title: ZF4_IPNV_24hr postinfection dyeswap sample 2

city: Taipei

first: Wei-Lun

last: Wang

address: No 128, Sect. 2, Academia Rd, Nankang, Taipei

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description:
Zebrafish ZF4 cell line derived from 24-hpf zebrafish embryos was purchased from the American Type Culture Collection (CRL-2050) and cultured in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum and penicillin-streptomycin. The isolated virus, E1-S, a member of the Ab strain of IPNV, was isolated from Japanese eels in Taiwan.
The commercial zebrafish 14K oligonucleotides set (MWG Biotech AG, Ebersbach, Germany) were obtained and were printed on UltraGAPS Coated slide (Corning, New York, NY ) with use of the OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI) according to the manufacture’s instructions. The 14,067 oligonucleotides represent 9666 genes (7009 singlet genes and 2657 redundant genes), and the redundancy of this chip is 31 %.

hyb_protocol: Amino-allay dye coupling was carried out using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) according to the manufacture’s instructions. We have optimized a reverse transcription labeling protocol using 40 μg total RNA, 5 μg of anchored oligo(dT) primer ((dT)20VN) and SuperScript III reverse transcriptase. After 3 hour incubation at 46°C, the reaction was stopped by incubating at 70°C for 15 min in the presence of 1N NaOH, and then neutralized the solution by adding 1N HCl. Bring the reaction mixture to a final volume of 100 μl with nuclease-free water. Purify the amine-modified DNA using a MinElute PCR Purification Kit (QIAGEN), following the instructions in the kit, except perform twice washes instead of one and elute the probe by 0.1M NaHCO3. Resuspend one aliquot of Alexa Flour Dye in 20 μl aa-cDNA labeled probe and then incubate at RT in the dark for overnight. Repeat the purification by MinElute PCR Purification kit and elute with elution EB buffer. Yeast tRNA (10 μg) were added to the sample, dried in a speedvac at 45°C and redissolved in 70 μl of hybridization buffer (formamide-based) purchased from MWG (Germany) . The mixture was denatured at 95°C for 2 min. The solution was collected by brief centrifugation and applied onto the oligo area on the microarray slides. Coverslips were applied (60 x 22 mm) and then immersed the chamber in a water bath for hybridization overnight at 42°C. Arrays were washed by 2x SSC, 0.1% SDS, followed by 1x SSC, 0.1% SDS, followed by 0.5 x SSC, followed by 0.1 x SSC only at room temperature for 5 min each time. Slides were subsequently dried by brief centrifugation. Arrays were scanned using an Axon GenePix 4000B scanner and median spot intensities collected using Axon GenePix Pro5.1 (Molecular Devices, Sunnyvale, CA)

scan_protocol: Scanning was performed with a ScanArray Gx scaner (PerkinElmer, Waltham, MA). The acquired images were analyzed using ScanArray Express 3.0 (PerkinElmer)and Genespring software (Aglient Technologies, Foster City, CA).

data_processing: Data files were imported into GeneSpring GX 7.3 (Agilent Technologies, Foster City, CA) for further analysis. ‘LOWESS Normalization’ was applied for data normalization for GeneSpring. Expression data sets must pass all the following quality control categories before they are used for cluster analysis. First, the hybridization results were not flagged as bad. Second, net intensities of both channels were equal to or greater then 500. Third, statistical analyses were applied to the triplicate data for each spot and repeat three times. For expression data, ratio values equal to or greater than 2 were considered up-regulated or down-regulated.

organism: Danio rerio

source_name: normal ZF4 cells

label_protocol: cDNA probes were synthesized by reverse transcription of 10 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen).The amine-modified DNA then was incubated with resuspend one aliquot of Cy5 Dye (Amersham Bioscience, Buckinghamshire, UK) at RT in the dark for overnight. Finally, the probe was purified by kit and was eluted with elution EB buffer.

extract_protocol: ZF4 cells were seeded in a 100-mm petri dish and cultivated for more than 24 h. At the completion of each incubation period, the culture medium was aspirated, and cells were wished with PBS. The total RNAs of ZF4 cells were also extracted with TRIzol reagent (Invitrogen) and were further purified by On-Column RNase-free DNase digestion (QIAGEN) to remove possible genomic DNA contamination. The RIN value of RNA samples before being applied to microarray was measured to be 10.0 by Agilent 2100 Bioanalyzer to confirm the RNA quality.

treatment_protocol: The ZF4 cell monolayer incubated at 18°C.

tag: cell line

value: ZF4 cells

tag: infection

source_name: ZF4 cells infected by IPNV at 24 h.p.i.

label_protocol: cDNA probes were synthesized by reverse transcription of 10 μg total RNA using a SuperScript indirect cDNA labeling system (Invitrogen).The amine-modified DNA then was incubated with resuspend one aliquot of Cy3 Dye (Amersham Bioscience, Buckinghamshire, UK) at RT in the dark for overnight. Finally, the probe was purified by kit and was eluted with elution EB buffer.

extract_protocol: ZF4 cells were seeded in a 100-mm petri dish and cultivated for more than 24 h. These cells were then infected with MOI of 5 of IPNV and incubated for 24h. At the completion of each incubation period, the culture medium was aspirated, and cells were wished with PBS. The total RNAs of ZF4 cells were also extracted with TRIzol reagent (Invitrogen) and were further purified by On-Column RNase-free DNase digestion (QIAGEN) to remove possible genomic DNA contamination. The RIN value of RNA samples before being applied to microarray was measured to be 10.0 by Agilent 2100 Bioanalyzer to confirm the RNA quality.

treatment_protocol: The E1S virus was propagated in ZF4 cell monolayer at a 5 multiplicity of infection (MOI) per cell. Infected cultures were incubated at 18°C and collected sample at 24hr post-infection.

value: IPNV

tag: time point


title: sporadic breast tumor, Invasive Ductal Carcinoma_C031_Q425B2

status: Public on Feb 01 2011

type: genomic

city: Amsterdam

first: Petra

last: Nederlof

address: Plesmanlaan 121

department: Pathology

country: Netherlands

institute: The Netherlands Cancer Institute

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

scan_protocol: ImaGene v6.0 software (BioDiscovery Inc) was used to translate the cy5/cy3 intensity ratios into average of the triplicates log2-ratio.

data_processing: average of triplicate Log2 ratios after Lowess pintip normalization

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE primary breast tumor material sporadic case

label_protocol: Sample and reference DNA were labeled with the Cy5- or Cy3-conjugates from the Universal Linkages System (ULS; Kreatech biotechnology, Amsterdam, The Netherlands)

extract_protocol: DNA isolation for arrayCGH was performed as described elsewhere. (20) In short, formalin-fixed paraffin-embedded FFPE tissue of uterine corpus cancer was used. Cases were discarded if the tumor cell percentage was below 70%.  Genomic DNA was isolated from 10*10µm thick paraffin slides. Slides were deparaffinized twice in xylene for 5 minutes, rehydrated in 100% (twice), 90%,70% ethanol and stained with hematoxylin. To remove formalin induced cross-links an overnight incubation in 1M NaSCN at 37°C was performed. Slides were subsequently washed in PBS twice for 10 minutes and air-dried. Tumor cells were collected by macro dissection by scraping from the slides and cells were transferred to a tube containing 200 µl ATL buffer (QIAamp® DNA Mini Kit cat 51304, Qiagen), 27 µl Proteinase-K was added and samples were incubated at 55°C while shaken at 450 rmp for at least 40 hours.  At intervals of 4, 16 and 24 hours additional 27 µl of Proteinase-K was added (Qiagen kit). Further isolation was done following the manufacturers instructions (Qiagen).

