title: Relapsed mesenchymal mammary tumor cell line 4, replicate 2

first: Keith

middle: L

last: Knutson

address: 200 First Street SW

department: Immunology

hyb_protocol: 15μg of each labeled probe was mixed with Affymetrix hybridization spike controls in a standard hybridization solution and heated to 95°C for 5 min, 45°C for 5 min, centrifuged to remove particulates and hybridized to Affymetrix Mouse 430_2 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: The data was analyzed using Affymetrix GCOS v1.3 software with a scaling target signal of 500 and a normalization of 1.

source_name: mammary tumor

label_protocol: Biotinylated cRNA probes were synthesized using a Message AMP II kit (Ambion).

growth_protocol: Cells grown in 10% FBS RPMI complete media, 80% confluent 10cm dishes

extract_protocol: RNA was isolated using RNeasy Plus Mini Kit (Qiagen) according to manufacturer's recommendations.

value: FVB/N, female, relapsed tumor resulting from injection of E cells


title: Relapsed mesenchymal mammary tumor cell line 4, replicate 1

status: Public on Apr 01 2009

type: RNA

city: Rochester

state: MN

country: USA

institute: Mayo Clinic

label: biotin

molecule: total RNA

organism: Mus musculus

tag: Strain


title: planktonic_exponential_rep2

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

country: Japan

institute: Hokkaido University

description: Planktonic sample

hyb_protocol: The labeled cRNA was fragmented, and 10 µg of the fragmented cRNA was hybridized to E. coli Antisense Genome Array (Affymetrix) For 16 hours at 45ºC according to the Affymetrix protocols.

scan_protocol: Affymetrix protocols

data_processing: Normalization was performed with dchip software using the Invariant Set Normalization method. Sample “At 1” was used as the baseline array.

organism: Escherichia coli

source_name: planktonic exponential phase in MOPS media with 0.2% glucose

label_protocol: The mRNA was purified from extracted total RNA with MICROBExpressTM (Ambion, Austin, TX) by removing the 16S and 23S ribosomal RNAs. The purified mRNA was polyadenylated with Poly(A) Polymerase (PAP), primed with an oligo(dT) primer bearing a T7 promoter by using MessageAmpTM II-Bacteria (Ambion). The second strand cDNA was synthesized from the obtained first strand cDNA. The cRNA was synthesized from the obtained second strand cDNA and biotin-labeled with GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix, Santa Clara, CA).

growth_protocol: Samples were grown in MOPS minimal media with 0.2% glucose.

extract_protocol: Samples were RNA-stabilized with Qiagen RNAProtect Bacterial Reagent, and total RNA was isolated with Qiagen RNeasy mini kit (Qiagen).

value: Escherichia coli MG1655


title: biofilm_maturation_rep1

description: Biofilm sample on glass surface

source_name: maturation process during biofilm formation in MOPS media with 0.2% glucose


title: Pineal_LD_ZT2

status: Public on May 01 2009

city: Tel Aviv

first: Yoav

last: Gothilf

address: Sherman Building, Room 405

department: Neurobiology, Faculty of Life Sciences

country: Israel

institute: Tel Aviv University

description: Gene expression data from zebrafish pineal

hyb_protocol: The target cRNA generated from each sample was fragmented and 15 micogram of the fragmented cRNA was added to the hybridization cocktail which includes in addition to the fragmented target, probe array controls (pre-mixed biotin-labeled bioB, bioC, bioD and cre, in staggered concentrations, ready to be added directly to the hybridization cocktail. These controls facilitate monitoring of the hybridization process for troubleshooting), BSA, and herring sperm DNA. It was then hybridized to the probe array during a 16-hour incubation at 45 deg (C). The array was then washed and stained  on the Affymetrix  fluidic station (using Streptavidin-Phycoerythrin which binds to the biotinylated UTP and CTP incorporated previously in the hybridized cRNA).

scan_protocol: The stained array was scanned on the Affymetrix scanner (450).

data_processing: The GCOS (Gene Operating System) generates the numerical data from the scanned intensities using the MAS 5 software (MicroArray suite 5.0; Affymetrix).

organism: Danio rerio

source_name: pineal at ZT2, 12-h light/12-h dark cycle

label_protocol: Double-strand cDNA was generated from 10-100 ng of mRNA by using a T7-linked oligo(dT) primer (Affymetrix). After second-strand synthesis, in vitro transcription was performed with MEGAscript® T7 Kit (Ambion, Inc.). The cRNA (600ng) was then used for second cycle first-strand cDNA (Affymetrix) by using a T7-linked oligo(dT) primer (Affymetrix). After 2nd cycle - second-strand synthesis, in vitro transcription was again performed; this time biotinylated UTP and CTP (Affymetrix) were incorporated in the cRNA, resulting in approximately 1800-fold amplification of labeled RNA.

growth_protocol: Adult zebrafish were raised in a light- and temperature-controlled recirculation water system under a 12-h light/12-h dark cycle at 28 °C and fed twice a day.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, Qiagen).

treatment_protocol: Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. 12 pineal glands were collected and pooled at each time point and at each light condition.

tag: Tg(aanat2:EGFP)Y8 transgenic zebrafish

tag: Age

value: adult (3-6 months)

tag: Gender

value: males and females


title: Pineal_DD_ZT2

source_name: pineal at ZT2, constant darkness


title: planktonic_exponential_rep1

description: Planktonic sample


title: Relapsed mesenchymal mammary tumor cell line 3, replicate 2


title: Pineal_DD_ZT2b

source_name: pineal at ZT2b, constant darkness


title: biofilm_colony formation_rep1

description: Biofilm sample on glass surface

source_name: colony formation process during biofilm formation in MOPS media with 0.2% glucose


title: biofilm_colony formation_rep2

description: Biofilm sample on glass surface


title: biofilm_colony formation_rep3

description: Biofilm sample on glass surface


title: biofilm_attachment_rep3

description: Biofilm sample on glass surface

source_name: attachment process during biofilm formation in MOPS media with 0.2% glucose


title: Relapsed mesenchymal mammary tumor cell line 3, replicate 1


title: Relapsed mesenchymal mammary tumor cell line 2, replicate 1


title: Relapsed mesenchymal mammary tumor cell line 1, replicate 2


title: Relapsed mesenchymal mammary tumor cell line 2, replicate 2


title: biofilm_attachment_rep2

description: Biofilm sample on glass surface


title: biofilm_attachment_rep1

description: Biofilm sample on glass surface


title: Spontaneous epithelial mammary tumor cell line, replicate 1

description: E

value: FVB/N-TgN(MMTVneu)202Mul, female, mammary adenocarcinoma


title: planktonic_exponential_rep3

description: Planktonic sample


title: Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk [Time 12 h vs. 4 h]

status: Public on Mar 24 2009

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

description: signal intensities (stored as TIFF files) were quantified, and the local background was subtracted using the QuantArray 3.0 software package (Packard BioScience).

scan_protocol: After acquisition of fluorescence intensities at 10-µm resolution using a ScanArray 4000 Microarray Scanner (Packard Biochip BioScience; Biochip Technologies LLC, Billerica, MA),

data_processing: data was log2 transformed and imported into JMP Genomics (SAS, Cary, NC). Loess normalization was applied to pre-processed data.  Following normalization, gene-specific effects were modeled in terms of the residuals.  A Mixed Model Analysis was applied to the pre-normalized data (Cui & Churchill, 2003). False discovery rate (FDR) was selected to adjust for the large number of multiple hypothesis tests across all genes. The default value of alpha (0.05) was used. The model-based approach, step-down quadratic regression method was applied to 791 significant genes for pattern recognition (Liu et al., 2005).

organism: Lactobacillus acidophilus NCFM

source_name: Time 12h

label_protocol: Reverse transcription and labeling of identical amounts (20 µg) of DNAse treated (Invitrogen, Carlsband, CA) RNA was performed with the SuperScript™ Indirect cDNA Labeling System for DNA Microarrays (Invitrogen) according to the manufacturer’s directions. Coupling of the Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ) to the AA-dUTP labeled cDNA and hybridization of samples to microarrays were performed according to the protocols outlined in the TIGR protocols website (www.tigr.org/tdb/microarray/protocolsTGR.shtml) and described previously (Azcarate-Peril et al., 2005).

extract_protocol: One-hundred ml aliquots of L. acidophilus cells growing in SM were harvested by centrifugation for 10 min at 3,220 x g, and frozen immediately in a dry ice/ethanol bath (the total time of each sampling process was 5 min).  RNA isolation was performed as described previously (Azcarate-Peril et al., 2005) with the following modifications: 5 ml Trizol® Reagent (Invitrogen, Carlsband, CA) was added to the cell pellets and they were homogenized in a Mini-Beadbeater-8 cell disruptor (Biospec Products, Bartlesville, OK) for seven 40-sec cycles (and chilled on ice for 40 sec between cycles), the phases were separated by centrifugation (3,220 x g, 20 min, 4º C).  The aqueous phase was removed to a fresh tube and 2.1 ml of Trizol and 1 ml of chloroform were added.  The mixture was vortexed for 15 s and centrifuged to separate the phases.  The Trizol step was repeated twice and RNA was precipitated from the final aqueous phase by adding 1 volume of isopropanol, followed by incubation at room temperature for 10 min and centrifugation (11,600 x g 10 min, 4º C).  Purity and quality of RNA samples were determined by electrophoresis on agarose gels. NanoDrop (ND-3300, NanoDrop Technologies, DE) was used as an UV/VIS spectrophotometer for quantification of the RNA samples.

tag: RNA samples were obtained from two biological replicates at time 12h (pH= 4.9; ≈ 1.5 X 108 cfu/ml)

source_name: Time 4h

tag: RNA samples were obtained from two biological replicates at time 4h (pH= 5.8; ≈ 3.8 X 107 cfu/ml)


title: Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk [Time 8h vs. 5 min]

hyb_protocol: Coupling of the Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ) to the AA-dUTP labeled cDNA and hybridization of samples to microarrays were performed according to the protocols outlined in the TIGR protocols website (www.tigr.org/tdb/microarray/protocolsTGR.shtml) and described previously (Azcarate-Peril et al., 2005).

tag: RNA samples were obtained from two biological replicates at time 8h (pH= 5.4; ≈ 7.1 X 107 cfu/ml)

source_name: Time 0 (5 min)

tag: RNA samples were obtained from two biological replicates at time 5  min


title: Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk [Time 8h vs. 12h]

source_name: Time 8h


title: Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk [time 4h vs. 8h]

tag: RNA samples were obtained from two biological replicates at time4h (pH= 5.8; ≈ 3.8 X 107 cfu/ml)


title: Relapsed mesenchymal mammary tumor cell line 1, replicate 1


title: Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk [Time 12h vs. 5min]

tag: RNA samples were obtained from two biological replicates at time 5  min (pH= 6.4; ≈ 2.1 X 107 cfu/ml)


title: Depomerai_heat_shock_2

status: Public on Mar 12 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: wild-type (N2) strain of C. elegans (originally obtained from the MRC Laboratory of Molecular Biology at Cambridge (UK))

hyb_protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit according to guidelines set out by Affymetrix, Santa Clara, CA.

