title: 12hMesoOA_Acet_3

city: Cincinnati

first: William

middle: J

last: Scott

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: Samples used for hybridization consisted of non-pooled (NP) RNA extracts from 8 groups in each of two time periods after drug administration: oil vehicle treated control embryonic limb bud mesoderm and ectoderm, phosphate buffered saline vehicle control embryonic limb bud mesoderm and ectoderm, acetazolamide treated embryonic limb bud mesoderm and ectoderm, and cadmium sulfate treated embryonic limb bud mesoderm and ectoderm. Forty-eight hybridization experiments were on non-pooled (NP) individual RNA extracts.

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains  0.067 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg.mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Ivitrogen), and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45?C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

label_protocol: Standard Affymetrix one-cycle target labeling protocol.

extract_protocol:
Total RNA was extracted from the murine ectoderms and mesoderms using Trizol kit (Invitrogen) and then purified two times using RNeasy columns (Qiagen)
Quality control steps:   RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used

treatment_protocol: pregnant mice injected, ip, with either 400 mg/kg of acetazolamide suspended in vegetable oil or 4 mg/kg of Cadmium sulfate in phosphate buffered saline on gestation day 9.5. Three and twelve hours post-treatment, embryos collected.  The right forelimb buds were removed, treated with 2% Crude trypsin in PBS, the ectoderm and mesoderm separated.  The mesoderm and ectoderms of severals litters were pooled to obtain RNA.

tag: embryonic limb bud mesoderm

tag: acetazolamide-treated


title: Female 3 hornfly cy3 vs male pool cy5

status: Public on Jun 19 2008

type: RNA

city: Lubbock

first: Scot

last: Dowd

state: TX

address: 4321 Marsha Sharp Fwy

department: MBRI

country: USA

institute: MBRI

hyb_protocol: Labeled cDNA was hybridized to the Agilent microarrays using the Gene Expression Hybridization kit (Agilent Technologies Inc.) following manufacturer’s protocols. Arrays were washed with Gene Expression Wash Buffer kit (Agilent Technologies Inc.)

scan_protocol: Microarray images were captured using a Genepix 4000B (Molecular Devices Corporation, Union City, CA) laser scanner and images processed using Genepix 6.0 software (Molecular Devices Corporation). Microarray data analyses were performed using Acuity 4.0 software. Slides were normalized using standard ratio-based methods. Data were analyzed based upon Log ratio (635/532) values. Genes were included in the final dataset that exhibit significance based upon a very conservative FDR less than 2.5% [27] and at least 2.0-fold comparative regulation.

data_processing: Data VALUES were generated in Acuity 6.0 based upon Log ratio (635/532) values.

molecule: total RNA

organism: Haematobia irritans

source_name: Female cy3 adult hornfly

label_protocol: In short, RNA from female horn flies was labeled and hybridized against labeled RNA from male horn flies in a dyeswap design. Similarly, RNA from first instar larvae was labeled and hybridized against labeled a 50:50 mix of RNA from adult male and female flies. All labeling, hybridization and washing procedures were performed according to respective manufacturer protocols. For each sample, 10 ug of total RNA and 50-fold dilution of Agilent two color spike-in control RNA kit (Agilent Technologies Inc.) were labeled with either CyDye3-dCTP or CyDye5-dCTP (Amersham Biosciences, Piscataway, NJ) using the LabelStar kit (Qiagen Inc., Valencia, CA) and oligo-dT and Random nonamers (Sigma-Aldrich Inc., St. Louis, MO).

extract_protocol: All procedures were performed according to respective manufacturer protocols. RNA was extracted from approximately 1 g of adult flies and 0.1 g larvae using the TotallyRNA Kit (Ambion, Inc., Austin, TX). DNA was removed using Turbo DNA Free Kit (Ambion, Inc.). Two RNA preparations were made from independent samplings of the fly materials. RNA was quantified using a NanoDrop ND-1000 device (NanoDrop Technologies, Wilmington, DE) and quality confirmed by electrophoresis.

tag: Female cy3 adult hornfly

source_name: Hornfly Male adult cy 5 pooled

tag: Hornfly Male adult cy 5 pooled


title: Nodal DLBCL 19N

type: genomic

city: Groningen

first: Marije

last: Booman

department: Pathology

country: Netherlands

institute: University Medical Center Groningen

description: Gender mismatch hybridisation

hyb_protocol: DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed by post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA).

scan_protocol: Slides were scanned on a GenePix 4100A scanner (Axon Instruments, Westburg BV).

data_processing: Scanned images were processed using GenePix Pro 4.1 software. Pixel intensities for each feature were integrated and median values were determined, and the local background was calculated. For each spot the intensities were corrected (pixel median values) by subtracting the local background (pixel median values) for both wavelengths. The median of the ratios of all spots was calculated and used to normalize all data points. As quality control, spots outside the 20% confidence interval of the average of the replicate were excluded. Only those targets presenting at least two spots within 20% confidence interval of their average were used. For each feature (3 spots), the log2 value of the average of the normalized ratios of the three spots was calculated.

