title: control embryos at 48hpf, biological rep 4

city: Dunedin

first: Julia

last: Horsfield

address: Cnr Hanover and Great King Streets

department: Pathology Department

country: New Zealand

institute: University of Otago

description: Gene Expression data from WT control embryos at 48hpf

hyb_protocol: see label protocol

scan_protocol: Arrays were scanned using a 7Gplus Affymetrix scanner.

data_processing: Cell file data was generated using  the Affymetrix Algorithm Feature extraction- 6.2.33. Data was normalized using  RMAExpress.

organism: Danio rerio

source_name: control embryos at 48hpf

label_protocol: 100ng of total RNA was labeled and hybridized as outlined in the Affymetrix IVT express kit protocol catalogue number 901229. Arrays were washed using an Affymetrix 450 wash station and Affymetrix wash protocol  FS450_0004

growth_protocol: Embryos were kept in embryo medium at 28.5 degrees Celcius until collected for RNA extraction.

extract_protocol: Total RNA was extracted from 4 replicates (50 embryos each) using Trizol (Invitrogen) and purified using Qiagen RNeasy columns according to the manufacturer’s instructions. RNA integrity was measured using the Agilent Bioanalyzer 2100 (RIN ≥ 9.5 for all samples).

treatment_protocol: Zebrafish were injected at the 1-cell stage with either an esco2 morpholino (esco2 MO) or with buffer only (control).

tag: tissue

value: dechorionated whole embryos

tag: genotype

value: wild type control

tag: age

value: 48 hpf


title: CLL CD4 cells - after stimulation - proband7

status: Public on Mar 01 2011

type: RNA

city: Freiburg

first: Petros

last: Christopoulos

address: Hugstetter Str. 55

department: Medizin I.

country: Germany

institute: Uniklinik Freiburg

description:
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CD4 cells - after stimulation - proband7 - rep1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.

extract_protocol: Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).

treatment_protocol: For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).

tag: cell type

value: peripheral blood CD4 cells

tag: disease state

value: CLL

tag: age in years

tag: used in fl/emzl vs healthy comparison (1-yes)

tag: used in cll vs healthy comparison (1-yes)

tag: used in mgus vs healthy comparison (1-yes)


title: WT_fedL1_rep3

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

country: USA

institute: HHMI/UCB

description: Synchronous L1s fed for 3 hours

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: Arrays were normalized by RMA (Robust Multichip Average) using Affymetrix Expression Consol software (Irizarry et al. 2003). Data were analyzed by ArrayStar. Statistical analysis was performed using a moderated t-test with FDR multiple testing correction (Benjamini-Hochberg method). Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. 2003. Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 4: 249-264.

organism: Caenorhabditis elegans

source_name: embryos from worms grown on NG plates

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Fed L1s used for microarray analysis were obtained by feeding synchronous L1 larvae with HB101 for 3 hours

extract_protocol: Gravid adults were bleached and hatched off for 24 hours in 1XM9 at 20 degrees celcius. Synchronous L1s were placed in S medium at a density of 10 worms/uL and fed with 10 mg/mL HB101 E.coli for 3 hours at 20 degrees celcius in liquid culture. Fed L1s were harvested as described (Portman, D.S, Wombook, Profiling C. elegans gene expression with DNA microarrays) and 100 µl aliquots snap frozen in liquid nitrogen and stored at -80∞C. An aliquot was thawed at 65∞C for 10 minutes, resuspended in 1ml Trizol (Invitrogen, Carlsbad, CA), vortexed vigorously to resuspend, and incubated for 20 minutes at room temperature. The sample was then centrifuged for 15 minutes at 12,000xg at 4∞C. The aqueous phase was transferred to a new tube and 100 µl of BCP (1-bromo-3-chloropropane) (MRC, Cincinnati, OH) was added, the sample was mixed by vortexing, incubated for 15 minutes at room temperature, and centrifuged for 10 minutes at 12,000xg at 4∞C. The aqueous phase was transferred to a new tube and nucleic acid was precipitated by addition of 500 µl of isopropanol. The sample was incubated for 10 minutes at room temperature, centrifuged at 12,000xg for 8 minutes, washed in 70% ethanol and air dried for 5 minutes. Nucleic acid was resuspended in 100 µl nuclease-free water and RNA quantified with a UV spectrophotometer. One hundred micrograms of RNA was then treated with 3 µl RQ1-DNAse (Promega, Madison, WI) and RNA isolated with the RNAeasy kit as per the manufacturer's protocol (Qiagen, Valencia, CA). RNA was again quantified with a UV spectrophotometer and cDNA was prepared from 5 µg RNA using the Protoscript Kit (NEB, Ipswich, MA) and diluted 1:15 in water.

tag: genotype/variation

value: wild type (N2)

tag: developmental stage

value: larval stage L1

tag: protocol

value: Synchronous L1s fed for 3 hours


title: ISC_GG U133 Plus 2.0

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Gene expression data from peripheral blood sample

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU133 Plus 2.0 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: The data were processed by the function mas5 from the Bioconductor affy package

source_name: Human peripheral blood sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA

extract_protocol: Qiagen RNeasy Mini extraction of total RNA was performed according to the manufacturer instructions

value: blood

value: Infective colitis


title: whole-blood_0_Rep9

city: CA

first: James

middle: A.

last: Wingrove

address: 2500 Faber Place

institute: CardioDx, Inc.

hyb_protocol: Labeled RNAs were hybridized using the Agilent protocol (Agilent, version 4.0.1)

scan_protocol: Agilent Feature Extraction Software (version 9.5.3.1) was used for background subtraction and LOWESS normalization.

data_processing: Agilent processed signal values were used;  values were scaled to a trimmed mean of 100 using an R script developed in-house at CardioDx.

label_protocol: 200 ng of each patient whole blood RNA was labeled with Cy3 using Agilent's Low RNA Input Linear Amplification Kit following the recommended protocol.

growth_protocol: Whole blood (2.5 ml) was collected via syringe during catheterization.

extract_protocol: RNA was extracted per manufacturers protocol (PreAnalytix, Franklin Lakes, NJ)

treatment_protocol: Collected blood was aliquoted into PaxGene tubes, inverted 10X and then frozen at -20 C until further processing

value: Control (0)


title: FL CD4 cells - after stimulation - proband5

source_name: CD4 cells - after stimulation - proband5 - rep1

value: FL


title: WT_fedL1_rep2

description: Synchronous L1s fed for 3 hours

treatment_protocol: Fed L1s used for microarray analysis were obtained by feeding synchronous L1 larvae with HB101 for 3 hours


title: WT BMDMs CpG 0hr

city: La Jolla

first: Alexander

last: Hoffmann

address: UCSD m/c 0375, NSB 3318 9500, Gilman Dr

department: Chemistry and Biochemistry

institute: UCSD

description: BMDM expression in response to LPS, CpG or IFNb

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized using Illumina Inc. BeadStudio

organism: Mus musculus

source_name: Bone marrow derived macrophages

label_protocol: Biotinylated cRNA was prepared with the Ambion Message Amp kit for Illumina arrays

