title: Gibson_prop_30h_c

status: Public on Apr 23 2008

city: Loughborough

first: Katherine

last: Smart

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

institute: University of Nottingham

description: yeast strain CB11 propagation 30hours after inoculation

hyb_protocol: Yeast Genome 2.0 GeneChip® arrays (Affymetrix) were hybridized with 15 micrograms of fragmented, labelled cRNA for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual. GeneChip® arrays were stained with streptavidin-phycoerythrin solution.

scan_protocol: Samples were scanned using a G2500A GeneArray Scanner (Affymetrix). Following scanning, non-scaled RNA signal intensity (CEL) files were generated using the GeneChip® operating system (GCOS version 5.0; Affymetrix). Non-scaled RNA CEL files contain the raw signal intensity values for each probe on the array, generated from the scanned image of the GeneChip® array. The RNA CEL file contains signal intensity values for the 11 perfect match probes and 11 mismatch probes within each probe set; more than 100,000 signal intensity values for the Yeast Genome 2.0 GeneChip® array.

data_processing:
The data was analysed using Robust Multichip Average (RMA)
The non-scaled RNA CEL files, representing replicates from each time point, were loaded into GeneSpring analysis software (GeneSpring 7.3; Agilent Technologies, USA) using the Robust Multichip Average (RMA) pre-normalization algorithm (Irizarry, et al., 2003). To establish the optimal hybridization threshold for interpreting transcriptional data, the non-scaled RNA CEL files were pre-normalized as a single experimental group. Per-gene normalizations were applied to the probe-set signal values as follows. For each replicate, probe-set signal values were standardized to the median probe-set signal value for all arrays in the experiment. Probe-sets with differential hybridization intensities between a given time point and the reference sample were identified using a two-step process: (i) genes that were at least 1.5-fold up- or down-regulated were selected, and (ii) a Welch's t-test was performed to identify genes that were differentially expressed between time points (P < 0.05).

organism: Saccharomyces cerevisiae

source_name: yeast strain CB11

label_protocol: Approximately 5 micrograms of total RNA was reverse-transcribed at 42°C for one hour to generate first-strand cDNA using 100 pmol oligo dT primer containing a 5'-T7 RNA polymerase promoter sequence, 1X Affymetrix First-Strand Master Mix, 10 mM dithiothreitol (DTT), 10 mM dNTPs and 200 units of SuperScript II reverse transcriptase (Invitrogen). Following first-strand synthesis, second-strand cDNA was synthesized using ten units of Escherichia coli polymerase I, ten units of E. coli DNA ligase and two units of RNase H in a reaction containing 1X Affymetrix Second-Strand Master Mix and 10 mM dNTPs. The second-strand synthesis reaction proceeded at 16°C for two hours before ten units of T4 DNA polymerase were added and the reaction allowed to continue for a further five minutes. The reaction was terminated by adding 0.5 M EDTA. Double-stranded cDNA products were purified using the GeneChip® Sample Cleanup Module (Affymetrix). The synthesized cDNAs were in vitro transcribed by T7 RNA polymerase (Enzo BioArray High Yield RNA Transcript Labelling Kit; Enzo Life Sciences Inc., Farmingdale, NY, USA) using biotinylated nucleotides to generate biotinylated complementary RNAs (cRNAs). The cRNAs were purified using the GeneChip® Sample Cleanup Module (Affymetrix). The cRNAs were then randomly fragmented at 94°C for 35 minutes in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate to generate molecules of approx. 35-200 bp.

growth_protocol:
Yeast sampling:
Triplicate samples of the lager yeast strain CB11 were sampled from a 140 hL (14,000 L) propagation vessel immediately after inoculation and at intervals throughout a 30-hour propagation period. The yeast batch had been incubated aerobically in an 8 hL propagation vessel prior to incubation in this principal (140 hL) vessel.  Propagation wort (85% malt and 15% sugar adjunct) contained 0.5 mg L-1 Zn2+ (added as zinc sulphate heptahydrate) and was oxygenated with a ramped supply of molecular oxygen (5-100 L min-1) to give a consistent dissolved oxygen concentration of 7-8 mg L-1. Temperature of the wort was maintained throughout at 20°C. Specific gravity of the wort was 17º Plato. Triplicate samples of the same yeast strain were also collected from a fourth-generation 3275hL wort fermentation, i.e. the yeast batch had been used in four fermentations previously. The cylindroconical fermentation vessel was filled in stages, with six successive batches of oxygenated wort (each between 520 and 570 hL) added. The wort used for fermentation was the same as that used for the propagation (85% malt and 15% sugar adjunct), contained 0.2 mg L-1 zinc sulphate and was oxygenated in line prior to vessel filling to achieve a dissolved oxygen concentration of 25 mg L-1. An in line oxygen meter (Orbisphere), upstream of yeast pitching, was used to measure dissolved oxygen. Yeast was pitched with the 2nd and 4th batches of wort. The first sample for analysis was taken 8 hours after all of the yeast had been pitched (and 5 hours after the last batch of oxygenated wort had been added to the fermentation vessel). The fermentation vessel's sample point was located on the vertical side of the vessel, 1 metre above the cone. The sample valves were hygienic needle-type valves. Samples were taken at intervals for up to 102 hours after pitching and were transported between the process vessels and the laboratory at 4ºC and in under 5 minutes. Cells and wort were separated by centrifugation at 4ºC. Cell pellets for RNA extraction were flash-frozen in liquid nitrogen and stored at -80°C until required.
Cell density and budding index:
Cell suspensions were diluted to an appropriate volume and density was measured using an Improved Neubauer counting chamber (Weber Scientific International Ltd, Middlesex, UK) and standard light microscope (Zeiss, Oberkocken, Germany) at 200x magnification. To determine budding index, a minimum of 500 cells were scored microscopically and the number of budded cells was calculated as a percentage of the total.

extract_protocol: RNA extraction was carried out following the method of Lyne et al. (Lyne, et al., 2003). Cell samples (1x108 cells) were washed with DEPC-treated water, pelleted by centrifugation (13,000 g; 5 minutes) and re-suspended in 750 microlitres TES. 750 microlitres of chilled (4°C) acidic phenol:chloroform (5:1; pH 4.7) (Sigma) was added and the samples were incubated on a heating block at 65°C for one hour with agitation of the sample by vortexing every ten minutes for 15 seconds. Samples were then cooled on ice and centrifuged (13,000 g; 4°C; five minutes). The upper phase was transferred to a 2.0 mL Eppendorf Phase Lock GelTM tube (Eppendorf AG, Hamburg, Germany), mixed by inversion and centrifuged (13,000 g; 4°C; five minutes). The upper phase was again removed and transferred to a fresh 2.0 mL Eppendorf Phase Lock GelTM tube containing 700 microlitres of chloroform:isoamyl alcohol (24:1; Sigma). The samples were mixed by inversion and centrifuged (13,000 g; 4°C; five minutes). The upper phase was transferred to an Eppendorf tube containing 1.5 mL ethanol (-20°C) and 50 microlitres 3 M sodium acetate pH 5 and agitated briefly by vortexing. RNA was precipitated from the sample by incubation at -70°C for one hour. The sample was then centrifuged (13,000 g; room temperature; five minutes). Supernatant was discarded and the RNA was washed with 70% ethanol (4°C). Ethanol was removed by aspiration and the RNA sample was allowed to dry. 100 microlitres of DEPC-treated water was added and the RNA sample incubated for ten minutes at room temperature.

