title: Third_instar_larval_midgut_STA_12h_rep1

source_name: Third instar larval midgut, starvation, 12 hr

treatment_protocol: Third instar of Drosophila melanogaster were starved for 12 hr. Insect larval midguts were dissected out in 214 mM NaCl solution, and then transferred to RNAlater® (Ambion Inc., Austin, TX). After dissecting, fifty midguts were pooled in the RNAlater and immediately frozen in liquid nitrogen, then transferred to -80°C. Fifty midguts represented a single replicate for each microarray experiment. Three biological replicates were performed, with one biological replicate per oligoarray for a total of three oligoarrays.

value: W1118 Age:Third instar, 108 hr, then starved for 12 hr


title: Third_instar_larval_midgut_STA_12h_rep3

status: Public on Oct 03 2008

type: RNA

city: Urbana

first: Hongmei

last: LI

state: IL

address: 505 S. Goodwin Ave

department: Entomology

country: USA

institute: University of Illinois at Urbana-Champaign

description: Gene expression data from the third instar Drosophila larval midgut

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45 C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with GCOS software (Affymetrix, Santa Clara, CA)

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Temp: 24°C Humid:60% Light/Dark cycle: 14:10

extract_protocol: Total RNA was isolated by using the TRIzol® Reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kit (Qiagen Inc., Valencia, CA) following the manufacturers’ protocol.

tag: Strain

tag: Tissue

value: midgut


title: KELS_FaDu-3

status: Public on Sep 30 2008

city: Providence

first: Michele

last: Avissar

state: RI

address: 70 Ship Street

department: Pathology

institute: Brown University

hyb_protocol: Labelled miRNA were hybridized for 16 hr at 42C on miRVANA Bioarrays. Following hybridization, bioarrays were washed 3x and dried.

scan_protocol: Bioarrays were scanned using the GenePix 4200AL scanner.

data_processing: The fluorescent signal associated with the probes and local background was extracted using GenePix Pro and background adjusted fluorescent values were normalized for each microRNA using a variation stabilization transformation method described by Huber et al

organism: Homo sapiens

source_name: HNSCC tumor cell_line

label_protocol: The 3’ ends of the RNA molecules were tailed and labeled using the mirVana™ miRNA Labeling Kit (Ambion) according to the manufacturer’s instructions. Amine-modified nucleotides were incorporated during the poly (A) polymerase mediated tailing reaction, and Cy5 succinimide esters (Amersham Biosciences (GE Healthcare)) were conjugated to the amine moieties on the microRNAs

extract_protocol: Total RNA extraction using mirVANA RNA Isolation Kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol for total RNA isolation. RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), aliquoted, and stored at –80°C until needed.


title: Third_instar_larval_midgut_WGA_12h_rep3

source_name: Third instar larval midgut, WGA, 12 hours

treatment_protocol: Third instar of Drosophila melanogaster fed 1% wheat germ agglutinin (WGA) for 12 hr. Insect larval midguts were dissected out in 214 mM NaCl solution, and then transferred to RNAlater® (Ambion Inc., Austin, TX). After dissecting, fifty midguts were pooled in the RNAlater and immediately frozen in liquid nitrogen, then transferred to -80°C. Fifty midguts represented a single replicate for each microarray experiment. Three biological replicates were performed, with one biological replicate per oligoarray for a total of three oligoarrays.

value: W1118 Age:Third instar, 108 hr, then feed on 1% WGA for 12 hr


title: Third_instar_larval_midgut_BBI_12h_rep3

description: Gene expression data from the third instar Drosophila larval midgut.

data_processing: The data were analyzed with GCOS software (Affymetrix, Santa Clara, CA).

source_name: Third instar larval midgut, BBI, 12 hours

treatment_protocol: Third instar of Drosophila melanogaster fed 0.3% BBI for 12 hr. Insect larval midguts were dissected out in 214 mM NaCl solution, and then transferred to RNAlater® (Ambion Inc., Austin, TX). After dissecting, fifty midguts were pooled in the RNAlater and immediately frozen in liquid nitrogen, then transferred to -80°C. Fifty midguts represented a single replicate for each microarray experiment. Three biological replicates were performed, with one biological replicate per oligoarray for a total of three oligoarrays.

value: W1118 Age:Third instar, 108 hr, then feed on 0.3% BBI for 12 hr


title: 59167T

source_name: Normal head and neck epithelium

tag: normal


title: Third_instar_larval_midgut_STA_12h_rep2


title: KELS_FaDu-2


title: Third_instar_larval_midgut_WGA_12h_rep2


title: Bmicroplus_larvae_amitraz_rep2 block2

status: Public on Dec 31 2008

city: Kerrville

first: Leonel

middle: (Leo)

last: Saldivar

state: TX

address: 2700 Fredericksburg Rd.

department: Agriculture

institute: USDA

description: Custom high-density single channel oligonucleotide arrays were constructed by NimbleGen Systems Inc. (Madison, WI) using ESTs sequences from BmiGI.  The design of the array is such that 14 50mer probes per target were used for 13,601 of the 13,642 potential coding regions.  No mismatch probes are included on the arrays, allowing twice as many probes per target than if mismatches are included.  Probes with randomly generated sequences were also included.  These probes were generated with sequences designed to match the melting temperature (Tm) of the other probes on the array.  These random probes reflect the distribution of non-specific signal intensities for binding events to probes with approximately the same composition as the perfect match probes but with random sequences.  Each microarray chip includes 2 in-slide replicates (spot replicates), which were treated as technical replicates.

hyb_protocol: Hybridizations done at NimbleGen Inc.  Five R. microplus pooled RNA samples were hybridized to the microarrays.  A control and four different acaricides: organophosphate, pyrethroid, ivermectin, and amitraz.  The hybridization was done twice, resulting in a total of ten array hybridizations, i.e. two technical replicates per treatment including control were used.  The oligonucleotide arrays were used to examine differential gene expression between the control and each acaricide.

scan_protocol: The hybridized arrays were scanned with an Axon scanner (Axon Instruments, Union City, CA)

data_processing: The intensity raw values were normalized using quantile normalization to adjust intensity values which arise from variation in the technology rather than from biological differences between the RNA samples. It is important to remove as much of the non-biological variation in signal intensity as possible.  One robust way is by using a ‘complete data method’ of normalization.  The method is called ‘complete data method’ because it makes use of data from all arrays in an experiment to form the normalizing relation.  Quantile normalization is a complete data method and this is what was implemented for our dataset.  The goal of this type of normalization is to equalize the distribution of probe intensities for each array in a set of arrays.   (Bolstad, 2001)   Gene Calls: The gene calls were generated using the Robust Multichip Average (RMA) algorithm.  (Irizarray,et al., 2003A,  Irizarray, et al., 2003B,  Bolstad, 2003)   The software package tools used for normalization and gene calling are available through Bioconductor project at:  www.bioconductor.org

organism: Rhipicephalus microplus

source_name: Larvae

label_protocol: Dye: CY3 single channel

extract_protocol: Total RNA was isolated from 0.1 g larval material, respectively, using two consecutive 40 sec runs in the FastPrep-24 Tissue and Cell Homogenizer and Lysing Matrix D (Qbiogene, Irvine, CA). A setting of 6.0 with a 3 min ice incubation between runs was used, followed by RNA isolation with the Fast RNA Pro Green Kit (Qbiogene) and subsequent lithium chloride precipitation using the Totally RNA Kit reagents (Ambion Inc., Austin, TX).  Approximately 50 mg total RNA was treated with Turbo DNA-free kit (Ambion Inc.) in two 100 ml aliquots each treated with 2 ml of Turbo DNAse per kit protocols.  RNA integrity was verified by formaldehyde gel electrophoresis and staining in GelStar Nucleic Acid Gel Stain (Cambrex Bio Science, Rockland, ME).  Twenty mg of each DNA-free RNA was sent to NimbleGen for use in microarray analysis.

tag: larvae

value: 12-16 days old


title: KELS_CAL27-3


title: Third_instar_larval_midgut_BBI_12h_rep1


title: KELS2816-2

source_name: primary HNSCC tumor


title: MR-1 nitrate sample to fumarate sample-1

status: Public on Oct 01 2008

city: Hangzhou

first: haichun

last: gao

address: 388 Yuhangtang Rd.

country: China

institute: Zhejiang University

description: Gao H, Wang Y, Liu X, Yan T et al. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol 2004 Nov;186 (22):7796-803.

organism: Shewanella oneidensis MR-1

source_name: MR-1 on nitrate

tag: Cells grown on nitrate under anaerobic conditions

source_name: MR-1 on fumarate

tag: Cells grown on fumarate under anaerobic conditions


title: MR-1 nitrate sample to fumarate sample-3

hyb_protocol: Gao H, Wang Y, Liu X, Yan T et al. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol 2004 Nov;186 (22):7796-803.


title: MR-1 nitrate sample to fumarate sample-2

scan_protocol: Gao H, Wang Y, Liu X, Yan T et al. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol 2004 Nov;186 (22):7796-803.