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: The non-scaled RNA CEL files, were loaded into GeneSpring analysis software (GeneSpring 7.3; Agilent Technologies, Geneva, Switzerland) using the Robust Multichip Average (RMA) pre-normalisation algorithm (Irizarry et al., 2003). Further normalisations were performed for each experiment using a three step process: (i) probe-sets with a signal value <0.01 were set to 0.01, (ii) per chip normalisation to the 50th percentile, (iii) each gene signal from the microwave treated sample was normalised to the corresponding sham sample and the sham samples normalised to themselves.

organism: Caenorhabditis elegans

label_protocol: RNA quality was analysed with the Agilent 2100 Bioanalyser (Agilent Technologies, Geneva, Switzerland) using the RNA 6000 nano kit. All 10 RNA samples were of sufficient quality for gene array analysis. Approximately 5 µg of total RNA from each sample was used to produce cDNA using the GeneChip® One-cycle cDNA synthesis kit (Affymetrix, USA), as per manufacturer's instructions. Double stranded cDNA products were purified using the GeneChip® Sample Cleanup Module (Affymetrix, Santa Clara, USA). The synthesised cDNAs were in-vitro transcribed by T7 RNA polymerase using biotinylated nucleotides to generate biotinylated complementary RNAs (cRNAs) using the GeneChip® HT IVT labeling kit (Affymetrix, Santa Clara, USA), according to the manufacturer's instructions. The cRNAs were purified using the GeneChip® Sample Cleanup Module (Affymetrix, Santa Clara, USA). The cRNAs were then randomly fragmented at 94°C for 35 minutes in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate to generate molecules of approximately 35 to 200bp. Affymetrix C. elegans Genome GeneChip® arrays were hybridised with 15 µg of fragmented labeled cRNA for 16 h at 45°C as described in the Affymetrix Technical Analysis Manual using the GeneChip® hybridization control kit and GeneChip® hybridisation, wash and stain kit (Affymetrix, Santa Clara, USA). GeneChip® arrays were stained with streptavidin-phycoerythrin solution and scanned with an Affymetrix G2500A GeneArray scanner. Following scanning, non-scaled RNA signal intensity (CEL) files were generated using GeneChip® operating software (GCOS; Affymetrix, Santa Clara, USA) and normalised data was generated with the GCOS software using the MAS 5 algorithm (Affymetrix microarray suite users guide).

growth_protocol: Worm culture: N2 worms were cultured at 15°C on large 14 cm Petri dishes containing Nematode Growth Medium (NGM) agar overlaid with a lawn of food bacteria (E. coli strain P90C), as described previously [Sulston & Hodgkin, 1988; Dawe et al, 2006]. Worms were then synchronised by egg isolation using bleach [Suslton & Hodgkin, 1988] and the L1 offspring were filtered using 5um nylon filters [Mutwakil et al, 1997]. These synchronised cultures were grown up to the L4 stage before exposure. L4 worms were washed off the plates using K-medium (53 mM NaCl, 32 mM KCl) [Williams & Dusenbery, 1990], filtered using 5um nylon filters to remove excess bacteria and then dispensed carefully using a magnetic stirrer into two equal groups of 6-well plates destined for microwave or sham exposure, respectively. The sample volume in each well was always 1.0 ml, as previously used for dosimetry and temperature measurements.

extract_protocol: Aliquots of L4 worms were either sham-exposed (control; no field) in the copper TEM cell, or else exposed to 1GHz, 0.5W for 2.5hours at 26C in the silver-plated TEM cell. Post exposure, the worms were quickly removed from the 6-well dishes using glass pipettes, pelleted by centrifugation (3000 x g for 3 min) and then dropped in small concentrated pellets (again using a glass pipette) into liquid nitrogen. These pellets were then crushed using a pre-cooled mortar and pestle (-80°C) in the presence of 2ml of Trizol (Invitrogen). The worm-Trizol slurry was transferred by spatula into a 50 ml tube, left to defrost at room temperature with regular agitation, and then transferred to 2 x 1.5 ml microcentrifuge tubes. A standard Trizol RNA extraction was then performed according to the manufacturer's instructions. All microcentrifuge tubes, the spatula and the mortar and pestle were autoclaved and pretreated with RNaseZap (Ambion, Huntingtdon, UK) and diethyl pyrocarbonate-treated water prior to use. RNA samples from three exposure runs (performed on different days) were combined for hybridization onto microarrays. Thus the results below derive from 5 sets of sham gene-arrays pooled from 15 sham exposures, compared against 5 sets of exposed gene-arrays pooled from 15 microwave exposures. RNA was transported on dry ice and storage was at -80°C.

treatment_protocol: Microwave exposure and dosimetry: One group of worms was exposed to the microwave field (CW; 1.8 GHz; 5-40 mW kg-1) for 2.5 h at 26°C in the modified silver-plated TEM cell described in Dawe et al [2006], whereas the other group was sham-exposed (no field) for the same length of time at the same temperature in an unmodified copper TEM cell. The temperature difference between exposed samples in the silver-plated cell and sham samples in the copper cell has previously been measured at 0.1°C [Dawe et al, 2006], thereby minimising thermal artefacts in this study. Both TLM (N. Vasic & D. Thomas, unpublished) and FDTD modelling (G. Bit-Babik & M. Swicord, unpublished) concur with actual field measurements (B. Loader & A. Gregory, unpublished) that the SAR experienced by worms crawling across the well floor in a microwave-exposed 24-well multiwell plate varies from 5 mW kg-1 in the central wells up to 40 mW kg-1 in the corner wells.

tag: Food source

value: 90C lac-deleted strain of E. coli used as a food source


title: Depomerai_heat_shock_1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Sham (de_Pomerai_9_S5_C.Elegans)

source_name: 9_S5_C.Elegans sham exposed

growth_protocol: Worm culture: N2 worms were cultured at 15°C on large 14 cm  Petri dishes containing Nematode Growth Medium (NGM) agar overlaid with a lawn of food bacteria (E. coli strain P90C), as described previously [Sulston & Hodgkin, 1988; Dawe et al, 2006].  Worms were then synchronised by egg isolation using bleach [Suslton & Hodgkin, 1988] and  the L1 offspring were filtered using 5um nylon filters [Mutwakil et al, 1997]. These synchronised cultures were grown up to the L4 stage before exposure. L4 worms were washed off the plates using K-medium (53 mM NaCl, 32 mM KCl) [Williams & Dusenbery, 1990], filtered using 5um nylon filters to remove excess bacteria and then dispensed carefully using a magnetic stirrer into two equal groups of 6-well plates destined for microwave or sham exposure, respectively. The sample volume in each well was always 1.0 ml, as previously used for dosimetry and temperature measurements.

extract_protocol: Aliquots of L4 worms were either sham-exposed (control; no field) in the copper TEM cell, or else exposed to 1GHz, 0.5W for 2.5hours at 26C in the silver-plated TEM cell.  Post exposure, the worms were quickly removed from the 6-well dishes using glass pipettes, pelleted by centrifugation (3000 x g for 3 min) and then dropped in small concentrated pellets (again using a glass pipette) into liquid nitrogen.   These pellets were then crushed using a pre-cooled mortar and pestle (-80°C) in the presence of 2ml of Trizol (Invitrogen).  The worm-Trizol slurry was transferred by spatula into a 50 ml tube, left to defrost at room temperature with regular agitation, and then transferred to 2 x 1.5 ml microcentrifuge tubes.  A standard Trizol RNA extraction was then performed according to the manufacturer's instructions.  All microcentrifuge tubes, the spatula and the mortar and pestle were autoclaved and pretreated with RNaseZap (Ambion, Huntingtdon, UK) and diethyl pyrocarbonate-treated water prior to use.  RNA samples from three exposure runs (performed on different days) were combined for hybridization onto microarrays.  Thus the results below derive from 5 sets of sham gene-arrays pooled from 15 sham exposures, compared against 5 sets of exposed gene-arrays pooled from 15 microwave exposures. RNA was transported on dry ice and storage was at -80°C.

treatment_protocol: Microwave exposure and dosimetry: One group of worms was exposed to the microwave field (CW; 1.8 GHz; 5-40 mW kg-1) for 2.5 h at 26°C in the modified silver-plated TEM cell described in Dawe et al [2006], whereas the other group was sham-exposed (no field) for the same length of time at the same temperature in an unmodified copper TEM cell.  The temperature difference between exposed samples in the silver-plated cell and sham samples in the copper cell has previously been measured at 0.1°C [Dawe et al, 2006], thereby minimising thermal artefacts in this study.  Both TLM (N. Vasic & D. Thomas, unpublished) and FDTD modelling (G. Bit-Babik & M. Swicord, unpublished) concur with actual field measurements (B. Loader & A. Gregory, unpublished) that the SAR experienced by worms crawling across the well floor in a microwave-exposed 24-well multiwell plate varies from 5 mW kg-1 in the central wells up to 40 mW kg-1 in the corner wells.