molecule: genomic DNA

organism: Homo sapiens

source_name: Nodal DLBCL

label_protocol: 450 ng genomic DNA was labeled using Cy3- or Cy5-dCTP in an overnight random prime labeling reaction (BioPrime Random Prime labelling Kit, Invitrogen). Labeled test and reference samples were pooled and precipitated in the presence of Cot1 DNA.

extract_protocol: Genomic DNA was isolated using high salt after overnight SDS/proteinase K digestion.

tag: Tissue

value: Nodal diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:DNA, Gender:Male

source_name: Pooled reference DNA

tag: commercially available female DNAs (Promega, Leiden, the Netherlands) that represent DNA pools derived from at least seven individuals


title: Nodal DLBCL 17N

description: Gender mismatch hybridisation


title: Hornfly Female adult cy 5 vs male adult cy3

source_name: Female adult hornfly cy5

tag: Female adult hornfly

source_name: Male adult hornfly cy3

tag: Male adult hornfly cy3


title: Nodal DLBCL 16N

description: Gender mismatch hybridisation

value: Nodal diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:DNA, Gender:Female

tag: commercially available male DNAs (Promega, Leiden, the Netherlands) that represent DNA pools derived from at least seven individuals


title: Female 2 cy3 vs male pool cy5

source_name: Female hornfly

tag: Female adult hornfly total RNA

source_name: Adult Male hornfly pooled sample

tag: Adult Male hornfly pooled cy 5


title: Nodal DLBCL 15N

description: Gender mismatch hybridisation


title: Nodal DLBCL 18N

description: Gender mismatch hybridisation


title: 12hMesoOA_Acet_2

label: biotin

organism: Mus musculus


title: naïve_2

status: Public on Jun 20 2008

city: Frederick

first: Shalini

last: Oberdoerffer

state: MD

address: 1050 Boyles Street

institute: National Cancer Institute

description: FileNumber: 1

hyb_protocol: microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450

scan_protocol: Genechip scanner 3000 7G

data_processing: The input files were normalized with full quantile normalization (Irizarry et al 2003).  For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points.  Next, the 6,553,590 probes were manipulated into the analysis values as follows.  Probes with GC count less than 6 and greater than 17 were excluded from the analysis.  Probe scores were then transformed by taking the Natural Logarithm of 0.1 plus the probe score.  Background CorrectionExon arrays do not use individual mis-match probes.  Background is established from a pool of probes designed for that purpose.  Background probes are stratified by CG content and are defined in the Human Exon 1.0 ST_antigenomic.bgp file.  BGP files can also be downloaded from www.affymetrix.com.  Each probe score was corrected for background by subtracting the median expression score of background probes with similar GC content.    The Human Exon 1.0 ST array contains 1,404,693 probe-sets (typically, but not always, groups of four probes).  Probe-set Expression Scores and Annotation FilteringThe expression score for a probe-set was defined to be the median of its probe expression scores and probe-sets with fewer than 1 probes (that pass all of the tests defined above) are excluded from further analysis.  Exon Array Probes are designed off of genomic sequence and hence the reliability of probes and probe-sets correspond to the quality of their parent genomic annotations.  Probe-set reliability is ranked from more to less reliable as Core, Extended, or Full.  For example 'Core' probe-sets include probe-sets that correspond to high quality genomic features like RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org) transcripts while 'full' and 'extended' probe-sets match less reliable annotations like EST hits and gene prediction algorithms.  For this analysis, only 'Core' probe-sets were analyzed.

source_name: naive

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

growth_protocol: Naïve CD4+ T cells were collected from human cord blood and maintained in IL-2 containing medium.

extract_protocol: Total RNA was isolated from unstimulated cells or cells that had been stimulated for 24 hours with anti-CD3 and anti-CD28 antibodies with RNeasy columns (Qiagen).

treatment_protocol: Activation was accomplished by stimulating cells for 24 hours with anti-CD3 and anti-CD28 antibodies.

tag: naive


title: Nodal DLBCL 13N

description: Gender mismatch hybridisation


title: 12hMesoOA_Acet_1


title: Female cy3 vs Male cy5 hornfly gene expression

source_name: Hornfly female RNA

tag: Total RNA extracted from adult females

source_name: Hornfly Male

tag: Hornfly adult Male


title: Nodal DLBCL 14N

description: Gender mismatch hybridisation


title: patient C1-22

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description: healthy patients

hyb_protocol: Hybridization of the [α 33P]-labelled targets onto a cDNA array was done after preincubating the membrane in a mixture (50mL) of 50% deionized formamide, 5xSSPE (20xSSPE is 3M NaCl, 0.23M NaH2PO4, 20mM EDTA, pH 7.4), 5x Denhardt's solution, 1% SDS, 5% dextran sulfate, 200μg/mL heatdenatured salmon sperm DNA at 42°C for 3h in a rolling bottle. The labelled targets in 25mL of the same mixture were next incubated with the membrane at 42°C for 18 hrs, prior to membrane washing (two washes at 68°C for one hour each) with 50mL of a 2xSSPE / 0.5% SDS mixture.

