 1851; diagnostic sample


title: FL sample number 1896; diagnostic sample


title: FL sample number 1887; diagnostic sample


title: FL sample number 1879; diagnostic sample


title: FL sample number 1873; diagnostic sample


title: FL sample number 1866; diagnostic sample


title: FL sample number 1905; diagnostic sample


title: FL sample number 1884; diagnostic sample


title: FL sample number 1870; diagnostic sample


title: FL sample number 1842; diagnostic sample


title: FL sample number 1874; diagnostic sample


title: FL sample number 1861; diagnostic sample


title: FL sample number 1863; diagnostic sample


title: FL sample number 1876; diagnostic sample


title: FL sample number 1857; diagnostic sample


title: FL sample number 1846; diagnostic sample


title: FL sample number 1855; diagnostic sample


title: FL sample number 1839; diagnostic sample


title: FL sample number 1835; diagnostic sample


title: FL sample number 1841; diagnostic sample


title: FL sample number 1834; diagnostic sample


title: FL sample number 1848; diagnostic sample


title: FL sample number 1864; diagnostic sample


title: FL sample number 1853; diagnostic sample


title: FL sample number 1850; diagnostic sample


title: FL sample number 1827; diagnostic sample


title: FL sample number 1797; diagnostic sample


title: FL sample number 1845; diagnostic sample


title: FL sample number 1828; diagnostic sample


title: FL sample number 1844; diagnostic sample


title: FL sample number 1830; diagnostic sample


title: FL sample number 1838; diagnostic sample


title: FL sample number 1792; diagnostic sample


title: FL sample number 1790; diagnostic sample


title: FL sample number 1836; diagnostic sample


title: FL sample number 1788; diagnostic sample


title: FL sample number 1825; diagnostic sample


title: FL sample number 1719; diagnostic sample


title: FL sample number 1735; diagnostic sample


title: FL sample number 1732; diagnostic sample


title: FL sample number 1771; diagnostic sample


title: FL sample number 1772; diagnostic sample


title: FL sample number 1799; diagnostic sample


title: FL sample number 1717; diagnostic sample


title: FL sample number 1811; diagnostic sample


title: FL sample number 1683; diagnostic sample


title: FL sample number 1720; diagnostic sample


title: FL sample number 1718; diagnostic sample


title: FL sample number 1684; diagnostic sample


title: FL sample number 1716; diagnostic sample


title: FL sample number 1761; diagnostic sample


title: FL sample number 1681; diagnostic sample


title: FL sample number 1675; diagnostic sample


title: FL sample number 1670; diagnostic sample


title: FL sample number 1729; diagnostic sample


title: FL sample number 1795; diagnostic sample


title: FL sample number 1664; diagnostic sample


title: FL sample number 1669; diagnostic sample


title: FL sample number 1656; diagnostic sample


title: FL sample number 1662; diagnostic sample


title: FL sample number 1661; diagnostic sample


title: FL sample number 1654; diagnostic sample


title: FL sample number 1648; diagnostic sample


title: FL sample number 1655; diagnostic sample


title: FL sample number 1660; diagnostic sample


title: FL sample number 1647; diagnostic sample


title: FL sample number 1645; diagnostic sample


title: FL sample number 1880; diagnostic sample


title: FL sample number 1643; diagnostic sample


title: FL sample number 1627; diagnostic sample


title: FL sample number 1637; diagnostic sample


title: FL sample number 1628; diagnostic sample


title: FL sample number 1624; diagnostic sample


title: FL sample number 1639; diagnostic sample


title: FL sample number 1768; diagnostic sample


title: FL sample number 1644; diagnostic sample


title: FL sample number 1638; diagnostic sample


title: FL sample number 1622; diagnostic sample


title: FL sample number 1611; diagnostic sample


title: FL sample number 1646; diagnostic sample


title: FL sample number 1615; diagnostic sample


title: FL sample number 1606; diagnostic sample


title: FL sample number 1625; diagnostic sample


title: FL sample number 1623; diagnostic sample


title: FL sample number 1595; diagnostic sample


title: FL sample number 1604; diagnostic sample


title: FL sample number 1594; diagnostic sample


title: FL sample number 1589; diagnostic sample