growth_protocol: BMDMs were cultured in L929 cell conditioned medium for 5 to 8 days

extract_protocol: Total RNA was extracted from BMDMs with Rneasy columns (Qiagen)

treatment_protocol: BMDMs were stimulated with LPS, CpG or IFNb

tag: strain

value: BMDM

value: wild type

tag: agent

value: CpG

tag: time


title: D_SZI U133 Plus 2.0

value: Diverticulitis


title: esco2 MO injected embryos at 48hpf, biological rep 3

description: Gene Expression data from esco2 morphant embryos at 48hpf

source_name: esco2 MO injected embryos at 48hpf

value: esco2 morphants


title: control embryos at 48hpf, biological rep 3

value: dechorionated whole embryos


title: esco2 MO injected embryos at 48hpf, biological rep 1


title: D_MKne U133 Plus 2.0


title: esco2 MO injected embryos at 48hpf, biological rep 4


title: IC_MT U133 Plus 2.0


title: esco2 MO injected embryos at 48hpf, biological rep 2


title: whole-blood_0_Rep7


title: D_RA div U133 Plus 2.0


title: whole-blood_0_Rep3


title: esco2 MO injected embryos at 24hpf, biological rep 2

description: Gene Expression data from esco2 morphant embryos at 24hpf

source_name: esco2 MO injected embryos at 24hpf

value: 24 hpf


title: whole-blood_0_Rep5


title: whole-blood_0_Rep4


title: whole-blood_0_Rep2


title: whole-blood_0_Rep6


title: whole-blood_0_Rep8


title: control embryos at 48hpf, biological rep 1

value: wild type control

value: 48 hpf


title: D_KJne div U133 Plus 2.0


title: control embryos at 24hpf, biological rep 4

description: Gene Expression data from WT control embryos at 24hpf

source_name: control embryos at 24hpf


title: esco2 MO injected embryos at 24hpf, biological rep 3


title: esco2 MO injected embryos at 24hpf, biological rep 1


title: HT-29_siLuc_72h

city: Hong Kong

first: William

middle: K. C.

last: Cheung

address: Pokfulam Road

department: Chemistry

country: China

institute: The University of Hong Kong

description: Microarray hybridization and image scanning was performed by the Genome Research Centre, The University of Hong Kong.

hyb_protocol: After fragmentation, 15 μg of cRNA was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array using Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 h. The microarray chips were then washed and stained using GeneChip Fluidics Station 400 (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The images were scanned by GeneChip Scanner 3000 (Affymetrix).

data_processing: Primary image analysis was performed with MicroArray Suite v5.0 (MAS5, Affymetrix).

source_name: HT-29 cells, siLuc

label_protocol: Total RNA was first amplified and labeled with MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion Inc., TX). Double strand cDNA was then reverse transcribed from 1 μg of amplified total RNA using Oligo(dT) primer bearing a T7 promoter. The double strand cDNA was used as a template for in vitro transcription to generate biotin-labeled cRNA.

extract_protocol: RNeasy Mini kit (Qiagen).

treatment_protocol: HT-29 cells were transfected with siRNAs targeting firefly luciferase and human IFITM1 mRNAs for 72 h. A siLuc-transfected sample was used as the baseline control.

tag: cell line

value: colorectal adenocarcinoma

tag: sirna

value: siLuc


title: esco2 MO injected embryos at 24hpf, biological rep 4

tag: tissue


title: Disc Tissue 22

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

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

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

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

source_name: Disc Tissue

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

extract_protocol: RNA was isolation via 1.) Cells were collected via laser capture mircodissection (LCM) and total RNA was isolated according to the Paradise reagent system 2.) tissue was homongenized and RNA isolated using TRIzol reagent

value: V

value: Homogenization

value: Surgical specimen


title: SW620_MOCK_KO

city: Seattle

first: Biaoyang

last: Lin

state: WA

address: 550 17th Ave, James Tower suite 550

department: Swedish Neuroscience Institute

institute: Swedish Medical Center

description: gene expression data from liver of ECM1 Ko mice

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133_plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: the chips were scanned withthe affymetrix genechip 7G plus, and AGCC is used for the image processing.

data_processing: RMA normalization using GeneSpring 7.3

source_name: Sw620 human colorectal cancer cell line with Mock knockdown

label_protocol: start with 250ng total RNA, and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, GeneChip 3 IVT Express Kit,(Lot no. 901228) is used in the experiment.

growth_protocol: cells were cultured in RPMI-1640 cell culture media

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

treatment_protocol: Sox2 was knockdown in sw620 cell lines  by lentivrus mediated ShRNA and mock no target conrtol ShRNA

value: Sw620 colorectal cancer


title: control embryos at 24hpf, biological rep 2

tag: genotype


title: control embryos at 24hpf, biological rep 3

tag: age


title: SW620_SOX2_KO

source_name: Sw620 human colorectal cancer cell line with Sox2 knockdown


title: HT-29_siIFITM1_72h

source_name: HT-29 cells, siIFITM1

tag: cell type


title: whole-blood_0_Rep1

tag: disease state

value: Control (0)


title: In vivo exp 1 LNCaP 10mg kg ABR-215050 24h

city: Lund

first: Johan

last: Vallon-Christersson

address: Lund University

department: Department of Oncology, Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Prior to hybridization, arrays were UV-cross-linked at 500 mJ/cm2 and pretreated using the Universal Microarray Hybridization Kit (Corning) according to manufacturers' instructions. Slides were hybridized using Corning Pronto Plus system 6 (Corning) on a MAUI®Hybridization System.

scan_protocol: Arrays were washed using Universal Microarray Hybridization Kit (Corning) according to manufacturers' instructions and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for treated sample were stored as channel 1 (ch1) whereas quantified intensities for control sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots that were flagged during image-analysis or had a background corrected intensity value >64999 signal units were removed and regarded as missing values. Spots with a background corrected intensity value <1 signal units were set to value 1. Spots from dye-swap hybridization were merged using geometric mean of ratios requiring presence in both replicates. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying Lowess on M values stratified into 8 separate groups defined spatially by pin-tip (8 neighboring pin-tips per group).

source_name: Experimental samples after 24h treatment.

label_protocol: Fluorescently labeled cDNA targets for hybridization were prepared according to manufacturers' instructions using the Corning Pronto Plus system 6 (Corning).

growth_protocol: Nude BALB/c mice (8-10 weeks old) were used for subcutaneous implantation of human prostate tumor cells LNCaP. Distribution for 24h of ABR-215050 at 10 mg/kg/day (administered orally via the drinking water (ad.lib.)) started on day 14 or day 21 after inoculation. All animal experiments were conducted in accordance with the Bioethics Committee guidelines in Lund, Sweden.

extract_protocol: Tumor samples were collected and stored at -70°C. About 50 mg of frozen tumor tissue were cut and cruched in LN2, followed by immediate addition of 1 ml Trizol® (Invitrogen). The total RNA was isolated by extracting the Trizol® samples with chloroform followed by separation and purification using a modified protocol for the RNeasy RNA extraction Kit (Qiagen). 1 µl RNAse inhibitor mix was added per 50 µl total RNA before treatment with DNAse for 20 min (DNA-free™; Ambion, Austin TX). The RNA concentration and purity was quality controlled by analysis with a Bioanalyser.