title: Third_instar_larval_midgut_BBI_12h_rep2


title: KELS2748


title: KELS_FaDu-1


title: KELS3687


title: KELS2801


title: 59167U


title: 58926T


title: KELS_CAL27-1


title: KELS3326


title: KELS3083


title: KELS3014


title: KELS2816-1


title: KELS2917


title: KELS2910


title: KELS2551


title: KELS2844


title: KELS2845


title: KELS3648


title: KELS_CAL27-2


title: 59166L


title: KELS2995


title: Foxf1 Hetz mouse lungs treated with CCl4

status: Public on Sep 04 2008

city: Chicago

first: Tanya

last: Kalin

address: 5841 S. Maryland Ave.

department: Medicine

institute: University of Chicago

description: sample contained a mixture of equal amounts of RNA from three distinct Foxf1 Hetz mice,  treated with CCl4 for 16 hours.

hyb_protocol: Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.

data_processing: Signal intensities across microarrays were normalized using the quantile-quantile method (www.bioconductor.org).

label: DIG-UTP

organism: Mus musculus

source_name: mouse lung

label_protocol: 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.

extract_protocol: Tissues were quickly removed and frozen in liquid nitrogen and stored at -80C for subsequent preparation of total RNA. Total RNA was isolated using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O supplemented with the RNase inhibitor Superasin (Ambion, Austin, TX) as per manufacturers directions. Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).

tag: total lung tissues from adult mice treated with CCl4


title: KELS2847


title: Wild type mouse lungs treated with CCl4

description: sample contained a mixture of equal amounts of RNA from three distinct WT mice,  treated with CCl4 for 16 hours.

tag: total lung RNA from mice treated with CCl4


title: PF382 CompE 24h rep2

status: Public on Aug 20 2008

city: New York

first: Adolfo

middle: A

last: Ferrando

state: NY

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: Standard Affymetrix procedure

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5 followed by  Dchip data normalization for adjustment of interarray intensity differences and calculation of  model based expression (VALUE).

source_name: PF382 human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h

label_protocol: Approx. 10 micrograms of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% fetal bovine serum plus antibiotics (pen/strep) in a humidified incubator with 5% CO2 atmosphere at 37C

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen) following the manufacturer?s instructions

treatment_protocol: Compound E (CompE) [ (2S)-2-{[ (3,5-Difluorophenyl)acetyl]amino}-N-[(3S)-1-methyl-2-oxo-5-phenyl-2,3-dihydro-1H-1,4-benzodiazepin-3-yl] propanamide] (Alexis Biochemicals) a cell permeable, potent, selective, non-transition state and non-competitive inhibitor of gamma-secretase treatment at 500nM in DMSO for 24h.

tag: T-cell acute lymphoblastic leukemia cell line


title: PF382 DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: PF382 human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h

extract_protocol: RNA was extracted with RNAqueous minikit (Ambion) following the manufacturer’s instructions

treatment_protocol: Vehicle treatment (DMSO) control for 24 h.


title: P12-ICHIKAWA DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: P12-ICHIKAWA human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: Illini R Green Fruit technical rep 2

status: Public on Aug 01 2008

city: Charleston

first: Patrick

last: Wechter

state: SC

address: 2700 Savannah Highway

department: U.S. Vegetable Laboratory

institute: USDA-ARS

description: no additional information

hyb_protocol: According to standard NimbleGen protocol.

data_processing:
Performed by NimbleGen Systems: quantile normalization method of Bolstad et al. (2003). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame (ORF) by using the robust multiarray average (RMA) procedure as previously described by Irizarry et al. (2003).

Raw data file (.pair) linked as supplementary file.

organism: Citrullus lanatus

source_name: fruit

growth_protocol: The watermelon plants were grown in a field plot located at the South Central Agricultural Research Laboratory at Lane, OK.

extract_protocol: Total RNA was isolated from watermelon fruits and leaves from all bioreps as previously described by Davis et al., HortScience 2006, 41:1292-1294.

treatment_protocol: Watermelon fruits at green flesh stage (12 DAP), pink flesh stage (24 DAP), and red flesh stage (36 DAP) from the cultivar ‘Illini Red’ were used for RNA isolation.  In addition, several leaves in different stages of development, immature (not fully expanded), young (fully expanded), and mature, were collected from the experimental plants, combined, and processed for RNA isolation.

tag: Watermelon, Cultivar Illini Red

tag: synonym

value: Citrullus lanatus (Thunb.) Matsum. & Nakai

tag: Field grown

tag: 12 days post-pollination


title: Illini R Red Fruit technical rep 1

description: no additional information

scan_protocol: According to standard NimbleGen protocol.

tag: 36 days post-pollination


title: Illini R Pink Fruit technical rep 2

description: no additional information

label_protocol: According to standard NimbleGen protocol.

tag: 24 days post-pollination


title: Illini R Red Fruit technical rep 2

description: no additional information


title: Illini R Leaf technical rep 2

description: no additional information

source_name: leaf


title: Illini R Pink Fruit technical rep 3

description: no additional information


title: Illini R Red Fruit technical rep 3

description: no additional information


title: MOLT3 DMSO control 24h rep2

description: Standard Affymetrix procedure

source_name: MOLT3  human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: P12-ICHIKAWA DMSO control 24h rep2

description: Standard Affymetrix procedure


title: Illini R Green Fruit technical rep 1

description: no additional information


title: Illini R Leaf technical rep 3

description: no additional information


title: Illini R Green Fruit technical rep 3

description: no additional information


title: P12-ICHIKAWA CompE 24h rep2

description: Standard Affymetrix procedure

source_name: P12-ICHIKAWA Human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: Illini R Pink Fruit technical rep 1

description: no additional information


title: P12-ICHIKAWA CompE 24h rep1

description: Standard Affymetrix procedure


title: MOLT3 CompE 24h rep2

description: Standard Affymetrix procedure

source_name: MOLT3 Human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: PF382 CompE 24h rep1

description: Standard Affymetrix procedure


title: PF382 DMSO control 24h rep2

description: Standard Affymetrix procedure

source_name: PF382  human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: MOLT3 DMSO control 24h rep1

description: Standard Affymetrix procedure

source_name: MOLT3 human T-cell lymphoblastic cell line vehicle only (DMSO) treatment control 24h


title: Illini R Leaf technical rep 1

description: no additional information


title: Patient 30

type: genomic

city: Salamanca

first: Olga

last: Lopez

address: P/ San Vicente 58-182

department: Hematology

country: Spain

institute: Hospital Universitario de Salamanca

description: For the array, 10 simultaneous hybridizations of normal male versus normal female and placenta:placenta (DNA reference) were performed to define the normal variation for the log2 ratio.

hyb_protocol: Labelled test and reference DNAs were mixed equitably, co-precipitated in presence of Cot-1 human DNA (Roche, Indianapolis, IN) with ethanol, washed, and resuspended in hybridization solution (50% Formamide, 10% Dextran sulfate, 2X standard saline citrate, 10 mM Tris pH 7.6, 2.7% sodium dodecyl sulfate and 10 μg/ μl of yeast tRNA). DNA mixtures were cohybridized to the arrays in the GENETAC for 48 hours at 37ºC according to the manufacturer’s recommended protocol.

scan_protocol: Images and signal intensities were acquired using GenePix4000B (Axon Instruments, Burlingame, CA) dual laser scanner in combination with GenePixPro4.0 (Axon Instruments) imaging software

data_processing: The Cy5/Cy3 intensity ratios of every spot were converted into log2 ratios. The log2 ratio of each clone was normalized to the median log2 ratio of the ten control hybridizations, after which the median of triplicate spots was calculated. Data from two-colour hybridizations for both DNA were normalized using the corresponding GEPAS5,6 module DNMAD.7 Regions of copy number gain and loss for the BAC array-CGH data were identified by creating sample specific thresholds.3,4 The clones with log2 ratios above or below +/- a control sample’s threshold value (0.4) were considered as gains or losses, respectively. A BAC clone with a log2 ratio of – 0.4 or less was defined as loss region and log2 ratio of +0.4 or more was defined as gain region. Moreover, spots with weak Cy3 or Cy5 below R2 < 0.2 intensity were excluded from analysis. Furthermore, clones with standard deviation more than 0.3 of triplicate spots were also excluded. In total, approximately 10% of clones were excluded.

molecule: genomic DNA

source_name: Control DNA

label_protocol: the digested DNAs were separately labelled using random primers (Bioprimer labelling kit, Invitrogen)  Cy5-dCTP fluorescent dye to paired hybridisation samples (Amersham Biosciences). The incorporated of the label nucleotide was quantified using the Nanodrop spectrophotometer.

extract_protocol: The DNA fresh-frozen samples was extracted with the standard phenol-chloroform method

tag: Control DNA

source_name: Mesenchymal cells DNA from myelodysplastic syndrome patient

label_protocol: the digested DNAs were separately labelled using random primers (Bioprimer labelling kit, Invitrogen)  Cy3-dCTP fluorescent dye to paired hybridisation samples (Amersham Biosciences). The incorporated of the label nucleotide was quantified using the Nanodrop spectrophotometer.

tag: Mesenchymal cells DNA


title: Patient 27


title: Patient 24


title: Patient 18


title: Patient 26


title: Patient 22


title: Patient 21


title: Patient 17


title: Patient 16


title: Patient 12


title: Patient 10


title: Patients 8

source_name: mesenchymal cells DNA from myelodysplastic syndrome patient


title: O157:H7 in model apple juice, exponential phase cells in MAJ vs. MOPS, rep 4

city: East Lansing

first: Thomas

middle: S

last: Whittam

state: MI

address: 165 Food Safety & Tox

department: Microbiology

institute: Michigan State University

description: There are probes on the array that target three different E. coli genomes. Those that were specific for genomes other than Sakai were excluded from the analysis.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5x SSC, and 1mg/mL BSA at 42C for 1 hour. After blocking, arrays were washed 2x 5 min in 0.1x SSC and 2x 30s in H2O. Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95C for 5 min and then mixed with 40uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array. Hybridizations were carried out at 47C for 16-18h. After hybridization, arrays were washed in 2x SSC, 0.5% SDS 37C for 5 min, followed by 2x 5 min in 0.1x SSC, 0.1% SDS 37C, and then 2x 2.5min in room temperature 0.1x SSC.