title: FL sample number 1619; diagnostic sample


title: FL sample number 1599; diagnostic sample


title: FL sample number 1581; diagnostic sample


title: FL sample number 1626; diagnostic sample


title: FL sample number 1608; diagnostic sample


title: FL sample number 1620; diagnostic sample


title: FL sample number 1610; diagnostic sample


title: FL sample number 1603; diagnostic sample


title: FL sample number 1617; diagnostic sample


title: FL sample number 1607; diagnostic sample


title: FL sample number 1598; diagnostic sample


title: FL sample number 1588; diagnostic sample


title: FL sample number 1476; diagnostic sample


title: FL sample number 1583; diagnostic sample


title: FL sample number 1478; diagnostic sample


title: FL sample number 1584; diagnostic sample


title: FL sample number 1474; diagnostic sample


title: FL sample number 1580; diagnostic sample


title: FL sample number 1472; diagnostic sample


title: FL sample number 1480; diagnostic sample


title: FL sample number 1579; diagnostic sample


title: FL sample number 1479; diagnostic sample


title: FL sample number 1432; diagnostic sample


title: FL sample number 1427; diagnostic sample


title: FL sample number 1419; diagnostic sample


title: FL sample number 1473; diagnostic sample


title: FL sample number 1445; diagnostic sample


title: FL sample number 1426; diagnostic sample


title: FL sample number 1422; diagnostic sample


title: FL sample number 1450; diagnostic sample


title: FL sample number 1477; diagnostic sample


title: FL sample number 1428; diagnostic sample


title: FL sample number 1425; diagnostic sample


title: FL sample number 1429; diagnostic sample


title: FL sample number 1436; diagnostic sample


title: FL sample number 1106; diagnostic sample


title: FL sample number 1416; diagnostic sample


title: FL sample number 1417; diagnostic sample


title: FL sample number 1102; diagnostic sample


title: FL sample number 1107; diagnostic sample


title: FL sample number 1184; diagnostic sample


title: FL sample number 1099; diagnostic sample


title: FL sample number 1591; diagnostic sample


title: FL sample number 1586; diagnostic sample


title: FL sample number 1097; diagnostic sample


title: FL sample number 1186; diagnostic sample


title: FL sample number 1183; diagnostic sample


title: FL sample number 1185; diagnostic sample


title: FL sample number 1087; diagnostic sample


title: FL sample number 1104; diagnostic sample


title: FL sample number 1081; diagnostic sample


title: FL sample number 1085; diagnostic sample


title: FL sample number 1083; diagnostic sample


title: FL sample number 1088; diagnostic sample


title: FL sample number 1077; diagnostic sample


title: FL sample number 1418; diagnostic sample


title: FL sample number 1075; diagnostic sample


title: FL sample number 1440; diagnostic sample


title: FL sample number 888; diagnostic sample


title: FL sample number 1080; diagnostic sample


title: FL sample number 1078; diagnostic sample


title: FL sample number 879; diagnostic sample


title: FL sample number 739; diagnostic sample


title: FL sample number 1098; diagnostic sample


title: FL sample number 1090; diagnostic sample


title: FL sample number 1086; diagnostic sample


title: C_frozen_Method 2

city: Portland

middle: A

last: Harrington

state: OR

address: 3303 SW Bond Ave

department: Gene Microarray Shared Resource

institute: Oregon Health and Science University

hyb_protocol: [see characteristics field for details]

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Affymetrix 3000 GeneArray laser scanner with the 7G upgrade.  Image inspection was performed manually immediately following each scan.  The array image scan was processed with Affymetrix Microarray Suite, version 5.0, (MAS 5.0) software.

data_processing: Low-level analysis (background correction, normalization, and gene summarization) of microarray data was performed with both Affymetrix Microarray Suite 5.0 (MAS 5.0) and Robust Multi-Array Average (RMA). Individual arrays were analyzed and scaled with MAS 5.0 using manufacturer’s default thresholds for detection calls and with target scaling factor set as 275.  For RMA analysis, arrays were normalized in four separate groups based on target labeling method using RMA implemented in Affymetrix Expression Console (version 1.1).