treatment_protocol: Tumor bearing mice (2 animals on each time point) were exposed to ABR-215050 at 10 mg/kg for 24 h at day 14 and day 21 after inoculation before the tumors were excised, frozen at -70°C, and used for RNA extraction.

value: LNCaP

source_name: Control samples no treatment.


title: CD19_selected_B-cells_after_FC_rep10

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

description: no additional information

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA

source_name: CD19 selected B-cells

label_protocol: Standard Affymetrix protocol.

extract_protocol: Trizol followed by RNeasy Mini kit (Qiagen)

tag: treatment

value: after FC


title: Disc Tissue 23


title: Disc Tissue 20

value: IV


title: CD19_selected_B-cells_after_FC_rep8

description: no additional information


title: In vivo exp 4 LNCaP 10mg kg ABR-215050 24h


title: control embryos at 24hpf, biological rep 1


title: Disc Tissue 18

value: II


title: In vivo exp 2 LNCaP 10mg kg ABR-215050 24h


title: Disc Tissue 21


title: Disc Tissue 17

value: III


title: CD19_selected_B-cells_after_FC_rep6

description: no additional information


title: Disc Tissue 19


title: CD19_selected_B-cells_after_FC_rep7

description: no additional information


title: In vivo exp 3 LNCaP 10mg kg ABR-215050 24h


title: CD19_selected_B-cells_after_FC_rep9

description: no additional information


title: CD19_selected_B-cells_after_FC_rep2

description: no additional information


title: Disc Tissue 15

value: LCM

value: CHTN specimen


title: Disc Tissue 13

value: I


title: Disc Tissue 16


title: CD19_selected_B-cells_after_FC_rep3

description: no additional information


title: CD19_selected_B-cells_after_FC_rep4

description: no additional information


title: CD19_selected_B-cells_after_FC_rep5

description: no additional information


title: Disc Tissue 12


title: Disc Tissue 14


title: CD19_selected_B-cells_before_FC_rep10

description: no additional information

value: before FC (control)


title: CD19_selected_B-cells_after_FC_rep1

description: no additional information


title: CD19_selected_B-cells_before_FC_rep9

description: no additional information


title: Disc Tissue 10


title: Disc Tissue 8


title: Disc Tissue 11


title: Disc Tissue 9


title: CD19_selected_B-cells_before_FC_rep8

description: no additional information


title: CD19_selected_B-cells_before_FC_rep6

description: no additional information


title: CD19_selected_B-cells_before_FC_rep5

description: no additional information


title: CD19_selected_B-cells_before_FC_rep7

description: no additional information


title: Phos_96h_4

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

country: United Kingdom

institute: Dstl

hyb_protocol: Test and control RNA was resuspended in 250ul of hybridisation buffer supplied by the microarray slide manufacturer (MWG Biotech, Ebersberg, Germany). Slides were hybridised overnight in hybridisation chambers (Qiagen, Crawley, West Sussex) for 16 hours at 42C in the dark and then washed in 3 different wash buffers for 5 minutes each wash. Wash buffer 1 consisted of 2 x SSC (buffered solution of sodium chloride and trisodium citrate), 0.1% SDS (Sigma, Poole), wash buffer 2 consisted of 1 x SSC and wash buffer 3 consisted of 0.5% SSC. All wash buffers were filter sterilised to prevent contaminating debris. The slides were dried by centrifugation at 500 x g for 5 minutes.

scan_protocol: Scanning was performed using a 428 nm scanner (GenePix 4000B, Axon, US) using the appropriate gain settings and filters for the Cy3 and Cy5 dyes (Cy3 = 532nm, 17mW, Cy5 = 635nm, 10mW).

data_processing: Image analysis was carried out using BlueFuse image analysis software (BlueGnome, Cambridge, UK). Statistical analysis of the array data was performed using GeneSpring software, version GX7.3 (Agilent Technologies, Berks, UK). Data were normalised using a Lowess curve fit to log-intensity versus log ratio plot, where 20% of the data were used for the Lowess normalisation. Agent data were then normalised to the respective sham time-matched control expression level for every spot on the chip (1509) using the “normalise to specific sample” algorithm within GeneSpring version GX7.3 (e.g. 24 hour agent normalised to 24 hour sham).

label_protocol: RNA was labelled using the LabelStar Array Kit (Qiagen, Crawley, West Sussex, UK). 3mg of test RNA (ricin or sham exposed) was labelled with Cyanine 3-dNTP (Cy3) (Ambion, Cambridgeshire, UK) and 3mg of universal mouse reference RNA (Stratagene Europe, Netherlands) labelled with Cyanine 5-dNTP (Cy5) (Ambion, Cambridgeshire, UK).

extract_protocol: Total RNA was extracted from each of the six lung tissue samples, after homogenisation with a rotor stator homogeniser, using the RNeasy Mini Kit (Qiagen, Crawley, West Sussex, UK) following the manufacturer’s protocol.

treatment_protocol: Phosgene or air only control

value: phosgene

tag: time point

value: Balb/c

tag: gender

value: Female

value: Lung

source_name: Stratagene Universal Reference RNA

value: Mixture of 11 cell lines


title: Disc Tissue 6

value: Surgical specimen


title: Disc Tissue 7


title: CD19_selected_B-cells_before_FC_rep4

description: no additional information


title: CD19_selected_B-cells_before_FC_rep3

description: no additional information


title: Phos_4h_4(2)


title: CD19_selected_B-cells_before_FC_rep1

description: no additional information


title: Disc Tissue 4


title: NB581

city: Gaithersburg

first: Javed

last: Khan

state: MD

address: 8717 Grovemont Circle

institute: National Cancer Institute

hyb_protocol: Microarrays were hybridized overnight with 5 ug biotin labelled ss-DNA, and washed in fluidics station wash protocol: FS450_0001

scan_protocol: Genechip scanner 3000 7G was used.

data_processing: We used Affymetrix Power Tool (APT) to get signal intensities for probesets and transcript clusters. Probeset signals were estimated by PLIER and a detection p-value was assigned to each probeset by DABG algorithm.