value: 90C lac-deleted strain of E. coli used as a food source (obtained from the MRC Laboratory of Molecular Biology at Cambridge (UK))


title: Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk Time 5 min vs. 4h


title: Sham (de_Pomerai_5_S3_C.Elegans)

source_name: 5_S3_C.Elegans sham exposed


title: Microwave (de_Pomerai_6_E3_C.Elegans)

source_name: 6_E3_C.Elegans microwave exposed


title: Microwave (de_Pomerai_2_E1_C.Elegans)

source_name: 2_E1_C.Elegans microwave exposed


title: Depomerai_heat_control_2


title: Spontaneous epithelial mammary tumor cell line, replicate 2


title: Microwave (de_Pomerai_4_E2_C.Elegans)

source_name: 4_E2_C.Elegans microwave exposed


title: Sham (de_Pomerai_3_S2_C.Elegans)

source_name: 3_S2_C.Elegans Sham exposed


title: Microwave (de_Pomerai_10_E5_C.Elegans)

source_name: 10_E5_C.Elegans microwave exposed


title: Sham (de_Pomerai_7_S4_C.Elegans)

source_name: 7_S4_C.Elegans sham exposed


title: Microwave (de_Pomerai_8_E4_C.Elegans)

source_name: 8_E4_C.Elegans microwave exposed


title: Sham (de_Pomerai_1_S1_C.Elegans)

source_name: S1_C.Elegans sham exposed


title: Depomerai_heat_control_1


title: 13690770 - U73343 4°C vs Control 4°C

status: Public on Mar 03 2009

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: Identification of genes induced with the cold via inhibition of the phospholipase C

hyb_protocol: Control 4°C Cy5 / U73343 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: Control 4°C

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

growth_protocol: whole plant - Media : ms/2	 Temperature : 22°C

extract_protocol: Control 4°C:1ug.

treatment_protocol: Name:Control 4°C - abiotic stress - temperature,temperature:quantity 4° time 4hour .

tag: Arabidopsis thaliana (columbia)  - harvest date:28-06-07

treatment_protocol: Name:U73343 4°C - compound based treatment - temperature,u73343:quantity 4° time 4hour . With U73343, an inactif homologue of the inibitor U73122 (inhibitor of the phospholipase C pathway).


title: 13690778 - U73343 4°C vs U73122 4°C

hyb_protocol: U73122 4°C Cy5 / U73343 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:U73122 4°C - compound based treatment - temperature,u73122:quantity 4° time 4hour . With U73122, an inhibitor of the phospholipase C pathway.


title: 13690769 - Control 4°C vs U73343 4°C

hyb_protocol: U73343 4°C Cy5 / Control 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690782 - U73122 4°C vs U73343 4°C

hyb_protocol: U73343 4°C Cy5 / U73122 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690768 - Control 4°C vs Control 22°C

hyb_protocol: Control 22°C Cy5 / Control 4°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Control 22°C

extract_protocol: Control 22°C:1ug.

treatment_protocol: no treatment


title: 13690767 - Control 22°C vs Control 4°C

hyb_protocol: Control 4°C Cy5 / Control 22°C Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: day 20 (day 2 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 3

status: Public on Mar 01 2009

city: college station

first: Huaijun

last: Zhou

state: TX

address: 101 Kleberg Center

department: Poultry Science

institute: Texas A&M University

description: spleen were collected before Clostridium perfringens infection at day 18 for 6 replicates, and each replicate has two birds pooled

hyb_protocol: The labeled probes were hybridized to the microarrays for 16 hours at 65C

scan_protocol: Scanned on ScanArray Express instrument and analyzed with the ScanArray Express software

data_processing: log2 (Cy5/Cy3) ratios, global LOWESS normalization

organism: Gallus gallus

source_name: total RNA from non-medicated spleen

label_protocol: Samples were concentrated to approximately 5 ul with Microcon YM-30 filters (Millipore), cDNA was then labelled with Cy3 or Cy5 monofunctional dye. The unincorporated dye was removed with the QIA-quick PCR Purification kit (Qiagen) and the labelled cDNA samples were dried in a speed-vac.

extract_protocol: Trizol

tag: non-medicated spleen

source_name: total RNA from medicated spleen

tag: medicated spleen


title: day 22 (day 4 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 1


title: day 22 (day 4 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 3


title: day 20 (day 2 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 6


title: day 22 (day 4 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 6


title: day 20 (day 2 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 2


title: day 20 (day 2 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 4


title: day 22 (day 4 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 2


title: day 19 (day 1 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 5


title: day 19 (day 1 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 6


title: day 22 (day 4 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 5


title: day 20 (day 2 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 5


title: day 19 (day 1 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 1


title: day 20 (day 2 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 1


title: day 19 (day 1 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 3


title: day 19 (day 1 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 4


title: day 22 (day 4 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 4


title: day 18 before Clostridium perfriengens infection non-medicated vs. medicated replicate 4


title: day 18 before Clostridium perfriengens infection non-medicated vs. medicated replicate 5


title: day 18 before Clostridium perfriengens infection non-medicated vs. medicated replicate 1

tag: non-medicated spleen, before infection

tag: medicated spleen, before infection


title: day 18 before Clostridium perfriengens infection non-medicated vs. medicated replicate 3


title: day 18 before Clostridium perfriengens infection non-medicated vs. medicated replicate 2

tag: non-medicated


title: day 19 (day 1 post Clostridium perfriengens infection) non-medicated vs. medicated replicate 2


title: Dll1 thymus_rep7

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: male, age

value: 17 weeks

source_name: Wt RNA pool thymus

tag: RNA pool; male, age


title: Dll1 thymus_rep5


title: Dll1 thymus_rep6


title: Dll1 spleen_rep4

source_name: Wt RNA pool spleen


title: Dll1 spleen_rep8


title: Dll1 spleen_rep7


title: Dll1 thymus_rep2


title: Dll1 liver_rep6

source_name: Wt RNA pool liver


title: Dll1 thymus_rep1


title: Dll1 liver_rep5


title: Dll1 liver_rep1


title: Dll1 liver_rep3


title: Dll1 spleen_rep6


title: Dll1 brain_rep6

source_name: Wt RNA pool brain


title: Dll1 spleen_rep3


title: Dll1 liver_rep2


title: Dll1 brain_rep5


title: Dll1 spleen_rep5


title: Dll1 brain_rep4


title: Dll1 thymus_rep4


title: Dll1 liver_rep8


title: Dll1 liver_rep7


title: Dll1 liver_rep4


title: Dll1 brain_rep3


title: Dll1 brain_rep7


title: Dll1 thymus_rep3


title: Dll1 brain_rep2


title: Dll1 brain_rep8


title: Dll1 spleen_rep1


title: Dll1 brain_rep1

label_protocol:
Channel 1 Label Protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562


title: Dll1 spleen_rep2


title: H1 hES cells

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: Effect of p53 in iPS cell generation

hyb_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).

data_processing:
Data were analyzed with GeneSpring GX 7.3.1. The parameters for normalization are as follows:
Data transformation: Set measurement less than 0.01 to 0.01
Per chip: Normalize to 50th percentile

organism: Homo sapiens

source_name: H1 human ES cells

extract_protocol: Total RNA was isolated with Trizol.

tag: H1 human ES cells


title: p53-null Nanog-GFP MEF

description: Origin of iPS cells

scan_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).

source_name: p53-null MEF

tag: p53-null mouse embryonic fibroblasts, containing Nanog-GFP reporter


title: wt.untr.3

status: Public on Feb 28 2009

city: Stockholm

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: HCT116 cell line

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: gcRMA

source_name: HCT116 cell line

label_protocol: One-Cycle Target Labeling and Control Reagents

extract_protocol: Qiagen RNEasy kit

treatment_protocol: HCT116 parental and HCT116 p53-null (HCT116 TP53-/-) cells were subjected to treatment with 1uM RITA for 12h, or left untreated.

tag: Sample type

value: cultured cell-line

tag: Tissue

value: colon carcinoma


title: wt.12h.1

description: HCT116 cell line, 1uM RITA, 12h

source_name: HCT116 cell line, 1uM RITA, 12h


title: Nanog-GFP ES cells

description: Origin of iPS cells

source_name: Nanog-GFP ES cells

label_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).

tag: RF8 ES cells containing Nanog-GFP reporter


title: null.12h.1

description: HCT116 TP53-/- cell line, 1uM RITA, 12h

source_name: HCT116 TP53-/- cell line, 1uM RITA, 12h

tag: Genetic modification

value: TP53 knocked out by homologous recombination


title: COPD, squamous cell lung carcinoma T34 (COPD-study)

status: Public on Feb 01 2009

city: Groningen

first: Mirjam

last: Boelens

address: Hanzeplein 1

country: Netherlands

institute: UMCG

hyb_protocol: Hybridization was performed with 750 ng of each labeled target together with fragmentation- and hybridization buffer at 60C for 17 hours onto Agilent Whole Human Genome oligoarrays following manufacturer’s protocol.

scan_protocol: The microarray slides were washed following the user manual instructions and scanned using the Agilent dual laser DNA microarray scanner. The microarray data were normalized using the Agilent feature extraction software v. 8.5 (Agilent Technologies, Palo Alto, CA) with regards to no background correction.