tag: Age

value: 30 hours


title: Gibson_prop_8h_b

type: RNA

middle: A

country: United Kingdom

description: yeast strain CB11 propagation 8hours after inoculation

label: biotin

molecule: total RNA

value: 8 hours

tag: Strain


title: ZHBTc4(Tc+), 0hr, #1

status: Public on Apr 24 2008

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

country: USA

institute: NIH

description: ZHBTc4(Tc+), 0hr

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Mus musculus

source_name: ZHBTc4(Tc+), 0hr

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: see Niwa et al. nature genetics, 24(2000) 372-376.

treatment_protocol: The sample were treated with ROSA-TET system, Tet inducible system, as described in [An efficient system to establish multiple embryonic stem cell lines carrying an inducible expression unit], Nucleic Acids Res. 2005; 33(4): e43.  Specifically, 5 ug of circular plasmid DNA of Tcl1 exchange vector (pZhC-Tcl1), which have only cds region of Tcl1 gene, and pCAGGS-Cre were co-transfected into EBRTcH3 ES cells. ES cells were cultured in regular medium within 18 ug/ml zeocin, and then, the clones of ES cells were isolated. Tet is present in the culture medium.

tag: embryonic stem cell

tag: Gender

value: male

tag: Genetic modification

value: gene knock in

tag: Individual Identifier

source_name: Universal Mouse Reference RNA

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: Gibson_prop_8h_a


title: Gibson_prop_30h_a


title: Gibson_prop_8h_c


title: Gibson_prop_0h_c

description: yeast strain CB11 propagation 0hours after inoculation

value: 0 hours


title: Gibson_prop_30h_b


title: Gibson_ferm_30hr_B_2

description: yeast strain CB11 fermented 30hours


title: Gibson_ferm_60h_b

description: yeast strain CB11 fermented 60hours

value: 60 hours


title: Gibson_ferm_8hr_A_2

description: yeast strain CB11 fermented 8hours


title: Glioblastoma GBM_152_acgh

status: Public on Apr 29 2008

type: genomic

city: Boston

first: Yonghong

last: Xiao

state: MA

address: 450 Brookline Ave., HIM218A

institute: Dana-Farber Cancer Institute

description: comparative genomic hybridization of human glioblastoma vs. normal genomic DNA

hyb_protocol: Genomic DNA hybridization to Agilent CGH arrays were performed as per manufacturer’s protocol

scan_protocol: Scanning was performed as per manufacturer's protocol

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

molecule: genomic DNA

organism: Homo sapiens

source_name: human glioblastoma tumor

label_protocol: Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.

extract_protocol: Total DNA extracted using PureGene kit following manufacturer's instructions (Gentra Systems).

tag: Human glioblastoma tumor

source_name: universal human male genomic DNA

tag: normal human male genomic DNA


title: Gibson_ferm_60h_c

description: yeast strain CB11 fermented 60hours


title: Gibson_ferm_30hr_C_2

description: yeast strain CB11 fermented 30hours


title: Gibson_prop_0h_a


title: Gibson_prop_0h_b


title: Gibson_ferm_8hr_B_2

description: yeast strain CB11 fermented 8hours


title: Gibson_ferm_8hr_C_2

description: yeast strain CB11 fermented 8hours


title: Gibson_ferm_60hr_A

description: yeast strain CB11 fermented 60hours


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb10

status: Public on Apr 22 2008

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description: Not applicable.

hyb_protocol: Following pooling of the appropriate cDNAs, samples were precipitated with linear acrylamide and resuspended in a 45 µL hybridization solution consisting of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, 1 mM EDTA, 4.0 µL LNA d(T) blocker, 2 µg sheared salmon testes DNA (Invitrogen) and 0.75 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 3´ 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 95°C in MilliQ-H2O, and dried by centrifugation (3 minutes 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 80°C for 10 min, then maintained at 65°C prior to adding to a microarray slide heated to 55°C, covered with a 22 ´ 60 ´ 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 48°C. Arrays were washed in 2´ SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65°C in the same solution, then three washes of 5 min in 2´ SSC at room temperature, and three washes of 5 min in 0.2´ 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 25% formamide, 4x SSC, 0.5% SDS, 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 48°C, 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 for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104). In order to assess performance of the poplar 15.5K microarray, a model containing a dye effect and a treatment effect for untreated control (C) minus C' was fit using data from four microarray slides. The C minus C' effect was computed by assigning two of the self-hybridized arrays to be Cy5-Cy3 and two to be Cy3-Cy5. Three analyses were done such that each self-hybridized array was paired with each other self-hybridized array only once, either as a Cy5-Cy3 or a Cy3-Cy5 combination. Expression variance was derived from technical variance between slides. The ratio of the C minus C' parameter estimate to the standard error was used to calculate a t statistic, from which a P value was obtained. In order to assess the biological response to FTC herbivory (H), a mixed effects model containing a dye effect and a treatment effect for H minus C was fit using data from ten microarray slides derived from five pairs of H versus C trees with a dye flip for each pair. Expression variance was obtained from two sources, biological and technical. The variance between hybridizations from the same H versus C tree pair is solely technical, whereas the variance between hybridizations in different tree pairs is a combination of biological and technical. Dye and H minus C effects, as well as biological and technical variation were estimated using a mixed effects model where the error term for the H minus C and dye effects was computed by pooling the biological and technical variation. Since all 10 slides contained technical variation but only 5 pairs have biological variation, the biological term was given twice the weight of the technical term in the pooled estimate. Next, the ratio of the H minus C 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 & Tibshirani, 2003 Proc. Natl. Acad. Sci. USA. 100: 9440-9445). All statistical analyses were performed within the R statistical package (www.r-project.org/).

organism: Populus trichocarpa x Populus deltoides

source_name: Hybrid poplar leaves, tree #3, untreated control

label_protocol: Hybridizations were performed using the Genisphere Array350 kit (Genisphere) following manufacturer’s instructions. Forty µg 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 65°C for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: Trees were grown under standard greenhouse conditions. See Ralph et al. (2006) Molecular Ecology 15: 1275-1297.

extract_protocol:
Total RNA was isolated according to procedures described in Kolosova et al. (2004) Biotechniques 36: 821-824.
Total RNA was quantified and quality checked by spectrophotometer and agarose gel. Poly(A)+ RNA was isolated by oligo d(T) cellulose using the Poly(A) Pure kit (Ambion, Austin, USA), following manufacturer's instructions. RNA was also evaluated for integrity and the presence of contaminants using reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, USA) with an oligo d(T18) primer and _P32 dGTP incorporation. After removal of unincorporated nucleotides using gel filtration columns (Microspin S-300 HR columns, Amersham Pharmacia Biotech, Buckinghamshire, UK) the resulting cDNA smear was resolved using a vertical 1% agarose alkaline gel and visualized using a Storm 860 phosphorimager (Amersham Pharmacia Biotech).

treatment_protocol: Trees were covered with mesh bags, but were otherwise left untreated.

tag: Six month old clonal trees grown under greenhouse conditions.  The five lowest, fully-expanded, healthy leaves with petioles removed were harvested.

tag: H11-11 genotype

source_name: Hybrid poplar leaves, tree #3, forest tent caterpillar feeding for 24 hours

treatment_protocol: For insect treatment, forest tent caterpillar (FTC) larvae (Malacosoma disstria) were kept without food on moist filter paper for 40 hours prior to placing caterpillars on trees. Five FTC were added to each of five trees under mesh bags on individual trees. Insects were caged on the five lowest, fully-expanded, healthy leaves of each tree.


title: ZHBTc4(Tc+), 24hr, #3

description: ZHBTc4(Tc+), 24hr

source_name: ZHBTc4(Tc+), 24hr


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb9

description: Not applicable.