scan_protocol: Quantitative signals were obtained by membrane autoradiography for 46-48 hours onto an europium screen that was next scanned with a 100µm resolution in a Phosphorimager SI (Molecular Dynamics)

data_processing: The scanned 16-bit in a Linux workstation and the spots were automatically identified and analyzed with XdotsReader software, version 1.8 (COSE, Le Bourget, France). A global background was calulated over the entire image as the mean of a local background measured around each spot and it was automatically substracted from every spot signal. Next, the mean signal associated to negative control spots was calculated over the entire image. For all genes under study, a spot whose signal was below a given threshold (2 SD above the average signal for negative controls) was considered to be non-significant (p<0.05). Finally, the mean signal associated to negative control spots was automatically substacted from the signal for every significant spot. Data normalization was based on the mean of the signals provided by the complete set of spots per image.

source_name: PBMCs

label_protocol: Within each RNA preparation prepared as above the target poly(A) mRNAs were labelled as follows : 10μg total RNAs in a 20μL solution containing dATP/dGTP/dTTP (0.5mM each) and 1μg 5'(dT23)VN3' oligonucleotide were heated at 65°C for 5min, cooled down to 4°C, added with 7μL 5x first-strand buffer (Tris-HCl buffer 250mM, pH 8.3, KCl 375mM, MgCl2 15mM), 2μL DTT 0.1M, 1μL (40u.) RNAse OUT as an RNAse inhibitor (Invitrogen) and 5μL [α 33P]dCTP (10mCi/mL, from Amersham) and incubated at 42°C for 2min prior to the addition of 200u. SuperScriptII RNAse H(-) reverse transcriptase (Invitrogen) and a further incubation at 42°C for 1h. A chase was done by adding 1μL dNTPs (10mM each) and 200u. SuperScriptII and incubating at 42°C for 1h. The RNAse inhibitor was next destroyed at 70°C for 15min and the RNA templates were digested with 2u. RNAseH (Invitrogen) at 37°C for 20min. Finally, free [α 33P]dCTP was eliminated by gel filtration onto a Nick Column G-50 (Amersham-Pharmacia Biotech) and the resulting, labelled cDNAs were immediately used for hybridization.

extract_protocol: Chomczynski, P., and Sacchi, N. 1987. Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159.

tag: Control

tag: pool


title: Nodal DLBCL 11N

description: Gender mismatch hybridisation


title: Nodal DLBCL 12N

description: Gender mismatch hybridisation


title: Nodal DLBCL 6N

description: Gender mismatch hybridisation


title: patient C1-21

description: healthy patients


title: patient C1-20

description: healthy patients


title: 12hMesoOA_Oil_2

tag: oil vehicle-treated control


title: Nodal DLBCL 1N

description: Gender mismatch hybridisation


title: Testicular DLBCL 18T

description: Gender mismatch hybridisation

source_name: Testicular DLBCL

value: Testicular diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:DNA, Gender:Male


title: patient C1-19

description: healthy patients


title: Testicular DLBCL 16T

description: Gender mismatch hybridisation


title: 12hEctoOA_Acet_2

tag: embryonic limb bud ectoderm


title: Testicular DLBCL 15T

description: Gender mismatch hybridisation


title: 12hEctoOA_Acet_1

tag: acetazolamide-treated


title: 12hMesoOA_Oil_1

tag: embryonic limb bud mesoderm


title: Testicular DLBCL 22T

description: Gender mismatch hybridisation


title: 12hEctoOA_Oil_3

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 12h;Ecto;acetazolamide group


title: patient C1-16

description: healthy patients


title: Testicular DLBCL 20T

description: Gender mismatch hybridisation


title: 12hEctoOA_Acet_3


title: patient C1-17

description: healthy patients


title: Testicular DLBCL 8T

description: Gender mismatch hybridisation


title: patient C1-15

description: healthy patients


title: 12hEctoOA_Oil_2


title: Testicular DLBCL 7T

description: Gender mismatch hybridisation


title: Testicular DLBCL 12T

description: Gender mismatch hybridisation


title: Testicular DLBCL 9T

description: Gender mismatch hybridisation


title: Testicular DLBCL 19T

description: Gender mismatch hybridisation


title: Testicular DLBCL 17T

description: Gender mismatch hybridisation


title: patient C1-18

description: healthy patients


title: patient C1-13

description: healthy patients


title: patient C1-14

description: healthy patients


title: Testicular DLBCL 11T

description: Gender mismatch hybridisation


title: Testicular DLBCL 6T

description: Gender mismatch hybridisation


title: CNS DLBCL 13C

description: Gender mismatch hybridisation

source_name: Central nervous system DLBCL

value: Central nervous system diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:DNA, Gender:Female