data_processing: The gene expression data were log transformed and quantile normalized (Cy3 and CY5 separate). For both Cy3 and Cy5, a filter was applied that excluded 50% of the probes with the lowest expression levels and 25% of the probes with the lowest expression range. Probes that had passed only one Cy-dye filter were excluded. The average of the normalized Cy3 and Cy5 data were used for further analysis.

label: Cy3 and Cy5

source_name: T34, COPD

label_protocol:
ULS LABELING
1. Take 1- 2 μg of aRNA. Ensure that the final concentration in the labeling reaction is above 50 ng/μL. Optimal modification degrees of the labeled material are not achieved if the final concentration of aRNA in the labeling mixture is below 50 ng/μL)
2. Add 1 μL of Cy5-ULS or Cy3-ULS per 1 μg aRNA (Always keep the ratio of μg of aRNA to μL ULS 1:1 when increasing or decreasing the amount to be labeled).
3. Add 1/10 volume of 10 x Labeling solution
4. Adjust with RNase-free water to final volume and mix by pipetting
5. Label sample by incubation for 15 minutes at 85°C
6. Place samples on ice, spin down to collect contents of tube before proceeding with purification using the KREApure columns
Dye Removal using KREApure Columns (Removal of free ULS label using KREApure columns
(20800 x g is equivalent to 14,000 rpm on eppendorf 5417C)):
1. Resuspend column material by vortexing
2. Loosen cap ¼ turn and snap off the bottom closure
3. Place the column in a 2 mL collection tube
4. Pre-spin the column for 1 minute at 20800 x g
5. Discard flow through and column cap, but re-use collection tube
6. Add 300 μL ultrapure water to the column and centrifuge for 1 min at 20,800g
7. Discard collection tube and flow-through
8. Place column in a new RNase free 1.5 mL microcentrifuge tube (not provided)
9. Add ULS-labeled aRNA onto column bed
10. Centrifuge column for 1 minute at 20800 x g
11. Flow through contains the purified labeled aRNA

extract_protocol:
LASER DISSECTION MICROSCOPY
- Frozen squamous cell lung carcinoma tissue sections of 8μm were used for laser dissection microscopy (LDM)
- Only vital tumor cells without apparent admixture of inflammatory cells through the tumor fields were isolated using laser dissection microscopy
- An area of approximately 20x106 μm2 was microdissected from the section using P.A.L.M. Microlaser Technology system (P.A.L.M., Bernried, Germany).
- Laser microdissected cells were collected in lysis buffer (Macherey-Nagel)
RNA ISOLATION
Total RNA was isolated and purified from the microdissected cells with a Nucleospin RNA II kit (Macherey-Nagel). The quantity of DNA-free total RNA was measured using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed by the presence and ratio of 18S and 28S rRNA bands combined with a low baseline, monitored with RNA 6000 PicoChip (Agilent, Palo Alto, CA) on the 2100 bioanalyzer (Agilent).
RNA AMPLIFICATION
For each sample, 150 ng total RNA was amplified using the MessageAmp II kit (Ambion, Austin, USA). Briefly, 150 ng total RNA was mixed with 1 ul of T7 Oligo(dT) primer in a total volume of 12 ul. Primer and template were denatured by incubating at 70C for 10 minutes and annealed by putting the reaction tubes on ice. The First Strand Reaction was performed by adding 8 µl Reverse Transcription Master Mix (containing 10x First Strand buffer, Ribonuclease Inhibitor, dNTP Mix and Reverse Transcriptase) and incubating at 42C for 2 hours. Second Strand cDNA Synthesis was done by adding 63 µl Nuclease-Free Water, 10 µl 10x Second Strand Buffer, 4µl dNTP Mix, 2µl DNA Polymerase and 1 µl RNase H and incubating at 16C for 2 hours. cDNA purification was done according manufacturers protocol (Ambion). In vitro transcription was initiated by addition of 2 µl aaUTP Solution (50mM), 12 µl ATP, CTP, GTP mix (25mM), 3 µl UTP Solution (50mM), 4 µl T7 10x Reaction Buffer and 4 µl T7 Enzyme Mix and incubated at 37C for 9 hours. Machery-Nagel RNA Clean up mini spin columns are used for purification of the cRNA.

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

value: male

tag: Age at time of surgery:	54

tag: Smoking status:		ex

tag: Packyears:			30

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		right lower lobe

tag: TNM stage:			T3N1M0

tag: Tumor stage:			IIIA

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	128 months

tag: Metastases:			lymph node

tag: Time to distant metastasis:	not applicable

tag: COPD:				COPD

tag: FEV1/FVC:			61 %

tag: GOLD stage:			GOLD II


title: wt.12h.2

description: HCT116 cell line, 1uM RITA, 12h

tag: Sample type

tag: Tissue


title: COPD, squamous cell lung carcinoma T31 (COPD-study)

source_name: T31, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

value: female

tag: Age at time of surgery:	61

tag: Smoking status:		current

tag: Packyears:			35

tag: Location tumor:		right upper lobe

tag: TNM stage:			T2N1M0

tag: Tumor stage:			IIB

tag: Survival as from surgery:	85 months

tag: FEV1/FVC:			65 %

tag: GOLD stage:			GOLD I


title: control shRNA

description: Effect of p53 in iPS cell generation

source_name: fibroblast, control shRNA

tag: control shRNA


title: null.12h.2

description: HCT116 TP53-/- cell line, 1uM RITA, 12h

tag: Genetic modification


title: No COPD, squamous cell lung carcinoma T30 (COPD-study)

source_name: T30, no COPD

tag: Age at time of surgery:	71

tag: Smoking status:		ex

tag: Packyears:			3

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		right lower lobe

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	71 months

tag: Metastases:			lymph node

tag: Time to distant metastasis:	not applicable

tag: COPD:				no COPD

tag: FEV1/FVC:			72 %

tag: GOLD stage:			not applicable


title: COPD, squamous cell lung carcinoma T26 (COPD-study)

source_name: T26, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	48

tag: Smoking status:		current

tag: Packyears:			25

tag: Type of Surgery:		bilobectomy

tag: Location tumor:		left lower lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Survival as from surgery:	34 months

tag: Metastases:			distant

tag: Time to distant metastasis:	19 months

tag: COPD:				COPD

tag: FEV1/FVC:			54 %

tag: GOLD stage:			GOLD II


title: No COPD, squamous cell lung carcinoma T28 (COPD-study)

source_name: T28, no COPD

tag: Age at time of surgery:	76

tag: Smoking status:		ex

tag: Packyears:			40

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left upper lobe

tag: TNM stage:			T3N1M0

tag: Tumor stage:			IIIA

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	58 months

tag: Metastases:			lymph node

tag: Time to distant metastasis:	not applicable

tag: COPD:				no COPD

tag: FEV1/FVC:			73 %

tag: GOLD stage:			not applicable


title: COPD, squamous cell lung carcinoma T27 (COPD-study)

source_name: T27, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	75

tag: Smoking status:		current

tag: Type of Surgery:		lobectomy

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Survival as from surgery:	6 months

tag: Metastases:			distant

tag: Time to distant metastasis:	2 months

tag: COPD:				COPD

tag: FEV1/FVC:			66 %


title: COPD, squamous cell lung carcinoma T35 (COPD-study)

source_name: T35, COPD

tag: Age at time of surgery:	62

tag: Smoking status:		ex

tag: Packyears:			25

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left upper lobe

tag: TNM stage:			T3N1M0

tag: Tumor stage:			IIIA

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	98 months

tag: Metastases:			lymph node

tag: Time to distant metastasis:	not applicable

tag: GOLD stage:			GOLD II


title: wt.untr.2

description: HCT116 cell line

tag: Sample type

tag: Tissue


title: null.untr.2

description: HCT116 TP53-/- cell line

source_name: HCT116 TP53-/- cell line

tag: Genetic modification


title: p53 shRNA

description: Effect of p53 in iPS cell generation

source_name: fibroblast, p53 shRNA

tag: shRNA2 from addgene


title: No COPD, squamous cell lung carcinoma T29 (COPD-study)

source_name: T29, no COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	58

tag: Smoking status:		unknown

tag: Packyears:			10

tag: Location tumor:		right lower lobe

tag: TNM stage:			T2N2M0

tag: Survival as from surgery:	130 months

tag: COPD:				no COPD

tag: FEV1/FVC:			71 %

tag: GOLD stage:			not applicable


title: wt.12h.3

description: HCT116 cell line, 1uM RITA, 12h


title: wt.untr.1

description: HCT116 cell line


title: Nanog-GFP MEF

description: Origin of iPS cells

source_name: Nanog-GFP MEF

tag: MEF containing Nanog-GFP reporter


title: AHDF

description: Effect of p53 in iPS cell generation

source_name: adult human dermal fibroblast

tag: adult human dermal fibroblast


title: COPD, squamous cell lung carcinoma T32 (COPD-study)

source_name: T32, COPD

tag: Age at time of surgery:	63

tag: Smoking status:		ex

tag: Packyears:			40

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left lower lobe

tag: TNM stage:			T2N1M0

tag: Tumor stage:			IIB

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	91 months

tag: Metastases:			lymph node

tag: Time to distant metastasis:	not applicable

tag: COPD:				COPD

tag: FEV1/FVC:			62 %

tag: GOLD stage:			GOLD I


title: null.12h.3

description: HCT116 TP53-/- cell line, 1uM RITA, 12h

tag: Sample type

tag: Tissue

tag: Genetic modification


title: null.untr.1

description: HCT116 TP53-/- cell line


title: COPD, squamous cell lung carcinoma T33 (COPD-study)

source_name: T33, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	51

tag: Smoking status:		current

tag: Packyears:			33

tag: Location tumor:		right middle lobe

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	69 months

tag: FEV1/FVC:			64 %


title: null.untr.3

description: HCT116 TP53-/- cell line


title: No COPD, squamous cell lung carcinoma T23 (COPD-study)