source_name: Whole blood, frozen, Globin PNAs_Affymetrix

label_protocol: Amplifications and labelings were performed for each donor using one of the following four methods with RNA extracted from fresh and frozen blood samples:  Method 1 - Affymetrix one-cycle cDNA synthesis/Affymetrix in vitro-transcription (IVT) on whole blood RNA; Method 2 - Affymetrix one-cycle cDNA/Affymetrix IVT with globin peptide nucleic acids (PNAs) inclusion during cDNA synthesis; and Method 3- RNA pre-treated with Ambion GLOBINclear beads to reduce globin transcripts prior to labeling with the Affymetrix one-cycle cDNA synthesis/Affymetrix IVT.  In Method 4- cDNA target was synthesized from whole blood RNA using the NuGEN Ovation Biotin RNA Amplification and Labeling System. See individual sample annotation for protocol details.

extract_protocol: [see characteristics field for details]

treatment_protocol: Unfractionated whole blood collection and RNA isolation were performed using the PAXgene Blood RNA Isolation System (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA).  With the approval of the OHSU Institutional Review Board, blood was collected from healthy donors using eight PAXGene tubes per individual (donor).  Four tubes per donor were frozen for subsequent processing and four tubes per donor were processed fresh (see individual sample annotation for storage state details).  Following RNA isolation, DNase-treatment was performed as per PAXGene manufacturer’s recommendation.  Samples were then pooled within donor and within RNA storage state (fresh/frozen) resulting in two tubes per donor (fresh/frozen).  RNA recovery and quality was then assessed by examining UV 260/280 absorbance ratios and RNA size distribution on RNA Nano LabChips (Agilent Technologies, Santa Clara, CA, USA) processed on the Agilent 2100 Bioanalyzer.  For inclusion in this study, the RNA mass per donor had to be greater than 12 µg for both fresh and frozen blood aliquots.  Samples from three of the four donors (Donors A, C, D) met the quantitative and qualitative criteria and were used in the microarray analysis.

tag: Gender

value: M

tag: Age

value: 25, Normal

tag: Biosource

value: Peripheral whole blood

tag: Donor ID

value: Donor C

tag: Sample storage state

value: frozen

tag: Sample protocol

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.

tag: Treatment protocol

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with PNA treatment of total RNA (Globin PNAs_Affymetrix):The standard Affymetrix amplification and labeling was performed with the following modification:four peptide nucleic acid (PNA) oligonucleotides (Applied Biosystems, Foster City, CA, USA) designed to anneal to human α- and β-globin mRNA were added to the total RNA preparations immediately prior to initiation of the target synthesis step in order to bind globin mRNA and block cDNA synthesis. The PNA oligonucleotide stocks were prepared on day of use at concentrations recommended by Affymetrix (www.affymetrix.com/support/technical/byproduct.affx?product=bloodrna). Globin reduction PNA master mix was prepared by adding equal amounts of the globin PNA stocks. Five µg of total RNA were incubated with oligo-dT primer and 1 µl PNA master mix for 10 minutes at 70C prior to first strand cDNA synthesis.

tag: Label protocol

value: Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.

tag: Target molecule

value: cRNA

tag: Hyb protocol

value: Labeled cRNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations.  The fragmented material was combined with Affymetrix hybridization controls:biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Following the manufacturer’s recommendations, 6.5 µg of target were hybridized with the GeneChip Human Genome Focus array (Affymetrix) for 16 hours at 45C.  Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.


title: A_fresh_Method 4

source_name: Whole blood, fresh, no depletion_NuGEN

value: 31, Normal

value: Donor A

value: fresh

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then RNA was isolated from the fresh sample.

value: NuGEN Ovation Biotin RNA Amplification and Labeling System v.1 (no depletion_NuGEN):No modifications of sample made prior to target synthesis.

value: NuGEN Ovation Biotin:Ovation labeling and amplification reagents were obtained from NuGEN Technologies, Inc (San Carlos, CA, USA) and biotinylated cDNA targets were prepared according to manufacturer’s instructions. Using a unique, chimeric primer, first strand cDNA was synthesized from 30 ng total RNA.  Second strand synthesis of double-stranded cDNA was followed by a linear isothermal amplification (SPIA Amplification™) to produce single-stranded cDNA (the target).  A proprietary fragmentation and direct labeling process attached biotin to the amplified target.  Target purifications were performed using DNA Clean and Concentrator – 25 (Zymo Research, Orange, CA, USA) and the DyeEx 2.0 Spin Kit (Qiagen).