source_name: Hybrid poplar leaves, tree #2, forest tent caterpillar feeding for 24 hours

source_name: Hybrid poplar leaves, tree #2, untreated control


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb7

description: Not applicable.

source_name: Hybrid poplar leaves, tree #5, untreated control

source_name: Hybrid poplar leaves, tree #5, forest tent caterpillar feeding for 24 hours


title: ZHBTc4(Tc+), 48hr, #3

description: ZHBTc4(Tc+), 48hr

source_name: ZHBTc4(Tc+), 48hr


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb3

description: Not applicable.

source_name: Hybrid poplar leaves, tree #1, untreated control

source_name: Hybrid poplar leaves, tree #1, forest tent caterpillar feeding for 24 hours


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb8

description: Not applicable.

source_name: Hybrid poplar leaves, tree #4, untreated control

source_name: Hybrid poplar leaves, tree #4, forest tent caterpillar feeding for 24 hours


title: Patient 10

first: Bruce

middle: H

last: Horwitz

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

description: A circumferential piece of tissue was obtained at the distal aspect of each specimen.  The tissue was flash frozen at -80 degrees for later processing.  Frozen specimens were homogenized into TriReagent  and RNA was isolated according to the manufacturer’s instruction.  RNA was processed and hybridized to Affymetrix microarray.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133A 2.0 arrrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The 13 data sets were first processed by Affymetrix GCOS V.1.4.0.036 software which computed present/absent calls for each probe set and the signal values were adjusted to an overall target intensity of 1500.  Data was then normalized in Genespring version 7.3.1 in 3 steps.  1. Data trasnformation: set measurements less than 0.01 to 0.01.  2. per chip: Normalization to 50th percentile.  3.  Per Gene: Normalize to median.

source_name: Patient 10 appendix

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

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

tag: appendix sample removed from patient who went to the operating room with the diagnosis of acute appendicitis


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb5

description: Not applicable.


title: Patient 13

source_name: Patient 13 appendix


title: Patient 9

source_name: Patient 9 appendix


title: Patient 19

source_name: Patient 19 appendix


title: Patient 4

source_name: Patient 4 appendix


title: Control 11

source_name: Control 11 appendix

tag: control appendix


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb6

description: Not applicable.


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb2

description: Not applicable.

source_name: Hybrid poplar leaves, tree #3,  forest tent caterpillar feeding for 24 hours

source_name: Hybrid poplar leaves, tree #3, untreated control


title: Control 25

source_name: Control 25 appendix


title: 340 hour rep 2

status: Public on Apr 17 2008

first: Hennie

middle: JJ

last: van Vuuren

address: 2205 East Mall

institute: UBC

description: yeast cells harvested after 340 hours

scan_protocol: as described by the manufacturer (Eukaryotic Arrays GeneChip Expression Analysis and Technical Manual, Affymetrix, Santa Clara, CA), using an Agilent G2500A GeneArray Scanner

data_processing: RMA applied to the whole series (as implemented in the 'affy' package in Bioconductor)

source_name: yeast cells harvested after 340 hours

label_protocol: Following ethanol precipitation, cRNA was prepared by in vitro transcription of the cDNA using the Enzo BioArray™ HighYield™ RNA Transcript Labeling kit (Farmingdale, NY, USA). The cRNA was purified with RNeasy spin columns (Qiagen, Mississauga, ON, Canada), followed by ethanol precipitation. Then, 20 μg of cRNA (0.5 μg μl-1) was fragmented by incubating at 94°C for 35 min in fragmentation buffer (40 mM Tris–acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate). Further details of procedures can be found in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA, USA).

extract_protocol: extraction of total RNA was done according to (Causton et al, Mol. Biol. Cell 12, 323–337,2001). Double-stranded cDNA was purified using phenol/chloroform/isoamyl alcohol (25:24:1) saturated with 10 mM Tris–HCl, pH 8.0, 1 mM EDTA (Ambion, Austin, TX, USA) and a Phase Lock Gel prepared according to the manufacturer's instructions (Eppendorf, Hamburg, Germany)

tag: An industrial wine strain of S. cerevisiae, Vin13 (Anchor Yeast, South Africa), was used. The dried yeast was resuspended (Marks et al, 2003) and inoculated into 1 L filter sterilized Riesling grape juice harvested from the Okanagan Valley in British Columbia, Canada in the 2000 growing season. The final cell count was 4 x 106 /ml. The grape juice contained 214 g/L sugar (equimolar amounts of glucose and fructose), 70 mg/ L ammonia, and 140 mg/L free alpha-amino nitrogen (Marks, 2003 et al, 2003). Incubation was at 20 °C


title: Control 26

source_name: Control 26 appendix


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb1

description: Not applicable.

hyb_protocol: Following pooling of the appropriate cDNAs, samples were precipitated with linear acrylamide and resuspended in a 45 µL hybridization solution consisting of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, 1 mM EDTA, 4.0 µL LNA d(T) blocker, 2 µg sheared salmon testes DNA (Invitrogen) and 0.75 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 3´ 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 95°C in MilliQ-H2O, and dried by centrifugation (3 minutes 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 80°C for 10 min, then maintained at 65°C prior to adding to a microarray slide heated to 55°C, covered with a 22 ´ 60 ´ 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 48°C.  Arrays were washed in 2´ SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65°C in the same solution, then three washes of 5 min in 2´ SSC at room temperature, and three washes of 5 min in 0.2´ 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 25% formamide, 4x SSC, 0.5% SDS, 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 48°C, then washed and dried as before.

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104). In order to assess performance of the poplar 15.5K microarray, a model containing a dye effect and a treatment effect for untreated control (C) minus C' was fit using data from four microarray slides. The C minus C' effect was computed by assigning two of the self-hybridized arrays to be Cy5-Cy3 and two to be Cy3-Cy5. Three analyses were done such that each self-hybridized array was paired with each other self-hybridized array only once, either as a Cy5-Cy3 or a Cy3-Cy5 combination.  Expression variance was derived from technical variance between slides. The ratio of the C minus C' parameter estimate to the standard error was used to calculate a t statistic, from which a P value was obtained. In order to assess the biological response to FTC herbivory (H), a mixed effects model containing a dye effect and a treatment effect for H minus C was fit using data from ten microarray slides derived from five pairs of H versus C trees with a dye flip for each pair. Expression variance was obtained from two sources, biological and technical. The variance between hybridizations from the same H versus C tree pair is solely technical, whereas the variance between hybridizations in different tree pairs is a combination of biological and technical. Dye and H minus C effects, as well as biological and technical variation were estimated using a mixed effects model where the error  term for the H minus C and dye effects was computed by pooling the biological and technical variation. Since all 10 slides contained technical variation but only 5 pairs have biological variation, the biological term was given twice the weight of the technical term in the pooled estimate. Next, the ratio of the H minus C 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 & Tibshirani, 2003 Proc. Natl. Acad. Sci. USA. 100: 9440-9445). All statistical analyses were performed within the R statistical package (www.r-project.org/).

source_name: Hybrid poplar leaves, tree #2, untreated control

label_protocol: Hybridizations were performed using the Genisphere Array350 kit (Genisphere) following manufacturer’s instructions.  Forty µg 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 65°C for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: Trees were grown under standard greenhouse conditions.  See Ralph et al. (2006) Molecular Ecology 15: 1275-1297.

source_name: Hybrid poplar leaves, tree #2, forest tent caterpillar feeding for 24 hours

treatment_protocol: For insect treatment, forest tent caterpillar (FTC) larvae (Malacosoma disstria) were kept without food on moist filter paper for 40 hours prior to placing caterpillars on trees.  Five FTC were added to each of five trees under mesh bags on individual trees.  Insects were caged on the five lowest, fully-expanded, healthy leaves of each tree.