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual.

extract_protocol: Total RNA is extracted using Trizol method

value: Neuroblastoma

tag: tumor stage


title: Disc Tissue 5


title: Disc Tissue 3


title: Phos_48h_4


title: Disc Tissue 2


title: Phos_24h_4


title: CD19_selected_B-cells_after_RFC_rep10

description: no additional information

value: after RFC


title: CD19_selected_B-cells_before_FC_rep2

description: no additional information


title: Disc Tissue 1


title: CD19_selected_B-cells_after_RFC_rep8

description: no additional information


title: Phos_7h_2


title: Phos_96h_2


title: NB541


title: NB547


title: NB545


title: CD19_selected_B-cells_after_RFC_rep7

description: no additional information


title: NB543


title: NB536


title: Phos_48h_2


title: NB548


title: Phos_4h_4


title: Phos_24h_2


title: NB515


title: Phos_1h_2(2)


title: CD19_selected_B-cells_after_RFC_rep5

description: no additional information


title: Phos_1h_2(3)


title: NB509


title: CD19_selected_B-cells_after_RFC_rep4

description: no additional information


title: Phos_96h_1


title: NB521


title: NB511


title: CD19_selected_B-cells_after_RFC_rep2

description: no additional information


title: CD19_selected_B-cells_after_RFC_rep3

description: no additional information


title: Phos_7h_1


title: NB510


title: CD19_selected_B-cells_after_RFC_rep6

description: no additional information


title: Phos_7h_1(2)


title: NB504


title: apum23 replicate 3

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Aerial parts of three-week old soil grown apum23-3 mutant.

hyb_protocol: After cleanup with a Sample Cleanup Module (Affymetrix), 10-15 ug of labeled cRNA was fragmented from 35 to 200 nt using fragmentation buffer (Affymetrix). Fragmented cRNA was hybridized to the Arabidopsis ATH1 Genome arrays (Affymetrix) at 45C for 16 h according to the Affymetrix standard protocol. After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a non-stringent wash buffer at 25C followed by a stringent wash buffer at 50C. After washing, the arrays were stained with a streptavidin-phycoerythrin complex.

scan_protocol: Intensities were determined with a GeneChip scanner 3000 (Affymetrix) controlled by GCOS Affymetrix software.

data_processing: The data were normalized and processed with cubic spline normalization using quantiles to adjust signal variations between chips [Workman, 2002 #327]. Gene-level summarization was performed by Robust Multi-Chip Analysis (RMA) using a median polish algorithm. This method identifies probes that are outliers in the overall behavior of the expression for a given gene, and the contribution by those outliers is reduced in the reported gene expression level. This improves the sensitivity and reproducibility of microarray results [Irizarry, 2003 #328].Multiple analysis was performed with the limma package in the R computing environment [Smyth, 2004 #329]. This package adopts the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes. Genes for which the adj. P. Value or false discovery was below 0.05 were collected and further selected to identify genes with expression levels that were higher than 1.0 or less than -1.0 as compared to those of wild type. To determine the significantly affected GO terms (cellular component, biological process and molecular function) in the apum23-1 mutant, GO analysis was performed with GoMiner [Ashburner, 2000 #330; Zeeberg, 2003 #331]. The Arabidopsis design ATH1 contains 23,288 genes annotated in TAIR8 version, and this number of genes was used as a total gene set in GoMiner for the analysis. Gominer first categorized each gene according to GO terms and mode of gene expression: down- or up- regulation. Modes of expression of the terms are denoted as Under, Over, and Change according to their regulated gene modes: down- and up-regulated genes and both of these. Gominer then calculated P-values with the one-sided Fisher exact test for the total number of categorized GO terms. False discovery rate (FDR) values were obtained from 100 randomizations. GO terms for which FDR were less than 0.05, at least at one condition (under, over, or change), were collected.

organism: Arabidopsis

source_name: apum23 plants grown on soil for 21 days

label_protocol: Total RNA was isolated from the aerial parts of Arabidopsis plants grown on composite soil for 3 weeks using TRIzol reagent (Invitrogen) and further purified using RNeasy Mini Kit (Qiagen). The purity and integrity of the total RNA were checked using the NanoDrop (NanoDrop Technologies) and the Experion (BioRad), respectively. Five micrograms of total RNA were used for probe labeling. Probe synthesis from total RNA samples, hybridization, detection, and scanning were performed according to standard protocols from Affymetrix, Inc. Briefly, cDNA was synthesized from total RNA using the One-Cycle cDNA Synthesis Kit (Affymetrix). Single stranded cDNA was synthesized using Superscript II reverse transcriptase and T7-oligo (dT) primers at 42¡ÆC for 1 h. Double stranded (ds)-cDNA was obtained by using DNA ligase, DNA polymerase I and RNase H at 16¡ÆC for 2 h, followed by T4 DNA polymerase at 16¡ÆC for 5 min for gap filling. After clean up with a Sample Cleanup Module (Affymetrix), ds-cDNA was used for in vitro transcription (IVT). cDNA was transcribed using the GeneChip IVT Labeling Kit (Affymetrix) in the presence of biotin-labeled CTP and UTP.

growth_protocol: Wild type (Col-3) and apum23-1 mutant seeds were grown on composite soil for 3 weeks under 8 h light/16 h dark cycles at 22C under white light conditions (120 umol photons m-2 s-1). Three-week old plants were harvested for total RNA isolation.

extract_protocol: TriZol procedure and sample were further purified using RNeasy Mini Kit (Qiagen).

tag: cultivar

tag: genotype/variation

value: apum23 mutant

value: aerial parts


title: CD19_selected_B-cells_after_R_rep10

description: no additional information

value: after Rituximab


title: CD19_selected_B-cells_after_RFC_rep1

description: no additional information


title: Phos_4h_1


title: apum23 replicate 2

description: Aerial parts of three-week old soil grown apum23-2 mutant.


title: Phos_48h_1


title: CD19_selected_B-cells_after_R_rep9

description: no additional information


title: Phos_24h_1


title: apum23 replicate 1

description: Aerial parts of three-week old soil grown apum23-1 mutant.


title: NB282


title: NB500


title: wild-type (Col-3) replicate 3

description: Aerial parts of three-week old soil grown wild-type (Col-3)

source_name: Wild type (Col-3) plants grown on soil for 21 days

value: wild type


title: NB508


title: wild-type (Col-3) replicate 2


title: Phos Sham_96h_3

value: air only control


title: CD19_selected_B-cells_after_R_rep7

description: no additional information


title: NB506


title: NB283


title: Phos_1h_1


title: CD19_selected_B-cells_after_R_rep6

description: no additional information


title: wild-type (Col-3) replicate 1


title: CD19_selected_B-cells_after_R_rep5

description: no additional information


title: NB278


title: NB269


title: NB275


title: NB266


title: NB540


title: Phos Sham_7h_3


title: Phos Sham_48h_3


title: CD19_selected_B-cells_after_RFC_rep9

description: no additional information


title: CD19_selected_B-cells_after_R_rep4

description: no additional information


title: NB503


title: Phos Sham_24h_3


title: Phos Sham_4h_3


title: CD19_selected_B-cells_after_R_rep2

description: no additional information


title: CD19_selected_B-cells_after_R_rep3

description: no additional information


title: NB238


title: NB265


title: NB237


title: Phos Sham_96h_2


title: Phos Sham_7h_2


title: NB210


title: CD19_selected_B-cells_after_R_rep8

description: no additional information


title: Phos Sham_1h_3


title: Phos Sham_48h_2


title: Phos Sham_24h_2


title: NB221


title: NB208


title: CD19_selected_B-cells_before_R_rep8

description: no additional information

value: before Rituximab (control)


title: Phos Sham_1h_2


title: CD19_selected_B-cells_after_R_rep1

description: no additional information


title: NB206


title: CD19_selected_B-cells_before_R_rep5

description: no additional information


title: CD19_selected_B-cells_before_R_rep7

description: no additional information


title: NB205


title: CD19_selected_B-cells_before_R_rep6

description: no additional information


title: CD19_selected_B-cells_before_R_rep4

description: no additional information


title: Phos Sham_7h_1


title: CD19_selected_B-cells_before_R_rep3

description: no additional information


title: arabinose-limited chemostat IMS0002 rep3

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description:
Saccharomyces cerevisiae IMS0002; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; selected for anaerobic growth on arabinose.
WWA08

hyb_protocol: Probe preparation and hybridization to Affymetrix Genechip YG-S98 microarrays were performed according to Affymetrix instructions, with the following modifications: double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA was monitored using the Agilent Bioanalyser 2100 (Agilent Technologies). Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChip® Operating Software (GCOS) version 1.2. Prior to comparison, all arrays were globally scaled to a target value of 150, using the average signal from all gene features, with GCOS (version 1.2).