value: cDNA

value: Labeled cDNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations.  The fragmented material was combined with Affymetrix hybridization controls:biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Following the manufacturer’s recommendations, 1.3 µg of target were hybridized with the GeneChip Human Genome Focus array (Affymetrix) for 18 hours at 45C.  Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.


title: D_frozen_Method 4

source_name: Whole blood, frozen, no depletion_NuGEN

value: M

value: 24, Normal

value: Donor D

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.  Treatment protocol:NuGEN Ovation Biotin RNA Amplification and Labeling System v.1 (no depletion_NuGEN):No modifications of sample made prior to target synthesis. Label protocol:NuGEN Ovation Biotin:Ovation labeling and amplification reagents were obtained from NuGEN Technologies, Inc (San Carlos, CA, USA) and biotinylated cDNA targets were prepared according to manufacturer’s instructions. Using a unique, chimeric primer, first strand cDNA was synthesized from 30 ng total RNA. Second strand synthesis of double-stranded cDNA was followed by a linear isothermal amplification (SPIA Amplification™) to produce single-stranded cDNA (the target).  A proprietary fragmentation and direct labeling process attached biotin to the amplified target.  Target purifications were performed using DNA Clean and Concentrator – 25 (Zymo Research, Orange, CA, USA) and the DyeEx 2.0 Spin Kit (Qiagen).


title: A_fresh_Method 3

source_name: Whole blood, fresh, GLOBINclear_Affymetrix

value: Peripheral whole blood

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with GLOBINclear treated total RNA (GLOBINclear_Affymetrix):Globin mRNA depletion was performed in three steps using the GLOBINclear Kit (Ambion, Austin, TX, USA).  First, species-specific biotinylated oligonucleotides complementary to human α- and β- globin mRNA were hybridized with total RNA (5 µg).  Second, magnetic streptavidin-coated beads were added to bind the biotinylated-oligonucleotide:globin RNA complexes.  Finally, a magnet was used to remove beads with the selectively bound α- and β-globin transcripts. After globin mRNA depletion, RNA quantity was determined by UV absorbance and RNA integrity was assessed using RNA Nano LabChips as described above.  RNA recovery following GLOBINclear treatment ranged from 2-5 µg.


title: A_frozen_Method 2

value: frozen

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with PNA treatment of total RNA (Globin PNAs_Affymetrix):The standard Affymetrix amplification and labeling was performed with the following modification:four peptide nucleic acid (PNA) oligonucleotides (Applied Biosystems, Foster City, CA, USA) designed to anneal to human α- and β-globin mRNA were added to the total RNA preparations immediately prior to initiation of the target synthesis step in order to bind globin mRNA and block cDNA synthesis. The PNA oligonucleotide stocks were prepared on day of use at concentrations recommended by Affymetrix (www.affymetrix.com/support/technical/byproduct.affx?product=bloodrna). Globin reduction PNA master mix was prepared by adding equal amounts of the globin PNA stocks. Five µg of total RNA were incubated with oligo-dT primer and 1 µl PNA master mix for 10 minutes at 70C prior to first strand cDNA synthesis.

value: Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.


title: D_fresh_Method 2

source_name: Whole blood, fresh, Globin PNAs_Affymetrix

value: cRNA

value: Labeled cRNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations.  The fragmented material was combined with Affymetrix hybridization controls:biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Following the manufacturer’s recommendations, 6.5 µg of target were hybridized with the GeneChip Human Genome Focus array (Affymetrix) for 16 hours at 45C.  Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.


title: FL sample number 1089; diagnostic sample


title: C_frozen_Method 4

value: 25, Normal

value: Donor C


title: C_fresh_Method 2

value: fresh

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then RNA was isolated from the fresh sample.


title: A_frozen_Method 4

value: 31, Normal

value: Donor A

value: cDNA

value: Labeled cDNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations.  The fragmented material was combined with Affymetrix hybridization controls:biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Following the manufacturer’s recommendations, 1.3 µg of target were hybridized with the GeneChip Human Genome Focus array (Affymetrix) for 18 hours at 45C.  Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.


title: FL sample number 1073; diagnostic sample


title: C_frozen_Method 1

source_name: Whole blood, frozen, no depletion_Affymetrix

value: M

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.  Treatment protocol:Affymetrix one-cycle cDNA synthesis/Affymetrix IVT (no depletion_Affymetrix):No modifications of sample made prior to target synthesis.