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: Raw intensity values for each array were normalized using pin-tip LOWESS in R (52) with the MAANOVA (v. 0.98-8) package. Signals from two replicate probes on each array were averaged and log2 transformation applied. Differences in transcript levels were determined using a mixed model ANOVA in R/MAANOVA which tested for significant differences due to growth phase (exponential or stationary), treatment (MOPS or MAJ) and the interaction of these two factors using the following linear model: array+dye+sample (biological replicate)+ phase+treatment+phase*treatment. The ANOVA modeling allows for consideration of appropriate error structures for experiments with multiple sources of variation in microarray measurements (37). The random effects of the model were biological replicate and array effects, whereas the fixed effects were growth phase, treatment, and dye effects (18). The Fs statistic, a shrinkage estimator for gene-specific variance components that makes no assumptions about the distribution of variances across genes, was estimated (19). Significant changes in expression over time were determined by calculating the p values for the Fs statistic for each gene using 1000 random permutations. The p-values were adjusted to correct for type I error with the Benjamini-Hochberg (B-H) linear step-up correction implemented in R/MAANOVA and a cutoff adjusted p-value of 0.05. Fold change in expression between treatments and growth phases was determined by calculating the difference in log2 expression between the treatments or growth phases of interest.

organism: Escherichia coli

source_name: O157:H7 Sakai, exponential phase cells in MOPS pH 7.4, 37C

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT, 400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM amino-allyl dUTP. 30uL reactions were incubated overnight at 42C. cDNA was purified using PCR cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5). Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.). Uncoupled dye was removed by another purfication using the PCR cleanup kit. Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

extract_protocol: A 1/10 volume of 10% phenol in ethanol stop solution was added to the 50 mL MAJ with culture, vortexed, and poured over 1% phenol, 10% ethanol ice. Samples were centrifuged immediately at 6000 rpm, 4ºC for 30 min to pellet cells. The supernatant was removed and cell pellets were suspended in 5 mL of lysis buffer (20 mM sodium actetate, 2mM EDTA) and immediately mixed with 5mL of hot acid phenol:chloroform. Samples were held at 65ºC with periodic shaking for at least 10 minutes before centrifuging at 4000 rpm for 20 min. Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1). RNA was precipitated overnight at –80ºC in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2. RNA samples were purified and treated with DNase using the Rneasy kit (Qiagen).

treatment_protocol: l 	At exponential phase (OD600=0.25, 3h after inoculation), 10mL of culture grown in MOPS minimal medium was mixed with 40mL of MOPS held at 37ºC for 10 min.

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 4

source_name: O157:H7 Sakai, exponential phase cells in MAJ pH 3.5, 37C

treatment_protocol: At exponential phase (OD600=0.25, 3h after inoculation), 10mL of culture grown in MOPS minimal medium was mixed with 40mL of MAJ held at 37ºC for 10 min.


title: Patient 1

hyb_protocol: For microarray hybridization, the digested DNAs were separately labelled using random primers (Bioprimer labelling kit, Invitrogen) and Cy3-dCTP and Cy5-dCTP fluorescent dye to paired hybridisation samples (Amersham Biosciences). The incorporated of the label nucleotide was quantified using the Nanodrop spectrophotometer. Labelled test and reference DNAs were mixed equitably, co-precipitated in presence of Cot-1 human DNA (Roche, Indianapolis, IN) with ethanol, washed, and resuspended in hybridization solution (50% Formamide, 10% Dextran sulfate, 2X standard saline citrate, 10 mM Tris pH 7.6, 2.7% sodium dodecyl sulfate and 10 μg/ μl of yeast tRNA). DNA mixtures were cohybridized to the arrays in the GENETAC for 48 hours at 37ºC according to the manufacturer’s recommended protocol.

scan_protocol: Images and signal intensities were acquired using GenePix4000B (Axon Instruments, Burlingame, CA) dual laser scanner in combination with GenePixPro4.0 (Axon Instruments) imaging softwar

data_processing: The Cy5/Cy3 intensity ratios of every spot were converted into log2 ratios. The log2 ratio of each clone was normalized to the median log2 ratio of the ten control hybridizations, after which the median of triplicate spots was calculated. Data from two-colour hybridizations for both DNA were normalized using the corresponding GEPAS5,6 module DNMAD.7 Regions of copy number gain and loss for the BAC array-CGH data were identified by creating sample specific thresholds.3,4 The clones with log2 ratios above or below +/- a control sample’s threshold value (0.4) were considered as gains or losses, respectively. A BAC clone with a log2 ratio of – 0.4 or less was defined as loss region and log2 ratio of +0.4 or more was defined as gain region. Moreover, spots with weak Cy3 or Cy5 below R2 < 0.2 intensity were excluded from analysis. Furthermore, clones with standard deviation more than 0.3 of triplicate spots were also excluded. In total, approximately 10% of clones were excluded

source_name: control DNA

extract_protocol: The DNA samples was extracted with the standard phenol-chloroform method . Normal DNA was prepared from human placenta of healthy donors. All DNAs were quantitated using the Nanodrop spectrophotometer. DNA quality was assessed by the 260:280 ratio and its integrity by agarose gel ethidium bromide visualization.1

tag: Control DNA Human

tag: mesemchymal cells DNA


title: O157:H7 in model apple juice, stationary phase cells in MAJ vs. MOPS, rep 4

source_name: O157:H7 Sakai, stationary phase cells in MOPS pH 7.4, 37C

treatment_protocol: At stationary phase (OD600=0.95, 6.5h after inoculation), 10mL of culture grown in MOPS minimal medium was mixed with 40mL of MOPS (without glucose) and held at 37ºC for 10 min.

source_name: O157:H7 Sakai, stationary phase cells in MAJ pH 3.5, 37C

treatment_protocol: At stationary phase (OD600=0.95, 6.5h after inoculation), 10mL of culture grown in MOPS minimal medium was mixed with 40mL of MAJ held at 37ºC for 10 min.


title: O157:H7 in model apple juice, exponential phase cells in MAJ vs. MOPS, rep 3

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 3

treatment_protocol: At exponential phase (OD600=0.25, 3h after inoculation), 10mL of culture grown in MOPS minimal medium was mixed with 40mL of MOPS held at 37ºC for 10 min.


title: O157:H7 in model apple juice, stationary phase cells in MAJ vs. MOPS, rep 5

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 5


title: O157:H7 in model apple juice, stationary phase cells in MAJ vs. MOPS, rep 3


title: O157:H7 in model apple juice, exponential phase cells in MAJ vs. MOPS, rep 1

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 1


title: O157:H7 in model apple juice, exponential phase vs stationary phase in MAJ, rep 4


title: O157:H7 in model apple juice, exponential phase cells in MAJ vs. MOPS, rep 2

tag: E. coli O157:H7 RIMD0509952 (Sakai) - culture replicate 2


title: O157:H7 in model apple juice, stationary phase cells in MAJ vs. MOPS, rep 2


title: O157:H7 in model apple juice, stationary phase cells in MAJ vs. MOPS, rep 1


title: O157:H7 in model apple juice, exponential phase vs stationary phase in MAJ, rep 2


title: O157:H7 in model apple juice, exponential phase cells in MAJ vs. MOPS, rep 5


title: Root sol2 rep2

status: Public on Jul 31 2008

city: Bunkyo-ku

first: Kuninori

last: Iwamoto

address: Hongo 7-3-1

country: Japan

institute: University of Tokyo

description: Arabidopsis root tip, sol2

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Scanning procedure was conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

data_processing: GCOS

organism: Arabidopsis thaliana

source_name: Arabidopsis root tip, sol2

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Seeds were sterilised with sodium hypochlorite 5 min, rinsed 4 times with sterile water, plated on MS media, and incubated at 23°C under the continuous light conditions for 4 days.