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: negative

tag: pr ihc

tag: her2 ihc

value: positive

source_name: genomic DNA from blood from 8 healthy females

tag: reference


title: Oral leukoplakia LM403

type: RNA

city: Houston

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

country: USA

institute: The University of Texas M.D. Anderson Cancer Center

description: RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol. RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit. For all experiments, the manufacturers' protocols were strictly followed. WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively. Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol. Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

data_processing: Raw data of microarrays were processed using quantile normalization and RMA algorithm (RMAExpress); expression values were log2 transformed

label: biotin

molecule: total RNA

source_name: Oral leukoplakia

growth_protocol: Biopsies of oral leukoplakia

treatment_protocol: Samples were OCT-embedded and frozen before RNA extraction

tag: Sex

value: male

tag: race

value: white

tag: alcohol habits

value: never

tag: smoking habits

value: former

tag: age

tag: treatment arm

value: retinyl palmitate

tag: histology at baseline (hyperplasia versus dysplasia)

value: dysplasia

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

value: high expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

value: oral cancer development

tag: time of biopsy

value: biopsy at baseline


title: ZF4_IPNV_24hr postinfection dyeswap sample 1

tag: cell line

value: ZF4 cells

tag: infection

tag: time point


title: Marginal zone B-cell lymphoma patient sample 08-240

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description:
08-240.CEL
Hybridized to 250K_Nsp

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

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

data_processing:
Data acquisition was performed using the GeneChip Operating Software (GCOS) v1.4 and Genotyping Analysis Software (GTYPE) v4.1. Genotype calls were calculated using the BRLMM algorithm. Mapping data for probes were derived from the National Center for Biotechnology Information (NCBI) Human Genome Build 36, as provided by Affymetrix, which was used for all subsequent analyses. The modified Bayesian Piecewise Regression (mBPCR) method was used to estimate the copy number (CN) starting from raw CN values obtained with Affymetrix CNAT 4.01 using a Gaussian bandwidth of 0 Kb and 46 Caucasian normal female samples of the HapMap Project as reference samples.
signal = log2ratio; loh = 0 or 1

label: Biotin

source_name: MZL patient sample 08-240

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: All clinical specimens were derived from involved sites and obtained in the course of routine diagnostic procedures before therapy initiation. Cases were selected based upon the availability of frozen material with a fraction of neoplastic cells in the specimen representing >70% of overall cellularity as determined by morphologic and/or immunophenotypic studies. Genomic DNA was extracted using the QIAamp DNA Mini Kit.

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: ZF4_IPNV_24hr postinfection sample 2

value: IPNV


title: Oral leukoplakia LM402

hyb_protocol: Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol.

scan_protocol: Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

label_protocol: WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols.

extract_protocol: RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.

tag: Sex

tag: race

value: hawaian

value: current

value: hyperplasia

value: low expression


title: sporadic breast tumor, Invasive Ductal Carcinoma_C032_Q425B5

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: positive

tag: pr ihc

tag: her2 ihc

value: negative

tag: reference

value: genomic DNA from blood from 8 healthy females


title: Marginal zone B-cell lymphoma patient sample 08-241

description:
08-241.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-241


title: sporadic breast tumor, Invasive Ductal Carcinoma_C030_Q430B4


title: Marginal zone B-cell lymphoma patient sample 08-238

description:
08-238.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-238


title: Marginal zone B-cell lymphoma patient sample 08-235

description:
08-235.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-235


title: Marginal zone B-cell lymphoma patient sample 08-234

description:
08-234.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-234


title: sporadic breast tumor, Invasive Ductal Carcinoma_C053_Q455D5


title: Oral leukoplakia LM401

value: male

value: white

tag: alcohol habits

value: former

tag: smoking habits

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy


title: Oral leukoplakia LM400

tag: Sex

tag: race

value: dysplasia

value: mild dysplasia

value: oral cancer development

value: biopsy at baseline


title: sporadic breast tumor, Invasive Lobular Carcinoma_C029_Q427C9

tag: gender

tag: tumor

tag: histology

value: Invasive lobular carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc


title: ZF4_IPNV_12hr postinfection dyeswap sample 1

tag: cell line

value: ZF4 cells

tag: infection

source_name: ZF4 cells infected by IPNV at 12 h.p.i.

extract_protocol: ZF4 cells were seeded in a 100-mm petri dish and cultivated for more than 24 h. These cells were then infected with MOI of 5 of IPNV and incubated for 12h. At the completion of each incubation period, the culture medium was aspirated, and cells were wished with PBS. The total RNAs of ZF4 cells were also extracted with TRIzol reagent (Invitrogen) and were further purified by On-Column RNase-free DNase digestion (QIAGEN) to remove possible genomic DNA contamination. The RIN value of RNA samples before being applied to microarray was measured to be 10.0 by Agilent 2100 Bioanalyzer to confirm the RNA quality.

treatment_protocol: The E1S virus was propagated in ZF4 cell monolayer at a 5 multiplicity of infection (MOI) per cell. Infected cultures were incubated at 18°C and collected sample at 12hr post-infection.

value: IPNV

tag: time point


title: Marginal zone B-cell lymphoma patient sample 08-233b

description:
08-233b.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-233b

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: Marginal zone B-cell lymphoma patient sample 08-237

description:
08-237.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-237


title: Marginal zone B-cell lymphoma patient sample 08-232

description:
08-232.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-232


title: ZF4_IPNV_12hr postinfection dyeswap sample 2


title: sporadic breast tumor, Invasive Ductal Carcinoma_C028_Q427D0

value: female

value: breast canrcinoma

value: Invasive ductal carcinoma

tag: pr ihc

tag: her2 ihc

tag: reference


title: sporadic breast tumor, Invasive Ductal Carcinoma_C027_Q425B7

value: positive

value: genomic DNA from blood from 8 healthy females


title: sporadic breast tumor, Invasive Ductal Carcinoma_C026_Q427B9

value: negative


title: Oral leukoplakia LM398

value: white

tag: alcohol habits

value: current

tag: smoking habits

value: never

tag: age

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

value: high expression

tag: podoplanin expression

value: low expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy


title: ZF4_IPNV_12hr postinfection sample 2

tag: cell line

tag: infection

tag: time point


title: Marginal zone B-cell lymphoma patient sample 08-239

description:
08-239.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-239

tag: cell type

tag: diagnosis


title: Marginal zone B-cell lymphoma patient sample 08-231

description:
08-231.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-231


title: ZF4_IPNV_24hr postinfection sample 1


title: Oral leukoplakia LM399

tag: Sex

value: male

tag: race

value: 13-cis-retinoic acid

value: oral cancer development

value: biopsy at 3 months after inclusion


title: ZF4_IPNV_12hr postinfection sample 1

value: ZF4 cells

value: IPNV


title: Marginal zone B-cell lymphoma patient sample 08-230

description:
08-230.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-230

value: marginal zone lymphoma

value: NMZL


title: sporadic breast tumor, Invasive Ductal Carcinoma_C023_Q430B3

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: positive

tag: pr ihc

tag: her2 ihc

tag: reference


title: sporadic breast tumor, Invasive Ductal Carcinoma_C025_Q425B6

value: negative

value: genomic DNA from blood from 8 healthy females


title: sporadic breast tumor, Invasive Ductal Carcinoma_C022_Q427C7


title: Oral leukoplakia LM397

value: white

tag: alcohol habits

value: former

tag: smoking habits

value: current

tag: age

tag: treatment arm

value: beta-carotene

tag: histology at baseline (hyperplasia versus dysplasia)

value: dysplasia

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy

value: biopsy at baseline


title: ZF4_IPNV_6hr postinfection_dyeswap sample 1

source_name: normal ZF4 cells

tag: cell line

value: ZF4 cells

tag: infection

source_name: ZF4 cells infected by IPNV at 6 h.p.i.

extract_protocol: ZF4 cells were seeded in a 100-mm petri dish and cultivated for more than 24 h. These cells were then infected with MOI of 5 of IPNV and incubated for 6h. At the completion of each incubation period, the culture medium was aspirated, and cells were wished with PBS. The total RNAs of ZF4 cells were also extracted with TRIzol reagent (Invitrogen) and were further purified by On-Column RNase-free DNase digestion (QIAGEN) to remove possible genomic DNA contamination. The RIN value of RNA samples before being applied to microarray was measured to be 10.0 by Agilent 2100 Bioanalyzer to confirm the RNA quality.

treatment_protocol: The E1S virus was propagated in ZF4 cell monolayer at a 5 multiplicity of infection (MOI) per cell. Infected cultures were incubated at 18°C and collected sample at 6hr post-infection.

tag: time point


title: Oral leukoplakia LM395

tag: Sex

value: male

tag: race

value: 13-cis-retinoic acid

value: high expression

value: oral cancer development

value: biopsy at 3 months after inclusion


title: Oral leukoplakia LM396

value: never

value: retinyl palmitate

value: hyperplasia

value: low expression


title: sporadic breast tumor, Invasive Ductal Carcinoma_C020_Q449D9

source_name: FFPE primary breast tumor material sporadic case

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: negative

tag: pr ihc

tag: her2 ihc

tag: reference

value: genomic DNA from blood from 8 healthy females


title: Oral leukoplakia LM394

value: white

tag: alcohol habits

tag: smoking habits

value: former

tag: age

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)


title: Oral leukoplakia LM393

tag: Sex

tag: race

value: beta-carotene

tag: outcome

tag: time of biopsy

value: biopsy at baseline


title: ZF4_IPNV_6hr postinfection sample 1

tag: cell line

value: ZF4 cells

tag: infection

value: IPNV

tag: time point


title: ZF4_IPNV_6hr postinfection sample 3


title: Oral leukoplakia LM391

value: hawaian

value: dysplasia

value: mild dysplasia

value: oral cancer development


title: Marginal zone B-cell lymphoma patient sample 08-226

description:
08-226.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-226

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: sporadic breast tumor, Invasive Ductal Carcinoma_C018_Q425A9

