title: Liver_phenobarbital_pool3

status: Public on Nov 27 2007

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: No additional data.

hyb_protocol: Sterolgene slides were washed before hybridization at room temperature 5 min in 2xSSC and 0.1%SDS, 3 min in 0.2xSSC and 2 min in MilliQ water and dried by centrifugation. Samples were denatured and hybridized in 3xSSC and 0.2% SDS hybridization buffer at 65˚C for 16 hours using humidified hybridization chambers (HybChambers, GeneMachines). After hybridizations slides were washed at room temperature for 5 min in 2xSSC and 0.5% SDS, followed by 5 min in 0.5xSSC, then 5 min in 0.05xSSC and dried by centrifugation.

scan_protocol: Slides were scanned using Tecan LS200 scanner. Images were analyzed using Array-Pro Analyzer 4.5 (Media Cybernetics). The median feature and local background intensities were extracted together with the estimates of their standard deviation.

data_processing: Features were filtered out according to the following criteria: coefficient of variation (CV, ratio between standard deviation of the background and the median feature intensity) above 0.5 and foreground to background ratio above 1.5. Saturated features were removed. Log2 ratios were normalized using LOESS fit to spike in control RNAs according to their average intensity. Two types of spike in controls were used: custom-made (Firefly luciferase) and commercial ArrayControl Spikes (Ambion). Filtration and normalization was done in Orange software. Normalized log ratios can be compared across samples.

source_name: liver, phenobarbital treated

label_protocol: 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol. Before labeling spike in RNAs were added to the total RNA in following quantities: 500 pg of Firefly luciferase mRNA (Promega) and sample mix (from 100 pg to 1500  pg of each RNA) prepared from ArrayControl Spikes (Ambion).

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were maintained in 12-hour light/12-hour dark cycle.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.

treatment_protocol: Animals were injected i.p. 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). After 10h they were sacrificed.

tag: Strain

value: male

value: 9 - 12 weeks

tag: Tissue

value: liver

tag: Treatment

value: 50 mg/kg of phenobarbital

source_name: liver, referenceV0

label_protocol: 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol. Before labeling spike in RNAs were added to the total RNA in following quantities: 500 pg of Firefly luciferase mRNA (Promega) and reference mix (500  pg of each RNA) prepared from ArrayControl Spikes (Ambion).

growth_protocol: Animals had free acess to food (standard laboratory chow diet) and water.

extract_protocol: Total RNA was isolated using TRI-reagent (Sigma) and purified by RNeasy Mini Kit (Qiagen) according to the manufacturers protocols. Total RNA from three males and three females was pooled.

treatment_protocol: No treatment.

value: male and female

value: 12 weeks

tag: RNA

value: pool of 3 males and 3 females


title: Liver_control_pool2

type: RNA

description: No additional data.

molecule: total RNA

organism: Mus musculus

source_name: liver, untreated

treatment_protocol: Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.

tag: Gender

tag: Age

value: vehicle only (5% DMSO in corn oil)


title: Liver_phenobarbital_pool1

description: No additional data.


title: Liver_cholesterol_pool1

description: No additional data.

source_name: liver, high cholesterol diet

growth_protocol: Animals had free acess to food (standard laboratory chow) and drinking water. They were maintained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1 % (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).

tag: Diet

value: 1 week 1% cholesterol diet


title: Liver_cholesterol_pool2

description: No additional data.


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 24 h post inoculation	5

status: Public on Nov 29 2007

city: Mountain Grove

first: Wenping

last: Qiu

state: MO

address: 9740 Red Spring Road

department: Agriculture

country: USA

institute: Missouri State University

description: Gene expression data from V. vinifera 'Cabernet Sauvignon' at 0 hour post inoculation of E. necator conidiospores

hyb_protocol: cRNA was cleaned up by the Affymetrix sample cleanup module which in included in the One-Cycle Target Labeling kit. Fifteen ug of cRNA at concentration of 1.301ug/ul were used for hybridization. Prior to hybridization, cRNA was heated at 94ºC for 35 min, and was fragmented to 35 to 200 nucleotides.  After adding hybridization buffer to the fragmented samples, hybridization cocktails were boiled for 5 min, incubated for 5 min at 45ºC, then centrifuged for 5 minutes prior to loading per standard one-cycle protocol. Hybridization took place in an Affy hybridization oven model 640, for 16h at 45ºC. All washing took place on the fluidics station (as per the recommended fluidics protocol) with non-stringent wash buffer (6X SSPE and 0.01% Tween-20) and Stringent wash buffer (100mM MES, 0.1M NaCl, 0.01% Tween-20). Fluorescence was amplified by first adding streptavidin-phycoerythrin (SAPE) stain, then adding a biotinylated antibody (anti-streptavidin) solution, followed by another SAPE staining (as per standard one-cycle protocol). The fluidics protocol Midi_Euk2v3 was used (as per V. vinifera microarray package insert) on fluidics station model 450.

scan_protocol: Affymetrix Scanner 3000 7G was used to collect at resolution of 1.56um with emission filter at a wavelength of 570nm and excitation wavelength of 532nm.

data_processing: Raw intensity data were processed using the GeneChip Operating Software Version 1.2 (GCOS 1.2; Affymetrix, 2001). Background correction and expression value calculation were performed as described by Affymetrix (2002). Normalization was done by global scaling, with a target intensity value of 150 (Affymetrix, 2001). Probe sets with missing values were deleted across all replicates and species to allow comparisons among datasets

label: biotin

organism: Vitis vinifera

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 24 hour after inoculation with E. necator conidiospores

label_protocol: The cDNA synthesis and antisense cRNA amplification/biotin labeling was performed using the One-Cycle Target Labeling Kit (Catalog number: 900493, Affymetrix, Santa Clara, California)

growth_protocol: 14 hours day/10 hours night. Light intensity: 500 umol m-2.  Light source: high pressure sodium and metal halide. Temperature: 25°C.  Relative humidity: 85%.

extract_protocol: Total RNA was extracted from each replicate sample individually. The leaves were ground in liquid nitrogen and homogenized in extraction buffer (2% Hexadecyltrimethyl Ammonium Bromide 1%  sodium dodecyl sulfate, 2.5M NaCl, 0.5M Tris, 50mM EDTA, 5% beta-mercaptoethanol, and 3% polyvinyl poly-pyrrolidone. Following a 30-min incubation at -80°C, the samples were thawed and centrifuged. The supernatant was supplemented with 1/30 volume of 3 M sodium acetate (pH5.2) and 1/10 volume of ethanol, incubated on ice and centrifuged three times at 7000g, 30 min 4 ºC, each time transferring the supernatant into a clean tube. The supernatant was supplemented with 1/9 volume of 3 M sodium acetate (pH5.2) and iso-propanol to a final concentration of 33%. Following 60-min incubation at -20°C, the RNA was collected by centrifugation at 12,000g, 30 min, 4 ºC. The RNA was then supplemented with 1/3 volume of 8 M LiCl and incubated overnight at 4 °C. RNA was then collected by centrifugation at 12,000g, 30 min, 4 ºC, washed with 75% ethanol, and resuspended in 40 ul DEPC water.  Ten micrograms of total RNA were treated with Turbo DNase I (Ambion) and purified with RNA purification kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: third or forth leaves were inocualted with E. necator conidiospores by touching 10 day-old powdery mildew colonies directly onto the target leaves

tag: Fully-expanded leaves at the third or fourth position from the top of each shoot were used for treatment


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 0 h post inoculation	1

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 0 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 8 h post inoculation	3

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 8 hour after inoculation with E. necator conidiospores


title: Liver_phenobarbital_pool2

description: No additional data.


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation	4

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 12 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 4 h post inoculation	2

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 4 hour after inoculation with E. necator conidiospores


title: Liver_control_pool1

description: No additional data.


title: Liver_TNFalpha_mouse3

description: No additional data.

source_name: liver, TNFalpha treated

label_protocol: 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol. Before labeling spike in RNAs were added to the total RNA in following quantities: 500 pg of Firefly luciferase mRNA (Promega) and sample mix (from 100 to 1500 pg of each RNA) prepared from ArrayControl Spikes (Ambion).

growth_protocol: Animals had free acess to food (standard laboratory chow diet) and drinking water. After treatment food was withdrawn.

extract_protocol: Total RNA was extracted using TRI-reagent (Sigma) according to the manufacturer's instructions and subjected to RNeasy Cleanup (Qiagen).

treatment_protocol: Animals were i.v. injected human recombinant TNFalpha (30 micrograms per animal) and food was withdrawn. After 20h animals were sacrified.

value: TNFalpha

value: fasting after treatment

source_name: liver, nontreated pool

label_protocol: 10 μg of total RNA was used for labeling using Agilent Fluorescent Direct Label Kit (Agilent) according to manufacturer protocol. Before labeling spike in RNAs were added to the total RNA in following quantities: 500 pg of Firefly luciferase mRNA (Promega) and refernce mix (500 pg of each RNA) prepared from ArrayControl Spikes (Ambion).

treatment_protocol: Animals were i.v. injected vehicle (saline). After 20h animals were sacrified.


title: Liver_fasted_mouse2

description: No additional data.

source_name: liver, fasted

treatment_protocol: Animals were i.v. injected vehicle (saline) and food was withdrawn. After 20h animals were sacrified.

value: 20h fasting prior sacrifice

growth_protocol: Animals had free acess to food (standard laboratory chow diet) and drinking water.


title: Liver_TNFalpha_mouse1

description: No additional data.


title: Liver_fasted_mouse3

description: No additional data.


title: Liver_TNFalpha_mouse2

description: No additional data.