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

organism: Saccharomyces cerevisiae

source_name: Anaerobic chemostat sample at D=0.03 h-1

growth_protocol: Anaerobic chemostat cultivation with strains IMS0001 and IMS0002 was carried out at 30 °C in 2 liter fermenters (Applikon, Schiedam, the Netherlands) with a working volume of 1 l. Cultures were performed in MY supplemented with 0.01 g l-1 ergosterol and 0.42 g l-1 Tween 80 dissolved in ethanol (Andreasen and Stier, 1953; Andreasen and Stier, 1954), silicon antifoam, vitamin solution and trace elements (Verduyn et al., 1992), and 20 g l-1 glucose (MYG) or arabinose (MYA), and was maintained at pH 5.0 by automatic addition of 2 M KOH. Cultures were stirred at 800 rpm and sparged with 0.5 l min-1 nitrogen gas (<10 ppm oxygen). To minimize oxygen diffusion, fermenters were equipped with Norprene tubing (Cole Palmer Instrument Company, Vernon Hills, USA). Absence of oxygen was verified with an oxygen electrode (Applisens, Schiedam, the Netherlands). After inoculation and completion of the batch phase, chemostat cultivation on MYA or MYG was initiated at a dilution rate of 0.03 h-1. The working volume of the culture was kept constant using an effluent pump controlled by an electric level sensor. Chemostats were assumed to be in steady state when, after at least five volume changes, dry weight and specific CO2 production rate changed by less than 2% over two further volume changes. Samples for microarray, biomass dry weight, extra- and intracellular metabolite analyses were taken between 7 and 9 volume changes after the onset of continuous cultivation.

value: arabinose limited

tag: sample type

value: chemostat culture steady state sample


title: Phos Sham_4h_1

tag: strain


title: Phos Sham_48h_1

tag: agent


title: arabinose-limited chemostat IMS0002 rep2

description:
Saccharomyces cerevisiae IMS0002; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; selected for anaerobic growth on arabinose.
WWA05

label_protocol: Probe preparation and hybridization to Affymetrix Genechip YG-S98 microarrays were performed according to Affymetrix instructions, with the following modifications: double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA was monitored using the Agilent Bioanalyser 2100 (Agilent Technologies). Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChip® Operating Software (GCOS) version 1.2. Prior to comparison, all arrays were globally scaled to a target value of 150, using the average signal from all gene features, with GCOS (version 1.2).


title: NB33


title: CD19_selected_B-cells_before_R_rep2

description: no additional information


title: CD19_selected_B-cells_before_R_rep1

description: no additional information


title: Phos Sham_1h_1


title: detached-A.thaliana-leaf_24hpi_rep2

city: Cape Town

first: Joseph

middle: Mary Kusasira

last: Mulema

state: Western Cape

address: Private Bag, Rondebosch

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

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

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

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

organism: Arabidopsis thaliana

source_name: Control A. thaliana leaves harvested after 24 hr

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

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

extract_protocol: Total RNA extracted using Phenol-Lithium chloride method

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

tag: ecotype

value: leaves

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

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


title: NB31


title: NB29


title: Sham_96h_3

extract_protocol: Total RNA was extracted from each of the 10 lung tissue samples, after homogenisation with a rotor stator homogeniser, using the RNeasy Mini Kit (Qiagen, Crawley, West Sussex, UK) following the manufacturer’s protocol.

treatment_protocol: Francisella tularensis or culture media aerosol exposure

value: vehicle (media only)


title: NB514


title: glucose-limited chemostat IMS0002 rep2

description:
Saccharomyces cerevisiae IMS0002; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; selected for anaerobic growth on arabinose.
WWA03

extract_protocol: Probe preparation and hybridization to Affymetrix Genechip YG-S98 microarrays were performed according to Affymetrix instructions, with the following modifications: double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA was monitored using the Agilent Bioanalyser 2100 (Agilent Technologies). Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChip® Operating Software (GCOS) version 1.2. Prior to comparison, all arrays were globally scaled to a target value of 150, using the average signal from all gene features, with GCOS (version 1.2).

value: glucose limited


title: CD19_selected_B-cells_before_R_rep10

description: no additional information


title: Sham_96h_2

value: Balb/c

value: Female


title: Phos Sham_24h_1

value: Lung

value: Mixture of 11 cell lines


title: NB30

value: Neuroblastoma


title: NB27


title: CD19_selected_B-cells_before_R_rep9

description: no additional information


title: Phos Sham_4h_2


title: Sham_96h_1


title: NB17


title: NB21


title: glucose-limited chemostat IMS0002 rep3

description:
Saccharomyces cerevisiae IMS0002; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; selected for anaerobic growth on arabinose.
WWA06

data_processing: Acquisition and quantification of array images and data filtering were performed using Affymetrix GeneChip® Operating Software (GCOS) version 1.2. Prior to comparison, all arrays were globally scaled to a target value of 150, using the average signal from all gene features, with GCOS (version 1.2).


title: glucose-limited chemostat IMS0002 rep1

description:
Saccharomyces cerevisiae IMS0002; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; selected for anaerobic growth on arabinose.
WWA02


title: Sham_48h_3


title: arabinose-limited chemostat IMS0002 rep1

description:
Saccharomyces cerevisiae IMS0002; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; selected for anaerobic growth on arabinose.
WWA01


title: NB8


title: S. rolfsii_EPSmax13_61h_rep2

city: Straubing

first: Jochen

last: Schmid

address: Schulgasse 16

department: Chair of Chemistry of Biogenic Resources

institute: Technische Universität München

description: Gene expression after 61hr in Exopolysaccharid production inducing media.

hyb_protocol: Oligomers for hybridizattion were designed by imaGenes (Berlin, Germany) using an in-house developed method for empirical selection of best performing probes for each gene (Pre Selection Strategy). Briefly, up to ten probes were designed for each of the unigenes (60 bp long oligomers). The 244K Agilent test array was hybridized with pooled Cy3-labeled cRNAs gained form EPSmax13 and EPSmin17 cultures and (in average) two of the best performing oligos were selected for each unigene. Microarray hybridization, was performes according to Agilent Gene Expression Hybridization Kit user guide (http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=34822&liid=4377).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to HDR Hi 100% and HDR lo 10%)  by imaGenes GmbH.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_ and Grid: 017067_D_F_20070615) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Expression data were analyzed by imaGenes GmbH using an in-house developed data analysis pipeline. After quantile normalization, genes were defined as differentially expressed if their expression levels varied at least 2 fold in samples of late growth phase (61 h) compared to samples of early growth phase (37 h) or in samples of EPSmax13 medium compared samples of EPSmin medium, and if the difference was statistically significant (Student’s t-test, P-value cut-off of 0.05).