title: Testicular DLBCL 4T

description: Gender mismatch hybridisation


title: CNS DLBCL 11C

description: Gender mismatch hybridisation


title: Testicular DLBCL 1T

description: Gender mismatch hybridisation


title: 3hMesoOA_Acet_2


title: CNS DLBCL 3C

description: Gender mismatch hybridisation

value: Central nervous system diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:DNA, Gender:Male


title: Testicular DLBCL 3T

description: Gender mismatch hybridisation


title: 3hMesoOA_Acet_1


title: 3hMesoOA_Oil_3

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 3h;Meso;acetazolamide group


title: CNS DLBCL 2C

description: Gender mismatch hybridisation


title: patient C1-11

description: healthy patients


title: patient C1-12

description: healthy patients


title: patient C1-10

description: healthy patients


title: patient C1-8

description: healthy patients


title: patient C1-9

description: healthy patients


title: 3hMesoOA_Acet_3


title: 3hMesoOA_Oil_2


title: CNS DLBCL 10C

description: Gender mismatch hybridisation


title: patient C1-7

description: healthy patients


title: CNS DLBCL 8C

description: Gender mismatch hybridisation


title: patient C1-6

description: healthy patients


title: CNS DLBCL 9C

description: Gender mismatch hybridisation


title: CNS DLBCL 12C

description: Gender mismatch hybridisation


title: 3hEctoOA_Acet_2


title: 3hEctoOA_Acet_3


title: patient C1-5

description: healthy patients


title: 3hEctoOA_Oil_3

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 3h;Ecto;acetazolamide group


title: 3hMesoOA_Oil_1


title: 12hEctoOA_Oil_1


title: 3hEctoOA_Acet_1


title: 3hEctoOA_Oil_2


title: patient C1-2

description: healthy patients


title: patient C1-3

description: healthy patients


title: patient NR7-2

description: RA patient treated with anakinra

tag: Non responder

tag: 73 year old woman


title: patient C1-1

description: healthy patients


title: patient NR7-1

description: RA patient treated with anakinra


title: patient NR5-2

description: RA patient treated with anakinra

tag: 61 year old woman


title: patient NR6-1

description: RA patient treated with anakinra

tag: 44 year old woman


title: 12hEctoPC_PBS_3

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 12h;Ecto;cadmium group

tag: phosphate buffered saline vehicle control


title: patient NR2-2

description: RA patient treated with anakinra

tag: 52 year old woman


title: 3hEctoOA_Oil_1


title: patientNR6-2

description: RA patient treated with anakinra


title: 12hMesoPC_Cd_2

tag: cadmium sulfate-treated


title: patient C1-4

description: healthy patients


title: patient NR2-1

description: RA patient treated with anakinra


title: 12hEctoPC_Cd_1


title: patientNR1-1

description: RA patient treated with anakinra

tag: 46 year old man


title: patient NR3-1

description: RA patient treated with anakinra

tag: 50 year old woman


title: CNS DLBCL 1C

description: Gender mismatch hybridisation

tag: Tissue

tag: commercially available female DNAs (Promega, Leiden, the Netherlands) that represent DNA pools derived from at least seven individuals


title: 12hMesoPC_Cd_1


title: 12hMesoPC_PBS_1


title: patient NR1-2

description: RA patient treated with anakinra


title: 3hMesoPC_PBS_3

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 3h;Meso;cadmium group


title: patient NR4-1

description: RA patient treated with anakinra

tag: 71 year old woman


title: patient R6-1

description: RA patient treated with anakinra

tag: Responder

tag: 43 year old woman


title: 12hMesoPC_PBS_3

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 12h;Meso;cadmium group


title: 12hMesoPC_Cd_3


title: 12hMesoPC_PBS_2


title: 3hMesoPC_PBS_2


title: patient R5-2

description: RA patient treated with anakinra

tag: 56 year old woman


title: 12hEctoPC_PBS_2

tag: embryonic limb bud ectoderm


title: patient R5-1

description: RA patient treated with anakinra


title: patient NR4-2

description: RA patient treated with anakinra


title: 3hMesoPC_Cd_3

tag: embryonic limb bud mesoderm


title: 12hEctoPC_PBS_1


title: patient R7-2

description: RA patient treated with anakinra

tag: 75 year old woman


title: patient R7-1

description: RA patient treated with anakinra


title: 3hMesoPC_Cd_1


title: 3hMesoPC_Cd_2


title: 12hEctoPC_Cd_3


title: 3hMesoPC_PBS_1


title: patientNR5-1

description: RA patient treated with anakinra

tag: Non responder


title: 3hEctoPC_Cd_3


title: patient R6-2

description: RA patient treated with anakinra


title: 12hEctoPC_Cd_2


title: 3hEctoPC_Cd_1


title: 3hEctoPC_Cd_2


title: patient R2-1

description: RA patient treated with anakinra


title: patient R3-2

description: RA patient treated with anakinra

tag: 31 year old woman


title: 3hEctoPC_PBS_3

data_processing:
Affymetrix murine U74Av2 gene chips were used.  GeneChip CEL  files were subjected to  RMAExpress  quantile normalization  using  the  GeneSpring GX 7.1; Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Reference normalization sample for the 3h;Ecto;cadmium group