title: Liver_fasted_mouse1

description: No additional data.


title: 68932

status: Public on Nov 01 2007

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

description: half scan-top D1= Day 1 -ae= lon- E. coli strain, growth in aerobic conditions Third replicate in this group (12 refers to the sample number overall out of the 24 analyzed)

hyb_protocol: Buffer (30 mM sodium citrate, 300 mM sodium chloride, 50% formamide, 0.4% SDS, pH 7.0) was held at 42 deg. C. Twelve ul was added to each sample along with 3 ul of 1:1 salmon sperm/tRNA blocker, heated for 2 min at 98 deg. C, centrifuged for 3 min at 14,000 x g, and then  20 ul was transferred into a microarray hybridization chamber (MAUI Mixer, Biomicro Systems).  After overnight hybridization at  45 deg. C, slides were inserted into a jig and submerged in Buffer A, comprised of 1X SSC and 0.05% SDS. The adhesive MAUI Mixer lid was removed and the slide placed in a rack in a jar containing fresh Buffer A. Once all slides were in the rack, they were agitated for 1 min, transferred to fresh Buffer A, agitated 2 min, transferred to Buffer B (0.1X SSC) for 2 min and then into fresh Buffer B. Slides were  centrifuged for 5 min starting at 220 rpm and increasing to 580 in increments of approximately 100 rpm. Once dry, the slides were removed from the centrifuge and scanned on a GenePix4000B Scanner (Axon Instruments/Molecular Devices).

scan_protocol: Image analysis was performed using GenePix Pro software (version 5.1, Axon Instruments/Molecular Devices). Relative mRNA expression levels measured by each probe spot were estimated by using median pixel intensity minus the mean background intensity. Arrays were normalized using the median spot intensity in each channel as a scaling factor. Log (base 2) transformation was applied to the Cy5/Cy3 ratios before further analysis. Correlation and hierarchical clustering calculations were performed using JMP statistical analysis software (version 5.1, SAS).

data_processing:
Feature pixel median minus background pixel mean;
ratio set to missing where SNR (feature mean - backround mean /  background SD) less than 2 in both channels ;
normalization subtracting array-median log2 ratio.

organism: Escherichia coli

source_name: Reference Pool

label_protocol:
Bacterial RNA was labeled following the protocol of the Microarray Research Facility at
the National Institute of Allergy and Infectious Diseases, except that no RNase inhibitor
was added.  Briefly, for each sample, 2.5 ug of RNA were reverse-transcribed/labeled
with Cy3, and 2.5 ug were reverse-transcribed/labeled with Cy5. Dyes were obtained
from Amersham Biosciences; all other reagents were from Invitrogen.  Cy3- and Cy5-
labeled samples were mixed and then concentrated in a Vivaspin 500 centrifigal
concentrator (10,000 MW cut-off; Vivascience). 400 ul TE buffer was added (10 mM
Tris, 1 mM EDTA, pH 8.0), and the samples were then centrifuged for 8 min at 12,000 x
g. The flow-through was discarded and 400 ul fresh TE was added to each tube and
mixed by pipette. These spinning and washing steps were repeated 3 more times, the
sample transferred to a new Vivaspin 500, washed with TE buffer, and centrifuged twice
more. The flow-through was again discarded, and sample was transferred to a fresh tube
and its volume adjusted to 9 ul by adding TE or by vacuum centrifugation, as appropriate.
Samples were then held on ice.

extract_protocol:
Cells were harvested on days 1 and 3 of glucose starvation, with samples taken from the
same cultures used for the viability assay. For each experimental condition, 15 aliquots of
1.8 ml (ca. 3E+9 cells) were pipetted into 2.0 ml tubes and immediately centrifuged at
16,000 g for 40 s at room temperature.  The supernatant was discarded, and cell pellets
were immediately frozen in liquid nitrogen and stored at -80 deg. C.  For RNA isolation,
triplicate samples were prepared by combining cells from 5 tubes each.  Each pellet was
re-suspended in 200 ul Trizol and combined for a total volume of 1 ml, then promptly
chilled in a dry ice/ethanol. bath.  After homogenization with glass beads,. RNA was
isolated by chloroform extraction and precipitation by isopropanol. Precipitated RNA
was washed with 70 percent ethanol, resuspended in 30 ul water, and held at 4 deg. C for
further processing

tag: pool of aliquots from all samples

tag: day

value: . strain:. oxygen:.


title: 68931

institute: National Institute of Allergy and Infectious Diseases

description: half scan-bottom D3= Day 3 +AN= lon+ E. coli strain, growth in anaerobic conditions Second replicate in this group (14 refers to the sample number overall out of the 24 analyzed)


title: 68933

description: half scan-bottom D3= Day 3 +AN= lon+ E. coli strain, growth in anaerobic conditions First replicate in this group (13 refers to the sample number overall out of the 24 analyzed)


title: 68930

description: half scan-top D1= Day 1 -ae= lon- E. coli strain, growth in aerobic conditions Second replicate in this group (11 refers to the sample number overall out of the 24 analyzed)


title: 68929

description: half scan-bottom D3= Day 3 +AN= lon+ E. coli strain, growth in anaerobic conditions Third replicate in this group (15 refers to the sample number overall out of the 24 analyzed)


title: 68927

description: half scan-bottom D3= Day 3 -AN= lon- E. coli strain, growth in anaerobic conditions First replicate in this group (16 refers to the sample number overall out of the 24 analyzed)


title: 68928

description: half scan-top D1= Day 1 -ae= lon- E. coli strain, growth in aerobic conditions First replicate in this group (10 refers to the sample number overall out of the 24 analyzed)


title: 68917

description: half scan-top D1= Day 1 -AN= lon- E. coli strain, growth in anaerobic conditions Second replicate in this group (5 refers to the sample number overall out of the 24 analyzed)


title: 68926

description: half scan-bottom D1= Day 1 +ae= lon+ E. coli strain, growth in aerobic conditions Third replicate in this group (9 refers to the sample number overall out of the 24 analyzed)


title: 68924

description: half scan-top D1= Day 1 +ae= lon+ E. coli strain, growth in aerobic conditions Third replicate in this group (8 refers to the sample number overall out of the 24 analyzed)


title: 68925

description: half scan-bottom D3= Day 3 -AN= lon- E. coli strain, growth in anaerobic conditions Second replicate in this group (17 refers to the sample number overall out of the 24 analyzed)


title: 68923

description: half scan-bottom D3= Day 3 -AN= lon- E. coli strain, growth in anaerobic conditions Third replicate in this group (18 refers to the sample number overall out of the 24 analyzed)


title: 68922

description: half scan-top D1= Day 1 +ae= lon+ E. coli strain, growth in aerobic conditions Third replicate in this group (7 refers to the sample number overall out of the 24 analyzed)


title: 68916

description: half scan-bottom D3= Day 3 +ae= lon- E. coli strain, growth in aerobic conditions Third replicate in this group (21 refers to the sample number overall out of the 24 analyzed)


title: 68912

description: half scan-top D1= Day 1 +AN= lon+ E. coli strain, growth in anaerobic conditions Third replicate in this group (3 refers to the sample number overall out of the 24 analyzed)


title: 68921

description: half scan-bottom D3= Day 3 +ae= lon+ E. coli strain, growth in aerobic conditions Third replicate in this group (19 refers to the sample number overall out of the 24 analyzed)


title: 68913

description: half scan-bottom D3= Day 3 -ae= lon- E. coli strain, growth in aerobic conditions First replicate in this group (22 refers to the sample number overall out of the 24 analyzed)


title: 68919

description: half scan-bottom D3= Day 3 +ae= lon+ E. coli strain, growth in aerobic conditions Second replicate in this group (20 refers to the sample number overall out of the 24 analyzed)


title: 68920

description: half scan-top D1= Day 1 -AN= lon- E. coli strain, growth in anaerobic conditions Third replicate in this group (6 refers to the sample number overall out of the 24 analyzed)


title: 68915

description: half scan-top D1= Day 1 -AN= lon- E. coli strain, growth in anaerobic conditions First replicate in this group (4 refers to the sample number overall out of the 24 analyzed)


title: 68911

description: half scan-top D3= Day 3 -ae= lon- E. coli strain, growth in aerobic conditions Second replicate in this group (23 refers to the sample number overall out of the 24 analyzed)


title: 10%Tryptone_Medium _Stationary_rep1_#10729

status: Public on Sep 01 2007

city: Saint Louis

first: Herbert

last: Chiang

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

description: Bacteroides thetaiotaomicron (BT2923::pGERM) harvested from growth in 10% tryptone medium at stationary phase.

hyb_protocol: According to Affymetrix's protocol.

scan_protocol: According to Affymetrix's protocol.

data_processing: MAS5; scaling = 500

organism: Bacteroides thetaiotaomicron

source_name: Bacteroides thetaiotaomicron (BT2923::pGERM), growth in 10% tryptone medium, Stationary phase

label_protocol: According to Affymetrix's protocol.

tag: Bacteroides thetaiotaomicron (BT2923::pGERM), stationary phase


title: S. pombe ployg mutant R5

status: Public on Sep 28 2007

city: Singapore

first: Zhaoqing

last: Chu

address: 60, Biopolis Streat

country: Singapore

institute: Genome Institute of Singapore

description: Schizosaccharomyces pombe ployg mutant cells growing in YES medium at 30 degree centigrade vs Schizosaccharomyces pombe asynchronized mid log phase WT cells (OD600 was around 0.3).

data_processing: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer’s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy5-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.  Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).  Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.

growth_protocol: Yeast cells were cultured at 30 degree centigrade.

extract_protocol: Total RNA of tissue samples were extracted using hot phenol methold describled in materials and metholds.

tag: Schizosaccharomyces pombe ployg mutant cells growing in YES medium to mid log phase.

source_name: Fission yeast wildtype cells.