organism: Agroathelia rolfsii

source_name: tRNA from S. rolfsii grown in EPSmax13 for 61h, replicate 2

label_protocol: For comparative expression profiling, total RNA was isolated from S. rolfsii, cultured for 37 h in EPSmax13 and EPSmin17 media as described above. Labelling was performed with the Agilent's low RNA Input Amplifikation Kit PLUS (http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=42629), which generates fluorescent cRNA (sample input 500 ng, The method uses T7 RNA polymerase, which simultaneously amplifies target material and incooperate cynine 3-labelled CTP. The labelled RNA was purified by Quiagen's RNeasy mini spin colums and quantified by using NanoDrop ND-1000 UV-VIS spectrophotometer version 3.2.1. by ImaGenes (Berlin)

growth_protocol: S. rolfsii strain ATCC15205 was cultivated at 28°C in shake flasks containing 50 ml EPS medium (C-source, N-source, 2 g/l K2HPO4, 0.5 g/l KCl, 0.5 g/l MgSO4*7H2O, 0.05 g/l FeSO4*7H2O, 1 g/l yeast extract, 0.7 g/l citric acid 7*H2O. pH 4.5). EPSmax13 contained 40 g/l glucose and 3.0 g/l NaNO3 as C- and N-sources, whereas EPSmin17 used 40 g/l fructose and 1.9 g/l NH4Cl, respectively. 2 cm2 of S. rolfsii mycelia grown on EPSmax13 plates (1.5% of agar) covered with cellophan was harvested, disintegrated with a scalpel and given into 50 ml of EPSmax13 medium or EPSmin 17 medium respectively

extract_protocol: After homogenization using a dismembrator (Braun Biotech), the pulverized homogenate was resuspended in 5 ml RNA extraction buffer (4 M guanidine isothiocyanate; 0.1 M Tris/HCl, pH 7.5; 1 % β-Mercaptoethanol, 0.5 % N-laurylsarcosine). After centrifugation (5000×g, 10 min, RT), the supernatant was subjected to ultracentrifugation using 5 M caesium chloride (30.,000×g, 19 h, RT). The resulting RNA pellet was precipitated using 2 volumes of ice-cold EtOH (96%) and 1/10 volumes of 8 M LiCl.

treatment_protocol: Due to the high amounts of EPS produced, extraction of intact total RNA from S. rolfsii cultures was only possible by using a caesium chloride-based ultracentrifugation method. In brief, 1 g of S. rolfsii mycelium was harvested by filtration and frozen in liquid nitrogen.

tag: condition

value: EPS inducing condition


title: glucose-limited chemostat IMS0001 rep2

description:
Saccharomyces cerevisiae IMS0001; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; does not grow on arabinose as sole carbon source
WWA07


title: detached-A.thaliana-leaf_12hpi_rep1

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

source_name: Control A. thaliana leaves harvested after 12 hr


title: S. rolfsii_EPSmin17_61h_rep1

description: Gene expression after 61hr in Exopolysaccharid production non-inducing media.

source_name: tRNA from S. rolfsii grown in EPSmin17 for 61h, replicate 1

value: EPS non-inducing condition


title: detached-A.thaliana-leaf_24hpi_rep1


title: glucose-limited chemostat IMS0001 rep3

description:
Saccharomyces cerevisiae IMS0001; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; does not grow on arabinose as sole carbon source
WWA10


title: S. rolfsii_EPSmin17_61h_rep3

source_name: tRNA from S. rolfsii grown in EPSmin17 for 61h, replicate 3


title: S. rolfsii_EPSmin17_61h_rep2

source_name: tRNA from S. rolfsii grown in EPSmin17 for 61h, replicate 2


title: S. rolfsii_EPSmax13_61h_rep1

source_name: tRNA from S. rolfsii grown in EPSmax13 for 61h, replicate 1


title: Sham_48h_2


title: S. rolfsii_EPSmax13_61h_rep3

source_name: tRNA from S. rolfsii grown in EPSmax13 for 61h, replicate 3


title: NB7


title: HsO2A-106_012714

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description:
M8 LPS+VEGFB vs LPS
Date: 2010/08/17

hyb_protocol: Agilent : 80 pmol at 60 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner Image intensity data were extracted with GenePix Pro 6.0 analysis software

data_processing: Lowess non linear normalization

source_name: M8 VEGFB+LPS 2

label_protocol: Amino Allyl MessageAmp aRNA Amplification Kit of Ambion, which incorporates amino allyl incorporation and aRNA amplification, as well as the Cy dyes.

extract_protocol: Qiagen

tag: patient

value: VEGFB+LPS

value: M8 VEGFB+LPS

value: Trizol

value: M8 VEGFB+LPSs

value: Macro

source_name: M8 LPS2

value: LPS

value: M8 LPS


title: NB32


title: NB207


title: NB9


title: NB24


title: Sham_48h_1

tag: tissue


title: Sham_1h_3


title: Sham_24h_2


title: Sham_24h_3


title: Sham_24h_1


title: HsO2A-104_012711

description:
M8 LPS+VEGFB vs LPS
Date: 2010/08/17


title: 13912510 - adg1 N3 vs WS N3

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves.

hyb_protocol: WS N3 Cy5 / adg1 N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

source_name: WS N3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette - Media: peat-based compost Hygrometry: approximately 60% during the day Temperature: 22°C during the day/ 17°C during the night Light: 16h light

extract_protocol: WS N3:6ug.

treatment_protocol: no treatment

tag: genotype

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: adg1 N3

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1-); age:5 week


title: 13912507 - WS N2 vs adg1 N2

hyb_protocol: adg1 N2 Cy5 / WS N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: adg1 N2

extract_protocol: adg1 N2:8ug.

source_name: WS N2


title: glucose-limited chemostat IMS0001 rep1

description:
Saccharomyces cerevisiae IMS0001; promoters of TKL1, TAL1, RPE1 and RKI1 replaced by strong TPI promoter;  transformed with plasmids containing Lactobacillus plantarum AraA, AraB and AraD; does not grow on arabinose as sole carbon source
WWA04

source_name: Anaerobic chemostat sample at D=0.03 h-1

value: glucose limited

value: chemostat culture steady state sample


title: Sham_1h_2

value: vehicle (media only)

value: Balb/c

value: Female

source_name: Stratagene Universal Reference RNA


title: detached-A.thaliana-leaf_12hpi_rep2

value: leaves


title: PBC_MMTV-MYC_validation_33

city: Durham

first: Erich

last: Huang

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized on Mouse Genome M430 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.

scan_protocol: GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).

data_processing:
Data processing was performed in a pilot revision control system entitled Quality-Auditable Data Repository and Analysis (QUADRA). For fully versioned and annotated source code and data objects, please see http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project.
Data were RMA normalized according to the source code found at http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project/human-dataprep.