tag: gender

value: female

tag: tumor

tag: histology

tag: age at diagnosis

tag: tumor grade

tag: er ihc

tag: pr ihc

tag: her2 ihc

source_name: genomic DNA from blood from 8 healthy females

tag: reference


title: Marginal zone B-cell lymphoma patient sample 08-225

description:
08-225.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-225


title: ZF4_IPNV_6hr postinfection sample 2


title: Oral leukoplakia LM390

source_name: Oral leukoplakia

tag: Sex

tag: race

tag: alcohol habits

value: current

tag: smoking habits

tag: age

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

value: high expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

value: biopsy at 3 months after inclusion


title: Patient 2 ALDH high cells

city: Lund

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

country: Sweden

institute: Lund University

hyb_protocol: According to the manufacturers specifications

data_processing:
Data management and normalization was carried out using BioArray Software Environment (BASE). Raw intensity values representing mean bead pool intensity values for each probe were background corrected, negative intensities were capped to zero, followed by addition of an intensity constant of 20 to all probe intensities. Data was normalized using a quantile normalization algorithm as implemented in BASE.  Only probes with an annotated gene symbol according to RefSeq Release 22 (NCBI build 36.2), and UniGene Build 199) were used in further analyses.
The final reporter intensity values (unlogged) that was used for downstream data analyses. Data is normalized and filtered as specified in the data processing section. Matrix non-normalized :Background corrected intensity values prior normalization and filtering.

source_name: Normal kidney cortex

label_protocol: Biotinylated cRNA were prepared with the Ambion Message Amp RNA Amplification kit according to the manufacturers specifications

extract_protocol: Total RNA was extracted using Trizol reagent followed by purification on RNeasy micro columns (Qiagen) according to the manufacturers recommendations

treatment_protocol: Normal renal tissue was obtained from nephrectomies performed due to malignancy. All specimens were collected after informed consent by the patient. The cortical tissue farthest from the tumor was selected and put in ice cold DMEM medium (Invitrogen) supplemented with 10% fetal calf serum (FCS) and 1% penicillin/streptomycin (PEST). The tissues were rinsed, minced and subjected to overnight collagenase treatment at 37oC in a processing medium consisting of Ham´s F12/Dulbecco´s modified Eagle´s medium (F12:DMEM, 1:1, (v:v); Invitrogen), supplemented with 5 % fetal calf serum, 1 % PEST and Collagenase IV at a concentration of 1 mg/ml (Invitrogen) and deoxyribonuclease I type II at 5 mg /ml, (Sigma-Aldrich). Following trituration by slow repeated pipetting through a 10 ml Steri Strip, the resulting tissue suspension was serially passed through tissue strainers with the mesh sizes 100 and 70 μm respectively, thereby excluding glomeruli from the preparation. The suspension was treated with 1X trypsin-EDTA for 5 minutes and passed through a 20 μm strainer, which resulted in single-cells. Cells obtained from freshly dissociated kidneys were suspended in ALDEFLUOR assay buffer(StemCell Technologies) containing the ALDH substrate BODIPY-aminoacetaldehyde, (BAAA) at a concentration of 1,5 μM per 1 x 10^6 cells, followed by incubation for 30 minutes at 37oC. As negative control an aliquot of the cell suspension was allowed to react in the presence of the specific ALDH inhibitor diethylaminobenzaldehyde (DEAB) at a concentration of 15 μM per 0,5 x 106 cells. To exclude non-viable cells from the FACS step, the cells were assayed for viability by exposure to 0.25 μg 7-Amino-Actinomycin D (7AAD, BD Biosciences) per 1x10^6 cells for ten minutes before sorting, according to the protocols of the manufacturer. FACS analysis was performed using BD FACSAria I (BD Biosciences), and analysis were done using FACS Diva software version 6.1.1 (BD Biosciences) and FlowJo software v7.5.4 (Tree star, Inc) enabeling isolation of three pairs of cell fractions with high and low ALDH activity respectively.

tag: phenotype

value: ALDH high

tag: cell type

value: renal proximal tubule cell


title: Patient 3 ALDH high cells

scan_protocol: According to the manufacturers specifications


title: Marginal zone B-cell lymphoma patient sample 08-228

description:
08-228.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-228

tag: diagnosis


title: Oral leukoplakia LM392

value: white

value: former

value: 13-cis-retinoic acid

tag: outcome

tag: time of biopsy


title: Patient 2 ALDH low cells

value: ALDH low


title: Patient 3 ALDH low cells


title: Oral leukoplakia LM389

value: never

value: beta-carotene

value: low expression

value: biopsy at baseline


title: Patient 1 ALDH high cells


title: Marginal zone B-cell lymphoma patient sample 08-223

description:
08-223.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-223

value: marginal zone lymphoma


title: sporadic breast tumor, Invasive Ductal Carcinoma_C019_Q425B0

tag: gender

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: positive

tag: pr ihc

tag: her2 ihc

value: negative

tag: reference

value: genomic DNA from blood from 8 healthy females


title: Marginal zone B-cell lymphoma patient sample 08-227

description:
08-227.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-227

value: SMZL


title: sporadic breast tumor, Invasive Ductal Carcinoma_C015_Q425B8

value: female


title: Marginal zone B-cell lymphoma patient sample 08-224

description:
08-224.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-224


title: Marginal zone B-cell lymphoma patient sample 08-220

description:
08-220.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-220


title: Marginal zone B-cell lymphoma patient sample 08-221

description:
08-221.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-221


title: Oral leukoplakia LM388

tag: Sex

tag: race

tag: alcohol habits

tag: smoking habits

tag: age

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

value: dysplasia

tag: histology at baseline (breakdown)

value: moderate dysplasia

tag: p63 expression

value: high expression

value: oral cancer development


title: sporadic breast tumor, Invasive Ductal Carcinoma_C006_Q425A4

tag: gender

tag: tumor


title: sporadic breast tumor, Invasive Ductal Carcinoma_C016_Q425A7

tag: histology

tag: age at diagnosis


title: Marginal zone B-cell lymphoma patient sample 08-206

description:
08-206.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-206

tag: cell type

tag: diagnosis


title: Patient 1 ALDH low cells

tag: phenotype

value: ALDH low

value: renal proximal tubule cell


title: sporadic breast tumor, Invasive Ductal Carcinoma_C010_Q425A5

tag: tumor grade

tag: er ihc

tag: pr ihc

tag: her2 ihc

tag: reference


title: Oral leukoplakia LM387

tag: Sex

value: male

tag: race

value: white

tag: alcohol habits

value: current

tag: smoking habits

tag: age

value: 13-cis-retinoic acid

value: hyperplasia

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy

value: biopsy at 3 months after inclusion


title: Marginal zone B-cell lymphoma patient sample 08-222

description:
08-222.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-222

tag: cell type

value: marginal zone lymphoma


title: Oral leukoplakia LM386

value: former

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

value: biopsy at baseline


title: sporadic breast tumor, Invasive Ductal Carcinoma_C013_Q427C3

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: er ihc

value: negative

tag: pr ihc

value: positive

value: genomic DNA from blood from 8 healthy females


title: Oral leukoplakia LM385

tag: Sex

tag: race

tag: alcohol habits

tag: smoking habits

tag: age

value: dysplasia

value: moderate dysplasia

value: high expression

value: oral cancer development


title: HUVEC_LSS75_rep3

city: Bristol

first: Stephen

middle: John

last: White

address: Level 7 Queens Building, Bristol Royal Infirmary

department: Bristol Heart Institute

country: United Kingdom

institute: University of Bristol

description: pooled donor batch 3

hyb_protocol: ServiceXS

scan_protocol: ServiceXS

data_processing: Array data were extracted using Illumina's BeadStudio software. Normalization and statistical analysis were performed using scripts in R/Biocunductor. Differential expression between the treatments of interest was assessed using a Baysian statistics moderated t-test23. Genes were considered significant if the P values, adjusted for multiple testing by using Benjamini and Hochberg's method24, were <0.05. The false discovery rate (FDR) was thereby controlled to be <5%.