title: patient R1-2

description: RA patient treated with anakinra

tag: 30 year old woman


title: patient R4-1

description: RA patient treated with anakinra

tag: 37 year old woman


title: 3hEctoPC_PBS_1

tag: phosphate buffered saline vehicle control


title: 3hEctoPC_PBS_2


title: 13501443 - F-MS-06h-3 vs F-H2O-06h-3

status: Public on Jun 17 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

institute: INRA

description: Dynamic analyses of transcriptomic response to urany l nitrate

hyb_protocol: F-H2O-06h-3 Cy5 / F-MS-06h-3 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,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

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.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 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: leaf - Plants are grown on sand and transfered in hydroponic culture during 2 days.

treatment_protocol: Name:H2O-06h - control buffer - control buffer,water:time 6hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then exposed to water at pH 4.5. Roots and leaves were collected independently after 6h of treament.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

treatment_protocol: Name:MS-06h - control buffer - control buffer,ms:time 6hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then exposed to MS (control). Roots and leaves were collected independently after 6h of treament.


title: patient R3-1

description: RA patient treated with anakinra


title: patient R4-2

description: RA patient treated with anakinra


title: 13501444 - F-H2O-06h-3 vs F-MS-06h-3

hyb_protocol: F-MS-06h-3 Cy5 / F-H2O-06h-3 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: 13501859 - F-MS-02h-3 vs F-H2O-02h-3

hyb_protocol: F-H2O-02h-3 Cy5 / F-MS-02h-3 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.

treatment_protocol: Name:H2O-02h - control buffer - control buffer,water:time 2hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then exposed to water at pH 4.5. Roots and leaves were collected independently after 2h of treament.

treatment_protocol: Name:MS-02h - control buffer - control buffer,ms:time 2hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then exposed to MS (control). Roots and leaves were collected independently after 2h of treament.


title: patient R2-2

description: RA patient treated with anakinra


title: patient R1-1

description: RA patient treated with anakinra


title: 13501440 - F-H2O-06h-1 vs F-MS-06h-1

hyb_protocol: F-MS-06h-1 Cy5 / F-H2O-06h-1 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: 13501861 - F-H2O-02h-3 vs F-MS-02h-3

hyb_protocol: F-MS-02h-3 Cy5 / F-H2O-02h-3 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: E11.5_wild-type_embryo#13

status: Public on Jun 18 2008

first: Andrei

middle: S

last: Zolotukhin

address: P.O. Box B

institute: NCI-Frederick

description: Mice harboring a low expression Ott1 allele were mated and embryos at day E11.5 were dissected and genotyped.

hyb_protocol: CodeLink Bioarrays were hybridized with the cRNA target and stained with Cy5-streptavidin.

scan_protocol: Slides were washed and then scanned on an Axon GenePix 4000B scanner.

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	14.23302186;
Normalized TrimMean Negative Control:	0.250135542;
Median:	56.90123749

source_name: Ott1 knockdown, wild-type embryo #13

label_protocol:
First and second strand cDNA was prepared from the total RNA samples using standard CodeLink protocol.
Biotinylated cRNA target was prepared from the DNA template and verified on the Bioanalyzer.
cRNA was fragmented to uniform size and verified on the Bioanalyzer.

extract_protocol:
Total RNA was extracted and purified using RiboPure RNA isolation (Ambion).
Total RNA samples were quantitated by UV spectrophotometry (OD260/280).
Quality of Total RNA was assessed using an Agilent Bioanalyzer.

treatment_protocol: Dissected embryos, snap-frozen in liquid nitrogen

tag: The mouse ES cell line XK135 (obtained from BayGenomics; funded by the National Heart, Lung, and Blood Institute, http://baygenomics.ucsf.edu), harbours a LacZ-neo fusion cassette inserted into the first coding exon of Ott1, 20 nt upstream the initiator codon, generating a low-expression Ott1XK135 allele. After injection into C57BL/6 blastocysts, the chimeric mice were bred for germline transmission. Genomic DNA from tail snips or yolk sacs was used for PCR genotyping. Ott1 alleles were detected by using primers, which span the XK135 insertion site.


title: E11.5_homozygous_embryo#2

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	16.95388803;
Normalized TrimMean Negative Control:	0.273318201;
Median:	62.02985382

source_name: Ott1 knockdown, homozygous embryo #2

tag: The mouse ES cell line XK135 (obtained from BayGenomics; funded by the National Heart, Lung, and Blood Institute, http://baygenomics.ucsf.edu), harbours a LacZ-neo fusion cassette inserted into the first coding exon of Ott1, 20 nt upstream the initiator codon, generating a low-expression Ott1XK135 allele. After injection into C57BL/6  blastocysts, the chimeric mice were bred for germline transmission. Genomic DNA from tail snips or yolk sacs was used for PCR genotyping. Ott1 alleles were detected by using primers, which span the XK135 insertion site.