title: Patient 6

source_name: Patient 6 appendix


title: 340 hour rep 1

description: yeast cells harvested after 340 hours

hyb_protocol: 20 μg of cRNA (0.5 μg μl-1) was fragmented by incubating at 94°C for 35 min in fragmentation buffer (40 mM Tris–acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate)


title: Patient 5

source_name: Patient 5 appendix


title: 340 hour rep 3

description: yeast cells harvested after 340 hours


title: Control 2

source_name: Control 2 appendix


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_HerbivoryHyb4

description: Not applicable.

source_name: Hybrid poplar leaves, tree #1, forest tent caterpillar feeding for 24 hours

source_name: Hybrid poplar leaves, tree #1, untreated control


title: Patient 7

source_name: Patient 7 appendix


title: Patient 22

source_name: Patient  22 appendix


title: 60 hour rep 2

description: yeast cells harvested after 60 hours

source_name: yeast cells harvested after 60 hours


title: 120 hour rep 2

description: yeast cells harvested after 120 hours

source_name: yeast cells harvested after 120 hours


title: 60 hour rep 1

description: yeast cells harvested after 60 hours


title: 48 hour rep 1

description: yeast cells harvested after 48 hours

source_name: yeast cells harvested after 48 hours


title: 24 hour rep 1

description: yeast cells harvested after 24 hours

source_name: yeast cells harvested after 24 hours


title: 48 hour rep 2

description: yeast cells harvested after 48 hours


title: 60 hour rep 3

description: yeast cells harvested after 60 hours


title: 48 hour rep 3

description: yeast cells harvested after 48 hours


title: 24 hour rep 2

description: yeast cells harvested after 24 hours


title: WT vs adk1 knock-out mutant

city: Paris

first: Laurent

last: Jourdren

address: 46 rue d'Ulm

department: Biologie

country: France

institute: École Normale Supérieure

description: Technical replicate 1 of 2.

hyb_protocol: 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65¡C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37¡C. The array slides are then air dryed and ready for scaning.

scan_protocol: Scanned on a genepix 4000B scanner (Axon)

data_processing:
Scanning software: GenePix Pro 6.1
Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/
Genepix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalisation method.

source_name: Total RNA extracted from adk1 knock-out mutant in BY4742 strain labeled with Cyanine-5 (red).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Cell growth 24 hours at 28°C in SD medium (Casaminoacid 0.2%, Adenin 300µM, Uracil 200µM, Tryptophan 200µM) to an OD = 1.0

extract_protocol: Hot phenol extract procedure followed by RNEasy Mini Kit purification step (Quiagen)

tag: adk1 knock-out in BY4742 (Mat alpha, his3D1, leu2D0, lys2D0, ura3D0) strain

source_name: Total RNA extracted from WT (BY4742) strain labeled with Cyanine-3 (green).

label_protocol: 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy3. The coupling is stoped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using QiaQuick column.

tag: WT BY4742 (Mat alpha, his3D1, leu2D0, lys2D0, ura3D0) strain


title: adk1 knock-out mutant vs WT (dye swap)

description: Technical replicate 2 of 2 (dye swap).

source_name: Total RNA extracted from WT (BY4742) strain labeled with Cyanine-5 (red).

source_name: Total RNA extracted from adk1 knock-out mutant in BY4742 strain labeled with Cyanine-3 (green).


title: 12 hour rep 3

description: yeast cells harvested after 12 hours

source_name: yeast cells harvested after 12 hours


title: 1 hour rep 1

description: yeast cells harvested after 1 hour

source_name: yeast cells harvested after 1 hour


title: 120 hour rep 1

description: yeast cells harvested after 120 hours


title: 24 hour rep 3

description: yeast cells harvested after 24 hours


title: 1 hour rep 2

description: yeast cells harvested after 1 hour


title: 12 hour rep 1

description: yeast cells harvested after 12 hours


title: 1 hour rep 3

description: yeast cells harvested after 1 hour


title: 12 hour rep 2

description: yeast cells harvested after 12 hours


title: YLK807 glucose vs mixed reference

status: Public on Apr 15 2008

city: Princeton

first: Erin

middle: N

last: Smith

state: NJ

address: 110 Carl Icahn Labs

department: Ecology and Evolutionary Biology

institute: Princeton University

description: YLK807 glucose vs mixed reference

hyb_protocol: Hybridization date : 2006-12-06 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2006-12-06 Scan Time : 14:00:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.1.3.1
Datafile type : Agilent result file

source_name: Mixed reference: BYg+BYE+RMg+RME

label_protocol:
Type of label : Cy3
Low RNA Input Fluorescent Linear Amplification Kit Protocol, Version 4, January 2006, Agilent Technologies, Publication 5185-58

growth_protocol: media : common reference: mixture of BY4716 and RM11-1a RNA from glucose and ethanol conditions

extract_protocol: Extraction method : "Hot acid/phenol, Qiagen Rneasy Kit"

tag: Strain Name

value: common reference:mixture of BY4716 and RM11-1a RNA from glucose and ethanol conditions

source_name: YLK807 glucose

label_protocol:
Type of label : Cy5
Low RNA Input Fluorescent Linear Amplification Kit Protocol, Version 4, January 2006, Agilent Technologies, Publication 5185-58

growth_protocol: media : "glucose carbon source: 6.7g/L YNB (Sigma Y0626), 20g/L glucose, 100 mg/L leucine, 100mg/L lysine, 20mg/L uracil"


title: YLK810 glucose vs mixed reference

description: YLK810 glucose vs mixed reference

hyb_protocol: Hybridization date : 2/27/07 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2007-02-27 Scan Time : 14:39:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: BYg+RMg+BYE+RME

source_name: YLK810 glucose


title: RM3g RM11-1a 0 2% glucose

description: RM3g RM11-1a 0 2% glucose

hyb_protocol: Hybridization date : 2005-12-09 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:26:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : Unknown
Datafile type : Agilent result file

source_name: RM3g RM11-1a 0 2% glucose


title: 9E 2_4_a YLK132 1% ethanol

description: 9E 2_4_a YLK132 1% ethanol

hyb_protocol: Hybridization date : 2005-12-11 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:56:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 9E 2_4_a YLK132 1% ethanol

growth_protocol: media : "ethanol carbon source: 6.7g/L YNB (Sigma Y0626), 10mL/L ethanol, 100 mg/L leucine, 100mg/L lysine, 20mg/L uracil"


title: BY3E BY4716 0 1% ethanol

description: BY3E BY4716 0 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:14:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY3E BY4716 0 1% ethanol


title: RM5g RM11-1a 0 2% glucose

description: RM5g RM11-1a 0 2% glucose

hyb_protocol: Hybridization date : 2005-12-10 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 14:11:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM5g RM11-1a 0 2% glucose


title: RM1g RM11-1a 0 2% glu

description: RM1g RM11-1a 0 2% glu

hyb_protocol: Hybridization date : 2005-12-14 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:08:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM1g RM11-1a 0 2% glu


title: 99g 20_3_c YLK494 2% glucose

description: 99g 20_3_c YLK494 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:16:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 99g 20_3_c YLK494 2% glucose


title: 9g 2_4_a YLK132 2% glu

description: 9g 2_4_a YLK132 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 15:19:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: BY5E BY4716 0 1% eth

description: BY5E BY4716 0 1% eth

hyb_protocol: Hybridization date : 2005-12-13 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 15:03:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY5E BY4716 0 1% eth