title: C_frozen_Method 3

source_name: Peripheral whole blood, frozen, GLOBINclear_Affymetrix

value: Peripheral whole blood

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.  Treatment protocol:Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with GLOBINclear treated total RNA (GLOBINclear_Affymetrix):Globin mRNA depletion was performed in three steps using the GLOBINclear Kit (Ambion, Austin, TX, USA). First, species-specific biotinylated oligonucleotides complementary to human α- and β-globin mRNA were hybridized with total RNA (5 µg). Second, magnetic streptavidin-coated beads were added to bind the biotinylated-oligonucleotide:globin RNA complexes. Finally, a magnet was used to remove beads with the selectively bound α- and β-globin transcripts. After globin mRNA depletion, RNA quantity was determined by UV absorbance and RNA integrity was assessed using RNA Nano LabChips as described above. RNA recovery following GLOBINclear treatment ranged from 2-5 µg.  Label protocol:Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.


title: FL sample number 1074; diagnostic sample


title: FL sample number 738; diagnostic sample


title: FL sample number 878; diagnostic sample


title: FL sample number 886; diagnostic sample


title: C_fresh_Method 4

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then RNA was isolated from the fresh sample.  Treatment protocol:NuGEN Ovation Biotin RNA Amplification and Labeling System v.1 (no depletion_NuGEN):No modifications of sample made prior to target synthesis. Label protocol:NuGEN Ovation Biotin:Ovation labeling and amplification reagents were obtained from NuGEN Technologies, Inc (San Carlos, CA, USA) and biotinylated cDNA targets were prepared according to manufacturer’s instructions. Using a unique, chimeric primer, first strand cDNA was synthesized from 30 ng total RNA. Second strand synthesis of double-stranded cDNA was followed by a linear isothermal amplification (SPIA Amplification™) to produce single-stranded cDNA (the target).  A proprietary fragmentation and direct labeling process attached biotin to the amplified target.  Target purifications were performed using DNA Clean and Concentrator – 25 (Zymo Research, Orange, CA, USA) and the DyeEx 2.0 Spin Kit (Qiagen).


title: FL sample number 735; diagnostic sample


title: FL sample number 1076; diagnostic sample


title: D_fresh_Method 4

value: 24, Normal

value: Donor D


title: D_frozen_Method 2

value: frozen

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with PNA treatment of total RNA (Globin PNAs_Affymetrix):The standard Affymetrix amplification and labeling was performed with the following modification:four peptide nucleic acid (PNA) oligonucleotides (Applied Biosystems, Foster City, CA, USA) designed to anneal to human α- and β-globin mRNA were added to the total RNA preparations immediately prior to initiation of the target synthesis step in order to bind globin mRNA and block cDNA synthesis. The PNA oligonucleotide stocks were prepared on day of use at concentrations recommended by Affymetrix (www.affymetrix.com/support/technical/byproduct.affx?product=bloodrna). Globin reduction PNA master mix was prepared by adding equal amounts of the globin PNA stocks. Five µg of total RNA were incubated with oligo-dT primer and 1 µl PNA master mix for 10 minutes at 70C prior to first strand cDNA synthesis.

value: Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.

value: cRNA


title: D_frozen_Method 3

source_name: Whole blood, frozen, GLOBINclear_Affymetrix

value: Labeled cRNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations.  The fragmented material was combined with Affymetrix hybridization controls:biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Following the manufacturer’s recommendations, 6.5 µg of target were hybridized with the GeneChip Human Genome Focus array (Affymetrix) for 16 hours at 45C.  Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.


title: D_fresh_Method 3

value: fresh

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then RNA was isolated from the fresh sample.