title: E11.5_wild-type_embryo#11

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	14.25612704;
Normalized TrimMean Negative Control:	0.252726666;
Median:	56.40927124

source_name: Ott1 knockdown, wild-type embryo #11


title: E11.5_homozygous_embryo#16

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	77.54683689;
Normalized TrimMean Negative Control:	0.876699799;
Median:	88.453125

source_name: Ott1 knockdown, homozygous embryo #16


title: E11.5_heterozygous_embryo#10

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	14.47337532;
Normalized TrimMean Negative Control:	0.297574033;
Median:	48.63789749

source_name: Ott1 knockdown, heterozygous embryo #10


title: E11.5_heterozygous_embryo#15

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	15.07386429;
Normalized TrimMean Negative Control:	0.307866972;
Median:	48.96226501

source_name: Ott1 knockdown, heterozygous embryo #15


title: E11.5_heterozygous_embryo#3

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	13.82897093;
Normalized TrimMean Negative Control:	0.238254448;
Median	58.04286575

source_name: Ott1 knockdown, heterozygous embryo #3


title: E11.5_homozygous_embryo#7

data_processing:
Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method:	Median-Normalization;
Computation Method for Median:	Spot Based;
Threshold Trim Percentage:	20;
Raw TrimMean Negative Control:	16.26547943;
Normalized TrimMean Negative Control:	0.26178759;
Median:	62.13235474

source_name: Ott1 knockdown, homozygous embryo #7


title: 13501425 - R-H2O-02h-3 vs R-MS-02h-3

hyb_protocol: R-MS-02h-3 Cy5 / R-H2O-02h-3 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: 13501430 - R-H2O-06h-3 vs R-MS-06h-3

hyb_protocol: R-MS-06h-3 Cy5 / R-H2O-06h-3 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: 13501427 - R-MS-06h-1 vs R-H2O-06h-1

hyb_protocol: R-H2O-06h-1 Cy5 / R-MS-06h-1 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: 13501438 - F-MS-06h-1 vs F-H2O-06h-1

hyb_protocol: F-H2O-06h-1 Cy5 / F-MS-06h-1 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: 13501422 - R-H2O-02h-1 vs R-MS-02h-1

hyb_protocol: R-MS-02h-1 Cy5 / R-H2O-02h-1 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: 13501116 - F-URA-02h-3 vs F-H2O-02h-3

hyb_protocol: F-H2O-02h-3 Cy5 / F-URA-02h-3 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.

treatment_protocol: Name:URA-02h - abiotic stress - compound addition,uranyle nitrate:quantity 0.05mM time 2hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then exposed to 50(u)M uranyl nitrate at pH 4.5 in water. Roots and leaves were collected independently after 2h of treament.


title: 13501115 - F-H2O-02h-3 vs F-URA-02h-3

hyb_protocol: F-URA-02h-3 Cy5 / F-H2O-02h-3 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: 13501439 - F-H2O-02h-1 vs F-MS-02h-1

hyb_protocol: F-MS-02h-1 Cy5 / F-H2O-02h-1 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: 13501435 - F-MS-02h-1 vs F-H2O-02h-1

hyb_protocol: F-H2O-02h-1 Cy5 / F-MS-02h-1 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: 13501122 - F-H2O-30h-3 vs F-URA-30h-3

hyb_protocol: F-URA-30h-3 Cy5 / F-H2O-30h-3 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.

treatment_protocol: Name:URA-30h - abiotic stress - compound addition,uranyle nitrate:quantity 0.05mM time 30hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then expose or not to 50(u)M uranyl nitrate at pH 4.5 in water. Roots and leaves were collected independently after 6h of treament.

treatment_protocol: Name:H2O-30h - control buffer - control buffer,water:time 30hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then exposed to water at pH 4.5. Roots and leaves were collected independently after 30h of treament.


title: 13501123 - F-URA-30h-3 vs F-H2O-30h-3

hyb_protocol: F-H2O-30h-3 Cy5 / F-URA-30h-3 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: 13501421 - R-MS-02h-1 vs R-H2O-02h-1

hyb_protocol: R-H2O-02h-1 Cy5 / R-MS-02h-1 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: 13501097 - R-URA-02h-3 vs R-H2O-02h-3

hyb_protocol: R-H2O-02h-3 Cy5 / R-URA-02h-3 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: 13501424 - R-MS-02h-3 vs R-H2O-02h-3

hyb_protocol: R-H2O-02h-3 Cy5 / R-MS-02h-3 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: 13501429 - R-H2O-06h-1 vs R-MS-06h-1

hyb_protocol: R-MS-06h-1 Cy5 / R-H2O-06h-1 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: 13501426 - R-MS-06h-3 vs R-H2O-06h-3

hyb_protocol: R-H2O-06h-3 Cy5 / R-MS-06h-3 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: 13501121 - R-H2O-30h-3 vs R-URA-30h-3

hyb_protocol: R-URA-30h-3 Cy5 / R-H2O-30h-3 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: 13501098 - R-URA-30h-3 vs R-H2O-30h-3

hyb_protocol: R-H2O-30h-3 Cy5 / R-URA-30h-3 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: 13500974 - F-URA-06h-3 vs F-H2O-06h-3

hyb_protocol: F-H2O-06h-3 Cy5 / F-URA-06h-3 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.