source_name: T23, no COPD

extract_protocol:
LASER DISSECTION MICROSCOPY
- Frozen squamous cell lung carcinoma tissue sections of 8μm were used for laser dissection microscopy (LDM)
- Only vital tumor cells without apparent admixture of inflammatory cells through the tumor fields were isolated using laser dissection microscopy
- An area of approximately 20x106 μm2 was microdissected from the section using P.A.L.M. Microlaser Technology system (P.A.L.M., Bernried, Germany).
- Laser microdissected cells were collected in lysis buffer (Macherey-Nagel)
RNA ISOLATION
Total RNA was isolated and purified from the microdissected cells with a Nucleospin RNA II kit (Macherey-Nagel). The quantity of DNA-free total RNA was measured using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed by the presence and ratio of 18S and 28S rRNA bands combined with a low baseline, monitored with RNA 6000 PicoChip (Agilent, Palo Alto, CA) on the 2100 bioanalyzer (Agilent).
RNA AMPLIFICATION
For each sample, 150 ng total RNA was amplified using the MessageAmp II kit (Ambion, Austin, USA). Briefly, 150 ng total RNA was mixed with 1 ul of T7 Oligo(dT) primer in a total volume of 12 ul. Primer and template were denatured by incubating at 70C for 10 minutes and annealed by putting the reaction tubes on ice. The First Strand Reaction was performed by adding 8 µl Reverse Transcription Master Mix (containing 10x First Strand buffer, Ribonuclease Inhibitor, dNTP Mix and Reverse Transcriptase) and incubating at 42C for 2 hours. Second Strand cDNA Synthesis was done by adding 63 µl Nuclease-Free Water, 10 µl 10x Second Strand Buffer, 4µl dNTP Mix, 2µl DNA Polymerase and 1 µl RNase H and incubating at 16C for 2 hours. cDNA purification was done according manufacturers protocol (Ambion). In vitro transcription was initiated by addition of 2 µl aaUTP Solution (50mM), 12 µl ATP, CTP, GTP mix (25mM), 3 µl UTP Solution (50mM), 4 µl T7 10x Reaction Buffer and 4 µl T7 Enzyme Mix and incubated at 37C for 9 hours. Machery-Nagel RNA Clean up mini spin columns are used for purification of the cRNA.

tag: Age at time of surgery:	60

tag: Packyears:			40

tag: Type of Surgery:		lobectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		right upper lobe

tag: TNM stage:			T3N0M0

tag: Tumor stage:			IIB

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	9 months

tag: Metastases:			distant

tag: Time to distant metastasis:	6 months

tag: COPD:				no COPD

tag: FEV1/FVC:			73 %

tag: GOLD stage:			not applicable


title: No COPD, squamous cell lung carcinoma T20 (COPD-study)

source_name: T20, no COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	71

tag: Smoking status:		current

tag: Packyears:			57

tag: Location tumor:		left upper lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Survival as from surgery:	28 months

tag: Time to distant metastasis:	28 months

tag: FEV1/FVC:			75 %


title: No COPD, squamous cell lung carcinoma T19 (COPD-study)

source_name: T19, no COPD

tag: Packyears:			51

tag: Type of Surgery:		lobectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	13 months

tag: Metastases:			distant

tag: Time to distant metastasis:	13 months

tag: FEV1/FVC:			79 %


title: COPD, squamous cell lung carcinoma T18 (COPD-study)

source_name: T18, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	70

tag: Packyears:			36

tag: Type of Surgery:		bilobectomy

tag: Location tumor:		right upper lobe

tag: Survival as from surgery:	23 months

tag: Time to distant metastasis:	9 months

tag: COPD:				COPD

tag: FEV1/FVC:			54 %

tag: GOLD stage:			GOLD I


title: No COPD, squamous cell lung carcinoma T17 (COPD-study)

source_name: T17, no COPD

tag: Age at time of surgery:	72

tag: Smoking status:		current

tag: Packyears:			60

tag: Tumor type:			squamous cell lung carcinoma

tag: TNM stage:			T3N0M0

tag: Tumor stage:			IIB

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	18 months

tag: Time to distant metastasis:	6 months

tag: COPD:				no COPD

tag: FEV1/FVC:			77 %

tag: GOLD stage:			not applicable


title: COPD, squamous cell lung carcinoma T09 (COPD-study)

source_name: T09, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	83

tag: Smoking status:		ex

tag: Packyears:			45

tag: Type of Surgery:		lobectomy

tag: Location tumor:		left upper lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Survival as from surgery:	37 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: FEV1/FVC:			64 %


title: No COPD, squamous cell lung carcinoma T01 (COPD-study)

source_name: T01, no COPD

tag: Age at time of surgery:	67

tag: Smoking status:		current

tag: Packyears:			30

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left lower lobe

tag: TNM stage:			T2N1M0

tag: Tumor stage:			IIB

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	43 months

tag: Metastases:			lymph node

tag: COPD:				no COPD

tag: FEV1/FVC:			80 %


title: No COPD, squamous cell lung carcinoma T08 (COPD-study)

source_name: T08, no COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	54

tag: Smoking status:		ex

tag: Packyears:			35

tag: Type of Surgery:		wedge resection

tag: Location tumor:		left upper lobe

tag: TNM stage:			T1N0M0

tag: Tumor stage:			IA

tag: Survival as from surgery:	97 months

tag: FEV1/FVC:			71 %

tag: GOLD stage:			not applicable


title: COPD, squamous cell lung carcinoma T10 (COPD-study)

source_name: T10, COPD

tag: Age at time of surgery:	74

tag: Packyears:			53

tag: Type of Surgery:		lobectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		right lower lobe

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	117 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: COPD:				COPD

tag: FEV1/FVC:			69 %

tag: GOLD stage:			GOLD I


title: COPD, squamous cell lung carcinoma T24 (COPD-study)

source_name: T24, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	67

tag: Smoking status:		current

tag: Packyears:			45

tag: Type of Surgery:		pneumectomy

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Survival as from surgery:	16 months

tag: Metastases:			distant

tag: Time to distant metastasis:	16 months

tag: FEV1/FVC:			63 %


title: No COPD, squamous cell lung carcinoma T05 (COPD-study)

source_name: T05, no COPD

tag: Age at time of surgery:	59

tag: Smoking status:		ex

tag: Packyears:			6

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left upper lobe

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	93 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: COPD:				no COPD

tag: FEV1/FVC:			77 %

tag: GOLD stage:			not applicable


title: COPD, squamous cell lung carcinoma T13 (COPD-study)

source_name: T13, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	51

tag: Smoking status:		current

tag: Packyears:			28

tag: Type of Surgery:		bilobectomy

tag: Location tumor:		right lower lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Survival as from surgery:	106 months

tag: COPD:				COPD

tag: FEV1/FVC:			64 %

tag: GOLD stage:			GOLD I


title: COPD, squamous cell lung carcinoma T12 (COPD-study)

source_name: T12, COPD

tag: Age at time of surgery:	73

tag: Packyears:			35

tag: Type of Surgery:		lobectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left upper lobe

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	92 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: FEV1/FVC:			68 %


title: No COPD, squamous cell lung carcinoma T06 (COPD-study)

source_name: T06, no COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	63

tag: Smoking status:		current

tag: Packyears:			47

tag: Type of Surgery:		pneumectomy

tag: Location tumor:		left lower lobe

tag: Survival as from surgery:	61 months

tag: COPD:				no COPD

tag: FEV1/FVC:			72 %

tag: GOLD stage:			not applicable


title: COPD, normal B26 (COPD-study)

source_name: B26, COPD

extract_protocol:
LASER DISSECTION MICROSCOPY
- Frozen bronchial wall of 8μm were used for laser dissection microscopy (LDM)
- Only histologically normal bronchial epithelial cells were isolated using laser dissection microscopy
- An area of approximately 25x106 μm2 was microdissected from the section using P.A.L.M. Microlaser Technology system (P.A.L.M., Bernried, Germany).
- Laser microdissected cells were collected in lysis buffer (Macherey-Nagel)
RNA ISOLATION
Total RNA was isolated and purified from the microdissected cells with a Nucleospin RNA II kit (Macherey-Nagel). The quantity of DNA-free total RNA was measured using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA quality was assessed by the presence and ratio of 18S and 28S rRNA bands combined with a low baseline, monitored with RNA 6000 PicoChip (Agilent, Palo Alto, CA) on the 2100 bioanalyzer (Agilent).
RNA AMPLIFICATION
For each sample, 150 ng total RNA was amplified using the MessageAmp II kit (Ambion, Austin, USA). Briefly, 150 ng total RNA was mixed with 1 l of T7 Oligo(dT) primer in a total volume of 12 l. Primer and template were denatured by incubating at 70C for 10 minutes and annealed by putting the reaction tubes on ice. The First Strand Reaction was performed by adding 8 µl Reverse Transcription Master Mix (containing 10x First Strand buffer, Ribonuclease Inhibitor, dNTP Mix and Reverse Transcriptase) and incubating at 42C for 2 hours. Second Strand cDNA Synthesis was done by adding 63 µl Nuclease-Free Water, 10 µl 10x Second Strand Buffer, 4µl dNTP Mix, 2µl DNA Polymerase and 1 µl RNase H and incubating at 16C for 2 hours. cDNA purification was done according manufacturers protocol (Ambion). In vitro transcription was initiated by addition of 2 µl aaUTP Solution (50mM), 12 µl ATP, CTP, GTP mix (25mM), 3 µl UTP Solution (50mM), 4 µl T7 10x Reaction Buffer and 4 µl T7 Enzyme Mix and incubated at 37C for 9 hours. Machery-Nagel RNA Clean up mini spin columns are used for purification of the cRNA.