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with GLOBINclear treated total RNA (GLOBINclear_Affymetrix):Globin mRNA depletion was performed in three steps using the GLOBINclear Kit (Ambion, Austin, TX, USA). First, species-specific biotinylated oligonucleotides complementary to human α- and β- globin mRNA were hybridized with total RNA (5 µg). Second, magnetic streptavidin-coated beads were added to bind the biotinylated-oligonucleotide:globin RNA complexes. Finally, a magnet was used to remove beads with the selectively bound α- and β-globin transcripts. After globin mRNA depletion, RNA quantity was determined by UV absorbance and RNA integrity was assessed using RNA Nano LabChips as described above. RNA recovery following GLOBINclear treatment ranged from 2-5 µg.


title: C_fresh_Method 3

value: 25, Normal

value: Donor C

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with GLOBINclear treated total RNA (GLOBINclear_Affymetrix):Globin mRNA depletion was performed in three steps using the GLOBINclear Kit (Ambion, Austin, TX, USA).  First, species-specific biotinylated oligonucleotides complementary to human α- and β- globin mRNA were hybridized with total RNA (5 µg).  Second, magnetic streptavidin-coated beads were added to bind the biotinylated-oligonucleotide:globin RNA complexes.  Finally, a magnet was used to remove beads with the selectively bound α- and β-globin transcripts. After globin mRNA depletion, RNA quantity was determined by UV absorbance and RNA integrity was assessed using RNA Nano LabChips as described above.  RNA recovery following GLOBINclear treatment ranged from 2-5 µg.  Label protocol:Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.


title: A_frozen_Method 3

value: M

value: 31, Normal

value: Peripheral whole blood

value: Donor A

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.  Treatment protocol:Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with GLOBINclear treated total RNA (GLOBINclear_Affymetrix):Globin mRNA depletion was performed in three steps using the GLOBINclear Kit (Ambion, Austin, TX, USA).  First, species-specific biotinylated oligonucleotides complementary to human α- and β-globin mRNA were hybridized with total RNA (5 µg).  Second, magnetic streptavidin-coated beads were added to bind the biotinylated-oligonucleotide:globin RNA complexes.  Finally, a magnet was used to remove beads with the selectively bound α- and β-globin transcripts. After globin mRNA depletion, RNA quantity was determined by UV absorbance and RNA integrity was assessed using RNA Nano LabChips as described above.  RNA recovery following GLOBINclear treatment ranged from 2-5 µg.  Label protocol:Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.


title: D_frozen_Method 1

value: 24, Normal

value: Donor D

value: frozen

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then transferred to a -80C freezer.  RNA was isolated from the frozen PAXGene tube after storage at -80C for at least one week.  Treatment protocol:Affymetrix one-cycle cDNA synthesis/Affymetrix IVT (no depletion_Affymetrix):No modifications of sample made prior to target synthesis.


title: NHMEC 99005 - replicate 6 - mAdbID:53410

first: Ofelia

middle: Ana

last: Olivero

address: 37 Convent Dr-MSC 4255

department: CDI

institute: NCI-CCR-

description: mAdb experiment ID: 53410

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

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.43028;; 3.84136 Temperature: 27.2423

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: NHMEC 99005 (untreated) - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Labeled with Cy3 by indirect coupling.

extract_protocol:
Trizol Extraction Protocol
Other: For isolation of RNA the cells were lysed with 1.0 mL of Trizol Reagent (Invitrogen Corp., Carlsbad, CA) and RNA was extracted according to manufacturer’s protocol.

value: female

tag: Tissue

value: mammary gland

tag: Cell line

value: NHMEC 99005

tag: Cell type

value: Normal Human Mammary Epithelial

source_name: NHMEC 99005 - TAM - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Labeled with Cy5 by indirect coupling.

treatment_protocol:
Treatment type: compound
Agent: Tamoxifen
Treatment dose: 10 uM
Treatment time: 48 hours
Treatment temperature: 37C
Other: Cells at passage 13 were plated at 1 x10^6 cells/15 cm plate or T-175 flask for DNA preparation, and at 1x10^6 cells/6-well plate for RNA preparation and survival, and grown for 48 hours prior to treatment with 10 uM TAM in vehicle (DMSO) for an additional 48 hours.


title: A_frozen_Method 1

value: Affymetrix One-Cycle:Target synthesis was performed following the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Using 1 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix, Santa Clara, CA, USA).  Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation.  In the second step, amplified and labeled cRNA (the target) was produced by a transcription reaction using T7 RNA polymerase and biotin-CTP (Affymetrix).  Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) followed by an ethanol precipitation of the labeled target.