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen)
and purified with RNeasy Micro Kit (QIAGEN).

tag: Utrecht, 4-day-old roots, 2 mm root tips


title: Root wt rep1

description: Arabidopsis root tip, wt

source_name: Arabidopsis root tip, wt

growth_protocol:
Seeds were sterilised with sodium hypochlorite 5
min, 4 rinses sterile water,  plated on MS media, and incubated at 23°C under the continuous light conditions for 4 days.


title: O157:H7 in model apple juice, exponential phase vs stationary phase in MAJ, rep 1

data_processing: Raw intensity values for each array were normalized using pin-tip LOWESS in R (52)  with the MAANOVA (v. 0.98-8) package.  Signals from two replicate probes on each array were averaged and log2 transformation applied. Differences in transcript levels were determined using a mixed model ANOVA in R/MAANOVA which tested for significant differences due to growth phase (exponential or stationary), treatment (MOPS or MAJ) and the interaction of these two factors using the following linear model: array+dye+sample (biological replicate)+ phase+treatment+phase*treatment.  The ANOVA modeling allows for consideration of appropriate error structures for experiments with multiple sources of variation in microarray measurements (37). The random effects of the model were biological replicate and array effects, whereas the fixed effects were growth phase, treatment, and dye effects (18).  The Fs statistic, a shrinkage estimator for gene-specific variance components that makes no assumptions about the distribution of variances across genes, was estimated (19).  Significant changes in expression over time were determined by calculating the p values for the Fs statistic for each gene using 1000 random permutations.  The p-values were adjusted to correct for type I error with the Benjamini-Hochberg (B-H) linear step-up correction implemented in R/MAANOVA and a cutoff adjusted p-value of 0.05.  Fold change in expression between treatments and growth phases was determined by calculating the difference in log2 expression between the treatments or growth phases of interest.

extract_protocol: A 1/10 volume of 10% phenol in ethanol stop solution was added to the 50 mL MAJ with culture, vortexed, and poured over 1% phenol, 10% ethanol ice. Samples were centrifuged immediately at 6000 rpm, 4ºC for 30 min to pellet cells.  The supernatant was removed and cell pellets were suspended in 5 mL of lysis buffer (20 mM sodium actetate, 2mM EDTA) and immediately mixed with 5mL of hot acid phenol:chloroform.  Samples were held at 65ºC with periodic shaking for at least 10 minutes before centrifuging at 4000 rpm for 20 min.  Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1).  RNA was precipitated overnight at –80ºC in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2.  RNA samples were purified and treated with DNase using the Rneasy kit (Qiagen).

treatment_protocol: At  stationary phase (OD600=0.95, 6.5h after inoculation), 10mL of culture grown in MOPS minimal medium was mixed with 40mL of MAJ held at 37ºC for 10 min.

source_name: O157:H7 Sakai, exponential cells in MAJ, pH 3.5 37C

treatment_protocol: At  exponential phase (OD600=0.25, 3h after inoculation), 10mL of culture grown in MOPS minimal medium was mixed with 40mL of MAJ held at 37ºC for 10 min.


title: O157:H7 in model apple juice, exponential phase vs stationary phase in MAJ, rep 3


title: Root wt rep2

description: Arabidopsis root tip, wt


title: (C1) CTH1cth2 in 100uM BPS replicate 1

status: Public on Jul 15 2008

city: Durham

first: Dennis

middle: J.

last: Thiele

state: NC

address: 3813 Research Drive

department: Pharmacology and Cancer Biology

institute: Duke University

description: Gene expression data from CTH1cth2 strain under iron limitation (using the iron chelator BPS - bathophenanthroline disulfonate)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: MAS5.0 ExpressionStat, GeneSpring 6.1

label: Biotin

organism: Saccharomyces cerevisiae

source_name: CTH1cth2 strain grown in SC-ura with 100uM BPS

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard glass beads method using acidic phenol:chloroform.

tag: [cth1::kan;cth2::HIS (pRS416-CTH1)]

tag: BY4741 parental


title: (T1) cth1CTH2 in 100uM BPS replicate 1

description: Gene expression data from cth1CTH2 strain under iron limitation (using the iron chelator BPS - bathophenanthroline disulfonate)

source_name: cth1CTH2 strain grown in SC-ura with 100uM BPS

tag: [cth1::kan;cth2::HIS (pRS416-CTH2)]

tag: Parental BY4741


title: (T2) cth1CTH2 in 100uM BPS replicate 2


title: (C2) CTH1cth2 in 100uM BPS replicate 2


title: (T3) cth1CTH2 in 100uM BPS replicate 3


title: (V2) cth1cth2 in 100uM BPS replicate 2

description: Gene expression data from cth1cth2 deletion strain under iron limitation (using the iron chelator BPS - bathophenanthroline disulfonate)

source_name: cth1cth2 strain grown in SC-ura with 100uM BPS

tag: [cth1::kan;cth2::HIS (pRS416)]


title: (V1) cth1cth2 in 100uM BPS replicate 1


title: new_160703_micro06_GFS2172

status: Public on Jun 12 2008

city: Castanet-Tolosan Cedex

first: Gwenola

last: Tosser-Klopp

address: Chemin de Borde-Rouge  BP 52627

country: France

institute: INRA

description: hybridation simultannée avec la membrane 3

data_processing: QIM_CONST mean normalization

organism: Sus scrofa

source_name: Ovaire 17 : 07/04/2003,96h après traitement Régumate  10 follicules de diamètre 5 à 6,5 mm (qualité de frottis 1)

tag: GF

tag: PF MF GF animaux

value: GF 17

tag: annotation PF/MF/GF

value: GF

tag: annotation animal

tag: annotation animal PF MF GF

value: 17 GF


title: AdEasy transduced HepG2 cells, UV treated

status: Public on Jul 01 2008

city: Singapore

first: Wah Heng

last: Lee

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: Transduction Control, UV treated

hyb_protocol: Hybridization is done according to the agilent 60-mer oligo microarray processing protocol. Appropriate volumes corresponding to 0.75 ug Cy3- and Cy5- labeled cRNA were pooled, 50 ?l 10x control target solution was added and finally filled with water to a volume of 240 ?l. To this mixture 10 ?l 25x fragmentation buffer was added and incubated for 30 min at 60°C. 250 ?l 2x hybridization buffer was added to terminate the fragmentation reaction. 500 ?l of this 1x hybridization solution was hybridized overnight (17 hours, 60°C) on Whole Human Genome Oligo Microarrays using Agilent's recommended hybridization chamber and oven.

scan_protocol: Scanned on an Agilent scanner by Miltenyi service centre and Images were quantified by Miltenyi service centre

data_processing:
Individual probes are normalized using Agilent's Feature Extraction algorithms. These algorithms were developed with the aim of reducing systematic errors that arise from labeling bias, irregular feature morphologies, mismatched sample concentrations and cross-hybridization.They quantify feature signals and their background, perform background subtraction, dye normalization, and calculate feature log ratios (Agilent's Processed Signal value) and error estimates. The error estimates, based on an extensive error model and pixel level statistics calculated from the feature and background for each spot, are used to generate a p-value for each log ratio.
From the processed normalized data provided by the Agilent certified centre, we selected genes that exhibit at least 2 fold differences in gene expression between the AdHBx- and AdEasy-infected cells when compared against the Control HepG2 cell.

label_protocol: 1ug of total RNA was used for cDNA synthesis and half of the reaction mixture was subsequently used for complementary RNA synthesis and fluorescent labeling according to agilent's recommended protocol (Serviced by Miltenyi)

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% FCS, AdEasy MOI 4, 8-16J/m2 UV treatment

extract_protocol: Extraction done by servicing agent from Miltenyi

source_name: Control RNA from Miltenyi

tag: Control RNA; Information can be retrieved from Miltenyi service centre


title: new_160703_micro07_MFS2163

description: hybridation simulatnée avec la membrane 17

source_name: Ovaires 12 : 10/09/99,24h après traitement Régumate  8 follicules de diamètre 3 à 3,5 mm (qualité de frottis 1)

tag: MF

value: MF 12

value: MF

value: 12 MF


title: new_160703_micro09_GFS2166

description: hybridation simulatnée avec la membrane 16

source_name: Ovaire 14 : 10/02/2000,96h après traitement Régumate 5 follicules de diamètre 5 à 6,5 mm (qualité de frottis 1)

value: GF 14

value: 14 GF


title: new_110703_micro09_GFS2166


title: (V3) cth1cth2 in 100uM BPS replicate 3


title: new_160703_micro08_PFS2165

description: hybridation simulatnée avec la membrane 12

source_name: Ovaire 9D : 09/07/99,24h après traitement Régumate  24 follicules de diamètre 2 mm (follicules de qualité de frottis 1, 1+)

tag: PF

value: PF 9

value: PF

value: 9 PF


title: new_110703_micro06_GFS2172


title: AdHBx transduced HepG2 cells, UV treated

description: HBx-over-expressing HepG2 cells, UV treated

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% FCS, AdHBx MOI 6, 8-16J/m2 UV treatment

tag: AdHBx (AdEasy vector carrying full length Hbx cDNA) transduced HepG2 cells, UV treated

label_protocol: Information can be retrieved from Miltenyi service centre


title: Control HepG2 cell UV treated

description: UV treatment control

source_name: HepG2 cells, UV treated (8-16 J/m2)