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Age at time of surgery:	52

tag: Smoking status:		ex

tag: Packyears:			18

tag: Surgery due to:		lung transplantation

tag: Type of Surgery:		lung-explantation

tag: Location tumor:		not applicable

tag: TNM stage:			not applicable

tag: COPD:				COPD

tag: FEV1/FVC:			33 %

tag: GOLD stage:			GOLD IV


title: COPD, squamous cell lung carcinoma T11 (COPD-study)

source_name: T11, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	76

tag: Packyears:			10

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left upper lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	105 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: FEV1/FVC:			54 %

tag: GOLD stage:			GOLD I


title: COPD, squamous cell lung carcinoma T14 (COPD-study)

source_name: T14, COPD

tag: Age at time of surgery:	72

tag: Smoking status:		ex

tag: Packyears:			53

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	84 months

tag: COPD:				COPD

tag: FEV1/FVC:			65 %

tag: GOLD stage:			GOLD II


title: COPD, squamous cell lung carcinoma T25 (COPD-study)

source_name: T25, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	66

tag: Smoking status:		current

tag: Packyears:			50

tag: Type of Surgery:		lobectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left upper lobe

tag: TNM stage:			T3N0M0

tag: Tumor stage:			IIB

tag: Survival as from surgery:	20 months

tag: Metastases:			distant

tag: Time to distant metastasis:	11 months

tag: FEV1/FVC:			58 %


title: COPD, normal B25 (COPD-study)

source_name: B25, COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Age at time of surgery:	59

tag: Smoking status:		ex

tag: Packyears:			29

tag: Surgery due to:		lung transplantation

tag: Type of Surgery:		lung-explantation

tag: Location tumor:		not applicable

tag: TNM stage:			not applicable

tag: COPD:				COPD

tag: FEV1/FVC:			29 %

tag: GOLD stage:			GOLD IV


title: No COPD, squamous cell lung carcinoma T07 (COPD-study)

source_name: T07, no COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	61

tag: Packyears:			25

tag: Type of Surgery:		lobectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		right lower lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	104 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: COPD:				no COPD

tag: FEV1/FVC:			78 %

tag: GOLD stage:			not applicable


title: COPD, squamous cell lung carcinoma T16 (COPD-study)

source_name: T16, COPD

tag: Sample code

tag: Age at time of surgery:	74

tag: Smoking status:		current

tag: Packyears:			39

tag: Type of Surgery:		bilobectomy

tag: Location tumor:		right upper lobe

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	75 months

tag: COPD:				COPD

tag: FEV1/FVC:			49 %

tag: GOLD stage:			GOLD II


title: COPD, normal B28 (COPD-study)

source_name: B28, COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	55

tag: Smoking status:		ex

tag: Surgery due to:		lung transplantation

tag: Type of Surgery:		lung-explantation

tag: Location tumor:		not applicable

tag: TNM stage:			not applicable

tag: FEV1/FVC:			21 %

tag: GOLD stage:			GOLD IV


title: No COPD, squamous cell lung carcinoma T22 (COPD-study)

source_name: T22, no COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Packyears:			30

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left upper lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	20 months

tag: Metastases:			distant

tag: Time to distant metastasis:	17 months

tag: COPD:				no COPD

tag: FEV1/FVC:			72 %

tag: GOLD stage:			not applicable


title: No COPD, squamous cell lung carcinoma T02 (COPD-study)

source_name: T02, no COPD

tag: Gender

tag: Age at time of surgery:	67

tag: Smoking status:		current

tag: Packyears:			25

tag: Type of Surgery:		lobectomy

tag: Survival as from surgery:	151 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: FEV1/FVC:			71 %


title: COPD, squamous cell lung carcinoma T15 (COPD-study)

source_name: T15, COPD

tag: Sample code

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Age at time of surgery:	47

tag: Packyears:			30

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		left lower lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Survival as from surgery:	72 months

tag: COPD:				COPD

tag: FEV1/FVC:			53 %

tag: GOLD stage:			GOLD II


title: No COPD, squamous cell lung carcinoma T03 (COPD-study)

source_name: T03, no COPD

tag: Gender

tag: Age at time of surgery:	53

tag: Smoking status:		current

tag: Packyears:			40

tag: Type of Surgery:		lobectomy

tag: Dead/alive at last follow-up:	alive

tag: Survival as from surgery:	173 months

tag: COPD:				no COPD

tag: GOLD stage:			not applicable


title: COPD, normal B27 (COPD-study)

source_name: B27, COPD

tag: Sample code

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Age at time of surgery:	58

tag: Smoking status:		ex

tag: Packyears:			80

tag: Surgery due to:		lung transplantation

tag: Type of Surgery:		lung-explantation

tag: Location tumor:		not applicable

tag: TNM stage:			not applicable

tag: FEV1/FVC:			49 %

tag: GOLD stage:			GOLD IV


title: No COPD, squamous cell lung carcinoma T21 (COPD-study)

source_name: T21, no COPD

tag: Cell type:			tumor cells that were laser microdissected from frozen squamous cell lung carcinoma tissue

tag: Gender

tag: Age at time of surgery:	69

tag: Packyears:			30

tag: Type of Surgery:		pneumectomy

tag: Tumor type:			squamous cell lung carcinoma

tag: Location tumor:		right middle lobe

tag: TNM stage:			T2N0M0

tag: Tumor stage:			IB

tag: Dead/alive at last follow-up:	dead

tag: Survival as from surgery:	6 months

tag: Metastases:			distant

tag: Time to distant metastasis:	4 months

tag: FEV1/FVC:			76 %


title: No COPD, squamous cell lung carcinoma T04 (COPD-study)

source_name: T04, no COPD

tag: Sample code

tag: Age at time of surgery:	76

tag: Smoking status:		ex

tag: Packyears:			55

tag: Type of Surgery:		lobectomy

tag: Location tumor:		left upper lobe

tag: Survival as from surgery:	72 months

tag: Metastases:			no

tag: Time to distant metastasis:	not applicable

tag: COPD:				no COPD

tag: FEV1/FVC:			70 %

tag: GOLD stage:			not applicable


title: COPD, normal B22 (COPD-study)

source_name: B22, COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	53

tag: Smoking status:		current

tag: Packyears:			40

tag: Surgery due to:		lung transplantation

tag: Type of Surgery:		lung-explantation

tag: Location tumor:		right upper lobe (adenocarcinoma)

tag: TNM stage:			T1N0M0

tag: COPD:				COPD

tag: FEV1/FVC:			34 %

tag: GOLD stage:			GOLD IV


title: COPD, normal B08 (COPD-study)

source_name: B08, COPD

tag: Sample code

tag: Age at time of surgery:	67

tag: Packyears:			13

tag: Surgery due to:		squamous cell carcinoma

tag: Type of Surgery:		lobectomy

tag: Location tumor:		right lower lobe

tag: FEV1/FVC:			60 %

tag: GOLD stage:			GOLD II


title: No COPD, normal B06 (COPD-study)

source_name: B06, no COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	58

tag: Smoking status:		ex

tag: Packyears:			25

tag: Surgery due to:		large cell carcinoma

tag: Location tumor:		right upper lobe

tag: COPD:				no COPD

tag: FEV1/FVC:			74 %

tag: GOLD stage:			not applicable


title: No COPD, normal B09 (COPD-study)

source_name: B09, no COPD

tag: Sample code

tag: Age at time of surgery:	72

tag: Smoking status:		current

tag: Packyears:			52

tag: Type of Surgery:		pneumectomy

tag: Location tumor:		left upper lobe

tag: TNM stage:			T2N1M0

tag: FEV1/FVC:			71 %


title: No COPD, normal B07 (COPD-study)

source_name: B07, no COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	67

tag: Packyears:			20

tag: Type of Surgery:		lobectomy

tag: Location tumor:		left lower lobe

tag: TNM stage:			T1N0M0

tag: FEV1/FVC:			81 %


title: No COPD, normal B10 (COPD-study)

source_name: B10, no COPD

tag: Age at time of surgery:	74

tag: Smoking status:		ex

tag: Packyears:			45

tag: Surgery due to:		squamous cell carcinoma

tag: COPD:				no COPD

tag: FEV1/FVC:			72 %

tag: GOLD stage:			not applicable


title: No COPD, normal B14 (COPD-study)

source_name: B14, no COPD

tag: Sample code

tag: Age at time of surgery:	53

tag: Smoking status:		current

tag: Packyears:			40

tag: TNM stage:			T2N0M0


title: COPD, normal B16 (COPD-study)

source_name: B16, COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	51

tag: Packyears:			60

tag: Type of Surgery:		pneumectomy

tag: Location tumor:		left upper lobe

tag: TNM stage:			T3N1M0

tag: COPD:				COPD

tag: FEV1/FVC:			61 %

tag: GOLD stage:			GOLD I


title: No COPD, normal B11 (COPD-study)

source_name: B11, no COPD

tag: Age at time of surgery:	65

tag: Smoking status:		ex

tag: Packyears:			26

tag: Surgery due to:		squamous cell carcinoma

tag: Location tumor:		right upper lobe

tag: COPD:				no COPD

tag: FEV1/FVC:			79 %


title: COPD, normal B15 (COPD-study)

source_name: B15, COPD

tag: Sample code

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Age at time of surgery:	76

tag: Packyears:			40

tag: Type of Surgery:		lobectomy

tag: Location tumor:		left lower lobe

tag: TNM stage:			T1N0M0

tag: FEV1/FVC:			59 %


title: No COPD, normal B12 (COPD-study)

source_name: B12, no COPD

tag: Gender

tag: Age at time of surgery:	52

tag: Smoking status:		current

tag: Packyears:			20

tag: Type of Surgery:		bilobectomy

tag: Location tumor:		right lower lobe

tag: TNM stage:			T2N1M0

tag: FEV1/FVC:			75 %

tag: GOLD stage:			not applicable


title: COPD, normal B23 (COPD-study)