value: cRNA

value: Labeled cRNA targets were chemically fragmented at 95C for 35 min as per Affymetrix’s recommendations.  The fragmented material was combined with Affymetrix hybridization controls:biotinylated control oligomer (B2) and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Following the manufacturer’s recommendations, 6.5 µg of target were hybridized with the GeneChip Human Genome Focus array (Affymetrix) for 16 hours at 45C.  Post-hybridization array processing was performed on the Fluidics Station 450 (Affymetrix); array staining and signal amplification were performed according to manufacturer’s recommendations.


title: A_fresh_Method 2

value: fresh

value: Whole blood was incubated in a PAXGene tube (PreAnalytiX, a Qiagen BD Company, Valencia, CA, USA) for two hours and then RNA was isolated from the fresh sample.

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT with PNA treatment of total RNA (Globin PNAs_Affymetrix):

tag: The standard Affymetrix amplification and labeling was performed with the following modification

value: four peptide nucleic acid (PNA) oligonucleotides (Applied Biosystems, Foster City, CA, USA) designed to anneal to human α- and β-globin mRNA were added to the total RNA preparations immediately prior to initiation of the target synthesis step in order to bind globin mRNA and block cDNA synthesis. The PNA oligonucleotide stocks were prepared on day of use at concentrations recommended by Affymetrix (www.affymetrix.com/support/technical/byproduct.affx?product=bloodrna).  Globin reduction PNA master mix was prepared by adding equal amounts of the globin PNA stocks. Five µg of total RNA were incubated with oligo-dT primer and 1 µl PNA master mix for 10 minutes at 70C prior to first strand cDNA synthesis.


title: NHMEC 99005 - dye swap - replicate 3 - mAdbID:53691

description: mAdb experiment ID: 53691

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.37321;; 3.85022 Temperature: 24.5262

source_name: NHMEC 99005 (untreated) - Cy5

source_name: NHMEC 99005 - TAM - Cy3


title: NHMEC 98016 - replicate 4 - mAdbID:53408

description: mAdb experiment ID: 53408

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.45286;; 3.7611 Temperature: 28.0663

source_name: NHMEC 98016 (untreated) - Cy3

value: NHMEC 98016

source_name: NHMEC 98016 - TAM - Cy5


title: NHMEC 98040 - replicate 3 - mAdbID:53076

description: mAdb experiment ID: 53076

scan_protocol: Creator: GenePix Pro 4.0.0.54 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.51421;; 3.96741 Temperature: 26.6015

source_name: NHMEC 98040 (untreated) - Cy3

value: NHMEC 98040

source_name: NHMEC 98040 - TAM - Cy5


title: NHMEC 98040 - dye swap - replicate 2 - mAdbID:47769

description: mAdb experiment ID: 47769

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.44157;; 3.6082 Temperature: 26.8151

source_name: NHMEC 98040 (untreated) - Cy5

source_name: NHMEC 98040 - TAM - Cy3


title: A_fresh_Method 1

source_name: Whole blood, fresh, no depletion_Affymetrix

label_protocol: Amplifications and labelings were performed for each donor using one of the following four methods with RNA extracted from fresh and frozen blood samples:  Method 1 - Affymetrix one-cycle cDNA synthesis/Affymetrix in vitro-transcription (IVT) on whole blood RNA; Method 2 - Affymetrix one-cycle cDNA/Affymetrix IVT with globin peptide nucleic acids (PNAs) inclusion during cDNA synthesis; and Method 3- RNA pre-treated with Ambion GLOBINclear beads to reduce globin transcripts prior to labeling with the Affymetrix one-cycle cDNA synthesis/Affymetrix IVT. In Method 4- cDNA target was synthesized from whole blood RNA using the NuGEN Ovation Biotin RNA Amplification and Labeling System. See individual sample annotation for protocol details.

value: M

value: 31, Normal

value: Peripheral whole blood

value: Donor A

value: Affymetrix one-cycle cDNA synthesis/Affymetrix IVT (no depletion_Affymetrix):No modifications of sample made prior to target synthesis.


title: NHMEC 98040 - replicate 1 - mAdbID:47767

description: mAdb experiment ID: 47767

scan_protocol: Creator: GenePix Pro 4.0.1.6 Scanner: GenePix 4000B [84573] ScanPower: 100;; 100 LaserPower: 3.44462;; 3.5374 Temperature: 26.0826

value: female

value: mammary gland