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.

label_protocol:
Purified total RNA (200 ng) was amplified using NuGEN Ovation™ RNA Amplification System (NuGEN Technologies, Inc., San Carlos, CA).
Biotinylated cRNA were prepared according to the standard Affymetrix IVT 1-cycle protocol from 2.5 ug total RNA.

extract_protocol:
Samples were collected using the submandibular (cheekpouch) method. Briefly, the vein that drains the face and cheek area was punctured by a lancet (GoldenRod animal lancet, MEDIpoint, Inc., Mineola, NY) and blood was captured in BD Microtainer™ tubes with potassium-EDTA anticoagulant (Becton Dickinson, Franklin Lakes, NJ). Tubes were immediately inverted 10-12 times and placed on ice.
Following erythrocyte lysis, total RNA was isolated from the leukocyte pellet using the QIAamp RNA Blood Mini Kit (Qiagen, Valencia, CA). Alternatively, the leukocyte pellet was immediately lysed, homogenized and stored at -80°C. RNA was isolated at a later date using the protocol described above or the adapted protocol associated with the QIAamp RNA Blood Mini Kit for use in the QIAcube (Qiagen, Valencia, CA).

value: FVB/NJ

value: MMTV/c-MYC transgenic

tag: phenotype

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

tag: data set

value: validation


title: NB34

tag: cell type

value: Neuroblastoma


title: HsO2A-105_012713

description:
M8 LPS+VEGFB vs LPS
Date: 2010/08/17

value: VEGFB+LPS

value: M8 VEGFB+LPS

value: Trizol

value: Macro


title: 13912508 - adg1 N2 vs WS N2

hyb_protocol: WS N2 Cy5 / adg1 N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Arabidopsis thaliana (wassilewskija); age:5 week

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1-); age:5 week


title: HsO2A-103_012535

description:
M8 LPS+VEGFB vs LPS
Date: 2010/08/17

value: LPS

value: M8 LPS


title: PBC_MMTV-MYC_validation_30


title: PBC_MMTV-MYC_validation_31


title: 13967995 - ss3 N2 vs Col0 N2

hyb_protocol: Col0 N2 Cy5 / ss3 N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 N2

value: Arabidopsis thaliana (col-0); age:5 week

source_name: ss3 N2

value: Arabidopsis thaliana (col-0)  mutant (ss3-); age:5 week


title: 13912509 - WS N3 vs adg1 N3

hyb_protocol: adg1 N3 Cy5 / WS N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HsO2A-096_012602

description:
M8 VEGFB vs Control
Date: 2010/07/27

source_name: M8 C1

value: Control

value: M8 Control

source_name: M8 VEGFB1

value: VEGFB

value: M8 VEGFB


title: Sham_1h_1

value: vehicle (media only)

value: Balb/c

value: Female

value: Lung

value: Mixture of 11 cell lines


title: PBC_MMTV-MYC_validation_32

value: FVB/NJ

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

value: validation


title: HsO2A-088_012603

description:
M8 LPS+VEGFB vs LPS
Date: 2010/07/29

source_name: M8 L+V1

value: VEGFB+LPS

value: M8 L+V1

value: Trizol

value: Macro

source_name: M8 LPS1

value: LPS

value: M8 LPS


title: PBC_MMTV-MYC_validation_29


title: FT_96h_6

value: aerosolised Francisella tularensis


title: 13967992 - Col0 N2 vs ss3 N2

hyb_protocol: ss3 N2 Cy5 / Col0 N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Arabidopsis thaliana (col-0)  mutant (ss3-); age:5 week

value: Arabidopsis thaliana (col-0); age:5 week


title: HsO2A-098_012604

description:
M8 VEGFB vs Control
Date: 2010/08/09

source_name: M8 VEGFB2

value: VEGFB

value: M8 VEGFB

source_name: M8 C2

value: Control

value: M8 Control


title: HsO2A-099_012527

description:
M8 VEGFB vs Control
Date: 2010/08/09


title: HsO2A-095_012601

description:
M8 VEGFB vs Control
Date: 2010/07/27


title: 13967990 - Col0 N1 vs ss3 N1

hyb_protocol: ss3 N1 Cy5 / Col0 N1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ss3 N1

extract_protocol: ss3 N1:8ug.

source_name: Col0 N1

extract_protocol: Col0 N1:11ug.


title: 13967989 - ss3 D3 vs Col0 D3

hyb_protocol: Col0 D3 Cy5 / ss3 D3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 D3

source_name: ss3 D3


title: 13967991 - ss3 N1 vs Col0 N1

hyb_protocol: Col0 N1 Cy5 / ss3 N1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBC_MMTV-MYC_validation_27

value: FVB/NJ

value: MMTV/c-MYC transgenic


title: HsO2A-093_012725

description:
M8 VEGFB vs Control
Date: 2010/07/27


title: PBC_MMTV-MYC_validation_28

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)


title: PBC_MMTV-MYC_validation_26

value: validation


title: HsO2A-094_012530

description:
M8 VEGFB vs Control
Date: 2010/07/27


title: 13912891 - abb N3 vs WS N3

hyb_protocol: WS N3 Cy5 / abb N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WS N3

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: abb N3

extract_protocol: abb N3:5.2ug.

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1- be2- be3-); age:5 week


title: PBC_MMTV-MYC_validation_24


title: FT_96h_5

hyb_protocol: Test and control RNA was resuspended in 250ul of hybridisation buffer supplied by the microarray slide manufacturer (MWG Biotech, Ebersberg, Germany). Slides were hybridised overnight in hybridisation chambers (Qiagen, Crawley, West Sussex) for 16 hours at 42C in the dark and then washed in 3 different wash buffers for 5 minutes each wash. Wash buffer 1 consisted of 2 x SSC (buffered solution of sodium chloride and trisodium citrate), 0.1% SDS (Sigma, Poole), wash buffer 2 consisted of 1 x SSC and wash buffer 3 consisted of 0.5% SSC. All wash buffers were filter sterilised to prevent contaminating debris. The slides were dried by centrifugation at 500 x g for 5 minutes.

value: Balb/c

value: Female

value: Lung

value: Mixture of 11 cell lines


title: PBC_MMTV-MYC_validation_25


title: FT_96h_1

value: aerosolised Francisella tularensis


title: 13967988 - Col0 D3 vs ss3 D3

hyb_protocol: ss3 D3 Cy5 / Col0 D3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Arabidopsis thaliana (col-0)  mutant (ss3-); age:5 week

value: Arabidopsis thaliana (col-0); age:5 week


title: FT_96h_4


title: FT_96h_3


title: FT_48h_6


title: HsO2A-090_012522

description:
M8 LPS+VEGFB vs LPS
Date: 2010/07/29

value: LPS

value: M8 LPS

value: Trizol

value: Macro

value: VEGFB+LPS

value: M8 L+V1


title: HsO2A-091_012723

description:
M8 VEGFB vs Control
Date: 2010/08/09

value: Control

value: M8 Control

value: VEGFB

value: M8 VEGFB


title: FT_96h_2

value: Balb/c


title: FT_48h_5

value: Female


title: PBC_MMTV-MYC_validation_22

value: FVB/NJ

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

value: validation


title: HsO2A-089_012521

description:
M8 LPS+VEGFB vs LPS
Date: 2010/07/29

value: LPS


title: HsO4E-056_359252

description:
M5 VEGFB vs Control
Date: 2009/09/16

source_name: M5 VEGFB2

value: M5 VEGFB

source_name: M5 C2

value: M5 Control


title: PBC_MMTV-MYC_validation_21

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.


title: 13912889 - abb N2 vs WS N2

hyb_protocol: WS N2 Cy5 / abb N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WS N2

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: abb N2

extract_protocol: abb N2:7.5ug.