source_name: HUVEC

label_protocol: ServiceXS

growth_protocol: Promocell large vessel endothelial growth media

extract_protocol: Qiagen Total RNA extraction kit

treatment_protocol: Media without hydrocortisone, supplemented with 3.35% dextran to raise viscosity to 1.5cP (equivalent to plasma)

tag: cell type

value: Human umbilical vein endothelial

tag: laminar shear stress

value: 75 dynes/cm2


title: HUVEC_LSS75_rep2

description: pooled donor batch 2


title: HUVEC_LSS75_rep4

description: pooled donor batch 4


title: Marginal zone B-cell lymphoma patient sample 08-208

description:
08-208.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-208

tag: diagnosis

value: SMZL


title: Marginal zone B-cell lymphoma patient sample 08-205

description:
08-205.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-205

value: marginal zone lymphoma


title: HUVEC_LSS75_rep1

description: pooled donor batch 1


title: sporadic breast tumor, Invasive Ductal Carcinoma_C004_Q427C6

source_name: FFPE primary breast tumor material sporadic case

tag: her2 ihc

tag: reference


title: Oral leukoplakia LM383

value: male

value: white

value: former

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy

value: biopsy at 3 months after inclusion


title: Marginal zone B-cell lymphoma patient sample 08-203

description:
08-203.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-203


title: Marginal zone B-cell lymphoma patient sample 08-200

description:
08-200.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-200


title: Marginal zone B-cell lymphoma patient sample 08-201

description:
08-201.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-201


title: Marginal zone B-cell lymphoma patient sample 08-202

description:
08-202.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-202


title: Oral leukoplakia LM384

source_name: Oral leukoplakia

tag: Sex

value: female

tag: race

value: never

value: current

value: biopsy at baseline


title: Oral leukoplakia LM382

tag: alcohol habits

tag: smoking habits

value: dysplasia

value: moderate dysplasia

value: low expression


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX496_HB393-11

source_name: FFPE primary breast tumor material BRCAx family

tag: gender

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: grade

tag: er ihc

value: 10-50% positive

tag: pr ihc

value: negative

value: strong positive

source_name: genomic DNA from blood from 8 healthy females


title: HUVEC_LSS15_rep4

description: pooled donor batch 4

tag: cell type

value: Human umbilical vein endothelial

tag: laminar shear stress

value: 15 dynes/cm2


title: Oral leukoplakia LM380

value: male

value: white

value: former

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

value: high expression

value: oral cancer development


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX495_HB375-23

value: female

tag: her2 ihc


title: sporadic breast tumor, Invasive Ductal Carcinoma_C002_Q425A6

tag: age at diagnosis

tag: tumor grade

value: positive

tag: reference

value: genomic DNA from blood from 8 healthy females


title: Oral leukoplakia LM381

tag: Sex

tag: race

tag: alcohol habits

value: current

tag: smoking habits

value: dysplasia

value: severe dysplasia

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy

value: biopsy at baseline


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX494_HB394-11

tag: gender

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive lobular carcinoma

tag: grade

tag: er ihc

value: 10-50% positive

tag: pr ihc

value: >=50% positive

value: negative


title: HUVEC_LSS15_rep3

description: pooled donor batch 3

tag: cell type

value: Human umbilical vein endothelial

tag: laminar shear stress

value: 15 dynes/cm2


title: sporadic breast tumor, Invasive Ductal Carcinoma_C001_Q425A3

value: Invasive ductal carcinoma

tag: age at diagnosis

tag: tumor grade

tag: her2 ihc

tag: reference


title: HUVEC_LSS15_rep2

description: pooled donor batch 2


title: Marginal zone B-cell lymphoma patient sample 08-199

description:
08-199.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-199

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: HUVEC_LSS15_rep1

description: pooled donor batch 1


title: Oral leukoplakia LM378

tag: Sex

value: male

tag: race

value: white

tag: alcohol habits

tag: smoking habits

value: former

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

value: high expression

tag: podoplanin expression

value: oral cancer development

value: biopsy at 3 months after inclusion


title: Oral leukoplakia LM379

value: female

value: current

value: never

value: beta-carotene

value: low expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy


title: Oral leukoplakia LM377

value: dysplasia

value: moderate dysplasia

value: biopsy at baseline


title: Marginal zone B-cell lymphoma patient sample 08-197

description:
08-197.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-197

tag: cell type

value: marginal zone lymphoma

value: SMZL


title: Oral leukoplakia LM376

value: male

value: white

value: mild dysplasia


title: Marginal zone B-cell lymphoma patient sample 08-198

description:
08-198.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-198


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX492_HB404-19

tag: gender

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: grade

tag: er ihc

value: 10-50% positive

tag: pr ihc

value: >=50% positive

tag: her2 ihc

value: negative


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX491_HB375-11

value: female

value: strong positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX490_HB375-10


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX489_HB375-09

value: unknown

value: <10% positive


title: Oral leukoplakia LM375

tag: Sex

tag: race

tag: alcohol habits

value: current

tag: smoking habits

value: former

tag: age

value: beta-carotene

value: hyperplasia

value: high expression

value: oral cancer development


title: Marginal zone B-cell lymphoma patient sample 08-196

description:
08-196.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-196

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: sporadic breast tumor, Invasive Ductal Carcinoma_C017_Q425A8

value: breast canrcinoma

tag: age at diagnosis

tag: tumor grade

value: positive

tag: reference

value: genomic DNA from blood from 8 healthy females


title: Oral leukoplakia LM374

value: male

value: white

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

value: low expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

value: no oral cancer development

tag: time of biopsy

value: biopsy at baseline


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX487_HB375-17

tag: gender

value: female

tag: tumor

tag: histology

value: Invasive ductal carcinoma

tag: grade

tag: er ihc

value: 10-50% positive

tag: pr ihc

value: negative

tag: her2 ihc


title: Marginal zone B-cell lymphoma patient sample 08-194

description:
08-194.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-194

tag: cell type

tag: diagnosis


title: Marginal zone B-cell lymphoma patient sample 08-192

description:
08-192.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-192


title: aneurysmal tissue: sample #3

city: Jinan

first: Fan

last: Jiang

state: Shandong

address: 107 Wen Hua Xi Road

country: China

institute: Shandong University

description: Gene expression data

hyb_protocol: Fragmented cRNA were hybridized according to the standard protocol in the GeneChip® Expression Analysis Technical Manual.

scan_protocol: Arrays were scanned using the Affymetrix® GeneChip® Scanner 3000.

data_processing: The data were analyzed with whole chip Robust Multi-chip Average (RMA) analysis.

source_name: Intracranial arterial aneurysm (unruptured)

label_protocol: Labeled cRNA was synthesized from cDNA using the GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol:
sample collection protocol: The arterial tissues were snap-frozen in liquid nitrogen, and stored at –80 ° C.
Total RNA was isolated using TRIzol (Invitrogen) and cleaned using RNeasy kit (Qiagen) following the manufacturers’ protocol. The integrity of total RNA was confirmed by agarose gel electrophoresis.

tag: tissue

value: arterial

tag: status

value: unruptured aneurysm


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX486_HB375-22

value: Invasive lobular carcinoma

value: <10% positive


title: Marginal zone B-cell lymphoma patient sample 08-193

description:
08-193.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-193

value: marginal zone lymphoma

value: SMZL


title: RRE2_SEN_HCl45_04_7DE1309

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: biological replicate, Date of Scan Fri Jun 13 11:35:30 2008

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv5_SP040504_adapforsmallpins_040817

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: SEN NalR total RNA after 10min exposure to HCl pH4.5 in TSB

label_protocol: incorporation of Cy3-dCTP with Superscript RT and random hexamers

extract_protocol: RNeasy kit (QIAGEN)

tag: strain

value: Salmonella Enteritidis NalR

tag: condition

value: log phase culture after 10min exposure to acidic conditions HCl pH4.5

tag: medium

value: TSB

source_name: SEN NalR total RNA in TSB

label_protocol: incorporation of Cy5-dCTP with Superscript RT and random hexamers

value: log phase culture


title: aneurysmal tissue: sample #2

description: Gene expression data


title: aneurysmal tissue: sample #1

description: Gene expression data


title: Oral leukoplakia LM372

tag: Sex

tag: race

value: white

tag: alcohol habits

value: never

tag: smoking habits

tag: age

tag: treatment arm

value: retinyl palmitate

tag: histology at baseline (hyperplasia versus dysplasia)

value: dysplasia

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

value: low expression

tag: podoplanin expression

value: high expression

tag: oral cancer-free survival time (years)


title: normal arterial tissue: sample #3

description: Gene expression data

source_name: normal superficial temporal artery

value: arterial

value: normal


title: Oral leukoplakia LM373

value: male

value: current

value: former

value: 13-cis-retinoic acid

value: hyperplasia

tag: outcome

value: no oral cancer development

tag: time of biopsy

value: biopsy at baseline


title: normal arterial tissue: sample #1

description: Gene expression data

tag: tissue

tag: status


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX483_HB375-21

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: LCIS

tag: grade

value: unknown

tag: er ihc

value: 10-50% positive

tag: pr ihc

tag: her2 ihc

value: negative


title: normal arterial tissue: sample #2

description: Gene expression data


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX485_HB375-16

value: Invasive ductal carcinoma


title: Oral leukoplakia LM371

tag: Sex

tag: race

value: white

tag: alcohol habits

tag: smoking habits

value: never

tag: age

tag: treatment arm

value: beta-carotene

value: low expression


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX482_HB393-10

value: >=50% positive


title: Oral leukoplakia LM369

value: male

value: current

tag: histology at baseline (hyperplasia versus dysplasia)