treatment_protocol: Name:URA-06h - abiotic stress - compound addition,uranyle nitrate:quantity 0.05mM time 6hour . Plants are grown on sand and transfert in hydroponic culture during 2 days and then expose or not to 50(u)M uranyl nitrate at pH 4.5 in water. Roots and leaves were collected independently after 6h of treament.


title: 13501096 - R-H2O-02h-3 vs R-URA-02h-3

hyb_protocol: R-URA-02h-3 Cy5 / R-H2O-02h-3 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: 13501118 - F-H2O-06h-3 vs F-URA-06h-3

hyb_protocol: F-URA-06h-3 Cy5 / F-H2O-06h-3 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: 13500969 - R-URA-06h-3 vs R-H2O-06h-3

hyb_protocol: R-H2O-06h-3 Cy5 / R-URA-06h-3 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: 13489217 - R-H2O-30h-2 vs R-URA-30h-2

hyb_protocol: R-URA-30h-2 Cy5 / R-H2O-30h-2 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: 13489218 - R-URA-30h-2 vs R-H2O-30h-2

hyb_protocol: R-H2O-30h-2 Cy5 / R-URA-30h-2 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: 13489216 - R-URA-06h-2 vs R-H2O-06h-2

hyb_protocol: R-H2O-06h-2 Cy5 / R-URA-06h-2 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: 13489213 - R-URA-02h-2 vs R-H2O-02h-2

hyb_protocol: R-H2O-02h-2 Cy5 / R-URA-02h-2 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: 13500970 - R-H2O-06h-3 vs R-URA-06h-3

hyb_protocol: R-URA-06h-3 Cy5 / R-H2O-06h-3 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: 13489214 - R-H2O-06h-2 vs R-URA-06h-2

hyb_protocol: R-URA-06h-2 Cy5 / R-H2O-06h-2 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: 13488705 - F-H2O-02h-2 vs F-URA-02h-2

hyb_protocol: F-URA-02h-2 Cy5 / F-H2O-02h-2 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: 13483897 - F-URA-06h-2 vs F-H2O-06h-2

hyb_protocol: F-H2O-06h-2 Cy5 / F-URA-06h-2 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: 13483898 - F-H2O-30h-2 vs F-URA-30h-2

hyb_protocol: F-URA-30h-2 Cy5 / F-H2O-30h-2 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: 13488699 - F-URA-30h-2 vs F-H2O-30h-2

hyb_protocol: F-H2O-30h-2 Cy5 / F-URA-30h-2 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: 13488711 - F-URA-02h-2 vs F-H2O-02h-2

hyb_protocol: F-H2O-02h-2 Cy5 / F-URA-02h-2 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: 13489212 - R-H2O-02h-2 vs R-URA-02h-2

hyb_protocol: R-URA-02h-2 Cy5 / R-H2O-02h-2 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: 13483896 - F-H2O-06h-2 vs F-URA-06h-2

hyb_protocol: F-URA-06h-2 Cy5 / F-H2O-06h-2 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: MPI-591

city: Regensburg

first: Stefan

last: Bentink

state: Bayern

address: Josef Engertstr. 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

description: Mature aggressive B-cell lymphoma

hyb_protocol: Affymetrix hybridization was carried with U133A GeneChips according to the manufacturer’s recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter.

scan_protocol: After hybridization of night (16 hours, 45 C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500).

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536).  Probe-set summarization was performed using the median polish method on the normalized data (Irrizary et al. Nucleic Acids Research 2003, PMID: 12582260).

label: Biotin

source_name: Frozen tissue

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation.

extract_protocol: RNA was isolated using RNeasy Mini Kit (both from QIAGEN).The concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed by analysis of an aliquot in the Agilent BioAnalyzer.

tag: Unique Identifier

tag: Age at diagnosis

tag: Sex of patient

value: male

tag: Consensus morphological diagnosis from expert hematopathologists

value: BL

tag: Immunohistochemistry

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):100

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):4

tag: Cytogenetics

value: Status of MYC translocation:IG-MYC

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

tag: ArrayCGH

value: Complexity/relative number of genomic gains and losses:1

tag: Cytogenetics/arryCGH

value: MYC-break with simple or complex karyotype:MYC.simple

tag: Ann Arbour Stage

tag: Gene expression

value: Diagnosis according to mBL gene expression signature:mBL

tag: Germinal center like/ activated B-cell like signature

value: GCB

tag: mBL index (>0.95 => mBL)


title: MPI-585

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Proportion of positive tumor cells BCL2 (>1 => pos):4