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer’s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy3-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.  Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).  Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade.


title: 10%Tryptone_Medium _Stationary_rep2_#10730


title: 68909

description: half scan-bottom D3= Day 3 -ae= lon- E. coli strain, growth in aerobic conditions Third replicate in this group (24 refers to the sample number overall out of the 24 analyzed)


title: 10%Tryptone_Medium _Stationary_rep2_#10726

description: Wild type Bacteroides thetaiotaomicron harvested from growth in 10% tryptone medium at stationary phase.

source_name: wt Bacteroides thetaiotaomicron, growth in 10% tryptone medium, Stationary phase

tag: wild type Bacteroides thetaiotaomicron, stationary phase


title: 68910

description: half scan-top D1= Day 1 +AN= lon+ E. coli strain, growth in anaerobic conditions Second replicate in this group (2 refers to the sample number overall out of the 24 analyzed)


title: Liver_control_pool3

description: No additional data.


title: 10%Tryptone_Medium _Mid_log_rep2_#10724

description: Wild type Bacteroides thetaiotaomicron harvested from growth in 10% tryptone medium at mid-log phase.

source_name: wt Bacteroides thetaiotaomicron, growth in 10% tryptone medium, Mid-log phase

tag: wild type Bacteroides thetaiotaomicron, mid-log phase


title: NMRIcecum_Stdchow_10d_rep3_#8771

description: Bacteroides thetaiotaomicron (BT2923::pGERM) monoassociated in gnotobiotic NMRI mice on a standard polysaccharide-rich diet, harvested from the cecum after 10 days.

source_name: Bacteroides thetaiotaomicron (BT2923::pGERM), monoassociation, cecum NMRI mice, 10days


title: 10%Tryptone_Medium _Stationary_rep1_#10725


title: 10%Tryptone_Medium _Mid_log_rep1_#10723


title: S. pombe ployg mutant R2

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.


title: 10%Tryptone_Medium _Mid_log_rep1_#10727

description: Bacteroides thetaiotaomicron (BT2923::pGERM) harvested from growth in 10% tryptone medium at mid-log phase.

source_name: Bacteroides thetaiotaomicron (BT2923::pGERM), growth in 10% tryptone medium, Mid-log phase

tag: Bacteroides thetaiotaomicron (BT2923::pGERM), mid-log phase


title: 68908

description: half scan-top D1=Day 1 +AN= lon+ strain of E.coli in anaerobic growth conditions First replicate of this group


title: S. pombe ployg mutant R1


title: NMRIcecum_Stdchow_10d_rep2_#8770

tag: Bacteroides thetaiotaomicron (BT2923::pGERM), monoassociation, cecum NMRI mice, 10days


title: B6cecum_Stdchow_10d_rep8_#7665

description: Bacteroides thetaiotaomicron (BT2923::pGERM) monoassociated in gnotobiotic B6 mice on a standard polysaccharide-rich diet, harvested from the cecum after 10 days.

source_name: Bacteroides thetaiotaomicron (BT2923::pGERM), monoassociation, cecum B6 mice, 10days


title: B6cecum_Stdchow_10d_rep4_#9586

tag: Bacteroides thetaiotaomicron (BT2923::pGERM), monoassociation, cecum B6 mice, 10days


title: B6cecum_Stdchow_10d_rep7_#7664


title: NMRIcecum_Stdchow_10d_rep1_#8769


title: B6cecum_Stdchow_10d_rep5_#8765


title: B6cecum_Stdchow_10d_rep6_#7663


title: B6cecum_Stdchow_10d_rep3_#8764


title: S. pombe ployg mutant R4


title: 10%Tryptone_Medium _Mid_log_rep2_#10728


title: B6cecum_Stdchow_10d_rep1_#9585


title: NMRIcecum_Stdchow_10d_rep1_#8766

description: Bacteroides thetaiotaomicron monoassociated in gnotobiotic NMRI mice on a standard polysaccharide-rich diet, harvested from the cecum after 10 days.

source_name: Bacteroides thetaiotaomicron, monoassociation, cecum NMRI mice, 10days


title: B6cecum_Stdchow_10d_rep2_#8763


title: NMRIcecum_Stdchow_10d_rep2_#8767

tag: Bacteroides thetaiotaomicron, monoassociation, cecum NMRI mice, 10days


title: NMRIcecum_Stdchow_10d_rep3_#8768


title: B6cecum_Stdchow_10d_rep9_#9401

description: Bacteroides thetaiotaomicron monoassociated in gnotobiotic B6 mice on a standard polysaccharide-rich diet, harvested from the cecum after 10 days.

source_name: Bacteroides thetaiotaomicron, monoassociation, cecum B6 mice, 10days


title: B6cecum_Stdchow_10d_rep10_#9402

tag: Bacteroides thetaiotaomicron, monoassociation, cecum B6 mice, 10days


title: B6cecum_Stdchow_10d_rep5_#9584


title: B6cecum_Stdchow_10d_rep6_#9398


title: B6cecum_Stdchow_10d_rep8_#9400


title: B6cecum_Stdchow_10d_rep7_#9399


title: NMRIcecum_Stdchow_10d_rep3_#5952


title: B6cecum_Stdchow_10d_rep2_#9583


title: NMRIcecum_Stdchow_10d_rep4_#5953


title: NMRIcecum_Stdchow_10d_rep2_#5951


title: NMRIcecum_Stdchow_10d_rep5_#5954


title: B6cecum_Stdchow_10d_rep3_#8761


title: NMRIcecum_Stdchow_10d_rep6_#5955


title: S. pombe ployg mutant R3


title: NMRIcecum_Stdchow_10d_rep1_#5950


title: TYG_Medium _8.8h_rep1_#5309

description: Wild type Bacteroides thetaiotaomicron harvested from batch fermentor growth in rich tryptone/yeast extract/glucose (TYG) medium at 8.8 hours.

source_name: wt Bacteroides thetaiotaomicron, chemostat growth, 8.8 h

tag: wild type Bacteroides thetaiotaomicron, chemostat, 8.8h


title: B6cecum_Stdchow_10d_rep1_#8760


title: TYG_Medium _6.5h_rep1_#5307

description: Wild type Bacteroides thetaiotaomicron harvested from batch fermentor growth in rich tryptone/yeast extract/glucose (TYG) medium at 6.5 hours.

source_name: wt Bacteroides thetaiotaomicron, chemostat growth, 6.5 h

tag: wild type Bacteroides thetaiotaomicron, chemostat, 6.5h


title: B6cecum_Stdchow_10d_rep4_#8762


title: TYG_Medium _8.8h_rep2_#5310


title: TYG_Medium _3.5h_rep2_#5278

description: Wild type Bacteroides thetaiotaomicron harvested from batch fermentor growth in rich tryptone/yeast extract/glucose (TYG) medium at 3.5 hours.

source_name: wt Bacteroides thetaiotaomicron, chemostat growth, 3.5 h

tag: wild type Bacteroides thetaiotaomicron, chemostat, 3.5h


title: TYG_Medium _4.5h_rep2_#5304

description: Wild type Bacteroides thetaiotaomicron harvested from batch fermentor growth in rich tryptone/yeast extract/glucose (TYG) medium at 4.5 hours.

source_name: wt Bacteroides thetaiotaomicron, chemostat growth, 4.5 h

tag: wild type Bacteroides thetaiotaomicron, chemostat, 4.5h


title: TYG_Medium _4.5h_rep1_#5303


title: TYG_Medium _5.5h_rep1_#5305

description: Wild type Bacteroides thetaiotaomicron harvested from batch fermentor growth in rich tryptone/yeast extract/glucose (TYG) medium at 5.5 hours.

source_name: wt Bacteroides thetaiotaomicron, chemostat growth, 5.5 h

tag: wild type Bacteroides thetaiotaomicron, chemostat, 5.5h


title: TYG_Medium _5.5h_rep2_#5306


title: TYG_Medium _6.5h_rep2_#5308


title: TYG_Medium _3.5h_rep1_#5277


title: rad001 12h, biological rep5

status: Public on Jul 01 2007

city: boston

first: qing

last: xu

state: MA

address: 44 binney st

department: Medical Oncology

institute: dana farber cancer institute

description: Gene expression data from ventral prostate of wild type FVB mice and FVB-AKT1 mice treated with placebo or rad001 for 12h, 2d, 6d, 9d, and 15d

hyb_protocol: standard procedure carried out at Broad Institute

data_processing: CEL files were normalized with dChip, then expression values were computed and merged and normalized again with dChip.

source_name: ventral prostate of transgenic FVB mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard mouse diet