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% FCS

tag: HepG2 cells, Human liver cancer cell line

extract_protocol: Information can be retrieved from Miltenyi service centre


title: new_040703_micro08_GFS2166

description: hybridation simulatnée avec la membrane 14


title: new_110703_micro08_PFS2165


title: new_110703_micro07_MFS2163


title: new_040703_micro07_PFS2165


title: new_030703_micro07_PFS2165


title: new_110703_micro17_MFS2163

description: hybridation simultannée avec la membrane 7


title: new_040703_micro17_GFS2176

description: hybridation simultannée avec la membrane 5

source_name: Ovaire 18 : 07/04/2003,96h après traitement Régumate  14 follicules de diamètre 5 à 6,5 mm (qualité de frottis 1)

value: GF 18

value: 18 GF


title: new_040703_micro09_GFS2170

description: hybridation simulatnée avec la membrane 15


title: new_030703_micro09_GFS2170


title: new_030703_micro17_GFS2176


title: new_160703_micro17_MFS2163


title: new_040703_micro16_PFS2165


title: Root sol2 rep1

description: Arabidopsis root tip, sol2


title: new_160703_micro16_GFS2166

description: hybridation simultannée avec la membrane 9


title: new_160703_micro15_PFS2174

source_name: Ovaires 12 : 10/09/99,24h après traitement Régumate  22 follicules de diamètre 1 à 2 mm (qualité de frottis 1)      Date added 2003-07-09

value: PF 12

value: 12 PF


title: new_030703_micro16_PFS2165


title: new_110703_micro16_GFS2166


title: new_030703_micro02_PFS2174

description: hybridation simulatnée avec la membrane 13


title: new_110703_micro15_PFS2174


title: (C3) CTH1cth2 in 100uM BPS replicate 3


title: new_030703_micro05_GFS2176


title: new_030703_micro04_MFS2163

description: hybridation simultanée avec la membrane 12


title: new_110703_micro03_GFS2172

description: hybridation simulatnée avec la membrane 6


title: new_030703_micro15_GFS2170


title: new_040703_micro04_MFS2163


title: new_110703_micro04_GFS2176


title: new_160703_micro14_GFS2170

description: hybridation simultannée avec la membrane 2


title: new_110703_micro02_GFS2170


title: new_040703_micro15_GFS2170


title: new_110703_micro05_PFS2174


title: new_040703_micro02_PFS2174


title: new_110703_micro14_GFS2170


title: new_160703_micro03_GFS2172


title: new_040703_micro13_PFS2174


title: new_040703_micro14_GFS2166

description: hybridation simultannée avec la membrane 8


title: new_040703_micro05_GFS2176

description: Cette hybridation est "fictive". C'est une exposition compl�mentaire de l'hybridation new_H2003-13.1_GFS2176 avec la sonde S2003-13.  Probl�me d� � la migration de BASE (�t� 2004)


title: new_110703_micro13_GFS2176

description: hybridation simultannée avec la membrane 4


title: new_160703_micro02_GFS2170


title: new_030703_micro14_GFS2166


title: new_160703_micro13_GFS2176


title: new_160703_micro05_PFS2174


title: new_160703_micro04_GFS2176


title: new_110703_micro12_PFS2165


title: new_030703_micro13_PFS2174


title: new_160703_micro12_PFS2165


title: new_040703_micro12_MFS2163


title: Whole heart at d49_12, biological rep3

status: Public on Jun 10 2008

city: Madison

first: wei

last: guo

state: WI

address: 1805 Linden Dr.

institute: University of Wisconsin-Madison

description: Gene expression data from wild type rat heart at day49

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 320 2.0 Genome Array. GeneChips were washed and stained in a GeneChip 640 hybridization oven.

scan_protocol: Images were scanned using a GeneArray scanner

data_processing: RMA

source_name: wild type rat heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: These wild type animals were crossed with Fisher 344 inbreds. Both strains were obtained from Harlan Sprague Dawley, Indianapolis, IN. Animals were maintained on standard rodent chow using protocols approved by the University of Wisconsin-Madison Animal Use and Care Committee.

tag: Genotype

tag: age

value: 49day after birth


title: new_030703_micro08_GFS2166

description: Cette hybridation est "fictive". C'est une exposition complémentaire de l'hybridation new_H2003-10.1_GFS2166 avec la sonde S2003-10.  Problème dï¿½ ï¿½ l amigration de BASE (ï¿½tï¿½ 2004)


title: Whole heart at d49_5, biological rep2


title: new_030703_micro12_MFS2163


title: Whole heart at d49_1D, biological rep1

description: Gene expression data from mutant rat heart at day49

source_name: mutant rat heart

treatment_protocol: The original rats in which the mutation was observed were from the Sprague-Dawley strain. These animals were crossed with Fisher 344 inbreds. Both strains were obtained from Harlan Sprague Dawley, Indianapolis, IN. Animals were maintained on standard rodent chow using protocols approved by the University of Wisconsin-Madison Animal Use and Care Committee.


title: Whole heart at d49_1H, biological rep2


title: Whole heart at d20_7, biological rep3

description: Gene expression data from wild type rat heart at day20

value: 20day after birth


title: Whole heart at d20_4, biological rep2


title: Whole heart at d20_11, biological rep3

description: Gene expression data from mutant rat heart at day20


title: Whole heart at d49_3, biological rep1


title: Whole heart at d1_2E, biological rep3

description: Gene expression data from mutant rat heart at day1

value: 1day after birth


title: Whole heart at d20_6, biological rep2


title: Whole heart at d1_1E, biological rep2

description: Gene expression data from wild type rat heart at day1


title: Whole heart at d20_3, biological rep1


title: Whole heart at d1_1A, biological rep1


title: Whole heart at d20_2, biological rep1


title: Whole heart at d1_D, biological rep2


title: Whole heart at d1_K, biological rep3


title: Whole heart at d49_1J, biological rep3


title: Whole heart at d1_E, biological rep1


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb18

status: Public on Jun 01 2008

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: No additional information provided.

hyb_protocol: Following pooling of the appropriate cDNAs, samples were precipitated with linear acrylamide and resuspended in a 45 μL hybridization solution consisting of 0.25M NaPO4, 0.5% SDS, 1x SSC, 2x Denhardt's solution, 1 mM EDTA, 2.75 μL LNA d(T) blocker, 2 μg sheared salmon testes DNA (Invitrogen) and 0.3 μL of Cy5-labeled GFP cDNA (Cy5-dUTP and Ready-To-Go labeling beads, Amersham Pharmacia Biotech). Immediately prior to use, arrays were pre-washed 2x in 0.1% SDS at room temperature for 5 min each, followed by two washes in MilliQ-H2O for 2 min each, 3 min at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat denatured at 80ºC for 10 min, then maintained at 65ºC prior to adding to a microarray slide heated to 55ºC, covered with a 22 x 60 x 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 60ºC. Arrays were washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, then three washes of 5 min in 2x SSC at room temperature, and three washes of 5 min in 0.2x SSC at room temperature, and dried by centrifugation. The Cy3 and Cy5 3DNA capture reagent (Genisphere) were then hybridized to the bound cDNA on the microarray in a 45 μL volume consisting of 0.25M NaPO4, 0.5% SDS, 1x SSC, 2x Denhardt's solution, 1 mM EDTA, 2.5 μL Cy3 capture reagent and 2.5 μL Cy5 capture reagent. The 3DNA capture reagent is bound to its complementary cDNA capture sequence on the Cy3 or Cy5 oligo d(T) primers. The second hybridization was performed for 3 h at 60ºC, then washed and dried as before.

scan_protocol: Fluorescent images of hybridized arrays were acquired by using ScanArray Express (PerkinElmer, Foster City, USA). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively. All scans were performed at the same laser power (90%), but with the photomultiplier tube settings for the two channels adjusted such that the ratio of the mean signal intensities was ~1, and the percentage of saturated array elements was < 0.5% but > 0%, while minimizing background fluorescence. Fluorescent intensity data were extracted by using the ImaGene 5.5 software (Biodiscovery, El Segundo, USA).

data_processing:
Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the variance stabilizing normalization (VSN) method of Huber et al. (2002).  A factorial hybridization design with dye balance was chosen to assess gene expression among the untreated control cells, the four time points of cells treated with chitsan (i.e., 15 min, 30 min, 45 min and 2h), and cells treated with the heat-killed Ceratocystis polonica fungus (30 min).  Each of the eight biological replicates for each treatment and time point were hybridized only once for a total of 24 hybridizations.  All microarray experiments were designed to comply with MIAME guidelines (Brazma et al., 2001).  To assess the biological response to chitosan and C. polonica treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of the 24 microarray slides.  The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point.  Expression variance was obtained from the eight biological replicates for each treatment and time point.  Next, the ratio of the treatment (chitosan or C. polonica) minus untreated control parameter estimate to the standard error was used to calculate a t statistic and P value. The Q value for each effect and gene was calculated for each of the two models to adjust for the false discovery rate (Storey and Tibshirani, 2003). All statistical analyses were performed within the R statistical package (www.r-project.org/).
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremr S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME) – toward standards for microarray data.  Nature Genetics 29:  365-371.
Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression.  Bioinformatics 18: S96-S104.
Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies.  Proc Natl Acad Sci USA 100: 9440-9445.