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1- be2- be3-); age:5 week


title: HsO2A-092_012724

description:
M8 VEGFB vs Control
Date: 2010/08/09

value: Trizol

value: Macro


title: PBC_MMTV-MYC_validation_23


title: HsO4E-055_359251

description:
M5 VEGFB vs Control
Date: 2009/09/16

value: Control


title: HsO2A-088_012599

description:
M8 LPS+VEGFB vs LPS
Date: 2010/07/29

value: VEGFB+LPS

value: M8 L+V1

value: M8 LPS


title: FT_48h_4

value: aerosolised Francisella tularensis

value: Balb/c

value: Female

value: Lung

source_name: Stratagene Universal Reference RNA

value: Mixture of 11 cell lines


title: FT_48h_3


title: FT_48h_2


title: 13912888 - WS N2 vs abb N2

hyb_protocol: abb N2 Cy5 / WS N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBC_MMTV-MYC_validation_19

value: FVB/NJ

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

value: validation


title: PBC_MMTV-MYC_validation_20


title: FT_48h_1


title: PBC_MMTV-MYC_validation_18


title: 13912885 - ss4-phs1 N3 vs WS N3

hyb_protocol: WS N3 Cy5 / ss4-phs1 N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: ss4-phs1 N3

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4- phs1-); age:5 week


title: 13912886 - WS N1 vs abb N1

hyb_protocol: abb N1 Cy5 / WS N1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: abb N1

extract_protocol: abb N1:9.2ug.

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1- be2- be3-); age:5 week

source_name: WS N1


title: HsO4E-053_359452

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/14

hyb_protocol: Agilent : 80 pmol at 60 degree_C during 17 hours

source_name: M5 LPS1

value: LPS

value: M5 LPS

value: Trizol

value: Macro

source_name: M5 VEGFB+LPS 1

value: M5 VEGFB+LPS


title: PBC_MMTV-MYC_validation_15


title: 13912881 - ss4-phs1 N1 vs WS N1

hyb_protocol: WS N1 Cy5 / ss4-phs1 N1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ss4-phs1 N1


title: HsO4E-051_359425

description:
M5 VEGFB vs Control
Date: 2009/09/14

source_name: M5 VEGFB1

value: VEGFB

value: M5 VEGFB

source_name: M5 C1

value: Control

value: M5 Control


title: HsO4E-054_359453

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/16

source_name: M5 LPS2

source_name: M5 VEGFB+LPS 2

value: VEGFB+LPS


title: HsO4E-052_359451

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/14


title: 13912890 - WS N3 vs abb N3

hyb_protocol: abb N3 Cy5 / WS N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: abb N3

source_name: WS N3


title: 13912887 - abb N1 vs WS N1

hyb_protocol: WS N1 Cy5 / abb N1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13912878 - WS N3 vs phs1 N3

hyb_protocol: phs1 N3 Cy5 / WS N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: phs1 N3

value: Arabidopsis thaliana (wassilewskija)  mutant (phs1-); age:5 week


title: 13912892 - WS N3 vs ss4-phs1 N3

hyb_protocol: ss4-phs1 N3 Cy5 / WS N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBC_MMTV-MYC_validation_16

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized on Mouse Genome M430 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.

value: FVB/NJ

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse


title: 13912879 - phs1 N3 vs WS N3

hyb_protocol: WS N3 Cy5 / phs1 N3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Arabidopsis thaliana (wassilewskija); age:5 week


title: FT_24h_4

value: aerosolised Francisella tularensis

value: Balb/c

value: Female

value: Lung

value: Mixture of 11 cell lines


title: FT_24h_5


title: HsO4E-046_359346

description:
M5 VEGFB vs Control
Date: 2009/09/30

source_name: M5 C2

value: Trizol

value: Macro

source_name: M5 VEGFB2


title: 13912880 - WS N1 vs ss4-phs1 N1

hyb_protocol: ss4-phs1 N1 Cy5 / WS N1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4- phs1-); age:5 week


title: PBC_MMTV-MYC_validation_13

value: total white blood cells (WBCs)

value: validation


title: PBC_MMTV-MYC_validation_17


title: FT_24h_2

source_name: Stratagene Universal Reference RNA


title: FT_24h_3


title: HsO4E-045_359269

description:
M5 VEGFB1 vs Control
Date: 2009/09/29

value: Control

value: M5 Control

value: VEGFB

value: M5 VEGFB


title: PBC_MMTV-MYC_validation_14

value: FVB/NJ

value: MMTV/c-MYC transgenic


title: 13912877 - phs1 N2 vs WS N2

hyb_protocol: WS N2 Cy5 / phs1 N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WS N2

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: phs1 N2

value: Arabidopsis thaliana (wassilewskija)  mutant (phs1-); age:5 week


title: 13912876 - WS N2 vs phs1 N2

hyb_protocol: phs1 N2 Cy5 / WS N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HsO4E-050_359179

description:
M5 VEGFB vs Control
Date: 2009/09/14


title: FT_24h_1

hyb_protocol: Test and control RNA was resuspended in 250ul of hybridisation buffer supplied by the microarray slide manufacturer (MWG Biotech, Ebersberg, Germany). Slides were hybridised overnight in hybridisation chambers (Qiagen, Crawley, West Sussex) for 16 hours at 42C in the dark and then washed in 3 different wash buffers for 5 minutes each wash. Wash buffer 1 consisted of 2 x SSC (buffered solution of sodium chloride and trisodium citrate), 0.1% SDS (Sigma, Poole), wash buffer 2 consisted of 1 x SSC and wash buffer 3 consisted of 0.5% SSC. All wash buffers were filter sterilised to prevent contaminating debris. The slides were dried by centrifugation at 500 x g for 5 minutes.

value: aerosolised Francisella tularensis

value: Balb/c


title: HsO4E-041_359424

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/29

value: LPS

value: M5 LPS

value: VEGFB+LPS

value: M5 VEGFB+LPS


title: HsO4E-040_359448

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/29

value: Trizol

value: Macro


title: HsO4E-035_359443

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/16


title: 13912875 - phs1 N1 vs WS N1

hyb_protocol: WS N1 Cy5 / phs1 N1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WS N1

source_name: phs1 N1