source_name: B23, COPD

tag: Sample code

tag: Age at time of surgery:	57

tag: Smoking status:		ex

tag: Packyears:			30

tag: Surgery due to:		lung transplantation

tag: Type of Surgery:		lung-explantation

tag: Location tumor:		not applicable

tag: TNM stage:			not applicable

tag: COPD:				COPD

tag: FEV1/FVC:			23 %

tag: GOLD stage:			GOLD IV


title: COPD, normal B24 (COPD-study)

source_name: B24, COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Packyears:			25

tag: FEV1/FVC:			29 %


title: COPD, normal B05 (COPD-study)

source_name: B05, COPD

tag: Age at time of surgery:	73

tag: Packyears:			27

tag: Surgery due to:		broncho alveolar carcinoma

tag: Type of Surgery:		lobectomy

tag: Location tumor:		left upper lobe

tag: TNM stage:			T2N0M0

tag: FEV1/FVC:			37 %

tag: GOLD stage:			GOLD II


title: COPD, normal B21 (COPD-study)

source_name: B21, COPD

tag: Sample code

tag: Age at time of surgery:	54

tag: Smoking status:		ex

tag: Packyears:			31

tag: Surgery due to:		lung transplantation

tag: Type of Surgery:		lung-explantation

tag: Location tumor:		not applicable

tag: FEV1/FVC:			38 %


title: COPD, normal B17 (COPD-study)

source_name: B17, COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	60

tag: Smoking status:		current

tag: Packyears:			40

tag: Surgery due to:		squamous cell carcinoma

tag: Location tumor:		left lower lobe

tag: TNM stage:			T2N1M0

tag: COPD:				COPD

tag: FEV1/FVC:			61 %

tag: GOLD stage:			GOLD I


title: COPD, normal B03 (COPD-study)

source_name: B03, COPD

tag: Sample code

tag: Age at time of surgery:	57

tag: Surgery due to:		adenocarcinoma

tag: Type of Surgery:		lobectomy

tag: Location tumor:		left upper lobe

tag: TNM stage:			T1N2M0

tag: FEV1/FVC:			58 %


title: COPD, normal B19 (COPD-study)

source_name: B19, COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	66

tag: Packyears:			50

tag: TNM stage:			T3N0M0

tag: GOLD stage:			GOLD II


title: COPD, normal B18 (COPD-study)

source_name: B18, COPD

tag: Age at time of surgery:	46

tag: Smoking status:		current

tag: Packyears:			25

tag: Surgery due to:		squamous cell carcinoma

tag: Type of Surgery:		pneumectomy

tag: TNM stage:			T2N0M0

tag: FEV1/FVC:			51 %


title: No COPD, normal B02 (COPD-study)

source_name: B02, no COPD

tag: Sample code

tag: Age at time of surgery:	59

tag: Smoking status:		ex

tag: Packyears:			30

tag: Surgery due to:		adenocarcinoma

tag: Type of Surgery:		lobectomy

tag: Location tumor:		right lower lobe

tag: TNM stage:			T1N0M0

tag: COPD:				no COPD

tag: FEV1/FVC:			71 %

tag: GOLD stage:			not applicable


title: No COPD, normal B13 (COPD-study)

source_name: B13, no COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	68

tag: Packyears:			45

tag: Location tumor:		left upper lobe

tag: TNM stage:			T2N1M0

tag: FEV1/FVC:			77 %


title: COPD, normal B20 (COPD-study)

source_name: B20, COPD

tag: Sample code

tag: Age at time of surgery:	73

tag: Surgery due to:		squamous cell carcinoma

tag: COPD:				COPD

tag: FEV1/FVC:			63 %

tag: GOLD stage:			GOLD II


title: Gene expression in mtsR mutant strain (Late_EXP3)

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

description: Part of the comparison of gene expression in MGAS315 and isogenic mtsR mutant

hyb_protocol: Overnight at 45C, standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: Raw data normalized to total signal intensity

organism: Streptococcus pyogenes

source_name: THY culture

label_protocol: Standard Affymetrix

growth_protocol: bacteria were grown in THY medium to OD600=1.2 (late exponential growth phase)

extract_protocol: 5ml culture was added to 10ml RNA protect (Qiagen), and GAS collected by centrifugation and stored at -80C. RNA was extracted from bacterial cell pellets through mechanical disruption using glass beads (MatrixB tubes) in a FastPrep machine. RNA was purified using hot acid phenol (Ambion) extraction and re-purified on Qiagen miRNeasy columns using standard protocol. DNA was removed with DNA-free (Ambion). RNA quality was assessed by bioanalyzer and O.D. measurements.

tag: strain MGAS315_delta_mtsR, late exponential phase of growth


title: Gene expression in mtsR mutant strain (Late_EXP2)


title: COPD, normal B04 (COPD-study)

source_name: B04, COPD

tag: Age at time of surgery:	63

tag: Smoking status:		current

tag: Packyears:			40

tag: Surgery due to:		adenocarcinoma

tag: Type of Surgery:		lobectomy

tag: TNM stage:			T1N0M0

tag: FEV1/FVC:			39 %


title: Gene expression in mtsR mutant strain (Late_EXP1)

growth_protocol: bacteria were grown in THY medium to OD600=1.2 (exponential growth phase)


title: Gene expression in mtsR mutant strain (EXP2)

growth_protocol: bacteria were grown in THY medium to OD600=0.5 (late exponential growth phase)

tag: strain MGAS315_delta_mtsR, exponential phase of growth


title: No COPD, normal B01 (COPD-study)

source_name: B01, no COPD

tag: Cell type:			histologically normal bronchial epithelial cells that were laser microdissected from frozen bronchial wall tissue

tag: Gender

tag: Age at time of surgery:	52

tag: Packyears:			35

tag: Location tumor:		right lower lobe

tag: TNM stage:			T2N0M0

tag: COPD:				no COPD

tag: FEV1/FVC:			78 %

tag: GOLD stage:			not applicable


title: Gene expression in mtsR mutant strain (EXP1)

growth_protocol: bacteria were grown in THY medium to OD600=0.5 (exponential growth phase)


title: Gene expression in mtsR mutant strain (EXP3)


title: Gene expression in strain MGAS315_(Late_EXP3)

tag: strain MGAS315, late exponential phase of growth


title: Gene expression in strain MGAS315_(EXP2)

data_processing: Raw data normalized to total signal inensity

tag: strain MGAS315, exponential phase of growth


title: Gene expression in strain MGAS315_(EXP1)

extract_protocol: 5ml culture was added to 10ml RNA protect (Qiagen), and GAS collected by centrifugation and stored at -80C. RNA was extracted from bacterial cell pellets through mechanical disruption using glass beads (MatrixB tubes) in  a FastPrep machine. RNA was purified using hot acid phenol (Ambion) extraction and re-purified on Qiagen miRNeasy columns using standard protocol. DNA was removed with DNA-free (Ambion). RNA quality was assessed by bioanalyzer and O.D. measurements.


title: Gene expression in strain MGAS315_(EXP3)


title: Gene expression in strain MGAS315_(Late_EXP2)


title: Gene expression in strain MGAS315_(Late_EXP1)


title: -gcn4, YNB + 0.1 mM 3AT, replicate 3

city: Cambridge

first: Joel

last: Moxley

state: MA

address: 77 Massachusettes Ave

institute: MIT

description: -gcn4, YNB + 0.1 mM 3AT, replicate 3

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Bioconductor with RMA background correction, qspline normalization, and Li-Wong expression value summaries

organism: Saccharomyces cerevisiae

source_name: S288C gcn4-delta MAT a

label_protocol: standard Affymetrix procedures

extract_protocol: Strains were aerobically cultured at 30C and pH 5 in a chemostat diluted at 0.10 hr^-1.  Samples were quenced in ice, spun for 3 min, and frozen on liquid N2.  Total RNA was extracted with trizol from cells ground at cold temperatures.

tag: genetic and environmental variation indicated in Sample_title


title: wild type, YNB + 10 mM 3AT, replicate 3

description: wild type, YNB + 10 mM 3AT, replicate 3

source_name: S288C MAT a


title: -gcn4, YNB + 0.1 mM 3AT, replicate 2

description: -gcn4, YNB + 0.1 mM 3AT, replicate 2


title: -gcn4, YNB + 0.1 mM 3AT, replicate 1

description: -gcn4, YNB + 0.1 mM 3AT, replicate 1


title: wild type, YNB + 10 mM 3AT, replicate 2

description: wild type, YNB + 10 mM 3AT, replicate 2


title: Zhong You 821 stem-72 hour Infection vs control-Replicate 3

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Biological replicate 3 of 3
The Amino Allyl MessageAmp II aRNA amplification kit was used for cDNA synthesis and RNA amplification (Ambion) with 1 mg of total RNA following the manufacturer’s instructions. In vitro transcription to prepare amplified RNA (aRNA) was conducted at 37°C for 14 h and then purified.

hyb_protocol: Hybridizations were performed at 37°C for 16 h in the dark, after which the slides were washed in 2 x SSC, 0.1 % SDS at 37°C for 5 min, followed by 2 washes in 1 x SSC for 2 min each and 2 washes in 0.1 x SSC for 1 min each. Washed slides were dried by centrifugation at 1000 rpm for 1 min at 20°C.

scan_protocol: The slides were scanned using a Virtek Chip Reader (Bio-Rad Laboratories). For each scan, the signal intensity of the two channels was initially adjusted based on the control spots so that an average red/green signal ratio of approximately 1 was achieved and the spots were not saturated.

data_processing: Spot intensities from scanned slides were quantified using ArrayPro 4.0 (Bio-Rad Laboratories) and the data imported into the BioArray Software Environment (BASE version 1.0). Spots with intensities lower than the background were eliminated. Gene Spring 7.3 (Agilent Technologies, Inc.) was used to select spots with intensity values > 50 in at least half of the samples (slides) for further analysis. Normalization was conducted using the per spot and per-chip Lowess normalization procedure with a smooth factor of 20. A one-way ANOVA with a parametric test and variances not assumed to be equal was performed. A multiple test correction (Benjamini and Hochberg, 1995) was applied and a False Discovery Rate (FDR) of < 0.0001 was used.

organism: Brassica napus

source_name: B. napus stem tissue, infected with Sclerotinia, 72 hours after infection

label_protocol: 5 mg aRNA was coupled with either Cy3 or Cy5 dye. The coupling reaction mixture was incubated at 20°C for 30 min, quenched with 4 M hydroxylamine for 15 min and purified. Cy3/Cy5 labelled aRNA was completely dried in a vacuum, dissolved in 9 ml ddH2O and fragmented by adding 1 ml of fragmentation reagent followed by incubation at 70°C for 15 min. The reaction was stopped with 1 ml of stop solution and 47 ml of hybridization solution was added.

growth_protocol: Seeds of ZY821 were sown in Redi-Earth soil mixture (Scotts Fertilizer Company) amended with coconut fibre to improve drainage and Osmocote 15-7-12 for controlled release of fertilizer. The plants were grown in a growth chamber under 200 mmol m-2 s-1 light with a 16 h photoperiod provided by fluorescent and incandescent light. The temperature was maintained at 20°C in the light and 16°C in the dark. Two seeds were planted in each of 36 cells and seedlings were thinned to one plant per cell eleven days after planting. Four week-old seedlings were vernalized in a cold room at 5 - 8°C for 4 weeks under an 8 h photoperiod and half of the previous light intensity. After vernalization, each plant was transplanted to a six-inch pot and returned to the growth chamber. Seeds of Westar were planted directly in six-inch pots and plants were grown under the same conditions as ZY821 except for the vernalization treatment. Excess plants were grown and only those with uniform stem size and architecture were used. Plants were selected for inoculation and sampling using a randomized design with three biological replicates for each cultivar.

extract_protocol: Total RNA was isolated from 1 g of ground tissue using the plant RNeasy kit (Qiagen) and stored at -80°C. RNase-Free DNase was applied during RNA isolation to remove any DNA contamination (Qiagen). The concentration of total RNA was determined using a Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and verified by agarose gel electrophoresis.

treatment_protocol: One replicate consisted of 60 plants for five time points (6, 12, 24, 48 and 72 h) and two treatments (inoculated and mock-inoculated controls). S. sclerotiorum isolate 321 generated from field canola plants were used throughout the experiment (Kohli and Kohn, 1995). When the plants were at the full flower stage, three sites of the main stem were inoculated at every other internodes with 8 mm plugs cut from the growing margin of a colony cultured on minimal salts-glucose agar (20.0 g glucose, 2.0 g NH4NO3, 1.0 g KH2PO4, 1.0 g NaOH, 0.1 g MgSO47H2O, 0.1 g malic acid and 20.0 g agar per 1000 ml distilled water) modified from (Cruickshank, 1983). Mock infected plants were inoculated with only an agar plug. Plugs were secured to the stem with Parafilm™. Each line yielded 180 inoculation sites per biological replicate or 540 sites in total. Epidermal stem tissues extending 10 mm beyond the inoculation site and 1 mm deep were harvested at 6, 12, 24, 48, and 72 h post inoculation (hpi) with a razor blade. The tissues from one biological replicate at each time point (six individual plants comprising 18 inoculation sites) were pooled as one sample. Harvested tissues were frozen immediately in liquid nitrogen and stored at -80°C.

tag: B. napus (Zhong You 821), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 72 hrs after infection with Scleotinia scleotiorum

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 72 hours after infection

tag: B. napus (Zhong You 821), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 72 hrs after mock infection


title: Zhong You 821 stem-72 hour Control vs Infection-Replicate 3


title: T-LBL_19

type: genomic

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Nijmegen Medical Centre

description: primary LBL diagnosis sample

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: copy number detection using CNAG2.0 software (http://www.genome.umin.jp/)

molecule: genomic DNA

source_name: Mediastinal mass

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

tag: Immunotype

value: T-cell; Age:4 yrs; Gender:F


title: Zhong You 821 stem-72 hour Infection vs control-Replicate 2

description:
Biological replicate 2 of 3
The Amino Allyl MessageAmp II aRNA amplification kit was used for cDNA synthesis and RNA amplification (Ambion) with 1 mg of total RNA following the manufacturer’s instructions. In vitro transcription to prepare amplified RNA (aRNA) was conducted at 37°C for 14 h and then purified.


title: Zhong You 821 stem-72 hour Control vs Infection-Replicate 2


title: wild type, YNB + 10 mM 3AT, replicate 1

description: wild type, YNB + 10 mM 3AT, replicate 1


title: male reference pool_250kNsp_M01

description: pool of 10 male individuals

source_name: Peripheral blood

tag: control sample


title: T-LBL_18

description: primary LBL diagnosis sample

source_name: Lymph node

value: T-cell; Age:17 yrs; Gender:M


title: Zhong You 821 stem-72 hour Infection vs control-Replicate 1

description:
Biological replicate 1 of 3
The Amino Allyl MessageAmp II aRNA amplification kit was used for cDNA synthesis and RNA amplification (Ambion) with 1 mg of total RNA following the manufacturer’s instructions. In vitro transcription to prepare amplified RNA (aRNA) was conducted at 37°C for 14 h and then purified.


title: female reference pool_250kNsp_F03

description: pool of 10 female individuals


title: Zhong You 821 stem-72 hour Control vs Infection-Replicate 1


title: preB-LBL_04

description: primary LBL diagnosis sample

value: B-cell; Age:11 yrs; Gender:F


title: Zhong You 821 stem-48 hour Control vs Infection-Replicate 3

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 48 hours after infection

tag: B. napus (Zhong You 821), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 48 hrs after mock infection

source_name: B. napus stem tissue, infected with Sclerotinia, 48 hours after infection

tag: B. napus (Zhong You 821), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 48 hrs after infection with Scleotinia scleotiorum


title: female reference pool_250kNsp_F02

description: pool of 10 female individuals


title: T-LBL_16

description: primary LBL diagnosis sample

value: T-cell; Age:6 yrs; Gender:M


title: preB-LBL_02

description: primary LBL diagnosis sample

source_name: Testis

value: B-cell; Age:2 yrs; Gender:M


title: T-LBL_14

description: primary LBL diagnosis sample

value: T-cell; Age:11 yrs; Gender:M


title: Zhong You 821 stem-48 hour Infection vs control-Replicate 3


title: preB-LBL_05

description: primary LBL diagnosis sample

value: B-cell; Age:14 yrs; Gender:F


title: Zhong You 821 stem-48 hour Control vs Infection-Replicate 2


title: T-LBL_11

description: primary LBL diagnosis sample

value: T-cell; Age:18 yrs; Gender:M


title: male reference pool_250kNsp_M03

description: pool of 10 male individuals


title: preB-LBL_03

description: primary LBL diagnosis sample

value: B-cell; Age:10 yrs; Gender:M


title: male reference pool_250kNsp_M02

description: pool of 10 male individuals


title: T-LBL_08

description: primary LBL diagnosis sample

value: T-cell; Age:14 yrs; Gender:F


title: T-LBL_15

description: primary LBL diagnosis sample

value: T-cell; Age:9 yrs; Gender:M


title: T-LBL_09

description: primary LBL diagnosis sample

value: T-cell; Age:16 yrs; Gender:M


title: preB-LBL_07

description: primary LBL diagnosis sample

value: B-cell; Age:4 yrs; Gender:M


title: T-LBL_10

description: primary LBL diagnosis sample


title: T-LBL_12

description: primary LBL diagnosis sample

value: T-cell; Age:7 yrs; Gender:M


title: T-LBL_17

description: primary LBL diagnosis sample

value: T-cell; Age:14 yrs; Gender:M


title: female reference pool_250kNsp_F01

description: pool of 10 female individuals


title: preB-LBL_06

description: primary LBL diagnosis sample

value: B-cell; Age:15 yrs; Gender:M


title: Zhong You 821 stem-48 hour Infection vs control-Replicate 2


title: Zhong You 821 stem-24 hour Control vs Infection-Replicate 3

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 24 hours after infection

tag: B. napus (Zhong You 821), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 24 hrs after mock infection

source_name: B. napus stem tissue, infected with Sclerotinia, 24 hours after infection

tag: B. napus (Zhong You 821), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 24 hrs after infection with Scleotinia scleotiorum


title: preB-LBL_01

description: primary LBL diagnosis sample

value: B-cell; Age:3 yrs; Gender:M


title: Zhong You 821 stem-48 hour Control vs Infection-Replicate 1


title: Zhong You 821 stem-12 hour Control vs Infection-Replicate 3

source_name: B. napus stem tissue, mock-infected (no sclerotinia), 12 hours after infection

tag: B. napus (Zhong You 821), stem tissue (mock innoculation site + 1 cm around site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 12 hrs after mock infection

source_name: B. napus stem tissue, infected with Sclerotinia, 12 hours after infection

tag: B. napus (Zhong You 821), stem tissue (innoculation site + 1 cm around innoculation site, 1mm deep), plant in full flower, grown in a growth chamber, tissue taken 12 hrs after infection with Scleotinia scleotiorum


title: Zhong You 821 stem-48 hour Infection vs control-Replicate 1


title: Zhong You 821 stem-12 hour Control vs Infection-Replicate 1


title: Zhong You 821 stem-12 hour Infection vs control-Replicate 2


title: Zhong You 821 stem-12 hour Control vs Infection-Replicate 2


title: Zhong You 821 stem-12 hour Infection vs control-Replicate 3


title: Zhong You 821 stem-12 hour Infection vs control-Replicate 1