title: BY1g BY4716 0 2% glucose

description: BY1g BY4716 0 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:49:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY1g BY4716 0 2% glucose


title: RM3E RM11-1a 0 1% ethanol

description: RM3E RM11-1a 0 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:08:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM3E RM11-1a 0 1% ethanol


title: YLK810 ethanol vs mixed reference

description: YLK810 ethanol vs mixed reference

scan_protocol: Pixel Size : 10 Scan Date : 2007-02-27 Scan Time : 14:23:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: YLK810 ethanol


title: YLK807 ethanol vs mixed reference

description: YLK807 ethanol vs mixed reference

source_name: YLK807 ethanol


title: RM9E RM11-1a 0 1% eth

description: RM9E RM11-1a 0 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 15:19:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM9E RM11-1a 0 1% eth


title: RM1E RM11-1a 0 1% eth

description: RM1E RM11-1a 0 1% eth

hyb_protocol: Hybridization date : 2005-12-12 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:31:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM1E RM11-1a 0 1% eth


title: BY7E BY4716 0 1% eth *repeat*

description: BY7E BY4716 0 1% eth *repeat*

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:40:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY7E BY4716 0 1% eth *repeat*


title: RM7E RM11-1a 0 1% eth

description: RM7E RM11-1a 0 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:15:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM7E RM11-1a 0 1% eth


title: BY5g BY4716 0 2% glu

description: BY5g BY4716 0 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:55:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY5g BY4716 0 2% glu

source_name: BYg+RMg+BYE+RME


title: RM5E RM11-1a 1% ethanol rep 1 vs mixed reference

scan_protocol: Pixel Size : 10 Scan Date : 2007-02-27 Scan Time : 14:06:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: RM5E RM11-1a 1% ethanol rep 1


title: BY3g BY4716 0 2% glucose

description: BY3g BY4716 0 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:21:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY3g BY4716 0 2% glucose


title: BY1E BY4716 0 1% eth

description: BY1E BY4716 0 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 12:57:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY1E BY4716 0 1% eth


title: RM11E RM11-1a 0 1% eth

description: RM11E RM11-1a 0 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:52:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM11E RM11-1a 0 1% eth


title: 97E 20_1_d YLK487 1% ethanol

description: 97E 20_1_d YLK487 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:22:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 97E 20_1_d YLK487 1% ethanol


title: 99E 20_3_c YLK494 1% eth

description: 99E 20_3_c YLK494 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:16:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 97g 20_1_d YLK487 2% glu

description: 97g 20_1_d YLK487 2% glu


title: BY11E BY4716 0 1% eth

description: BY11E BY4716 0 1% eth


title: 98g 20_2_d YLK491 2% glucose

description: 98g 20_2_d YLK491 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:31:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 98g 20_2_d YLK491 2% glucose


title: 98E 20_2_d YLK491 1% eth

description: 98E 20_2_d YLK491 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:03:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 120 hour rep 3

description: yeast cells harvested after 120 hours

scan_protocol: as described by the manufacturer (Eukaryotic Arrays GeneChip Expression Analysis and Technical Manual, Affymetrix, Santa Clara, CA), using an Agilent G2500A GeneArray Scanner

source_name: yeast cells harvested after 120 hours


title: 86g 17_5_b YLK441 2% glu

description: 86g 17_5_b YLK441 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:11:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 92g 19_1_c YLK466 2% glu

description: 92g 19_1_c YLK466 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:48:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 85g 17_4_a YLK436 2% glu

description: 85g 17_4_a YLK436 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:37:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 95g 19_4_b YLK477 2% glucose

description: 95g 19_4_b YLK477 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:25:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 95g 19_4_b YLK477 2% glucose


title: 95E 19_4_b YLK477 1% ethanol

description: 95E 19_4_b YLK477 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:16:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 95E 19_4_b YLK477 1% ethanol


title: 96E 19_5_b YLK481 1% eth

description: 96E 19_5_b YLK481 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:07:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 90g 18_4_c YLK458 2% glu

description: 90g 18_4_c YLK458 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:13:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 87E 18_1_d YLK447 1% ethanol

description: 87E 18_1_d YLK447 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:17:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 87E 18_1_d YLK447 1% ethanol


title: 92E 19_1_c YLK466 1% ethanol

description: 92E 19_1_c YLK466 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:56:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 92E 19_1_c YLK466 1% ethanol


title: 87g 18_1_d YLK447 2% glu

description: 87g 18_1_d YLK447 2% glu


title: 93g 19_2_c YLK470 2% glucose

description: 93g 19_2_c YLK470 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:24:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 93g 19_2_c YLK470 2% glucose


title: 8g 2_3_d YLK131 2% glu

description: 8g 2_3_d YLK131 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:32:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 84E 17_2_d YLK435 1% ethanol

description: 84E 17_2_d YLK435 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 14:27:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 84E 17_2_d YLK435 1% ethanol


title: 94E 19_3_c YLK474 1% ethanol

description: 94E 19_3_c YLK474 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 11:44:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 94E 19_3_c YLK474 1% ethanol


title: 8E 2_3_d YLK131 1% eth

description: 8E 2_3_d YLK131 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 12:49:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 93E 19_2_c YLK470 1% ethanol

description: 93E 19_2_c YLK470 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:26:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 93E 19_2_c YLK470 1% ethanol


title: 86E 17_5_b YLK441 1% ethanol

description: 86E 17_5_b YLK441 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:36:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 86E 17_5_b YLK441 1% ethanol


title: 94g 19_3_c YLK474 2% glu

description: 94g 19_3_c YLK474 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:16:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BYg+RMg+BYE+RME


title: 88E 18_2_d YLK451 1% eth

description: 88E 18_2_d YLK451 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 15:27:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 88g 18_2_d YLK451 2% glucose

description: 88g 18_2_d YLK451 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:48:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 88g 18_2_d YLK451 2% glucose


title: 83E 17_1_a YLK428 1% eth

description: 83E 17_1_a YLK428 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:20:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 82E 16_1_d YLK427 1% ethanol

description: 82E 16_1_d YLK427 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:32:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 82E 16_1_d YLK427 1% ethanol


title: 84g 17_2_d YLK435 2% glucose

description: 84g 17_2_d YLK435 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:37:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 84g 17_2_d YLK435 2% glucose


title: 80g 15_5_b YLK417 2% glucose

description: 80g 15_5_b YLK417 2% glucose

source_name: 80g 15_5_b YLK417 2% glucose


title: 96g 19_5_b YLK481 2% glucose

description: 96g 19_5_b YLK481 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:44:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 96g 19_5_b YLK481 2% glucose


title: 83g 17_1_a YLK428 2% glucose

description: 83g 17_1_a YLK428 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:31:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 83g 17_1_a YLK428 2% glucose


title: 82g 16_1_d YLK427 2% glucose

description: 82g 16_1_d YLK427 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:56:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 82g 16_1_d YLK427 2% glucose


title: 85E 17_4_a YLK436 1% eth

description: 85E 17_4_a YLK436 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:52:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 7g 2_2_d YLK127 2% glu

description: 7g 2_2_d YLK127 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:53:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 74E 14_5_b YLK393 1% ethanol

description: 74E 14_5_b YLK393 1% ethanol

source_name: 74E 14_5_b YLK393 1% ethanol


title: 77E 15_2_d YLK407 1% ethanol

description: 77E 15_2_d YLK407 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:47:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 77E 15_2_d YLK407 1% ethanol


title: 71g 14_2_c YLK382 2% glu

description: 71g 14_2_c YLK382 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:11:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 79g 15_4_d YLK415 2% glu