value: dysplasia

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome


title: Marginal zone B-cell lymphoma patient sample 08-184

description:
08-184.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-184

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: NMZL


title: Marginal zone B-cell lymphoma patient sample 08-191

description:
08-191.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-191

value: SMZL


title: Oral leukoplakia LM370

value: female

value: former

value: 13-cis-retinoic acid

value: hyperplasia

value: high expression

value: no oral cancer development

tag: time of biopsy

value: biopsy at baseline


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX481_HB393-09

tag: gender

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: grade

tag: er ihc

value: 10-50% positive

tag: pr ihc

value: <10% positive


title: Marginal zone B-cell lymphoma patient sample 08-183

description:
08-183.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-183


title: Oral leukoplakia LM368

source_name: Oral leukoplakia

tag: Sex

value: male

tag: race

value: white

tag: alcohol habits

value: current

tag: smoking habits

tag: age

value: low expression


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX480_HB404-02

source_name: FFPE primary breast tumor material BRCAx family

tag: her2 ihc


title: Marginal zone B-cell lymphoma patient sample 08-190

description:
08-190.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-190

value: marginal zone lymphoma


title: Marginal zone B-cell lymphoma patient sample 08-182

description:
08-182.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-182

value: SMZL


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX479_HB376-17

value: female

value: negative

value: strong positive

source_name: genomic DNA from blood from 8 healthy females


title: Marginal zone B-cell lymphoma patient sample 08-180

description:
08-180.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-180


title: Pt20 whole subcutaneous adipose tissue, biological rep1

city: Boston

first: Frank

middle: H

last: Lau

state: MA

address: 185 Cambridge St - CPZN 4500

institute: Center for Regenerative Medicine

hyb_protocol: Following fragmentation, cRNA was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array following standard protocols.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Whole subcutaneous adipose tissue, patient 20

label_protocol: Biotinylated cRNA were prepared according to the standard protocols from 1.2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: No growth was involved; these are operating room specimens.

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

treatment_protocol: Adipocytes isolated by digestion with collagenase for 1 hour, 37C, 220 rpm shaker. Floating fraction collected.

tag: tissue

value: whole subcutaneous adipose tissue

tag: patient


title: Pt11 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 11


title: Marginal zone B-cell lymphoma patient sample 08-181

description:
08-181.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-181

tag: cell type

value: EMZL


title: Pt14 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 14


title: Pt20 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 20

value: whole pericardial adipose tissue


title: Pt17 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 17


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX477_HB393-08

value: positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX478_HB375-15

value: breast canrcinoma

value: Invasive lobular carcinoma


title: Oral leukoplakia LM365

value: asian

value: never

value: former

tag: treatment arm

value: retinyl palmitate

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

value: no oral cancer development

value: biopsy at baseline


title: Pt21 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 21


title: Oral leukoplakia LM366

value: male

value: current

value: beta-carotene

value: low expression

tag: time of biopsy


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX476_HB393-07

tag: gender

value: female

tag: tumor

tag: histology

value: Invasive ductal carcinoma

tag: grade

tag: er ihc

value: negative

tag: pr ihc


title: Oral leukoplakia LM363

tag: Sex

tag: race

value: white

tag: alcohol habits

tag: smoking habits

tag: age

value: dysplasia

value: mild dysplasia

value: biopsy at 3 months after inclusion


title: Marginal zone B-cell lymphoma patient sample 08-179

description:
08-179.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-179

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: Oral leukoplakia LM367

value: never

tag: treatment arm

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: podoplanin expression


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX475_HB376-16

tag: gender

tag: tumor

value: breast canrcinoma

value: 10-50% positive

tag: her2 ihc

value: strong positive


title: Oral leukoplakia LM364

value: male

value: 13-cis-retinoic acid

tag: oral cancer-free survival time (years)

tag: outcome

value: no oral cancer development

tag: time of biopsy

value: biopsy at baseline


title: Pt14 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 14

tag: tissue

value: whole pericardial adipose tissue

tag: patient


title: Oral leukoplakia LM362

tag: Sex

value: female

tag: race

tag: alcohol habits

tag: smoking habits

value: current

value: retinyl palmitate

value: hyperplasia

value: low expression


title: Marginal zone B-cell lymphoma patient sample 08-157

description:
08-157.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-157

tag: cell type

tag: diagnosis


title: Pt12 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 12


title: Pt19 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 19


title: Pt13 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 13

value: whole subcutaneous adipose tissue


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX473_HB394-17

source_name: FFPE primary breast tumor material BRCAx family

tag: histology

value: Invasive ductal carcinoma

tag: grade

tag: er ihc

value: negative

tag: pr ihc


title: Marginal zone B-cell lymphoma patient sample 08-158

description:
08-158.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-158

value: marginal zone lymphoma

value: SMZL


title: Pt10 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 10


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX469_HB376-23

tag: gender

tag: tumor

value: breast canrcinoma

value: >=50% positive

value: <10% positive

source_name: genomic DNA from blood from 8 healthy females


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX467_HB393-21

value: 10-50% positive

tag: her2 ihc

value: positive


title: Oral leukoplakia LM361

source_name: Oral leukoplakia

value: white

value: former

tag: age

tag: treatment arm

value: beta-carotene

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

value: high expression

tag: podoplanin expression

tag: oral cancer-free survival time (years)

tag: outcome

value: no oral cancer development

value: biopsy at baseline


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX466_HB393-03

value: female


title: Pt10 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 10

tag: tissue

value: whole pericardial adipose tissue

tag: patient


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX465_HB393-02

tag: histology

value: Invasive ductal carcinoma

value: strong positive


title: Oral leukoplakia LM359

tag: Sex

value: male

tag: race

tag: alcohol habits

value: current

tag: smoking habits

value: retinyl palmitate

value: hyperplasia

value: low expression

tag: time of biopsy

value: biopsy at 3 months after inclusion


title: Oral leukoplakia LM357

value: 13-cis-retinoic acid


title: Oral leukoplakia LM360

value: white


title: Marginal zone B-cell lymphoma patient sample 08-155

description:
08-155.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-155

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: NMZL


title: Oral leukoplakia LM358

value: never

tag: age

tag: treatment arm

value: beta-carotene


title: Pt8 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 8

value: whole subcutaneous adipose tissue


title: Marginal zone B-cell lymphoma patient sample 08-152

description:
08-152.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-152


title: Marginal zone B-cell lymphoma patient sample 08-154

description:
08-154.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-154


title: Marginal zone B-cell lymphoma patient sample 08-156

description:
08-156.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-156

value: SMZL


title: Marginal zone B-cell lymphoma patient sample 08-153

description:
08-153.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-153


title: Oral leukoplakia LM356

value: female

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

value: no oral cancer development

value: biopsy at baseline


title: Marginal zone B-cell lymphoma patient sample 08-151

description:
08-151.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-151

value: EMZL


title: Pt7 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 7


title: Oral leukoplakia LM355

value: current

tag: p63 expression

value: high expression

tag: podoplanin expression


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX460_HB393-01

tag: gender

tag: tumor

value: breast canrcinoma

value: Invasive lobular carcinoma

tag: grade

tag: er ihc

value: 10-50% positive

tag: pr ihc

tag: her2 ihc

value: <10% positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX462_HB376-15

tag: histology

value: Invasive ductal carcinoma

value: negative

value: strong positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX459_HB394-10


title: Marginal zone B-cell lymphoma patient sample 08-149

description:
08-149.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-149

value: marginal zone lymphoma


title: Marginal zone B-cell lymphoma patient sample 08-146

description:
08-146.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-146


title: Pt8 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 8

tag: tissue

value: whole pericardial adipose tissue

tag: patient


title: Marginal zone B-cell lymphoma patient sample 08-150

description:
08-150.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-150

tag: cell type


title: Marginal zone B-cell lymphoma patient sample 08-147

description:
08-147.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-147

tag: diagnosis


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX455_HB393-14

source_name: FFPE primary breast tumor material BRCAx family

value: positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX457_HB393-16

value: >=50% positive

source_name: genomic DNA from blood from 8 healthy females


title: Pt7 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 7


title: Oral leukoplakia LM354

source_name: Oral leukoplakia

tag: Sex

value: male

tag: race

value: white

tag: alcohol habits

value: never

tag: smoking habits

value: former

tag: age

value: beta-carotene

value: hyperplasia

value: low expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX456_HB393-15

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: grade


title: Marginal zone B-cell lymphoma patient sample 08-148

description:
08-148.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-148

value: EMZL


title: Pt5 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 5


title: Oral leukoplakia LM353

value: current

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: podoplanin expression

value: high expression

value: no oral cancer development

value: biopsy at baseline


title: Pt2 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 2

tag: tissue

value: whole subcutaneous adipose tissue

tag: patient


title: Pt3 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 3

value: whole pericardial adipose tissue


title: Oral leukoplakia LM351

tag: Sex

value: male

tag: race


title: Pt4 whole pericardial adipose tissue, biological rep1

source_name: Whole pericardial adipose tissue, patient 4


title: Pt1 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 1


title: Oral leukoplakia LM350

value: white

tag: alcohol habits

tag: smoking habits


title: Marginal zone B-cell lymphoma patient sample 08-145

description:
08-145.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-145

tag: cell type

value: marginal zone lymphoma

tag: diagnosis


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX454_HB393-13

tag: histology

value: Invasive ductal carcinoma

tag: er ihc

value: negative

tag: pr ihc

tag: her2 ihc

value: strong positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX451_HB384-48

tag: gender

tag: tumor

value: Invasive lobular carcinoma

tag: grade

value: positive


title: Marginal zone B-cell lymphoma patient sample 08-144

description:
08-144.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-144


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX450_HB404-08

value: female

value: breast canrcinoma

value: >=50% positive

value: 10-50% positive


title: Oral leukoplakia LM348

value: former

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: hyperplasia

tag: histology at baseline (breakdown)

tag: p63 expression

value: low expression

tag: oral cancer-free survival time (years)

tag: outcome

tag: time of biopsy


title: Oral leukoplakia LM346

tag: Sex

tag: race

tag: alcohol habits

value: never

tag: smoking habits

value: retinyl palmitate

value: dysplasia

value: moderate dysplasia

value: high expression

tag: podoplanin expression

value: no oral cancer development

value: biopsy at baseline


title: Pt11 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 11

tag: tissue

value: isolated pericardial adipocytes

tag: patient


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX448_HB384-38

tag: gender

tag: tumor

tag: histology

value: Invasive ductal carcinoma

tag: er ihc

tag: pr ihc

tag: her2 ihc

value: <10% positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX446_HB407-06

value: female

value: breast canrcinoma

value: Invasive lobular carcinoma

tag: grade

value: positive


title: Oral leukoplakia LM345

value: male

value: white

value: current

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: oral cancer-free survival time (years)

value: biopsy at 3 months after inclusion


title: Oral leukoplakia LM344

tag: Sex

tag: race

value: asian

tag: alcohol habits

value: never

tag: smoking habits

value: retinyl palmitate

value: dysplasia

value: mild dysplasia

value: low expression

tag: outcome

tag: time of biopsy


title: Marginal zone B-cell lymphoma patient sample 08-143

description:
08-143.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-143

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: EMZL


title: Oral leukoplakia LM343

value: former

value: hyperplasia

value: high expression

tag: podoplanin expression

value: no oral cancer development

value: biopsy at baseline


title: Marginal zone B-cell lymphoma patient sample 08-141

description:
08-141.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-141


title: Marginal zone B-cell lymphoma patient sample 08-142

description:
08-142.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-142


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX445_HB384-36

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: er ihc

value: >=50% positive

tag: pr ihc

value: 10-50% positive

tag: her2 ihc

value: positive


title: Pt5 whole subcutaneous adipose tissue, biological rep1

source_name: Whole subcutaneous adipose tissue, patient 5

tag: tissue

value: whole subcutaneous adipose tissue

tag: patient


title: Pt11 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 11

value: isolated subcutaneous adipocytes


title: Pt21 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 21

value: isolated pericardial adipocytes


title: Pt17 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 17


title: Pt17 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 17


title: Pt20 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 20


title: Marginal zone B-cell lymphoma patient sample 08-139

description:
08-139.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-139


title: Marginal zone B-cell lymphoma patient sample 08-134

description:
08-134.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-134


title: Oral leukoplakia LM341

source_name: Oral leukoplakia

tag: Sex

value: male

value: white

value: current

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: dysplasia

tag: histology at baseline (breakdown)

value: moderate dysplasia

tag: p63 expression

tag: oral cancer-free survival time (years)

value: biopsy at 3 months after inclusion


title: Marginal zone B-cell lymphoma patient sample 08-136

description:
08-136.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-136

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: EMZL


title: Marginal zone B-cell lymphoma patient sample 08-140

description:
08-140.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-140


title: Marginal zone B-cell lymphoma patient sample 08-135

description:
08-135.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-135


title: Marginal zone B-cell lymphoma patient sample 08-133

description:
08-133.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-133


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX434_HB394-24

source_name: FFPE primary breast tumor material BRCAx family

tag: gender

value: female

value: breast canrcinoma

value: Invasive lobular carcinoma

tag: grade

value: unknown

source_name: genomic DNA from blood from 8 healthy females


title: Oral leukoplakia LM340

tag: race

tag: alcohol habits

tag: smoking habits

value: former

value: severe dysplasia

tag: podoplanin expression

tag: outcome

value: no oral cancer development

tag: time of biopsy


title: Pt16 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 16

tag: tissue

value: isolated subcutaneous adipocytes

tag: patient


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX432_HB375-13

tag: tumor

tag: histology

value: Invasive ductal carcinoma

tag: er ihc

tag: pr ihc

tag: her2 ihc


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX430_HB394-22

value: 10-50% positive

value: negative


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX441_HB384-32

value: <10% positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX428_HB394-21


title: Oral leukoplakia LM337

tag: Sex

value: white

value: never

value: current

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

tag: histology at baseline (hyperplasia versus dysplasia)

value: dysplasia

tag: histology at baseline (breakdown)

value: mild dysplasia

tag: p63 expression

value: low expression

tag: oral cancer-free survival time (years)

value: biopsy at baseline


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX435_HB376-14

tag: gender

value: female

value: breast canrcinoma

tag: grade


title: Pt14 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 14


title: Oral leukoplakia LM339

tag: race

tag: alcohol habits

tag: smoking habits

value: hyperplasia

tag: podoplanin expression

tag: outcome

tag: time of biopsy


title: Oral leukoplakia LM349

value: male

value: high expression

value: no oral cancer development

value: biopsy at 3 months after inclusion


title: Oral leukoplakia LM336


title: Pt15 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 15

tag: tissue

value: isolated subcutaneous adipocytes

tag: patient


title: Pt16 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 16

value: isolated pericardial adipocytes


title: Oral leukoplakia LM338

tag: Sex

value: white


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX426_HB375-02

tag: tumor

tag: histology

value: Invasive ductal carcinoma

tag: er ihc

value: unknown

tag: pr ihc

tag: her2 ihc


title: Marginal zone B-cell lymphoma patient sample 08-124

description:
08-124.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-124

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: EMZL


title: Pt13 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 13


title: Pt15 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 15


title: Marginal zone B-cell lymphoma patient sample 08-131

description:
08-131.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-131


title: Oral leukoplakia LM335

value: never

tag: age

tag: treatment arm

value: beta-carotene

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: oral cancer-free survival time (years)


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX425_HB375-20

tag: gender

tag: grade

value: negative


title: Marginal zone B-cell lymphoma patient sample 08-123

description:
08-123.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-123


title: Oral leukoplakia LM334

value: female

tag: race

tag: alcohol habits

value: current

tag: smoking habits

value: former

value: 13-cis-retinoic acid

value: low expression

tag: podoplanin expression

tag: outcome

tag: time of biopsy

value: biopsy at baseline


title: Pt13 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 13

tag: tissue

tag: patient


title: Marginal zone B-cell lymphoma patient sample 08-128

description:
08-128.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-128

tag: cell type

tag: diagnosis


title: Oral leukoplakia LM342

source_name: Oral leukoplakia

tag: Sex

tag: age

tag: treatment arm

value: dysplasia

value: mild dysplasia

value: high expression

value: no oral cancer development


title: Pt12 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 12

value: isolated pericardial adipocytes


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX419_HB404-05

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: er ihc

value: 10-50% positive

tag: pr ihc

tag: her2 ihc


title: Oral leukoplakia LM333

tag: race

value: white

tag: alcohol habits

value: never

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: oral cancer-free survival time (years)


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX422_HB375-08

tag: gender

tag: grade

value: negative


title: Pt10 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 10

tag: tissue

value: isolated subcutaneous adipocytes

tag: patient


title: Marginal zone B-cell lymphoma patient sample 08-120

description:
08-120.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-120

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: EMZL


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX437_HB375-14

source_name: FFPE primary breast tumor material BRCAx family

value: female

tag: tumor

value: strong positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX418_HB375-04

tag: histology

source_name: genomic DNA from blood from 8 healthy females


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX421_HB384-04

tag: er ihc


title: Pt19 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 19


title: Marginal zone B-cell lymphoma patient sample 08-122

description:
08-122.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-122


title: Marginal zone B-cell lymphoma patient sample 08-126

description:
08-126.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-126


title: Oral leukoplakia LM329

tag: Sex

value: black

value: current

tag: smoking habits

tag: age

tag: treatment arm

value: 13-cis-retinoic acid

value: hyperplasia

value: low expression

tag: podoplanin expression

tag: outcome

tag: time of biopsy

value: biopsy at baseline


title: Oral leukoplakia LM331

value: male

tag: race

tag: alcohol habits

value: former

value: beta-carotene

tag: histology at baseline (hyperplasia versus dysplasia)

tag: histology at baseline (breakdown)

tag: p63 expression

tag: oral cancer-free survival time (years)

value: oral cancer development


title: Marginal zone B-cell lymphoma patient sample 08-125

description:
08-125.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-125

tag: cell type

tag: diagnosis


title: Pt8 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 8

tag: tissue

value: isolated pericardial adipocytes

tag: patient


title: Pt10 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 10


title: Marginal zone B-cell lymphoma patient sample 08-119

description:
08-119.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-119


title: Oral leukoplakia LM328

tag: Sex

value: white

value: never

value: retinyl palmitate

value: dysplasia

value: mild dysplasia

value: high expression

value: no oral cancer development

value: biopsy at 3 months after inclusion


title: Pt7 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 7

value: isolated subcutaneous adipocytes


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX417_HB407-04

tag: gender

value: female

tag: tumor

value: breast canrcinoma

tag: histology

value: Invasive ductal carcinoma

tag: grade

tag: er ihc

value: negative

tag: pr ihc

tag: her2 ihc


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX416_HB404-11

value: >=50% positive


title: Marginal zone B-cell lymphoma patient sample 08-115

description:
08-115.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-115

value: marginal zone lymphoma

value: EMZL


title: Marginal zone B-cell lymphoma patient sample 08-114

description:
08-114.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-114

value: NMZL


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX407_HB375-07


title: Pt5 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 5

value: isolated pericardial adipocytes


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX406_HB376-20

value: 10-50% positive


title: Marginal zone B-cell lymphoma patient sample 08-112

description:
08-112.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-112


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX414_HB375-05


title: Marginal zone B-cell lymphoma patient sample 08-111

description:
08-111.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-111


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX408_HB394-19

value: <10% positive


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX412_HB384-16


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX405_HB375-19


title: Pt4 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 4


title: Pt4 isolated pericardial adipocytes, biological rep2

source_name: Isolated pericardial adipocytes, patient 4


title: non-BRCA1/2 hereditary breast tumor (BRCAx)_BX403_HB376-13

source_name: FFPE primary breast tumor material BRCAx family

value: positive


title: Pt4 isolated pericardial adipocytes, biological rep1


title: Pt2 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 2


title: Pt3 isolated pericardial adipocytes, biological rep1

source_name: Isolated pericardial adipocytes, patient 3


title: Marginal zone B-cell lymphoma patient sample 08-107

description:
08-107.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-107


title: Pt3 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 3


title: Marginal zone B-cell lymphoma patient sample 08-110

description:
08-110.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-110

value: SMZL


title: Marginal zone B-cell lymphoma patient sample 08-084

description:
08-084.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-084


title: Marginal zone B-cell lymphoma patient sample 08-108

description:
08-108.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-108


title: Marginal zone B-cell lymphoma patient sample 08-085

description:
08-085.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-085


title: Pt1 isolated subcutaneous adipocytes, biological rep1

source_name: Isolated subcutaneous adipocytes, patient 1


title: Pt1 isolated subcutaneous adipocytes, biological rep2


title: 39 6475 + 24h C

first: Jame

last: Versalovic

state: TX

address: 1 Baylor Plaza, BCM 315

institute: Baylor College of Medicine

description: JVGXMO_36 / mouse 39

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data exported from Illumina Genome Studio was entered into Genespring GX 11.5.  Normalization and bacground correction as follows: threshold set at 1.0, Quantile normlaziation, log transformed (base 2),  Present call lower cut off 0.8; Absent call upper cut off 0.6

organism: Mus musculus

source_name: Mouse ileum epithelial cells

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

growth_protocol: 11-day-old male and female specific pathogen-free CD1 mouse pups received 1 of 3 treatments.  Intestinal epithelial cells from the distal-most 4 cm of ileum were isolated by laser capture microdissection 4 or 24 hours later.

extract_protocol: Epithelial cells from 24 ileum sections were harvested per animal  (ArcturusXT Microdissection System, Applied Biosystems, Carlsbad, CA) and isolated with PicoPure RNA Isolation Kit (Applied Biosystems), according to the manufacturer's protocols. Quality control was performed with Agilent Bioanalyzer and NanoDrop.

treatment_protocol: Each mouse received a single orogastric gavage of sterile vehicle (50 uL PBS) or Lactobacillus reuteri DSM 17938 (10^8 cfu/50 uL PBS) or L. reuteri ATCC PTA 6475 (10^8 cfu/50 uL PBS).

tag: strain

tag: age

value: 12 days old

value: Ileum epithelial cells

tag: agent

value: L. reuteri ATCC PTA 6475

tag: time

tag: replicate


title: 30 PBS + 24h C

description: JVGXMO_35 / mouse 30

value: PBS


title: Marginal zone B-cell lymphoma patient sample 08-083

description:
08-083.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-083

tag: cell type


title: Healthy donor, 24 hours GC treatment

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor taken 24 hours after GC administration.

RPK-II-24h

hyb_protocol: 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.

data_processing: The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).

source_name: Mononuclear cells, healthy donor, 24 hours after GC administration

label_protocol: 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: None.

extract_protocol: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.

treatment_protocol: Single administration of the glucocorticoid dexamethasone (20 mg/m2).

value: peripheral blood

value: mononuclear cells

tag: disease state

value: healthy

tag: treatment

value: dexamethasone

value: 24 hrs


title: DvH_60min._JW707_6500_ppm_nitrate_Nitrate_set955

type: mixed

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with JW707, 6500 ppm nitrate,  Nitrate.  Treatment time point = 60 min.

hyb_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P. Wall, J. D. and Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72:4370-4381.

scan_protocol: ImaGene software

data_processing: For a given time point (control or treatment), three microarray slides corresponding to three biological replicates were used. To estimate the average log (base 2) expression levels from replicate arrays, log expression levels from each array were normalized globally. This was calculated as follows. First, the net signal of each spot was calculated by subtracting out the background and adding a pseudosignal of 100 to enforce a positive value. If the resulting net signal was still less than 50, a value of 50 was used. Next, the expression level for each spot was calculated from the ratio of the two channels (mRNA over genomic DNA). Finally, the mean expression level and standard deviation of each spot were estimated, requiring n > 1, where n is the number of scorable replicates. To estimate the differential gene expression between the control and treatment conditions, normalized log ratios were calculated.  Each log ratio was calculated as log2(treatment)  log2(control). This log ratio was normalized using LOWESS (locally weighted scatterplot smoothing) on the difference versus the sum of the log expression level (12). Since sector-based artifacts were detected, each log ratio was further normalized by subtracting the median of all spots within each sector. The final normalized log ratio (log2R) was calculated from the average ratio of spots for each gene. To assess the significance of the normalized log ratio, a Z score was calculated by the following equation (0.25 is a pseudovariance term): Z = log2(treatment/control)/(0.25 + variance).

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 60min. JW707, 6500 ppm nitrate,  Nitrate

growth_protocol: Inoculate 200 ml of log-phase inoculum culture to 2000 ml of defined PIPES buffered medium LS4D. Grow culture in six 2L glass bottles placed in the anaerobic chamber at 30oC till OD of ~0.3. Three bottles will be the control(Ph 7.0, sterile water added) and the other three bottles will be the varibles (105 mM sodium nitrate). Harvest 50 ml of cells from each of the six bottles at 30, 60, 120, 240 and 480 min after treatment. All sampling occur in the anaerobic chamber. Samples were chilled and pumped through stainless steel tubing in ice-water into centrifuge bottlessurrounded by ice. Harvested biomass was centrifuged at 11,000  g for 10 min at 4oC.  Cell pellets were washed in 50ml anoxic 10mM phosphate buffered saline and centrifuged as above.  Cell pellets were immediately frozen in liquid N2 and stored at -80oC until RNA isolation.

extract_protocol: RNA extraction, purification, and labeling were performed independently on each cell sample. Total cellular RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer's protocol. RNA extracts were purified according to the RNeasy Mini Kit (QIAGEN, Valencia, CA) instructions, and on-column DNase digestion was performed with an RNase-free DNase set (QIAGEN, Valencia, CA) to remove genomic DNA contamination, according to the manufacturer's procedure.

treatment_protocol: 60min. JW707, 6500 ppm nitrate,  Nitrate.

value: Hildenborough, Fur knockout JW707

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, Fur knockout JW707, genomic DNA.

extract_protocol: Genomic DNA was extracted from D. vulgaris cultures at stationary phase using a standard protocol detailed elsewhere and labeled with the fluorophore Cy3-dUTP (Amersham Biosciences, Piscataway, NJ). The efficiency of labeling was routinely monitored by measuring the absorbance at 260 nm (for DNA concentration), 550 nm (for Cy3), or 650 nm (for Cy5).


title: DvH_60min._JW707_6500_ppm_nitrate_Nitrate_set951

label_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P. Wall, J. D. and Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72:4370-4381.


title: Healthy donor, 6 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor taken 6 hours after GC administration.