organism: Picea abies

source_name: Norway spruce cultured cells, vial #6, 2 hour exposure to chitosan

label_protocol: Hybridizations were performed using the Genisphere Array350 kit (Genisphere, Hatfield, USA) following manufacturer's instructions. Thirty-five micrograms total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen) and oligo d(T18) primers with a 5' unique sequence overhang specific to either the Cy3 or Cy5 labeling reactions. The RNA strand of the resulting cDNA:RNA hybrid was hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: The Norway spruce cell suspension cultures were maintained in HLM medium at 24°C in the dark while shaking at 100 rpm. For each replicate at each time point, a 30 mL culture in a 125 mL flask was used.

extract_protocol: Total RNA was isolated using the Ambion RNAqueous Midi kit according to manufacturer’s instructions (Ambion, Austin, TX, USA).  Total RNA was quantified and quality checked using an Agilent 2100 Bioanalyzer and the Agilent RNA 6000 Nano kit according to manufacturer’s instructions (Agilent, Santa Clara, CA, USA).

treatment_protocol: The elicitation was performed by adding a chitosan stock to the spruce cultures to a final conc of 100 µg/mL. The chitosan stock was prepared by dissolving chitosan in an acidic 50 mM acetate buffer. After 2 hours, cells were vacuum filtered onto Whatman No. 2 filter paper then transferred immediately to a 15 mL sterile Falcon tube with a clean spatula. The cells were maintained under vacuum for 10 seconds until visibly dry and were immediately flash frozen in liquid nitrogen.

tag: Somatic embryogenic cultures were initiated from mature Norway spruce seeds and were developed as described (Bishop-Hurley, Zabkiewicz et al. 2001; Phillips, Walter et al. 2007).

tag: Bishop-Hurley, S. L., R. C. Zabkiewicz, et al. (2001). "Conifer genetic engineering

value: transgenic Pinus radiata (D. Don) and Picea abies (Karst) plants are resistant to the herbicide Buster." Plant Cell Rep 20:235-243.

tag: Phillips, M. A., M. H. Walter, et al. (2007). "Functional identification and differential expression of 1-deoxy-D-xylulose 5-phosphate synthase in induced terpenoid resin formation of Norway spruce (Picea abies)." Plant Mol Biol 65(3)

source_name: Norway spruce cultured cells, vial #7, untreated control

treatment_protocol: Untreated control.


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb19

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #6, 45 minute exposure to chitosan

treatment_protocol: The elicitation was performed by adding a chitosan stock to the spruce cultures to a final conc of 100 µg/mL. The chitosan stock was prepared by dissolving chitosan in an acidic 50 mM acetate buffer. After 45 minutes, cells were vacuum filtered onto Whatman No. 2 filter paper then transferred immediately to a 15 mL sterile Falcon tube with a clean spatula. The cells were maintained under vacuum for 10 seconds until visibly dry and were immediately flash frozen in liquid nitrogen.

source_name: Norway spruce cultured cells, vial #7, 2 hour exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb20

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #6, 30 minute exposure to chitosan

treatment_protocol: The elicitation was performed by adding a chitosan stock to the spruce cultures to a final conc of 100 µg/mL. The chitosan stock was prepared by dissolving chitosan in an acidic 50 mM acetate buffer. After 30 minutes, cells were vacuum filtered onto Whatman No. 2 filter paper then transferred immediately to a 15 mL sterile Falcon tube with a clean spatula. The cells were maintained under vacuum for 10 seconds until visibly dry and were immediately flash frozen in liquid nitrogen.

source_name: Norway spruce cultured cells, vial #7, 45 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb23

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #8, untreated control

source_name: Norway spruce cultured cells, vial #8, 30 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb16

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #6, 30 minute exposure to Ceratocystis polonica

treatment_protocol: The elicitation was performed by adding a heat-killed C. polonica stock to the spruce cultures. After 30 minutes, cells were vacuum filtered onto Whatman No. 2 filter paper then transferred immediately to a 15 mL sterile Falcon tube with a clean spatula. The cells were maintained under vacuum for 10 seconds until visibly dry and were immediately flash frozen in liquid nitrogen.

source_name: Norway spruce cultured cells, vial #6, 15 minute exposure to chitosan

treatment_protocol: The elicitation was performed by adding a chitosan stock to the spruce cultures to a final conc of 100 µg/mL. The chitosan stock was prepared by dissolving chitosan in an acidic 50 mM acetate buffer. After 15 minutes, cells were vacuum filtered onto Whatman No. 2 filter paper then transferred immediately to a 15 mL sterile Falcon tube with a clean spatula. The cells were maintained under vacuum for 10 seconds until visibly dry and were immediately flash frozen in liquid nitrogen.


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb24

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #8, 30 minute exposure to Ceratocystis polonica

source_name: Norway spruce cultured cells, vial #8, 45 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb17

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #6, untreated control

source_name: Norway spruce cultured cells, vial #7, 30 minute exposure to Ceratocystis polonica


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb12

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #4, 30 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #4, 30 minute exposure to Ceratocystis polonica


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb13

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #5, 2 hour exposure to chitosan

source_name: Norway spruce cultured cells, vial #5, 15 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb11

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #3, 30 minute exposure to Ceratocystis polonica

source_name: Norway spruce cultured cells, vial #4, 2 hour exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb9

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #4, 15 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #4, untreated control


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb10

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #3, 2 hour exposure to chitosan

source_name: Norway spruce cultured cells, vial #3, 30 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb21

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #7, 15 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #7, 30 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb5

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #1, 30 minute exposure to Ceratocystis polonica

source_name: Norway spruce cultured cells, vial #2, untreated control


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb4

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #1, untreated control

source_name: Norway spruce cultured cells, vial #2, 2 hour exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb8

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #3, untreated control

source_name: Norway spruce cultured cells, vial #4, 45 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb15

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #5, 45 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #5, 30 minute exposure to Ceratocystis polonica


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb6

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #2, 15 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #2, 30 minute exposure to Ceratocystis polonica


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb14

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #5, 30 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #5, untreated control


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb3

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #1, 2 hour exposure to chitosan

source_name: Norway spruce cultured cells, vial #2, 45 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb7

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #3, 45 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #3, 15 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb1

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #1, 30 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #1, 15 minute exposure to chitosan


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb2

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #1, 45 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #2, 30 minute exposure to chitosan


title: A2B5/OTMP+ chipB biological replicate-3

city: Bethesda

first: Joe

last: Nielsen

state: MD

address: 49 Convent Drive BD49,5A75

institute: NIH/NINDS

description: Flow Cytometry was used to isolate A2B5/OTMP+ oligodendrocytes from postnatal day 7 rat brain. 4 bioloical replicates were obtained. This data can be compared to the previously submitted oligodendrocyte expression data (GSE5940).

hyb_protocol: Affymetrix standard protocols were followed using the hybridization oven 640, and washing with the fluidics station 450

scan_protocol: The microarrays were scanned with a genchip scanner 3000 7G

data_processing: Cel files were imported into Genespring for preprocessing using RMA, and normalization using a global per-chip and per-gene normalization strategy

organism: Rattus norvegicus

source_name: A2B5/OTMP+ oligodendrocytes

label_protocol: Affymetrix small sample labeling protocol

extract_protocol: Qiagen RNAeasy

tag: Fluorescent activated cell sorted A2B5/OTMP+ oligodendrocytes isolated from post-natal day 7 rat whole brain


title: A2B5/OTMP+ chipB biological replicate-2


title: NorwaySpruce_CulturedCells_Chitosan_&_C.polonica_Stress_Hyb22

description: No additional information provided.

source_name: Norway spruce cultured cells, vial #8, 15 minute exposure to chitosan

source_name: Norway spruce cultured cells, vial #8, 2 hour exposure to chitosan


title: A2B5/OTMP+ chipA biological replicate-1

source_name: A2B5/OTMP+ purified oligodendrocytes


title: A2B5/OTMP+ chipA biological replicate-4


title: A2B5/OTMP+ chipA biological replicate-2


title: A2B5/OTMP+ chipA biological replicate-3


title: A2B5/OTMP+ chipB biological replicate-1


title: HIGK cells infected with serB mutant of Pg33277, biological rep2

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

description: Gene expression data from an isogenic mutant of serB in Porphyromonas gingivalis-infected HIGK cells. (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)

hyb_protocol: Following fragmentation,  human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).

scan_protocol: GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.

data_processing: The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Human Immortalized Gingival Keratinocyte

label_protocol: cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted, DNAse-treated, purified and quantified according to standard  methods (Qiagen and Affymetrix).