description: 79g 15_4_d YLK415 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:21:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 68E 13_4_a YLK368 1% ethanol

description: 68E 13_4_a YLK368 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:43:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 68E 13_4_a YLK368 1% ethanol


title: 66E 13_2_c YLK362 1% eth

description: 66E 13_2_c YLK362 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:47:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 64g 12_2_b YLK353 2% glu

description: 64g 12_2_b YLK353 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:08:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 69E 13_5_c YLK374 1% ethanol

description: 69E 13_5_c YLK374 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:33:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 69E 13_5_c YLK374 1% ethanol


title: 64E 12_2_b YLK353 1% eth

description: 64E 12_2_b YLK353 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:39:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 75g 14_6_d YLK399 2% glucose

description: 75g 14_6_d YLK399 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:03:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 75g 14_6_d YLK399 2% glucose


title: 68g 13_4_a YLK368 2% glucose

description: 68g 13_4_a YLK368 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:00:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 68g 13_4_a YLK368 2% glucose


title: 67E 13_3_b YLK365 1% ethanol

description: 67E 13_3_b YLK365 1% ethanol

source_name: 67E 13_3_b YLK365 1% ethanol


title: 76g 14_7_c YLK402 2% glucose

description: 76g 14_7_c YLK402 2% glucose

source_name: 76g 14_7_c YLK402 2% glucose


title: 73g 14_4_a YLK388 2% glu

description: 73g 14_4_a YLK388 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:24:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 7E 2_2_d YLK127 1% ethanol

description: 7E 2_2_d YLK127 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:51:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 7E 2_2_d YLK127 1% ethanol


title: 65E 13_1_a YLK356 1% ethanol

description: 65E 13_1_a YLK356 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:59:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 65E 13_1_a YLK356 1% ethanol

source_name: BYg+RMg+BYE+RME


title: 67g 13_3_b YLK365 2% glucose

description: 67g 13_3_b YLK365 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:28:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 67g 13_3_b YLK365 2% glucose


title: 80E 15_5_b YLK417 1% ethanol

description: 80E 15_5_b YLK417 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:32:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 80E 15_5_b YLK417 1% ethanol


title: 63g 12_1_d YLK351 2% glucose

description: 63g 12_1_d YLK351 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:00:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 63g 12_1_d YLK351 2% glucose


title: 76E 14_7_c YLK402 1% eth

description: 76E 14_7_c YLK402 1% eth


title: 65g 13_1_a YLK356 2% glucose

description: 65g 13_1_a YLK356 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:08:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 65g 13_1_a YLK356 2% glucose


title: 75E 14_6_d YLK399 1% eth

description: 75E 14_6_d YLK399 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:45:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 77g 15_2_d YLK407 2% glucose

description: 77g 15_2_d YLK407 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 11:52:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 77g 15_2_d YLK407 2% glucose


title: 69g 13_5_c YLK374 2% glucose

description: 69g 13_5_c YLK374 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:58:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 69g 13_5_c YLK374 2% glucose


title: 78E 15_3_b YLK409 1% eth

description: 78E 15_3_b YLK409 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:21:31 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 66g 13_2_c YLK362 2% glu

description: 66g 13_2_c YLK362 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 15:03:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 74g 14_5_b YLK393 2% glu

description: 74g 14_5_b YLK393 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:29:25 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 71E 14_2_c YLK382 1% eth

description: 71E 14_2_c YLK382 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:40:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 70g 14_1_b YLK377 2% glucose

description: 70g 14_1_b YLK377 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:40:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 70g 14_1_b YLK377 2% glucose


title: 79E 15_4_d YLK415 1% eth

description: 79E 15_4_d YLK415 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:12:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 63E 12_1_d YLK351 1% ethanol

description: 63E 12_1_d YLK351 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:56:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 63E 12_1_d YLK351 1% ethanol


title: 61E 11_2_d YLK343 1% ethanol

description: 61E 11_2_d YLK343 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:42:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 61E 11_2_d YLK343 1% ethanol


title: 60g 11_1_a YLK336 2% glucose

description: 60g 11_1_a YLK336 2% glucose

source_name: 60g 11_1_a YLK336 2% glucose


title: 61g 11_2_d YLK343 2% glucose

description: 61g 11_2_d YLK343 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:40:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 61g 11_2_d YLK343 2% glucose


title: 62E 11_3_b YLK345 1% ethanol

description: 62E 11_3_b YLK345 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:45:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 62E 11_3_b YLK345 1% ethanol


title: 5E 1_5_c YLK118 1% ethanol

description: 5E 1_5_c YLK118 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:24:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 5E 1_5_c YLK118 1% ethanol


title: 59g 10_4_d YLK335 2% glucose

description: 59g 10_4_d YLK335 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:55:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 59g 10_4_d YLK335 2% glucose


title: 54g 9_6_d YLK315 2% glucose

description: 54g 9_6_d YLK315 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:51:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 54g 9_6_d YLK315 2% glucose


title: 55g 9_7_d YLK319 2% glucose

description: 55g 9_7_d YLK319 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:47:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 55g 9_7_d YLK319 2% glucose


title: 58g 10_3_c YLK330 2% glucose

description: 58g 10_3_c YLK330 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:16:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 58g 10_3_c YLK330 2% glucose

source_name: BYg+RMg+BYE+RME


title: 57g 10_2_d YLK327 2% glu

description: 57g 10_2_d YLK327 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:24:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 59E 10_4_d YLK335 1% eth

description: 59E 10_4_d YLK335 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:24:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 56g 10_1_c YLK322 2% glu

description: 56g 10_1_c YLK322 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:08:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 60E 11_1_a YLK336 1% ethanol

description: 60E 11_1_a YLK336 1% ethanol

source_name: 60E 11_1_a YLK336 1% ethanol


title: 62g 11_3_b YLK345 2% glu

description: 62g 11_3_b YLK345 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 12:57:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 56E 10_1_c YLK322 1% ethanol

description: 56E 10_1_c YLK322 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:15:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 56E 10_1_c YLK322 1% ethanol


title: 55E 9_7_d YLK319 1% eth

description: 55E 9_7_d YLK319 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:31:45 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 52E 9_4_d YLK307 1% eth

description: 52E 9_4_d YLK307 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:23:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 50g 9_2_d YLK299 2% glucose

description: 50g 9_2_d YLK299 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:06:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 50g 9_2_d YLK299 2% glucose


title: 4g 1_4_d YLK115 2% glu

description: 4g 1_4_d YLK115 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:12:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 50E 9_2_d YLK299 1% ethanol

description: 50E 9_2_d YLK299 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:50:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 50E 9_2_d YLK299 1% ethanol


title: 58E 10_3_c YLK330 1% eth

description: 58E 10_3_c YLK330 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 12:49:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 53E 9_5_d YLK311 1% ethanol

description: 53E 9_5_d YLK311 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:58:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 53E 9_5_d YLK311 1% ethanol


title: 5g 1_5_c YLK118 2% glucose

description: 5g 1_5_c YLK118 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:48:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 5g 1_5_c YLK118 2% glucose


title: 4E 1_4_d YLK115 1% eth

description: 4E 1_4_d YLK115 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:00:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 51g 9_3_d YLK303 2% glucose

description: 51g 9_3_d YLK303 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:59:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 51g 9_3_d YLK303 2% glucose


title: 49g 9_1_d YLK295 2% glucose

description: 49g 9_1_d YLK295 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:52:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 49g 9_1_d YLK295 2% glucose


title: 54E 9_6_d YLK315 1% ethanol

description: 54E 9_6_d YLK315 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:20:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 54E 9_6_d YLK315 1% ethanol