RPK-II-6h

source_name: Mononuclear cells, healthy donor, 6 hours after GC administration

tag: tissue

value: 6 hrs


title: 29 17938 + 24h C

description: JVGXMO_34 / mouse 29

value: L. reuteri DSM 17938


title: DvH_30min._JW707_6500_ppm_nitrate_Nitrate_set954

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with JW707, 6500 ppm nitrate,  Nitrate.  Treatment time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 30min. JW707, 6500 ppm nitrate,  Nitrate

treatment_protocol: 30min. JW707, 6500 ppm nitrate,  Nitrate.


title: DvH_30min._JW707_6500_ppm_nitrate_Nitrate_set950


title: Marginal zone B-cell lymphoma patient sample 08-080

description:
08-080.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-080

value: marginal zone lymphoma

tag: diagnosis


title: 22 6475 + 4h C

description: JVGXMO_33 / mouse 22

value: 11 days old


title: Healthy donor, 2 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor taken 2 hours after GC administration.

RPK-II-2h

source_name: Mononuclear cells, healthy donor, 2 hours after GC administration

value: 2 hrs


title: Marginal zone B-cell lymphoma patient sample 08-081

description:
08-081.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-081


title: Marginal zone B-cell lymphoma patient sample 08-082

description:
08-082.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-082


title: Marginal zone B-cell lymphoma patient sample 08-079

description:
08-079.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-079


title: Marginal zone B-cell lymphoma patient sample 08-078

description:
08-078.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-078


title: DvH_120min._JW707_6500_ppm_nitrate_Nitrate_set956

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with JW707, 6500 ppm nitrate,  Nitrate.  Treatment time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. JW707, 6500 ppm nitrate,  Nitrate

treatment_protocol: 120min. JW707, 6500 ppm nitrate,  Nitrate.


title: DvH_120min._JW707_6500_ppm_nitrate_Nitrate_set952


title: Epilepsy patient E5, 6 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 taken 6 hours after GC administration.

E5-6h

source_name: Mononuclear cells, epilepsy patient E5, 6 hours after GC administration

value: epilepsy, non-leukemic

tag: patient


title: DvH_0min._JW707_6500_ppm_nitrate_0_min_Nitrate_set949

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with JW707, 6500 ppm nitrate, 0 min  Nitrate.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. JW707, 6500 ppm nitrate, 0 min  Nitrate

treatment_protocol: 0min. JW707, 6500 ppm nitrate, 0 min  Nitrate.

treatment_protocol: 0min. JW707


title: DvH_240min._JW707_6500_ppm_nitrate_Nitrate_set953

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with JW707, 6500 ppm nitrate,  Nitrate.  Treatment time point = 240 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 240min. JW707, 6500 ppm nitrate,  Nitrate

treatment_protocol: 240min. JW707, 6500 ppm nitrate,  Nitrate.


title: DvH_240min._JW707_6500_ppm_nitrate_Nitrate_set957


title: 21 6475 + 4h B

description: JVGXMO_27 / mouse 21

source_name: Mouse ileum epithelial cells


title: 23 PBS + 4h C

description: JVGXMO_31 / mouse 23


title: Marginal zone B-cell lymphoma patient sample 08-075

description:
08-075.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-075

value: SMZL


title: Healthy donor, untreated sample

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor before administration of GC.

RPK-II-0h

source_name: Mononuclear cells, healthy donor, before administration of GC

value: untreated

value: 0 hrs


title: 38 6475 + 24h B

description: JVGXMO_30 / mouse 38

value: 12 days old

value: Ileum epithelial cells

value: L. reuteri ATCC PTA 6475


title: Epilepsy patient E5, 2 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 taken 2 hours after GC administration.

E5-2h

source_name: Mononuclear cells, epilepsy patient E5, 2 hours after GC administration

value: peripheral blood

value: mononuclear cells


title: Epilepsy patient E5, 24 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 taken 24 hours after GC administration.

E5-24h

source_name: Mononuclear cells, epilepsy patient E5, 24 hours after GC administration

value: dexamethasone


title: 33 PBS + 24h B

description: JVGXMO_28 / mouse 33

value: PBS


title: 28 17938 + 24h B

description: JVGXMO_29 / mouse 28


title: Marginal zone B-cell lymphoma patient sample 08-076

description:
08-076.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-076


title: Epilepsy patient E5, untreated sample

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 before administration of GC.

E5-0h

source_name: Mononuclear cells, epilepsy patient E5, before administration of GC


title: 11 17938 + 4h B

description: JVGXMO_26 / mouse 11


title: Marginal zone B-cell lymphoma patient sample 08-077

description:
08-077.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-077


title: 9 PBS + 4h B

description: JVGXMO_25 / mouse 9


title: Epilepsy patient E4, 24 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 taken 24 hours after GC administration.

E4-24h

source_name: Mononuclear cells, epilepsy patient E4, 24 hours after GC administration

value: 24 hrs


title: Marginal zone B-cell lymphoma patient sample 08-074

description:
08-074.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-074


title: Marginal zone B-cell lymphoma patient sample 08-073

description:
08-073.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-073


title: Marginal zone B-cell lymphoma patient sample 08-038

description:
08-038.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-038


title: Epilepsy patient E4, 2 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 taken 2 hours after GC administration.

E4-2h

source_name: Mononuclear cells, epilepsy patient E4, 2 hours after GC administration


title: Epilepsy patient E3, 6 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 taken 6 hours after GC administration.

E3-6h

source_name: Mononuclear cells, epilepsy patient E3, 6 hours after GC administration

value: 6 hrs


title: Epilepsy patient E4, untreated sample

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 before administration of GC.

E4-0h

source_name: Mononuclear cells, epilepsy patient E4, before administration of GC


title: Marginal zone B-cell lymphoma patient sample 08-036

description:
08-036.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-036


title: Marginal zone B-cell lymphoma patient sample 08-037

description:
08-037.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-037

value: NMZL


title: Epilepsy patient E3, 2 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 taken 2 hours after GC administration.

E3-2h

source_name: Mononuclear cells, epilepsy patient E3, 2 hours after GC administration


title: 31 PBS + 24 h A

description: JVGXMO_23 / mouse 31

source_name: Mouse ileum epithelial cells


title: Epilepsy patient E3, untreated sample

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 before administration of GC.

E3-0h

source_name: Mononuclear cells, epilepsy patient E3, before administration of GC


title: 25 17938 + 24h A

description: JVGXMO_21 / mouse 25

value: L. reuteri DSM 17938


title: 18 6475 + 4h A

description: JVGXMO_22 / mouse 18

value: 11 days old


title: 10 17938 + 4h A

description: JVGXMO_20 / mouse 10


title: Epilepsy patient E3, 24 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 taken 24 hours after GC administration.

E3-24h

source_name: Mononuclear cells, epilepsy patient E3, 24 hours after GC administration


title: GC sensitive clone C7H2-S15 treated for 6 hours with GC

description: GC sensitive clone C7H2-S15 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's gcrma package).

label_protocol: Total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: Cell lines were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity. The cells were free of mycoplamsa infection.

extract_protocol: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.

treatment_protocol: Cells were treated with 100nM dexametasone (Sigma, Vienna, Austria) or 0.1% ethanol as carrier control.

value: lymphoblastic leukemia

tag: gc resistant

value: FALSE

value: GC


title: Marginal zone B-cell lymphoma patient sample 08-035

description:
08-035.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-035

value: marginal zone lymphoma

value: SMZL


title: 36 6475 + 24 h A

description: JVGXMO_24 / mouse 36

value: 12 days old


title: GC sensitive clone C7H2-S2 treated for 6 hours with GC

description: GC sensitive clone C7H2-S2 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: GC sensitive clone C7H2-S10 treated for 6 hours with GC

description: GC sensitive clone C7H2-S10 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: 3 PBS + 4h A

description: JVGXMO_19 / mouse 3

value: Ileum epithelial cells


title: Marginal zone B-cell lymphoma patient sample 08-033

description:
08-033.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-033


title: 14 17938 + 4h C

description: JVGXMO_32 / mouse 14


title: Marginal zone B-cell lymphoma patient sample 08-034

description:
08-034.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-034


title: Marginal zone B-cell lymphoma patient sample 08-031

description:
08-031.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-031


title: Marginal zone B-cell lymphoma patient sample 08-027

description:
08-027.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-027

value: EMZL