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

treatment_protocol: rad001 for 12h

tag: Genotype

value: transgenic

tag: Age

value: 8-10 weeks


title: rad001 15d, biological rep3

scan_protocol: standard procedure carried out at Broad Institute

treatment_protocol: rad001 for 15d


title: rad001 12h, biological rep4


title: rad001 15d, biological rep2


title: rad001 15d, biological rep4


title: rad001 48h, biological rep1

treatment_protocol: rad001 for 48h


title: rad001 48h, biological rep2


title: rad001 15d, biological rep6


title: placebo 15d, biological rep9

treatment_protocol: placebo for 15d


title: rad001 48h, biological rep5


title: placebo 15d, biological rep10


title: rad001 15d, biological rep1


title: placebo 15d, biological rep8


title: rad001 12h, biological rep3


title: rad001 48h, biological rep4


title: rad001 12h, biological rep1


title: placebo 15d, biological rep4


title: placebo 15d, biological rep1


title: placebo 48h, biological rep5

treatment_protocol: placebo for 48h


title: rad001 15d, biological rep7


title: placebo 15d, biological rep2


title: rad001 12h, biological rep2


title: placebo 15d, biological rep6


title: placebo 48h, biological rep2


title: placebo 48h, biological rep3


title: placebo 48h, biological rep4


title: placebo 48h, biological rep1


title: placebo 12h, biological rep4

treatment_protocol: placebo for 12h


title: placebo 12h, biological rep3


title: wild type placebo 15d, biological rep2

source_name: ventral prostate of wild type FVB mice

treatment_protocol: placebo for d15

value: wild type


title: wild type placebo 15d, biological rep1


title: wild type placebo 48h, biological rep4


title: placebo 12h, biological rep2


title: placebo 12h, biological rep1


title: wild type placebo 12h, biological rep2


title: wild type placebo 48h, biological rep1


title: wild type placebo 15d, biological rep3


title: wild type placebo 48h, biological rep2


title: wild type placebo 12h, biological rep1


title: wild type placebo 12h, biological rep4


title: wild type placebo 48h, biological rep3


title: metanephric mesenchyme, ANX, 5 days, biological rep1

city: Berlin

first: Kai

middle: Martin

last: Schmidt-Ott

address: Robert-Roessle-Str. 10

department: Differentiation and Regeneration of Kidney Epithelia

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

description: Gene expression data from rat metanephric mesenchymes cultured for 5 days in the presence of the ANX fraction

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with robust multichip analysis (RMA) using the Affymetrix microarray *.cel image file and GeneTraffic(R) (Silicon Genetics) software

organism: Rattus norvegicus

source_name: rat E13.5 embryo, metanephric mesenchyme

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 microg total RNA (One-Cycle cDNA Synthesis Kit Technical Manual, 2003, Affymetrix).

growth_protocol: freshly dissected metanephric mesenchymes were either directly subjected to RNA isolation or grown on transwell filters (Corning, Collagen coated, pore size 0.4 microm) in DMEM/F12 with insulin (5 microg/ml), transferrin (5 microg/ml), selenium (5 ng/ml), dexamethasone (5 microg/ml), prostaglandin (5 microg/ml), T3 (5 microg/ml) (Sigma), recombinant FGF (50 ng/ml), recombinant TGF? (20 ng/ml) with or without any one of three inducers (LIF, NGAL, ANX) and harvested for extraction of total RNA after the indicated time period

extract_protocol: extraction of total RNA using Rneasy mini kit (Qiagen) was performed according to the manufacturer's instructions with on-column DNase digestion.

treatment_protocol: metanephric kidneys were microdissected on day 13.5, metanephric mesenchymes were separated from the ureteric bud using minutien pins following digestion in the presence of trypsin (1 mg/ml) and Dnase (100 U/ml) at 37 deg Celsius for 5 min

tag: Timepoint

tag: Inducer

value: ANX


title: metanephric mesenchyme, ANX, 5 days, biological rep2


title: metanephric mesenchyme, ANX, 7 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 7 days in the presence of the ANX fraction


title: metanephric mesenchyme, ANX, 4 days, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of the ANX fraction


title: metanephric mesenchyme, ANX, 4 days, biological rep1


title: metanephric mesenchyme, ANX, 1 day, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 1 day in the presence of the ANX fraction


title: metanephric mesenchyme, ANX, 7 days, biological rep2


title: metanephric mesenchyme, ANX, 3 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 3 days in the presence of the ANX fraction


title: metanephric mesenchyme, ANX, 2 days, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of the ANX fraction


title: metanephric mesenchyme, ANX, 3 days, biological rep2


title: metanephric mesenchyme, ANX, 1 day, biological rep1


title: metanephric mesenchyme, ANX, 2 days, biological rep1


title: metanephric mesenchyme, NGAL, 7 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 7 days in the presence of NGAL

value: NGAL


title: metanephric mesenchyme, NGAL, 7 days, biological rep2


title: wild type placebo 12h, biological rep3


title: metanephric mesenchyme, NGAL, 5 days, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 5 days in the presence of NGAL


title: 58888 H33FL_1/INPUT_2

status: Public on Dec 01 2007

type: genomic

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.

hyb_protocol: Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/product s/chip/index.html). Set MAUI hybridization unit to 42 deg C and allow time for the temperatu re to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents  in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to completely dissolve the sample. Spin the tube down briefly to collect the contents in the bo ttom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5  microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microlite r Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are included in the hybridization as controls that hybridize to alignment features on the Nimble Gen arrays. They are required for proper extraction of array data from the scanned image. Mi x the tube briefly then spin down to collect the contents in the bottom and place at 95 deg C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at  this temperature until you are are ready for sample loading. Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disas sembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put th e array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up to temperature. Load the sample using the pipet supplied with the MAUI Station and following  manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sampl e may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If ther e are, very gently massage any bubbles to either of the ends, away from the center of the ar ray. Avoid applying too much pressure since this will force liquid out of the ports. Place t he loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Clo se the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm th at the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours. Prior to removing the array from the MAUI Hybridization Station, prepare the following solut ions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One d ish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded  in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works w ell. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften t he adhesive on the hybridization chamber; this will help prevent braking the array. Place th e remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I:  225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25 ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash  Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C.  Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not l et the surface of the slide dry out at any point during washing. While the chip is submerged , carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfe r the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agita tion. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wa sh over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation.  Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dar k desiccator.

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/ chip/index.html). Axon Scanner (model 4000B). Turn on the power of the scanner. The switch i s on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow l asers to warm. Open the scanner door and open the side carriage. Place chip in carriage so t hat array is face down and barcode end is closest to you. Move the black lever on the left s ide of the carriage left until the array is lying flat in the carriage. Release the lever so  that the arry is pushed over gently to the right side of the carriage and held firmly. Clos e the carriage (you should hear a click) and slide the scanner door shut. Open the hardware settings. Select the following settings for scanning: Wavelength (532=Cy3, 635=Cy5). Set the  532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750. Power=100%. Pixel Size=5m. Lin es to average=1. Focus position=0micrometer. Select Image/Ratio to view both channels simult aneously. Perform a preview scan by clicking on the fast-forward icon. Stop scan once the fu ll arry is in view by pressing the stop icon. Switch to zoom mode by clicking on the array i mage and pressing Z. Click and drag the mouse on the area in which you want to zoom. Center the image of the entire array area within the viewing window. Under Tools on the left side o f the screen, click the Scan Area icon. Click and drag to define a box that bounds the visib ile array area. The box dimensions should be stretched to create a box just slightly larger than the array area. It is critical to include all of the corner probes within the scan imag e. Scan chip by clicking the play icon. While scanning, set the zoom level to view the whole im age and adjust the brightness and contrast of the displayed image to eliminate visible satur ation. Based on the appearance of the array features, adjust the PMT setting as appropriate.  The features should be mostly yellow. If your features are mostly green, either decrease th e 532 PMT or raise the 635 PMT. If the features are mostly red or orange, either raise the 5 32 PMT or decrease the 635 PMT. Zoom the view to a region scanned under the most recent PMT settings and click on the Histogram tab at the top of the left side of the screen to check g lobal intensity of the features. On the top left side of the screen make sure you have the 5 32 and 635 wavelength boxes checked so both wavelength histograms are displayed. Make sure t he Log Axis box is checked. You want the red and green curves to be as close as possible to one another. If the red curve is above the green, lower the red PMT setting or raise the gre en PMT setting. You want the curve to have 1e-5 normalized counts at the 65,000 intensity le vel (saturation). This means that you have about 1% of the features saturated. The position of the two curves on top of each other is more important than hitting the 1% saturation mark .  The histogram only graphs the area of the image that is viewable in the screen on the ima ge tab. If the histogram is no longer changing then either the chip is done scanning or the area that you can see on the image screen has been scanned. After the PMT settings are prope rly adjusted, stop the current scan, do not save this image. Restart the scan under the new settings and wait until the scan has completed. Save the images. Make sure you save both the  532nm and 635nm images as separate single image tif files.

data_processing: Log base 2 (58888_635/58888_532) ratios were bi-weight mean centered

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Chromatin affinity-purified DNA with tagged histone H3.3 region from Drosophila S2 cells

label_protocol:
Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.

source_name: Input DNA

label_protocol:
Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.

tag: Input DNA


title: metanephric mesenchyme, NGAL, 4 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of NGAL


title: metanephric mesenchyme, NGAL, 3 days, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 3 days in the presence of NGAL


title: metanephric mesenchyme, NGAL, 4 days, biological rep2


title: metanephric mesenchyme, NGAL, 3 days, biological rep1


title: metanephric mesenchyme, NGAL, 5 days, biological rep1


title: metanephric mesenchyme, NGAL, 2 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of NGAL


title: metanephric mesenchyme, NGAL, 1 day, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 1 day in the presence of NGAL


title: metanephric mesenchyme, LIF, 4 days, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 4 days in the presence of LIF

value: LIF


title: metanephric mesenchyme, LIF, 5 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 5 days in the presence of LIF


title: metanephric mesenchyme, LIF, 7 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 7 days in the presence of LIF


title: metanephric mesenchyme, LIF, 7 days, biological rep2


title: metanephric mesenchyme, LIF, 4 days, biological rep1


title: metanephric mesenchyme, NGAL, 1 day, biological rep1


title: metanephric mesenchyme, LIF, 3 days, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 3 days in the presence of LIF


title: metanephric mesenchyme, NGAL, 2 days, biological rep2


title: metanephric mesenchyme, LIF, 2 days, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 2 days in the presence of LIF


title: metanephric mesenchyme, LIF, 2 days, biological rep1


title: metanephric mesenchyme, LIF, 1 day, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 1 day in the presence of LIF


title: metanephric mesenchyme, LIF, 3 days, biological rep1


title: metanephric mesenchyme, LIF, 5 days, biological rep2


title: metanephric mesenchyme, LIF, 1 day, biological rep2


title: metanephric mesenchyme, control, 1 day, biological rep2

description: Gene expression data from rat metanephric mesenchymes cultured for 1 day in the absence of inducers


title: freshly dissected metanephric mesenchyme, biological rep1

description: Gene expression data from rat metanephric mesenchymes freshly dissected


title: metanephric mesenchyme, control, 2 days, biological rep1

description: Gene expression data from rat metanephric mesenchymes cultured for 2 days in the absence of inducers


title: freshly dissected metanephric mesenchyme, biological rep2


title: metanephric mesenchyme, control, 1 day, biological rep1


title: OVA sensitized_OVA challenged_UCP exposure_rep2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

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

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

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

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

source_name: Lung, OVA sensitized and OVA challenged, UCP exposure

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

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

tag: Lungs of groups of six ovalbumin sensitized and OVA challenged mice, UCP containing air, BALB/cJ mice

source_name: Lung, OVA sensitized and OVA challenged, particle free air

tag: Lungs of groups of six ovalbumin sensitized and OVA challenged mice, particle free air, BALB/cJ mice


title: OVA sensitized_OVA challenged_UCP exposure_rep1


title: OVA sensitized, OVA challenged, UCP exposure_rep2

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro6.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

source_name: lung, OVA sensitized, OVA challanged, UCP exposure

tag: Lungs of groups of six ovalbumin sensitized and ovalbumin challenged mice, UCP containing air, BALB/cJ mice

source_name: lung, UCP exposure

tag: Lungs of groups of six non-sensitized and non-challenged mice, UCP containing air, BALB/cJ mice


title: OVA sensitized, OVA challenged, UCP exposure_rep1

source_name: lung, OVA sensitized, OVA challanged,  UCP exposure

tag: Lungs of groups of six ovalbumin sensitized ovalbumin challenged mice, UCP containing air, BALB/cJ mice


title: OVA sensitized_UCP exposure_rep2

source_name: Lung, OVA sensitized, UCP exposure

tag: Lungs of groups of six ovalbumin sensitized mice, UCP containing air, BALB/cJ mice

source_name: Lung, OVA sensitized, particle free air

tag: Lungs of groups of six ovalbumin sensitized mice, particle free air, BALB/cJ mice


title: OVA sensitized, OVA challenged_rep2

source_name: lung, OVA sensitized, OVA challanged, particle free air

tag: Lungs of groups of six ovalbumin sensitized and ovalbumin challenged mice, particle-free air, BALB/cJ mice

source_name: lung, particle free air

tag: Lungs of groups of six non-sensitized and non-challenged mice, particle-free air, BALB/cJ mice


title: metanephric mesenchyme, control, 2 days, biological rep2


title: OVA sensitized_UCP exposure_rep1

organism:
Homo sapiens
Mus musculus


title: Calf 112 (salmonella) gd T cells time 24

status: Public on Jun 30 2007

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

description: gd T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 24hr post infection

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GeneChip Operating Software V.1.2

organism: Bos taurus

source_name: gd T cells

label_protocol: RNA was amplified using Affymetrix Two-cycle protocol with approximately 100 ng of total RNA as described in the GeneChip® Expression Analysis Technical Manual (June 2004).

extract_protocol: lymphatic cells were stained with GD3.8 directly conjugated to FITC, washed, and sorted on a Vantage SE cell sorter (BD Immunocytometry Systems) as previously described, directly into trizol buffer, then frozen at -80°C.  RNA was extracted following the manufacturer’s protocol for Trizol (Invitrogen) RNA extraction.

tag: gd T cells derived from lymphatic fluid


title: Calf 112 (salmonella) gd T cells time 0

description: gd T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 0hr post infection


title: Calf 112 (salmonella) gd T cells time 72

description: gd T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 72hr post infection


title: OVA sensitized and challange_praticle free air_rep1

source_name: lung, praticle free air

tag: Lungs of groups of six non-sensitized and non-challanged mice, particle-free air, BALB/cJ mice


title: Calf 112 (salmonella) ab T cells time 72

description: ab T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 72hr post infection

source_name: ab T cells

tag: ab T cells derived from lymphatic fluid


title: Calf 112 (salmonella) gd T cells time 6

description: gd T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 6hr post infection


title: Calf 112 (salmonella) ab T cells time 0

description: ab T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 0hr post infection


title: Calf 162 (salmonella) gd T cells time 48

description: gd T cells derived from lymphatic fluid of calf 162 (salmonella infection) at time 48hr post infection

label_protocol: RNA was amplified using Affymetrix One-cycle protocol with approximately 1.6 micrograms of total RNA as described in the GeneChip® Expression Analysis Technical Manual (June 2004).

extract_protocol: lymphatic cells were stained with GD3.8 directly conjugated to FITC, washed, and sorted on a Vantage SE cell sorter (BD Immunocytometry Systems) as previously described, suspended in Buffer RLT and immediately lysed using Qiashredder columns then frozen at -80°C. RNA was extracted following the manufacturer’s protocol for RNeasy (Qiagen) column purification.


title: Calf 162 (salmonella) gd T cells time 0

description: gd T cells derived from lymphatic fluid of calf 162 (salmonella infection) at time 0hr post infection


title: Calf 112 (salmonella) gd T cells time 48

description: gd T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 48hr post infection


title: Calf 112 (salmonella) ab T cells time 24

description: ab T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 24hr post infection


title: Calf 162 (salmonella) ab T cells time 48

description: ab T cells derived from lymphatic fluid of calf 162 (salmonella infection) at time 48hr post infection


title: Calf 156 (mock) gd T cells time 48

description: gd T cells derived from lymphatic fluid of calf 156 (mock infection) at time 48hr post infection


title: Calf 156 (mock) gd T cells time 0

description: gd T cells derived from lymphatic fluid of calf 156 (mock infection) at time 0hr post infection


title: Calf 156 (mock) ab T cells time 0

description: ab T cells derived from lymphatic fluid of calf 156 (mock infection) at time 0hr post infection


title: Calf 112 (salmonella) ab T cells time 6

description: ab T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 6hr post infection


title: Calf 162 (salmonella) ab T cells time 0

description: ab T cells derived from lymphatic fluid of calf 162 (salmonella infection) at time 0hr post infection


title: Patient5D

status: Public on Jun 07 2007

city: Atlanta

first: Michael

last: Zilliox

state: GA

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University School of Medicine

description: PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls.  All samples were normalized with quantile normalization and summarized using RMA.

data_processing: Robust Multi-array Analysis

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells


title: Patient5E

tag: PBMCs from children with acute measles at hospital (e)ntry, (d)ischarge and (f)ollow-up as well as non-infected controls.


title: Calf 112 (salmonella) ab T cells time 48

description: ab T cells derived from lymphatic fluid of calf 112 (salmonella infection) at time 48hr post infection


title: Patient3D


title: Patient3E


title: Patient2E


title: Patient4E


title: Patient4D


title: Patient1D


title: Patient4F


title: Patient2F


title: Patient2D


title: Control2


title: nai1-1 vs Col-0, rep4

status: Public on Jun 04 2007

city: Kitashirakawa, Sakyoku

first: Ikuko

last: Hara-Nishimura

state: Kyoto

address: Oiwakecho

department: Depertment of Botany

country: Japan

institute: Kyoto University

description: Comparison of gene expression between a ER body-deficient mutant (nai1-1) and wild-type plants (Col-0). Roots of the 20-day-old plants. Total RNA was purified from 3 plants of each genotype.

hyb_protocol: Agilent Arabidopsis2 oligo microarray hybridization protocol

scan_protocol: Dual-laser Microarray scanner Agilent Technologies, 10µm resolution, 10% PMT for Cy3, 20% PMT for Cy5

data_processing: Spot intensities on the DNA microarray were quantified by Feature Extraction Software ver.7.1. 1 (Agilent Technologies) with default parameters.

organism: Arabidopsis thaliana

source_name: nai1-1 root

label_protocol: Five micro-gram of total RNA was fluorescently labeled using a Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies).

growth_protocol: Seeds were surface sterilized and then sown onto 0.5% (w/v) Gellan Gum (Wako, Tokyo, Japan) with MS medium (Wako) and 1% (w/v) sucrose and were grown at 22˚C under continuous light conditions.

extract_protocol: RNeasy plant mini kit (Qiagen, Valencia, CA)

treatment_protocol: No treatment

tag: Three roots of 20-day-old plants

source_name: Col-0 root


title: nai1-1 vs Col-0, rep3

scan_protocol: Dual-laser Microarray scanner Agilent Technologies, 10µm resolution, 30% PMT for Cy3, 20% PMT for Cy5


title: nai1-1 vs Col-0, rep2


title: Patient3F


title: Control3


title: Patient1F


title: Patient1E


title: Calf 156 (mock) ab T cells time 48

description: ab T cells derived from lymphatic fluid of calf 156 (mock infection) at time 48hr post infection


status: Public on Jun 01 2007

first: Denise

last: Mauldin

address: 1100 Fairview Ave N D4-100

department: Human Biology

description: Mouse 129X1/SvJ D, L, V, A Prostate 129-1 from 8-9 weeks mouse 129X1/SvJ hybridized against Mouse Normal Variation Gold Standard.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA).  The image intensity data were gridded and extracted using GenePix Pro 4.1 software.

data_processing: For each array spot, the expression levels of the two fluorophores were obtained by subtracting median background intensity from median foreground intensity.  A gene was only considered expressed if the fluorescence intensity of the corresponding spot was at least 6 foreground pixels greater than 4 standard deviations above background in at least half of the arrays per strain. Array spot not meeting these criteria were designated NA. For each gene, the logarithm base 2 ratios (referred henceforth as log ratios) of the two channels were calculated to quantify the relative expression levels of genes between the experimental and reference samples. To allow for inter-array comparisons, each array was normalized to remove systematic sources of variation.  This was accomplished by means of a print-tip-specific intensity-based normalization method [35].  A scatter-plot smoother, which uses robust locally linear fits, was applied to capture the dependence of the log ratios on overall log-spot intensities. The log ratios were normalized by subtracting the fitted values based on the print-tip-specific scatter-plot smoother from the log ratios of experimental and control channels. After normalization, spots were removed from further analysis if they had more then 3 NA values or if they were in the lower third quantile of abundance across all 20 arrays.

source_name: D, L, V, A Prostate 129-1 from 129X1/SvJ Mouse

label_protocol: The protocol used for indirect labeling of cDNAs was a modification of a method described elsewhere (http://cmgm.stanford.edu/pbrown/protocols/aadUTPCouplingProcedure.htm). Briefly, cDNA probes were made from 2 µg of amplified RNA in a reaction volume of 30 µl containing 170 ng random hexamer primers, 0.2 mM 5-(3-aminoallyl)-2_-deoxyuridine-5_-triphosphate (amino acid-dUTP; Sigma-Aldrich), 0.3 mM dTTP, 0.5 mM each dATP, dCTP, and dGTP, and 380 units of Superscript II reverse transcriptase (Life Technologies) incubated at 42oC for 120 minutes.  After RNA hydrolysis, purified cDNA was combined with either Cy3 or Cy5 monoreactive fluors (Amersham Pharmacia) that covalently couple to the cDNA incorporated aminoallyl linker in the presence of 50 mM NaHCO3 (pH 9.0). The coupling reaction was quenched with Hydroxylamine and reference and experimental probes were combined, filtered, and competitively hybridized to microarrays under a coverslip for 16 h at 63°C. Slides were washed sequentially with 1X saline sodium citrate (SSC)/0.03% sodium dodecyl sulfate (SDS), 1X SSC, 0.2X SSC, 0.05X SSC, and spun dry. To account for dye bias, half of the biological experimental samples per strain were labeled with Cy3 dye and the reference with Cy5 dye, and in the other half the labeling was inversed.

extract_protocol: Prostate tissues were homogenized using a Polytron and total RNA was isolated using the RNeasy extraction kit (Qiagen). Equal amounts of total RNA (0.7 µg) from each of the four pooled lobes/strain were combined to produce secondary pools, and amplified with the MessageAmpTM aRNA kit (Ambion). Amplified RNA from each secondary pool (four pools per strain) was hybridized separately to cDNA microarrays for a total of 4 independent biological replicates per strain (12 mice, 4 pools of 3 mice per strain for a total of 4 microarray experiments per strain; see Figure 1). A common reference sample was created by combining equal amounts of RNA from all the samples from all strains.

tag: Mouse 129X1/SvJ D, L, V, A Prostate 129-1. Lobe

value: DP, LP, VP and AP Specimen_ID:129-1 Age:8-9 weeks Strain:129X1/SvJ Pool_Components:129X1/SvJ; mouse #1, 5 and 12

source_name: Equal amounts of RNA from all samples from all strains (129X1/SvJ, BALB/c, C57BL/6J, DBA/2, FVB/NJ)

tag: Mouse Normal Variation Gold Standard


title: Control1


description: Mouse 129X1/SvJ D, L, V, A Prostate 129-4 from 8-9 weeks mouse 129X1/SvJ hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate 129-4 from 129X1/SvJ Mouse

tag: Mouse 129X1/SvJ D, L, V, A Prostate 129-4. Lobe

value: DP, LP, VP and AP Specimen_ID:129-4 Age:8-9 weeks Strain:129X1/SvJ Pool_Components:129X1/SvJ; mouse #4, 8 and 10


title: nai1-1 vs Col-0, rep1

scan_protocol: Dual-laser Microarray scanner Agilent Technologies, 10µm resolution, 50% PMT


description: Mouse 129X1/SvJ D, L, V, A Prostate 129-2 from 8-9 weeks mouse 129X1/SvJ hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate 129-2 from 129X1/SvJ Mouse

tag: Mouse 129X1/SvJ D, L, V, A Prostate 129-2. Lobe

value: DP, LP, VP and AP Specimen_ID:129-2 Age:8-9 weeks Strain:129X1/SvJ Pool_Components:129X1/SvJ; mouse #2, 7 and 11


description: Mouse C57BL/6J D, L, V, A Prostate C57-2 from 8-9 weeks mouse C57BL/6J hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate C57-2 from C57BL/6J Mouse

tag: Mouse C57BL/6J D, L, V, A Prostate C57-2. Lobe

value: DP, LP, VP and AP Specimen_ID:C57-2 Age:8-9 weeks Strain:C57BL/6J Pool_Components:C57BL/6J; mouse #2, 7 and 10


description: Mouse 129X1/SvJ D, L, V, A Prostate 129-3 from 8-9 weeks mouse 129X1/SvJ hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate 129-3 from 129X1/SvJ Mouse

tag: Mouse 129X1/SvJ D, L, V, A Prostate 129-3. Lobe

value: DP, LP, VP and AP Specimen_ID:129-3 Age:8-9 weeks Strain:129X1/SvJ Pool_Components:129X1/SvJ; mouse #3, 6 and 9


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger05

type: mixed

city: Stanford

first: Susan

middle: Nelle

last: Thayer

state: CA

address: 260 Panama St.

department: Plant Biology

institute: Carnegie Institution of Washington

hyb_protocol: The combined labeled G. dissectum cDNA samples and Arabidopsis genomic DNA were hybridized to the microarrays in a hybridization buffer containing 0.16 µg yeast tRNA, 0.47 µg PolyA, 0.02 µg PolyT in 5X SSC, 25% formamide and 0.3% SDS in a total of 42.47 uL in a 42°C water bath for 16 h using ArrayIt Hybridization Cassettes. After hybridization, slides were washed sequentially with 2X SSC/0.03% SDS, followed by 1X SSC then 0.05X SSC (2 minutes each) and spun dry before scanning.

scan_protocol: Used a Genepix (Axon) 4000B scanner (Molecular Devices, Sunnyvale, CA). Images were quantified using SpotReader Software (Niles Scientific, Portola Valley, CA)

data_processing: Only features having >90% of Ch1 pixels above background were included. Flagged (saturated, low signal or bad) features were omitted, arrays were print tip normalized in Genespring v7.2 (Agilent Technologies), quantile normalized using Microsoft Excel, features with normalized Ch2/Ch1 ratio <0.65 omitted.

source_name: Columbia strain

label_protocol: We labeled 2 ug of the Arabidopsis genomic DNA using random primers, the Klenow enzyme (Amersham) and Cy5 dUTP (Amersham). The reaction products were purified using QiaQuick columns (Qiagen)and concentrated in a speed vac.

growth_protocol: sterilized seeds grown axenically on agar

extract_protocol: Tissue was ground in liquid nitrogen and extracted using an equal volume of buffer containing 100 mM Tris pH 8.0, 50 mM EDTA, 750 mM NaCl and 10 mM ?-mercaptoethoanol. Per 15 mL extraction buffer, 1 mL 20% SDS and 50 uL 20 mg/mL Proteinase K were added and incubated at 65 ºC for 20-30 min. with gentle mixing 2-3 times during incubation. To this 1/7 volume 5 M NaCl was added and mixed gently. Then 0.1 volume 10% hexadecyltrimethylammonium bromide (CTAB), 0.7 M NaCl was added, mixed gently, incubated at 37 ºC for 15-30 min., and then extracted with chloroform/isoamyl alcohol (24:1, vol:vol). To the aqueous phase, 0.1 volume 10% CTAB, 0.7M NaCl was added; mixed gently and re-extracted with chloroform:isoamyl alcohol. To the aqueous phase, 2 volumes of 1% CTAB, 100 mM Tris pH 8.0, 50 mM EDTA was added to precipitate the DNA. After overnight incubation at 37 ºC, the precipitate was suspended in 10 mM Tris pH 8.0, 10 mM EDTA containing 1 M NaCl, warming to 65 ºC as needed. The DNA was precipitated in isopropanol, dried and treated with RNaseA. The DNA was precipitated and washed with 70% ethanol.

tag: genomic DNA sheared to 1000 bp

organism: Geranium dissectum

source_name: Total RNA from multiple individuals in experimental field plot.

label_protocol: cDNA was made from 18.6 to 50 µg of total RNA using Invitrogen Superscript II. Any remaining RNA was then degraded with RNase A and H. cDNAs were purified using Microcon YM-30 columns (Millipore). We labeled the second strand using random primers, the Klenow enzyme (Amersham) and Cy5 dUTP (Amersham). The reaction products were purified using QiaQuick columns (Qiagen)and concentrated using a speed vac.

growth_protocol: natural grassland plants grown in 2001-2002 growing season subjected to 4 global change factors each at 2 levels: ambient or elevated CO2, ambient temperature or ambient + 1 degree C warming, natural rainfall (601.2 mm/yr) or natural rainfall supplemented with 50% of every storm added immediately following each storm with a 3 week season extension, ambient growth nitrogen or ambient supplemented with 7 g N m-2 y-1, supplied as Ca(NO3)2. There were 16 treatments applied in a nested design.

extract_protocol: Tissue ground in liquid nitrogen and then homogenized and extracted using a CTAB-based extraction buffer (Pine Tree Method, Chang and Puryear, 1993). Following two chloroform:isoamyl alcohol extractions, the RNA was precipitated overnight at 4°C, after adding isopropanol and 0.8M sodium citrate/1.2M sodium chloride using half the volume of the aqueous phase each. The precipitate was washed with cold 75% ethanol and resuspended in nuclease-free water. Genomic DNA and a contaminant that was labeled by Cy dyes were removed by precipitation with 2M LiCl for 1 h at -20°C.

tag: naturally growing in Jasper Ridge Global Change experiment, Stanford, CA

tag: leaf tissue

tag: harvested between 10 AM and 2 PM

tag: plants were vegetative at time of harvest


title: Mouse DBA/2 D, L, V, A Prostate DBA-4

description: Mouse DBA/2 D, L, V, A Prostate DBA-4 from 8-9 weeks mouse DBA/2 hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate DBA-4 from DBA/2 Mouse

tag: Mouse DBA/2 D, L, V, A Prostate DBA-4. Lobe

value: DP, LP, VP and AP Specimen_ID:DBA-4 Age:8-9 weeks Strain:DBA/2 Pool_Components:DBA/2; mouse #4, 7 and 10


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger44


title: Mouse BALB/c D, L, V, A Prostate Balb-3

description: Mouse BALB/c D, L, V, A Prostate Balb-3 from 8-9 weeks mouse BALB/c hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate Balb-3 from BALB/c Mouse

tag: Mouse BALB/c D, L, V, A Prostate Balb-3. Lobe

value: DP, LP, VP and AP Specimen_ID:Balb-3 Age:8-9 weeks Strain:BALB/c Pool_Components:BALB/c; mouse #3, 6 and 11


title: Patient5F


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger114


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger60


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger46


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger74


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger56


title: Treatment 16:elevated CO2, elevated temperature, added rainfall, added nitrogen Trt16Ger93


title: Mouse DBA/2 D, L, V, A Prostate DBA-3

description: Mouse DBA/2 D, L, V, A Prostate DBA-3 from 8-9 weeks mouse DBA/2 hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate DBA-3 from DBA/2 Mouse

tag: Mouse DBA/2 D, L, V, A Prostate DBA-3. Lobe

value: DP, LP, VP and AP Specimen_ID:DBA-3 Age:8-9 weeks Strain:DBA/2 Pool_Components:DBA/2; mouse #3, 6 and 9


title: Mouse DBA/2 D, L, V, A Prostate DBA-2

description: Mouse DBA/2 D, L, V, A Prostate DBA-2 from 8-9 weeks mouse DBA/2 hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate DBA-2 from DBA/2 Mouse

tag: Mouse DBA/2 D, L, V, A Prostate DBA-2. Lobe

value: DP, LP, VP and AP Specimen_ID:DBA-2 Age:8-9 weeks Strain:DBA/2 Pool_Components:DBA/2; mouse #2, 5 and 12


title: Treatment 15:elevated CO2, elevated temperature, added rainfall, ambient nitrogen Trt15Ger41


description: Mouse C57BL/6J D, L, V, A Prostate C57-1 from 8-9 weeks mouse C57BL/6J hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate C57-1 from C57BL/6J Mouse

tag: Mouse C57BL/6J D, L, V, A Prostate C57-1. Lobe

value: DP, LP, VP and AP Specimen_ID:C57-1 Age:8-9 weeks Strain:C57BL/6J Pool_Components:C57BL/6J; mouse #1, 6 and 11


title: Treatment 15:elevated CO2, elevated temperature, added rainfall, ambient nitrogen Trt15Ger55


description: Mouse C57BL/6J D, L, V, A Prostate C57-3 from 8-9 weeks mouse C57BL/6J hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate C57-3 from C57BL/6J Mouse

tag: Mouse C57BL/6J D, L, V, A Prostate C57-3. Lobe

value: DP, LP, VP and AP Specimen_ID:C57-3 Age:8-9 weeks Strain:C57BL/6J Pool_Components:C57BL/6J; mouse #3, 4 and 9


title: Mouse FVB/NJ D, L, V, A Prostate FVB-2

description: Mouse FVB/NJ D, L, V, A Prostate FVB-2 from 8-9 weeks mouse FVB/NJ hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate FVB-2 from FVB/NJ Mouse

tag: Mouse FVB/NJ D, L, V, A Prostate FVB-2. Lobe

value: DP, LP, VP and AP Specimen_ID:FVB-2 Age:8-9 weeks Strain:FVB/NJ Pool_Components:FVB/NJ; mouse #2, 7 and 11


title: Mouse DBA/2 D, L, V, A Prostate DBA-1

description: Mouse DBA/2 D, L, V, A Prostate DBA-1 from 8-9 weeks mouse DBA/2 hybridized against Mouse Normal Variation Gold Standard.

tag: Mouse Normal Variation Gold Standard

source_name: D, L, V, A Prostate DBA-1 from DBA/2 Mouse

tag: Mouse DBA/2 D, L, V, A Prostate DBA-1. Lobe

value: DP, LP, VP and AP Specimen_ID:DBA-1 Age:8-9 weeks Strain:DBA/2 Pool_Components:DBA/2; mouse #1, 8 and 11


description: Mouse C57BL/6J D, L, V, A Prostate C57-4 from 8-9 weeks mouse C57BL/6J hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate C57-4 from C57BL/6J Mouse

tag: Mouse C57BL/6J D, L, V, A Prostate C57-4. Lobe

value: DP, LP, VP and AP Specimen_ID:C57-4 Age:8-9 weeks Strain:C57BL/6J Pool_Components:C57BL/6J; mouse #5, 8 and 12


title: Mouse BALB/c D, L, V, A Prostate Balb-1

description: Mouse BALB/c D, L, V, A Prostate Balb-1 from 8-9 weeks mouse BALB/c hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate Balb-1 from BALB/c Mouse

tag: Mouse BALB/c D, L, V, A Prostate Balb-1. Lobe

value: DP, LP, VP and AP Specimen_ID:Balb-1 Age:8-9 weeks Strain:BALB/c Pool_Components:BALB/c; mouse #1, 5 and 12


title: Treatment 15:elevated CO2, elevated temperature, added rainfall, ambient nitrogen Trt15Ger58


title: Mouse FVB/NJ D, L, V, A Prostate FVB-4

description: Mouse FVB/NJ D, L, V, A Prostate FVB-4 from 8-9 weeks mouse FVB/NJ hybridized against Mouse Normal Variation Gold Standard.

source_name: Equal amounts of RNA from all samples from all strains (129X1/SvJ, BALB/c, C57BL/6J, DBA/2, FVB/NJ)

source_name: D, L, V, A Prostate FVB-4 from FVB/NJ Mouse

tag: Mouse FVB/NJ D, L, V, A Prostate FVB-4. Lobe

value: DP, LP, VP and AP Specimen_ID:FVB-4 Age:8-9 weeks Strain:FVB/NJ Pool_Components:FVB/NJ; mouse #4, 8 and 10


title: Mouse FVB/NJ D, L, V, A Prostate FVB-3

description: Mouse FVB/NJ D, L, V, A Prostate FVB-3 from 8-9 weeks mouse FVB/NJ hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate FVB-3 from FVB/NJ Mouse

tag: Mouse FVB/NJ D, L, V, A Prostate FVB-3. Lobe

value: DP, LP, VP and AP Specimen_ID:FVB-3 Age:8-9 weeks Strain:FVB/NJ Pool_Components:FVB/NJ; mouse #3, 6 and 9


title: Mouse FVB/NJ D, L, V, A Prostate FVB-1

description: Mouse FVB/NJ D, L, V, A Prostate FVB-1 from 8-9 weeks mouse FVB/NJ hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate FVB-1 from FVB/NJ Mouse

tag: Mouse FVB/NJ D, L, V, A Prostate FVB-1. Lobe

value: DP, LP, VP and AP Specimen_ID:FVB-1 Age:8-9 weeks Strain:FVB/NJ Pool_Components:FVB/NJ; mouse #1, 5 and 12


title: Treatment 14:elevated CO2, elevated temperature, ambient rainfall, added nitrogen Trt14Ger6

tag: genomic DNA sheared to 1000 bp

tag: naturally growing in Jasper Ridge Global Change experiment, Stanford, CA

tag: leaf tissue


title: Treatment 15:elevated CO2, elevated temperature, added rainfall, ambient nitrogen Trt15Ger48

tag: harvested between 10 AM and 2 PM

tag: plants were vegetative at time of harvest


title: Treatment 14:elevated CO2, elevated temperature, ambient rainfall, added nitrogen Trt14Ger43


title: Treatment 14:elevated CO2, elevated temperature, ambient rainfall, added nitrogen Trt14Ger45


title: Treatment 14:elevated CO2, elevated temperature, ambient rainfall, added nitrogen Trt14Ger75


title: Treatment 15:elevated CO2, elevated temperature, added rainfall, ambient nitrogen Trt15Ger7


title: Treatment 13:elevated CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt13Ger47


title: Treatment 14:elevated CO2, elevated temperature, ambient rainfall, added nitrogen Trt14Ger59


title: Treatment 14:elevated CO2, elevated temperature, ambient rainfall, added nitrogen Trt14Ger54


title: Treatment 15:elevated CO2, elevated temperature, added rainfall, ambient nitrogen Trt15Ger96


title: Treatment 13:elevated CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt13Ger8


title: Treatment 12:elelvated CO2, ambient temperature, added rainfall, added nitrogen Trt12Ger38


title: Treatment 13:elevated CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt13Ger42


title: Mouse BALB/c D, L, V, A Prostate Balb-2

description: Mouse BALB/c D, L, V, A Prostate Balb-2 from 8-9 weeks mouse BALB/c hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate Balb-2 from BALB/c Mouse

tag: Mouse BALB/c D, L, V, A Prostate Balb-2. Lobe

value: DP, LP, VP and AP Specimen_ID:Balb-2 Age:8-9 weeks Strain:BALB/c Pool_Components:BALB/c; mouse #2, 7 and 10


title: Treatment 13:elevated CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt13Ger76

source_name: Columbia strain


title: Treatment 14:elevated CO2, elevated temperature, ambient rainfall, added nitrogen Trt14Ger115

source_name: Total RNA from multiple individuals in experimental field plot.


title: Treatment 13:elevated CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt13Ger53


title: Treatment 12:elelvated CO2, ambient temperature, added rainfall, added nitrogen Trt12Ger112


title: Treatment 11:elevated CO2, ambient temperature, added rainfall, ambient nitrogen Trt11Ger97


title: Treatment 11:elevated CO2, ambient temperature, added rainfall, ambient nitrogen Trt11Ger16


title: Treatment 11:elevated CO2, ambient temperature, added rainfall, ambient nitrogen Trt11Ger110


title: Treatment 12:elelvated CO2, ambient temperature, added rainfall, added nitrogen Trt12Ger99


title: Treatment 11:elevated CO2, ambient temperature, added rainfall, ambient nitrogen Trt11Ger81


title: Treatment 12:elelvated CO2, ambient temperature, added rainfall, added nitrogen Trt12Ger84


title: Treatment 11:elevated CO2, ambient temperature, added rainfall, ambient nitrogen Trt11Ger27


title: Treatment 12:elelvated CO2, ambient temperature, added rainfall, added nitrogen Trt12Ger51


title: Treatment 10:elelvated CO2, ambient temperature, ambient rainfall, added nitrogen Trt10Ger111


title: Treatment 10:elelvated CO2, ambient temperature, ambient rainfall, added nitrogen Trt10Ger14


title: Treatment 10:elelvated CO2, ambient temperature, ambient rainfall, added nitrogen Trt10Ger49


title: Treatment 10:elelvated CO2, ambient temperature, ambient rainfall, added nitrogen Trt10Ger98


title: Treatment 9:elevated CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt09Ger28


title: Treatment 9:elevated CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt09Ger82


title: Treatment 9:elevated CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt09Ger50


title: Treatment 9:elevated CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt09Ger109


title: Treatment 8:ambient CO2, elevated temperature, added rainfall, added nitrogen Trt08Ger77


title: Mouse BALB/c D, L, V, A Prostate Balb-4

description: Mouse BALB/c D, L, V, A Prostate Balb-4 from 8-9 weeks mouse BALB/c hybridized against Mouse Normal Variation Gold Standard.

source_name: D, L, V, A Prostate Balb-4 from BALB/c Mouse

tag: Mouse BALB/c D, L, V, A Prostate Balb-4. Lobe

value: DP, LP, VP and AP Specimen_ID:Balb-4 Age:8-9 weeks Strain:BALB/c Pool_Components:BALB/c; mouse #4, 8 and 9


title: Treatment 9:elevated CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt09Ger40


title: Treatment 10:elelvated CO2, ambient temperature, ambient rainfall, added nitrogen Trt10Ger83


title: Treatment 9:elevated CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt09Ger100


title: Treatment 8:ambient CO2, elevated temperature, added rainfall, added nitrogen Trt08Ger85


title: Treatment 8:ambient CO2, elevated temperature, added rainfall, added nitrogen Trt08Ger11


title: Treatment 8:ambient CO2, elevated temperature, added rainfall, added nitrogen Trt08Ger21


title: Treatment 8:ambient CO2, elevated temperature, added rainfall, added nitrogen Trt08Ger62


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger23


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger78


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger10


title: Treatment 13:elevated CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt13Ger113


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger102


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger117


title: Treatment 6:ambient CO2, elevated temperature, ambient rainfall, added nitrogen Trt06Ger35


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger36


title: Treatment 6:ambient CO2, elevated temperature, ambient rainfall, added nitrogen Trt06Ger119


title: Treatment 6:ambient CO2, elevated temperature, ambient rainfall, added nitrogen Trt06Ger80


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger87


title: Treatment 5:ambient CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt05Ger79


title: Treatment 6:ambient CO2, elevated temperature, ambient rainfall, added nitrogen Trt06Ger61


title: Treatment 6:ambient CO2, elevated temperature, ambient rainfall, added nitrogen Trt06Ger104


title: Treatment 8:ambient CO2, elevated temperature, added rainfall, added nitrogen Trt08Ger118


title: Treatment 5:ambient CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt05Ger34


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger31


title: Treatment 5:ambient CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt05Ger12


title: Treatment 3:ambient CO2, ambient temperature, added rainfall, ambient nitrogen Trt03Ger18


title: Treatment 5:ambient CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt05Ger86


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger121


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger4


title: Treatment 5:ambient CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt05Ger103


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger20


title: Treatment 3:ambient CO2, ambient temperature, added rainfall, ambient nitrogen Trt03Ger108


title: Treatment 3:ambient CO2, ambient temperature, added rainfall, ambient nitrogen Trt03Ger65


title: Treatment 5:ambient CO2, elevated temperature, ambient rainfall, ambient nitrogen Trt05Ger22


title: Treatment 3:ambient CO2, ambient temperature, added rainfall, ambient nitrogen Trt03Ger91


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger92


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger106


title: Treatment 7:ambient CO2, elevated temperature, added rainfall, ambient nitrogen Trt07Ger64


title: Treatment 2:ambient CO2, ambient temperature, ambient rainfall, added nitrogen Trt02Ger32


title: Treatment 2:ambient CO2, ambient temperature, ambient rainfall, added nitrogen Trt02Ger89


title: Treatment 3:ambient CO2, ambient temperature, added rainfall, ambient nitrogen Trt03Ger29


title: Treatment 3:ambient CO2, ambient temperature, added rainfall, ambient nitrogen Trt03Ger127


title: Treatment 2:ambient CO2, ambient temperature, ambient rainfall, added nitrogen Trt02Ger128


title: Treatment 2:ambient CO2, ambient temperature, ambient rainfall, added nitrogen Trt02Ger17


title: Treatment 4:ambient CO2, ambient temperature, added rainfall, added nitrogen Trt04Ger126


title: Treatment 2:ambient CO2, ambient temperature, ambient rainfall, added nitrogen Trt02Ger105


title: Treatment 2:ambient CO2, ambient temperature, ambient rainfall, added nitrogen Trt02Ger122


title: Treatment 1:ambient CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt01Ger66


title: Treatment 1:ambient CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt01Ger90


title: Treatment 1:ambient CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt01Ger107


title: Treatment 1:ambient CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt01Ger19


title: Treatment 1:ambient CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt01Ger30


title: Treatment 1:ambient CO2, ambient temperature, ambient rainfall, ambient nitrogen Trt01Ger125


title: Treatment 10:elelvated CO2, ambient temperature, ambient rainfall, added nitrogen Trt10Ger37


title: JIR3528 gdn43

status: Public on May 01 2007

city: Melbourne

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

description: Random primers were annealed to 2ug of restriction-digested genomic DNA and labelled and unlabelled nucleotides were added using Klenow polyermase

data_processing: Expression and p-values are attached to series file

organism: Dichelobacter nodosus

tag: D. nodosus strain JIR3528

source_name: Wild-type JIR3356

tag: D. nodosus wild-type strain JIR3356


title: Hoof agar gdn53

description: Experiment looking at differences in gene expression when growth on solid surface was in the presence or absence of ground hoof

source_name: Wild-type JIR3356 hoof agar

label_protocol: 3ug labelled using the Genisphere Array 900 MPX kit

tag: Wild-type grown on EYE hoof agar

source_name: Wild-type JIR3356 agar

tag: Wild-type grown on EYE agar


title: JIR3528 gdn41


title: JIR1474 gdn39

description: Random primers were annlealed to 2ug of restriction digested genomic DNA and cy-labelled and unlabelled dNTP's were added using Klenow polymerase.

tag: D. nodosus strain JIR1474


title: Hoof agar gdn65


title: Hoof agar gdn51


title: JIR3356 gdn29


title: Hoof agar gdn55


title: JIR3350 gdn26

tag: D. nodosus strain JIR3350


title: JIR3209 gdn27

tag: D. nodosus strain JIR3209


title: JIR1474 gdn45


title: JIR1461 gdn22

description: Random primers were annealed to 2ug of restriction-digested genomic DNA and labelled and unlabelled nucleotide were added using Klenow polyermase.

tag: D. nodosus strain JIR1461

source_name: JIR3356 wild-type

tag: D. nodosus wild-type JIR3356


title: JIR1244 gdn30

tag: D. nodosus strain JIR1244


title: JIR1244 gdn36


title: JIR3350 gdn28


title: JIR3209 gdn21


title: JIR3356 gdn31


title: JIR1461 gdn49