title: 53g 9_5_d YLK311 2% glu

description: 53g 9_5_d YLK311 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:00:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 51E 9_3_d YLK303 1% eth

description: 51E 9_3_d YLK303 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:36:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 49E 9_1_d YLK295 1% eth

description: 49E 9_1_d YLK295 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 15:19:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 48E 8_7_b YLK289 1% ethanol

description: 48E 8_7_b YLK289 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:01:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 48E 8_7_b YLK289 1% ethanol


title: 48g 8_7_b YLK289 2% glucose

description: 48g 8_7_b YLK289 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:32:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 48g 8_7_b YLK289 2% glucose


title: 46g 8_5_b YLK281 2% glucose

description: 46g 8_5_b YLK281 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:22:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 46g 8_5_b YLK281 2% glucose


title: 45E 8_4_c YLK278 1% ethanol

description: 45E 8_4_c YLK278 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:30:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 45E 8_4_c YLK278 1% ethanol


title: 46E 8_5_b YLK281 1% ethanol

description: 46E 8_5_b YLK281 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:21:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 46E 8_5_b YLK281 1% ethanol


title: 47E 8_6_c YLK286 1% eth

description: 47E 8_6_c YLK286 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:28:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 45g 8_4_c YLK278 2% glucose

description: 45g 8_4_c YLK278 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:23:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 45g 8_4_c YLK278 2% glucose


title: 44g 8_3_a YLK272 2% glu

description: 44g 8_3_a YLK272 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:32:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 44E 8_3_a YLK272 1% eth

description: 44E 8_3_a YLK272 1% eth


title: 47g 8_6_c YLK286 2% glucose

description: 47g 8_6_c YLK286 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:12:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 47g 8_6_c YLK286 2% glucose


title: 42g 8_1_a YLK264 2% glucose

description: 42g 8_1_a YLK264 2% glucose

source_name: BYg+RMg+BYE+RME

source_name: 42g 8_1_a YLK264 2% glucose


title: 43g 8_2_d YLK271 2% glu

description: 43g 8_2_d YLK271 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:13:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 41g 7_8_d YLK263 2% glu

description: 41g 7_8_d YLK263 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:43:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 41E 7_8_d YLK263 1% eth

description: 41E 7_8_d YLK263 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:40:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 39g 7_6_c YLK254 2% glucose

description: 39g 7_6_c YLK254 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:34:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 39g 7_6_c YLK254 2% glucose


title: 39E 7_6_c YLK254 1% ethanol

description: 39E 7_6_c YLK254 1% ethanol

source_name: 39E 7_6_c YLK254 1% ethanol


title: 3E 1_3_d YLK111 1% eth

description: 3E 1_3_d YLK111 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:48:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 40g 7_7_c YLK258 2% glu

description: 40g 7_7_c YLK258 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:16:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 3g 1_3_d YLK111 2% glu

description: 3g 1_3_d YLK111 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:07:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 37E 7_4_c YLK246 1% ethanol

description: 37E 7_4_c YLK246 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:09:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 37E 7_4_c YLK246 1% ethanol


title: 37g 7_4_c YLK246 2% glucose

description: 37g 7_4_c YLK246 2% glucose

source_name: 37g 7_4_c YLK246 2% glucose


title: 36g 7_3_d YLK243 2% glu

description: 36g 7_3_d YLK243 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 15:03:53 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 40E 7_7_c YLK258 1% ethanol

description: 40E 7_7_c YLK258 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:45:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 40E 7_7_c YLK258 1% ethanol


title: 35E 7_2_c YLK238 1% eth

description: 35E 7_2_c YLK238 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:35:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 36E 7_3_d YLK243 1% ethanol

description: 36E 7_3_d YLK243 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:42:33 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 36E 7_3_d YLK243 1% ethanol


title: 34E 7_1_d YLK235 1% ethanol

description: 34E 7_1_d YLK235 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:25:17 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 34E 7_1_d YLK235 1% ethanol


title: 38g 7_5_d YLK251 2% glu

description: 38g 7_5_d YLK251 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:27:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 32E 6_6_d YLK227 1% eth

description: 32E 6_6_d YLK227 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:47:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 38E 7_5_d YLK251 1% ethanol

description: 38E 7_5_d YLK251 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:36:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 38E 7_5_d YLK251 1% ethanol


title: 33E 6_7_d YLK231 1% ethanol

description: 33E 6_7_d YLK231 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:07:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 33E 6_7_d YLK231 1% ethanol


title: 32g 6_6_d YLK227 2% glucose

description: 32g 6_6_d YLK227 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:14:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 32g 6_6_d YLK227 2% glucose


title: 34g 7_1_d YLK235 2% glucose

description: 34g 7_1_d YLK235 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:03:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 34g 7_1_d YLK235 2% glucose


title: 35g 7_2_c YLK238 2% glucose

description: 35g 7_2_c YLK238 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:24:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 35g 7_2_c YLK238 2% glucose


title: 30E 6_4_d YLK219 1% eth

description: 30E 6_4_d YLK219 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:43:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 33g 6_7_d YLK231 2% glu

description: 33g 6_7_d YLK231 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:08:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 31E 6_5_d YLK223 1% eth

description: 31E 6_5_d YLK223 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 15:11:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 29g 6_3_c YLK214 2% glu

description: 29g 6_3_c YLK214 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 15:11:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 29E 6_3_c YLK214 1% ethanol

description: 29E 6_3_c YLK214 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 14:19:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 29E 6_3_c YLK214 1% ethanol


title: 30g 6_4_d YLK219 2% glucose

description: 30g 6_4_d YLK219 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:41:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 30g 6_4_d YLK219 2% glucose


title: Soybean-S03W4-5-RMA

city: Ste-Anne-de-Bellevue

first: Martina

last: Stromvik

state: Quebec

address: 21,111 Lakeshore Rd

department: Department of Plant Science

institute: McGill University

description: Sample 5 from the S03W4 soybean strain.  The fifth of five samples for this strain.

hyb_protocol: Target preparation, hybridization and scanning were carried out at the McGill University and Genome Quebec Innovation Centre Microarray platform using the protocol recommended by Affymetrix ().  Labelled cRNA were cleaned and fragmented using the Sample Cleanup Module reagents (Qiagen).  Spike controls B2, bio-B, bio-C, bio-D, and Cre-x were added to the hybridization cocktail before overnight hybridization at 45°C for 16 h.

scan_protocol: Arrays were washed and stained in an Affymetrix fluidics Station prior to scanning on the GeneChip Scanner 3000 (Affymetrix).  Image acquisition and processing was done with the Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: R and the BioConductor packages (Gentleman et al., 2004) such as affy, limma, cluster, and made4 were used for data analysis.  This sample was pre-processed using the RMA method.

organism: Glycine max

source_name: Soybean strain S03W4

label_protocol: 5µg of total RNA was used to generate double-stranded cDNA using a T7-linked oligo(dT) primer and SuperScript II reverse transcriptase (Invitrogen) following the instructions for the One cycle-cDNA synthesis kit (from Affymetrix).  cRNA were synthesized using the IVT labelling kit from Affymetrix, resulting in biotinylated cRNA.

growth_protocol: Grown in growth changers in ambient humidity, 16h photoperiod, and 25/19°C day/night temperatures.  10 seeds sown into two 20 cm pots.

extract_protocol: At the V2 growth stage (Fehr et al. 1971), completely unrolled first trifoliate leaves were harvested by cutting  the petiole a few millimeters below the leaflets, immediately frozen in liquid nitrogen and stored at -80°C.  RNA was extracted using the RNeasy Plant Mini Kit (Quiagen, Valencia, CA).