treatment_protocol: Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 100 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.

tag: HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).

tag: HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.


title: HIGK cells infected with serB mutant of Pg33277, biological rep3


title: HIGK cells infected with serB mutant of Pg33277, biological rep4


title: Germ Cell Tumour, Histology 2, Biological replicate 18

status: Public on May 31 2008

city: Cambridge

first: Roger

middle: David

last: Palmer

address: Box 197 Hills Road

department: MRC Cancer Cell Unit

country: United Kingdom

institute: Hutchison/MRC Research Centre

description: Gene expression data from malignant germ cell tumor

hyb_protocol: Target cRNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) at Geneservice Ltd (Cambridge Science Park, Cambridge, UK), formerly MRC Geneservice. Briefly, spike controls were added to 15 µg fragmented cRNA before overnight hybridization with the Genechip Human Genome U133A arrays (Affymetrix).

scan_protocol: Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner.

data_processing: The array, once scanned, was used to generate an image file (with the extension .dat). GeneChip Operating Software (GCOS) was then used to compute cell intensity data from the image file and this data was saved in a file with the extension .cel. The .cel (CEL) files were provided by Geneservice Ltd and used for subsequent data analysis. Pre-processing of microarray data (including background correction and normalization) relied on the Robust Multi-Array Average (RMA) method within R.

source_name: Yolk sac tumor

label_protocol: Total RNA from each sample was used to prepare biotinylated target RNA in a one-cycle target labeling procedure, with minor modifications from the manufacturer’s recommendations available at: http://www.affymetrix.com/support/technical/manual/expression_manual.affx. Briefly, 10 µg of cleaned total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 10-fold amplification of RNA.

growth_protocol: Fresh frozen tumor material (pre-chemotherapy) was provided by the individual banking centers across the UK and from Düsseldorf, Germany

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

tag: Within teratoma, CNS, male, age 12, stage 1


title: Germ Cell Tumour, Histology 2, Biological replicate 17

tag: Within teratoma, SCT, female, age 3, stage 5


title: Germ Cell Tumour, Histology 2, Biological replicate 12

tag: Pure, ovarian, female, age 13, stage 2


title: HIGK cells infected with serB mutant of Pg33277, biological rep1


title: Germ Cell Tumour, Histology 2, Biological replicate 15

tag: Pure, ovarian, female, age 14, stage 4


title: Germ Cell Tumour, Histology 2, Biological replicate 9

tag: Pure, ovarian, female, age 9, stage 2


title: Germ Cell Tumour, Histology 2, Biological replicate 14

tag: Pure, ovarian, female, age 14, stage 1


title: Germ Cell Tumour, Histology 2, Biological replicate 13

tag: Pure, ovarian, female, age 13, stage 3


title: Germ Cell Tumour, Histology 2, Biological replicate 10

tag: Pure, ovarian, female, age 12, stage 1


title: Germ Cell Tumour, Histology 2, Biological replicate 11


title: A2B5/OTMP+ chipB biological replicate-4


title: Germ Cell Tumour, Histology 2, Biological replicate 8

tag: Pure, ovarian, female, age 0, stage 2


title: Germ Cell Tumour, Histology 2, Biological replicate 5

tag: Pure, testicular, male, age 1, stage 1


title: Germ Cell Tumour, Histology 2, Biological replicate 6

tag: Pure, testicular, male, age 4, stage 1


title: Germ Cell Tumour, Histology 2, Biological replicate 2

tag: Pure, testicular, male, age 0, stage 1


title: Germ Cell Tumour, Histology 2, Biological replicate 4


title: Germ Cell Tumour, Histology 2, Biological replicate 3


title: Germ Cell Tumor, Histology 1, Biological replicate 9

source_name: Seminoma (Dysgerminoma)

tag: Within teratoma, ovarian, female, age 12, stage 2


title: Germ Cell Tumor, Histology 1, Biological replicate 8

source_name: Seminoma (Germinoma)

tag: Pure, CNS, male, age 16, stage 1


title: Germ Cell Tumour, Histology 2, Biological replicate 16

tag: Within teratoma, SCT, female, age 2, stage 4


title: Germ Cell Tumour, Histology 2, Biological replicate 1


title: Germ Cell Tumor, Histology 1, Biological replicate 4


title: Germ Cell Tumor, Histology 1, Biological replicate 5

tag: Pure, ovarian, female, age 13, stage 1


title: Germ Cell Tumor, Histology 1, Biological replicate 7

tag: Pure, CNS, female, age 10, stage 1


title: Germ Cell Tumor, Histology 1, Biological replicate 6


title: Germ Cell Tumor, Histology 1, Biological replicate 3


title: Germ Cell Tumor, Histology 1, Biological replicate 1

tag: Pure, ovarian, female, age 10, stage 1


title: Oestrogen treated primary human fetal mixed neuronal/glial cell culture

status: Public on May 28 2008

city: Stockholm

first: Linda

middle: Alexandra Csöregh

last: Nord

address: Karolinska University Hospital, Solna, C4:U1

department: Dept. of Women's and Children's Health

country: Sweden

institute: Karolinska Institute

description: Primary mixed neuronal/glial cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. A total of 23 tissue samples yielding 9 cell cultures were used in this experiment. Half of the cell cultures were treated with β-oestradiol the day after seeding. The duration of the oestrogen treatment was 7 days and the cells were harvested after 8 days of culturing for RNA extraction.

hyb_protocol: Hybridization was performed at the Cancer Centre Karolinska Microarray Core Facility at the Karolinska University Hospital in Solna according to the manufactureres protocol.

scan_protocol: Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.

data_processing: Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS). Transcripts with signal intensities <100 in both samples were excluded.

label: Affymetrix single-stage biotin

source_name: Human fetal material, 8-12 weeks, from legal abortions

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

growth_protocol: Primary mixed neuronal/glial cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. Procedures were approved by the local Ethics committee at the Karolinska University Hospital, Stockholm. The cells were grown on Poly-D-lysine in DMEM medium supplemented with 10% newborn calf serum, L-Glutamine and Antibiotic-antimycotic. The cells were grown for 8 days.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit, followed by further cleaning and concentration by using RNeasy MinElute Cleanup Kit.

treatment_protocol: The cell cultures were treated with 2µM β-oestradiol, the day after seeding. Medium was not changed during the culture period. The duration of oestrogen treatment was 7 days and then cells were harvested for RNA extraction.

tag: Primary cell culture grown in medium containing oestradiol


title: Primary human fetal mixed neuronal/glial cell culture

description: Primary mixed neuronal/glial cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. Procedures were approved by the local Ethics committee at the Karolinska University Hospital, Stockholm. A total of 23 tissue samples yielding 9 cell cultures were used in this experiment. The cells were harvested after 8 days of culturing for RNA extraction.

tag: Primary cell culture


title: Germ Cell Tumor, Histology 1, Biological replicate 2


title: Germ Cell Tumour, Histology 2, Biological replicate 7

tag: Pure, testicular, male, age 2, stage 2


title: UV-SeV PI day 21 rep 1, Array 430B

status: Public on May 17 2008

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description: mouse whole lung gene expression, 21 days post-UV-inactivated Sendai virus infection, C57BL/6J, male

hyb_protocol: standard Affymetrix procedures

scan_protocol: Chips were scanned, and hybridization data were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software.

data_processing: Microarray normalization and statistical analysis were carried out using packages from the Bioconductor project (Gentleman RC et al, 2004, ver 2.0), executed in the R programming environment. Data was normalized using the empirical Bayes version of the GCRMA algorithm as implemented in the GCRMA package (Wu Z et al, 2004). Differential expression was assessed by using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package (Smyth GK, 2004). Differences in gene expression were considered significant if the P values were <0.05 after adjustment for multiple testing (Benjamini & Hochberg, 1995), and thus, false discovery rate was controlled to be <5%. Visualization and plotting were performed using Spotfire DecisionSite for Functional Genomics (Spotfire, Somerville, MA).

source_name: whole lung, UV-SeV PI day 21 rep 1

label_protocol: Second-strand cDNA synthesis, was performed using a T7-promoter coupled oligo(d)T primer (GeneChip T7-Oligo(d)T Promoter Primer Kit, Affymetrix, Santa Clara, CA), after which an in vitro transcription (IVT) reaction was performed using an Enzo BioArray High Yield RNA transcript labeling kit (Affymetrix).

growth_protocol: Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.

extract_protocol: Mice were sacrificed 21 days post-infection with Sendai virus. Lungs were flash frozen liquid nitrogen, and subsequently, total RNA was isolated by the acid guanidinium thiocyanate-phenol-chloroform extraction method (Trizol, Invitrogen, Carlsbad, CA).

treatment_protocol: Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Mice were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) intranasally. 3-5 week old male C57BL/6J mice were obtained from Jackson Laboratory. Airway hyperreactivity was assessed 21 days post infection as previously described (Patel et al, 2005), after which mice were sacrificed and lungs were harvested, right for RNA, left for histology and analysis of goblet cell metaplasia.