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):70

value: Percentage of positive tumor cells BCL6 (>1 => pos):3

value: Status of MYC translocation:neg

value: Breakpoint at BCL6-locus detected:pos

value: Complexity/relative number of genomic gains and losses:7

value: MYC-break with simple or complex karyotype:MYC.neg

value: Diagnosis according to mBL gene expression signature:non-mBL


title: MPI-583

description: Mature aggressive B-cell lymphoma

value: female

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):NA

value: Signal intensity BCL2:NA

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):NA

value: Status of MYC translocation:IG-MYC

value: Breakpoint at BCL6-locus detected:neg

value: Complexity/relative number of genomic gains and losses:4

value: Diagnosis according to mBL gene expression signature:intermediate


title: MPI-596

description: Mature aggressive B-cell lymphoma

value: DLBCL

value: Proportion of positive tumor cells CD10 (>1 => pos):NA

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):90

value: Percentage of positive tumor cells BCL6 (>1 => pos):3

value: IgH-BCL2 Fusion:neg

value: Complexity/relative number of genomic gains and losses:15

value: MYC-break with simple or complex karyotype:MYC.complex

value: IV

value: GCB


title: MPI-587

description: Mature aggressive B-cell lymphoma

value: male

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Signal intensity BCL2:NA

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Complexity/relative number of genomic gains and losses:1

value: MYC-break with simple or complex karyotype:MYC.simple


title: MPI-579

description: Mature aggressive B-cell lymphoma

value: female

value: BL

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Status of MYC translocation:IG-MYC

value: Breakpoint at BCL6-locus detected:neg

value: Complexity/relative number of genomic gains and losses:4

value: Diagnosis according to mBL gene expression signature:mBL


title: MPI-580

description: Mature aggressive B-cell lymphoma

value: Proportion of positive tumor cells BCL2 (>1 => pos):2

value: Signal intensity BCL2:1

value: Percentage of positive tumor cells BCL6 (>1 => pos):4

value: IgH-BCL2 Fusion:neg


title: MPI-588

description: Mature aggressive B-cell lymphoma

value: male

value: aggressive B-NHL.unclassifiable

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Complexity/relative number of genomic gains and losses:3

value: GCB


title: MPI-575

description: Mature aggressive B-cell lymphoma

value: female

value: FL

value: Proportion of positive tumor cells CD10 (>1 => pos):0

value: Proportion of positive tumor cells BCL2 (>1 => pos):4

value: Signal intensity BCL2:2

value: Percentage Ki-67 of positive tumor cells (proliferative index):75

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Status of MYC translocation:neg

value: Complexity/relative number of genomic gains and losses:0

value: MYC-break with simple or complex karyotype:MYC.neg

value: Diagnosis according to mBL gene expression signature:non-mBL


title: MPI-576

description: Mature aggressive B-cell lymphoma

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):1

value: Signal intensity BCL2:1

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Percentage of positive tumor cells CD5 (>1 => pos):4

value: Percentage of positive tumor cells BCL6 (>1 => pos):4

value: Status of MYC translocation:IG-MYC

value: Breakpoint at BCL6-locus detected:neg

value: IgH-BCL2 Fusion:neg

value: Complexity/relative number of genomic gains and losses:1

value: MYC-break with simple or complex karyotype:MYC.simple

value: Diagnosis according to mBL gene expression signature:mBL


title: MPI-574

description: Mature aggressive B-cell lymphoma

value: male

value: BL

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):99

value: Percentage of positive tumor cells CD5 (>1 => pos):0

value: Percentage of positive tumor cells BCL6 (>1 => pos):2

value: Complexity/relative number of genomic gains and losses:2

value: I

value: Diagnosis according to mBL gene expression signature:intermediate

value: GCB


title: MPI-568

description: Mature aggressive B-cell lymphoma

value: Proportion of positive tumor cells CD10 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):NA

value: Signal intensity BCL2:NA

value: Percentage Ki-67 of positive tumor cells (proliferative index):90

value: Percentage of positive tumor cells BCL6 (>1 => pos):NA

value: Status of MYC translocation:IG-MYC

value: Breakpoint at BCL6-locus detected:neg

value: Complexity/relative number of genomic gains and losses:9

value: MYC-break with simple or complex karyotype:MYC.complex


title: MPI-529

description: Mature aggressive B-cell lymphoma

value: female

value: BL

value: Proportion of positive tumor cells CD20 (>1 => pos):4

value: Proportion of positive tumor cells BCL2 (>1 => pos):0

value: Signal intensity BCL2:0

value: Percentage Ki-67 of positive tumor cells (proliferative index):95

value: Percentage of positive tumor cells BCL6 (>1 => pos):3

value: IgH-BCL2 Fusion:neg

value: MYC-break with simple or complex karyotype:MYC.simple

value: Diagnosis according to mBL gene expression signature:mBL