tag: Growth stage


title: Soybean-S03W4-4-RMA

description: Sample 4 from the S03W4 soybean strain.  The fourth of five samples for this strain.

tag: Strain


title: Soybean-S03W4-2-RMA

description: Sample 2 from the S03W4 soybean strain.  The second of five samples for this strain.


title: Soybean-S03W4-3-RMA

description: Sample 3 from the S03W4 soybean strain.  The third of five samples for this strain.


title: 28g 6_2_b YLK209 2% glucose

description: 28g 6_2_b YLK209 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:44:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 28g 6_2_b YLK209 2% glucose

source_name: BYg+RMg+BYE+RME


title: 27E 6_1_d YLK207 1% ethanol

description: 27E 6_1_d YLK207 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:12:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 27E 6_1_d YLK207 1% ethanol


title: 26E 5_5_d YLK203 1% ethanol

description: 26E 5_5_d YLK203 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 14:03:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 26E 5_5_d YLK203 1% ethanol


title: 26g 5_5_d YLK203 2% glucose

description: 26g 5_5_d YLK203 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:20:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 26g 5_5_d YLK203 2% glucose


title: 28E 6_2_b YLK209 1% eth

description: 28E 6_2_b YLK209 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:55:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 25E 5_4_d YLK199 1% eth

description: 25E 5_4_d YLK199 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:51:15 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 23g 5_2_d YLK191 2% glu

description: 23g 5_2_d YLK191 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:24:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 27g 6_1_d YLK207 2% glu

description: 27g 6_1_d YLK207 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:28:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 24g 5_3_d YLK195 2% glucose

description: 24g 5_3_d YLK195 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:01:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 24g 5_3_d YLK195 2% glucose


title: Soybean-S03W4-1-RMA

description: Sample 1 from the S03W4 soybean strain.  The first of five samples for this strain.


title: 22g 5_1_d YLK187 2% glu

description: 22g 5_1_d YLK187 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:44:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 22E 5_1_d YLK187 1% ethanol

description: 22E 5_1_d YLK187 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:07:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 22E 5_1_d YLK187 1% ethanol


title: Soybean-Mandarin-3-RMA

description: Sample 3 from the Mandarin soybean strain.  The second of five samples for this strain.

source_name: Soybean strain Mandarin

value: Mandarin (Ottawa)


title: Soybean-Mandarin-4-RMA

description: Sample 4 from the Mandarin soybean strain.  The third of five samples for this strain.


title: Soybean-PS46R-1-RMA

description: Sample 1 from the PS46R soybean strain.  The first of five samples for this strain.

source_name: Soybean strain PS46R


title: Soybean-PS46R-2-RMA

description: Sample 2 from the PS46R soybean strain.  The second of five samples for this strain.


title: Soybean-Mandarin-6-RMA

description: Sample 6 from the Mandarin soybean strain.  The fourth of five samples for this strain.


title: Soybean-PS46R-4-RMA

description: Sample 4 from the PS46R soybean strain.  The fourth of five samples for this strain.

extract_protocol: At the V2 growth stage (Fehr et al. 1971), completely unrolled first trifoliate leaves were harvested by cutting  the petiole a few millimeters below the leaflets, immediately frozen in liquid nitrogen and stored at -80°C.  RNA was extracted using RNeasy Plant Mini Kit (Quiagen, Valencia, CA).


title: Soybean-PS46R-3-RMA

description: Sample 3 from the PS46R soybean strain.  The third of five samples for this strain.


title: Soybean-Mandarin-7-RMA

description: Sample 7 from the Mandarin soybean strain.  The fifth of five samples for this strain.


title: 21E 4_4_d YLK183 1% eth

description: 21E 4_4_d YLK183 1% eth


title: Soybean-PS46R-5-RMA

description: Sample 5 from the PS46R soybean strain.  The fifth of five samples for this strain.


title: Soybean-Mandarin-1-RMA

description: Sample 1 from the Mandarin soybean strain.  The first of five samples for this strain.


title: Soybean-Bayfield-5-RMA

description: Sample 5 from the Bayfield soybean strain.  The fifth of five samples for this strain.

source_name: Soybean strain Bayfield

value: Bayfield


title: 20E 4_3_d YLK179 1% eth

description: 20E 4_3_d YLK179 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 11:23:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 25g 5_4_d YLK199 2% glucose

description: 25g 5_4_d YLK199 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 11:52:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 25g 5_4_d YLK199 2% glucose


title: RM9g RM11-1a 0 2% glu

description: RM9g RM11-1a 0 2% glu

source_name: RM9g RM11-1a 0 2% glu


title: 20g 4_3_d YLK179 2% glucose

description: 20g 4_3_d YLK179 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:15:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 20g 4_3_d YLK179 2% glucose


title: 18g 4_1_c YLK170 2% glu

description: 18g 4_1_c YLK170 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:00:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 18E 4_1_c YLK170 1% eth

description: 18E 4_1_c YLK170 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:32:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 1E 1_1_d YLK103 1% ethanol

description: 1E 1_1_d YLK103 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:16:24 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 1E 1_1_d YLK103 1% ethanol


title: Soybean-Bayfield-4-RMA

description: Sample 4 from the Bayfield soybean strain.  The fourth of five samples for this strain.

scan_protocol: Arrays were washed and stained in an Affymetrix fluidics Station prior to scanning on the GeneChip Scanner 3000 (Affymetrix).  Image acquisition and processing was done with the Microarray Analysis Suite 5.0 (Affymetrix).


title: 17g 3_5_d YLK167 2% glucose

description: 17g 3_5_d YLK167 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:36:50 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 17g 3_5_d YLK167 2% glucose


title: Soybean-Bayfield-3-RMA

description: Sample 3 from the Bayfield soybean strain.  The third of five samples for this strain.


title: 16E 3_4_d YLK163 1% eth

description: 16E 3_4_d YLK163 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:53:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Soybean-2601R-5-RMA

description: Sample 5 from the 2601R soybean strain.  The fourth of five samples for this strain.

source_name: Soybean strain 2601R


title: RM7g RM11-1a 0 2% glucose

description: RM7g RM11-1a 0 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:56:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM7g RM11-1a 0 2% glucose


title: 13E 3_1_d YLK151 1% ethanol

description: 13E 3_1_d YLK151 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 14:03:58 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 13E 3_1_d YLK151 1% ethanol


title: 17E 3_5_d YLK167 1% ethanol

description: 17E 3_5_d YLK167 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:55:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 17E 3_5_d YLK167 1% ethanol

source_name: BYg+RMg+BYE+RME


title: Soybean-2601R-4-RMA

description: Sample 4 from the 2601R soybean strain.  The third of five samples for this strain.

tag: Growth Stage


title: RM11g RM11-1a 0 2% glucose

description: RM11g RM11-1a 0 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:28:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: RM11g RM11-1a 0 2% glucose


title: 12E 2_7_a YLK144 1% ethanol

description: 12E 2_7_a YLK144 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:24:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 12E 2_7_a YLK144 1% ethanol


title: 1g 1_1_d YLK103 2% glu

description: 1g 1_1_d YLK103 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 15:11:47 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 13g 3_1_d YLK151 2% glucose

description: 13g 3_1_d YLK151 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:32:13 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 13g 3_1_d YLK151 2% glucose


title: 11g 2_6_d YLK143 2% glu

description: 11g 2_6_d YLK143 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:37:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 11E 2_6_d YLK143 1% eth

description: 11E 2_6_d YLK143 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:36:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1