tag: Strain

tag: Time

value: 21 days post-infection

tag: Infection

value: UV-inactivated Sendai virus

tag: Gender

value: Male


title: SeV PI day 21 rep 3, Array 430B

description: mouse whole lung gene expression, 21 days post-Sendai virus infection, C57BL/6J, male

source_name: whole lung, SeV PI day 21 rep 3

value: active Sendai virus


title: Adult female murine tibialis anterior muscle #3

status: Public on May 09 2008

city: Philadelphia

first: Elisabeth

middle: R

last: Barton

state: PA

address: 240 S. 40th Street

department: Anatomy and Cell Biology

institute: University of Pennsylvania Dental School

description: Profiling measurements were completed at the Penn Microarray Core Facility utilizing Affymetrix Mouse 430 2A chips.  All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

hyb_protocol: see above protocol

data_processing: The Affymetrix Microarray Suite 5.0 algorithm in GeneChip® Operating Software (GCOS) was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

label: streptavidin-phycoerythrin

source_name: adult tibialis anterior

label_protocol: Total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to microarray. The microarray was then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

extract_protocol: Total RNA was isolated from the frozen muscle samples (Trizol, Invitrogen, Carlsbad, CA), and further purified using RNeasy columns (Qiagen, Valencia, CA). RNA integrity was confirmed by gel electrophoresis

tag: control tissue from C57Bl/6 mouse


title: UV-SeV PI day 21 rep 3, Array 430A

source_name: whole lung, UV-SeV PI day 21 rep 3


title: UV-SeV PI day 21 rep 1, Array 430A


title: SeV PI day 21 rep 1, Array 430A

source_name: whole lung, SeV PI day 21 rep 1


title: UV-SeV PI day 21 rep 2, Array 430A

source_name: whole lung, UV-SeV PI day 21 rep 2


title: SeV PI day 21 rep 2, Array 430B

source_name: whole lung, SeV PI day 21 rep 2


title: SeV PI day 21 rep 2, Array 430A


title: Adult female murine tibialis anterior muscle #2

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.


title: Adult female murine tibialis anterior muscle #1


title: Adult female murine masseter muscle #3

source_name: adult superficial masseter


title: UV-SeV PI day 21 rep 2, Array 430B


title: SeV PI day 21 rep 1, Array 430B


title: UV-SeV PI day 21 rep 3, Array 430B


title: SeV PI day 21 rep 3, Array 430A


title: Adult female murine masseter muscle #1


title: PTZ-VGB-NF_14-4(Dyeswap)

status: Public on May 03 2008

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

country: India

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: The data in the file is ratio normalized.

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations

source_name: Drosophila melanogaster, males, unmated, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche) and purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle, and flies from identical cultures were first allowed to lay eggs in bottles containing NF. Flies were transferred to fresh bottle every 12 hr. After discarding first 4 batches of bottles, only those flies that emerged in subsequent bottles were used.Flies were collected within 1-2 days after removing flies that emerged initially, to ensure virgin collection, at every 4 hr interval thereafter. Followed by anesthetizing with diethyl ether, males and females were separated immediately under a microscope. Male flies were thereafter maintained for another 3-4 days on NF.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF twice, in the order : 7days+ 3 days + 4 days. On 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

value: Oregon R

tag: Sex

tag: Tissue

value: Head

source_name: Drosophila melanogaster, males, unmated, treated

extract_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche) and purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Vigabtarin (VGB)(mixed in normal fly food at a concentration of 8 and 24 mg/ml, respectively), in the order: PTZ-7days+ VGB-3 days+ NF-4days.On the final day of treatment, i.e. 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Adult female murine masseter muscle #2


title: PTZ-VGB-NF_14-3(Dyeswap)

label_protocol: Target Purification Kit (Roche), according to the manufacturer’s protocol. This cDNA was used for synthesizing labeled cRNA with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled cRNA was purified by Microarray Target Purification Kit (Roche).


title: PTZ-NaVP-NF_14-3(Dyeswap)

treatment_protocol: 3-4 day old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF twice, in the order : 7days+ 3 days + 4 days. On 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Sodium Valproate (NaVP)(mixed in normal fly food at a concentration of 8 and 0.33 mg/ml, respectively) , and transferred to normal food (NF) for 4 more days, in the order: PTZ-7days+ NaVP-3 days+ NF-4days.On the final day of treatment, i.e. 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-NF-NF_14-3(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ), and transferred to normal food (NF) twice, in the order: PTZ-7days+ NF-3 days+ NF-4days.On the final day of treatment, i.e. 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-NF-NF_14-1

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF twice, in the order : 7days+ 3 days + 4 days. On 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: PTZ-ETH-NF_14-1

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Ethosuximide (ETH)(mixed in normal fly food at a concentration of 8 and 3.48 mg/ml, respectively), and transferred to normal food (NF) for 4 more days, in the order: PTZ-7days+ ETH-3 days+ NF-4days.On the final day of treatment, i.e. 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-NaVP-NF_14-1

treatment_protocol: 3-4 day old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF twice, in the order : 7days+ 3 days + 4 days. On 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: PTZ-NF-NF_14-4(Dyeswap)


title: PTZ-NaVP-NF_14-2


title: PTZ-ETH-NF_14-4(Dyeswap)


title: PTZ-ETH-NF_14-3(Dyeswap)


title: PTZ-VGB-NF_14-2


title: PTZ-VGB-NF_14-1


title: PTZ-NaVP-NF_14-4(Dyeswap)


title: PTZ-VGB_10-4(Dywswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. : 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Vigabatrin (VGB)(mixed in normal fly food at a concentration of 8 and 24 mg/ml, respectively) , in the order: PTZ-7days+ VGB-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-ETH-NF_14-2


title: PTZ-GBP_10-3(Dyeswap)

treatment_protocol: 3-4 day old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. : 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Gabapentin (GBP)(mixed in normal fly food at a concentration of 8 and 16 mg/ml, respectively) , in the order: PTZ-7days+ GBP-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-GBP-NF_14-3(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Gabapentin (GBP)(mixed in normal fly food at a concentration of 8 and 16 mg/ml, respectively) , and transferred to normal food (NF) for 4 more days, in the order: PTZ-7days+ ETH-3 days+ NF-4days.On the final day of treatment, i.e. 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-GBP_10-4(Dyeswap)


title: PTZ-GBP-NF_14-1


title: PTZ-NF-NF_14-2


title: PTZ-NaVP_10-4(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Sodium Valproate (NaVP)(mixed in normal fly food at a concentration of 8 and 0.33 mg/ml, respectively) , in the order: PTZ-7days+ NaVP-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-NaVP_10-3(Dyeswap)


title: PTZ-GBP-NF_14-4(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Gabapentin (GBP)(mixed in normal fly food at a concentration of 8 and 16 mg/ml, respectively) , and transferred to normal food (NF) for 4 more days, in the order: PTZ-7days+ GBP-3 days+ NF-4days.On the final day of treatment, i.e. 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-NaVP_10-2

treatment_protocol: 3-4 day old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. : 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: PTZ-GBP-NF_14-2


title: PTZ-VGB_10-3(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. : 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: PTZ-VGB_10-1


title: PTZ-VGB_10-2


title: PTZ-GBP_10-2

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Gabapentin (GBP)(mixed in normal fly food at a concentration of 8 and 16 mg/ml, respectively) in the order: PTZ-7days+ GBP-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: 3-4 day old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: PTZ-NaVP_10-1


title: PTZ-ETH_10-3(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, i.e. 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Ethosuximide (ETH)(mixed in normal fly food at a concentration of 8 and 3.48 mg/ml, respectively) in the order: PTZ-7days+ ETH-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-GBP_10-1


title: PTZ-LEV-NF_14-1

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Levetiracetam (LEV)(mixed in normal fly food at a concentration of 8 and 5 mg/ml, respectively) , and transferred to normal food (NF) for 4 more days, in the order: PTZ-7days+ LEV-3 days+ NF-4days.On the final day of treatment, i.e. 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-LEV-NF_14-3(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF twice, in the order : 7days+ 3 days + 4 days. On 14th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: PTZ-LEV-NF_14-4(Dyeswap)


title: PTZ-LEV_10-3(Dyeswap)

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Levetiracetam (LEV)(mixed in normal fly food at a concentration of 8 and 5 mg/ml, respectively) , in the order: PTZ-7days+ LEV-3 days.On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: PTZ-LEV-NF_14-2


title: PTZ-ETH_10-4(Dyeswap)


title: PTZ-LEV_10-1


title: PTZ-ETH_10-1

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were treated with Pentylenetetrazole (PTZ) followed by Ethosuximide (ETH)(mixed in normal fly food at a concentration of 8 and 3.48 mg/ml, respectively) in the order: PTZ-7days+ ETH-3 days. On the final day of treatment, i.e. 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: 3-4 days old flies(maintained at 24 +/- 1ºC) were kept in normal fly food (NF) for 7 days and transferred to new vials containing NF, for 3 more days i.e. 7days+ 3 days. On 10th day, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC