title: 53-N2-5_v_46-N2-5 (array 1of2)

description: 53 days node2 vs 46 days node2 replication number 5. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 67-N1-6_v_46-N1-6 (array 1of2)

status: Public on Jun 26 2008

type: RNA

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

country: USA

institute: Iowa State University

description: 67 days node1 vs 46 days node1 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

hyb_protocol: Fluorescent targets were hybridized as described in the cDNA microarray protocol file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Each microarray chip (134 total) was scanned four times in ascending amounts of laser power and PMT gain settings using a ProScanArray scanner (PerkinElmer, Boston, MA). Two scans (one scan for each channel) from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide.

data_processing: The lowess normalization method of Dudoit, Yang, Callow, and Speed (2002) was applied to the log of background-corrected raw signal intensities to remove signal-intensity-dependent dye effects from each slide.  Normalization was carried out separately for each slide to avoid introducing dependencies among biological replications. Following lowess normalization, the normalized data for each slide/dye combination were median centered so that expression measures would be comparable across slides.  Median-centering involves subtracting the median value for a particular slide/dye combination from each individual value associated with the particular slide/dye combination. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

molecule: total RNA

organism: Oryza sativa

source_name: Node 1 of 46 day old seedlings

label_protocol: Targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/

growth_protocol: Seeds were incubated in water at 42C for 24hrs prior to planting. Initial watering contained a mixture of 1 to 1 Scotts Excel 21-5-20 All Purpose Water Soluble Fertilizer and Scotts Excel 15-5-15 Cal-Mg Water Soluble Fertilizer. Subsequent watering contained no fertilizer mix and was applied to maintain water levels high enough to submerse the seed. Seedlings were grown in a Percival PGC-105 growth chamber with settings of 12hrs light at 28C with 85% humidity and 12hrs dark at 22C with 60% humidity.

extract_protocol: RNA was isolated using RNeasy Plant Mini kit (Qiagen), following the manufacturer's protocol.

tag: Genotype

value: Nipponbare

tag: Developmental Stage

value: 46 days

tag: Tissue

value: node 1

tag: Replicate

source_name: Node 1 of 67 day old seedlings

value: 67 days


title: 46-N1-3_v_67-N1-3 (array 1of2)

description: 46 days node1 vs 67 days node1 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N1-6_v_53-N1-6 (array 1of2)

description: 46 days node1 vs 53 days node1 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 1 of 53 day old seedlings

value: 53 days


title: 60-N1-3_v_53-N1-3 (array 1of2)

description: 60 days node1 vs 53 days node1 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 1 of 60 day old seedlings

value: 60 days


title: 46-N1-3_v_67-N1-3 (array 2of2)


title: 67-N1-3_v_60-N1-3 (array 2of2)

description: 67 days node1 vs 60 days node1 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 53-N1-6_v_60-N1-6 (array 1of2)

description: 53 days node1 vs 60 days node1 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: 46-N2-6_v_53-N2-6 (array 1of2)

description: 46 days node2 vs 53 days node2 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 2 of 53 day old seedlings

value: node 2

source_name: Node 2 of 46 day old seedlings


title: 53-N2-6_v_60-N2-6 (array 2of2)

description: 53 days node2 vs 60 days node2 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.

source_name: Node 2 of 60 day old seedlings


title: 46-N1-6_v_53-N1-6 (array 2of2)


title: 60-N1-6_v_67-N1-6 (array 2of2)

description: 60 days node1 vs 67 days node1 replication number 6. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: gDNA 106/1(76I) no CQ-treatment, biological rep2

type: genomic

city: Rockville

first: Hongying

last: Jiang

state: MD

address: 12735 Twinbrook Parkway

institute: NIAID/NIH

hyb_protocol: After fragmentation, 10 ug of cRNA and DNA were hybridized for 16 hr at 45C on GeneChip Plasmodium/Anopheles Array. GeneChips were washed and stained following the Affymetrix’s EukGE-WS2v5 protocol. Affymetrix 20X hybridization control was used to make the hybridization cocktail.

scan_protocol: The chips were scanned at 570 nm emission wavelength using Affymetrix scanner 3000.

data_processing: Image CEL files were processed and normalized using the Robust Multi-array Analysis with correction for GC content of the oligos(GC-RMA).

label: biotin

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: Pf 106/1(76I), no CQ treatment

label_protocol: Five microgram total RNA was labeled following Affymetrix standard protocols for eukaryotes using One Cycle Target Labeling and Control Reagent Kit. Ten microgram of genomic DNA was fragmented to an average size of 50–150 bp with DNase I and subsequently end-labeled using terminal deoxynucleotidyl transferase (TdT) and a biotin labeling kit.

growth_protocol: parasites were maintained in RPMI 1640 medium containing 5% human O+ erythrocytes, 0.5% Albumax, 24 mM sodium bicarbonate and 10 µg/ml gentamycin at 37°C with 5% CO2, 5% O2, and 90% N2.

extract_protocol: Total RNA is extracted following Trizol extraction protocol according to the manufacturer’s instruction. Genomic DNA was extracted from saponin-lysed parasite pellets using Wizard Genomic DNA Purification Kit.

treatment_protocol: Parasites were synchronized in three steps using successive 5% sorbitol treatments, followed by a Percoll-sorbitol (80%:40%) gradient purification after 24 h and another round of 5% sorbitol treatment, then total RNAs were extracted after another 24 h. Three hours before total RNA extraction, a low dose CQ (IC25, based on previous study) were given to each parasite culture.

tag: parasite line

value: selected from 106/1K76 under 100nM CQ

tag: pfcrt key mutation


title: gDNA 106/1(76I) no CQ-treatment, biological rep1


title: gDNA 106/1 no CQ-treatment, biological rep2

source_name: Pf 106/1, no CQ treatment

value: Sudan isolate


title: gDNA 106/1 no CQ-treatment, biological rep1


title: 53-N1-6_v_60-N1-6 (array 2of2)


title: 46-N2-6_v_53-N2-6 (array 2of2)


title: gDNA 106/1(76I_352K) no CQ-treatment, biological rep2

source_name: Pf 106/1(76I_352K), no CQ treatment

value: selected from under 100nM quine (QN)


title: 53-N1-3_v_46-N1-3 (array 1of2)

description: 53 days node1 vs 46 days node1 replication number 3. Sample Prep: nodes from 7 to 9 plants were pooled and ground using mortars and pestles. RNA was isolated using RNeasy Plant Mini kit by Qiagen following the manufacturer's suggested protocol. RNA were labeled and pooled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the appropriate GEO platform. Due to the loop design (Fig. 1) in supplementary file, a total of six biological replications were performed.


title: gDNA 106/1(76I_352K) no CQ-treatment, biological rep1


title: 60-N1-3_v_53-N1-3 (array 2of2)


title: 53-N1-3_v_46-N1-3 (array 2of2)


title: 67-N1-6_v_46-N1-6 (array 2of2)


title: RNA 106/1(76I) CQ-treated, biological rep1

source_name: Pf 106/1(76I), CQ IC25 treated, 3h, synchronized


title: RNA 106/1(76I_352K) no CQ-treatment, biological rep1

source_name: Pf 106/1(76I_352K), no CQ treatment, synchronized


title: RNA 106/1(76I_352K) CQ-treated, biological rep1

source_name: Pf 106/1(76I_352K), CQ IC25 treated, 3h, synchronized


title: RNA 106/1(76I) no CQ-treatment, biological rep2

source_name: Pf 106/1(76I), no CQ treatment, synchronized


title: RNA 106/1(76I_352K) CQ-treated, biological rep2


title: RNA 106/1(76I_352K) no CQ-treatment, biological rep2


title: RNA 106/1 no CQ-treatment, biological rep3

source_name: Pf 106/1, no CQ treatment, synchronized


title: RNA 106/1(76I) CQ-treated, biological rep2


title: RNA 106/1 CQ-treated, biological rep2

description: RNA 106/1 CQ-treated, biological rep2

source_name: Pf 106/1, CQ IC25 treated, 3h, synchronized


title: RNA 106/1 CQ-treated, biological rep3

description: RNA 106/1 CQ-treated, biological rep3


title: RNA 106/1 no CQ-treatment, biological rep1


title: RNA 106/1(76I) no CQ-treatment, biological rep1


title: RNA 106/1(76I) no CQ-treatment, biological rep3


title: RNA 106/1(76I_352K) CQ-treated, biological rep3


title: RNA 106/1(76I) CQ-treated, biological rep3


title: Dehydration of baker's yeast at 4h-1

status: Public on Jun 25 2008

city: Tsukuba

first: Yoshinori

last: Murata

state: Ibaraki

address: 1-1 Ohwashi

department: Post-harvest Science and Technology Division

country: Japan

institute: Japan International Research Center for Agricultural Science

description:
Normalized ratio data included in supplementary file:
Values below 0.01 were set to 0.01. Each measurement was divided by the 50.0th percentile of all measurements in that sample. Specific samples were normalized to one another: All samples (1h, 2h, 4h, and 8h samples) were normalized against the median of the control samples (0h sample). Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples. "Normalization value = [Raw value]/[Control value]".
The value of "control" column is calculated as follows: Normalization value was decided from intensity of raw accoring to the Normalization scenario of 1.  After that, control value was calculated from this formula, "Normalization value = [Raw value]/[Control value]". i.e. [Control value] = [Raw value]/[Normalization value]

hyb_protocol: At 45degree for 16-18h

scan_protocol: GeneChip scanner

data_processing: GeneChip operating system (GCOS)

label: The biotinyated cRNA

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Baker's yeast

label_protocol: According to the Affymetrix user's mannual

growth_protocol: Fed-batch culture

extract_protocol: Poly A RNA was enriched from total RNA with Oligotex dT30.

treatment_protocol: The compressed yeast cells were put on the alminium tray, and dried by air blow at 37degree in dry oven.

tag: Dry 4h-1


title: RNA 106/1 no CQ-treatment, biological rep2


title: Dehydration of baker's yeast at 2h-2

label: The biotinyated RNA

label_protocol: Accoding to the Affymetrix user's mannual

tag: Dry 2h-2


title: Dehydration of baker's yeast at 8h-1

tag: Dry 8h-1


title: Dehydration of baker's yeast at 1h-2

tag: Dry 1h-2


title: Dehydration of baker's yeast at 2h-1

tag: Dry 2h-1


title: RNA 106/1(76I_352K) no CQ-treatment, biological rep3


title: Dehydration of baker's yeast at 4h-2

tag: Dry 4h-2


title: Dehydration of baker's yeast at 0h-1

scan_protocol: GeneChips scanner

tag: Dry 0h-1


title: Dehydration of baker's yeast at 0h-2

tag: Dry 0h-2


title: Dehydration of baker's yeast at 1h-1

tag: Dry 1h-1


title: Dehydration of baker's yeast at 8h-2

tag: Dry 8h-2


title: RNA 106/1 CQ-treated, biological rep1

description: RNA 106/1 CQ-treated, biological rep1


title: Expression of genes from UPEC U17 during chicken infection relative to that in vitro

city: yangzhou

first: zhao

last: lixiang

address: 88 Daxue road

department: verterinary school

country: China

institute: Yanzhou university

description: RNAs were  extracted from the blood of inoculated chicken and that grown in LB.

hyb_protocol: Labeled contro and test samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into 12 uL hybridization solution.  DNA in hybridization solution was denatured at 95 ℃ for 3 min prior loading on a microarray. Hybridization was performed under LifterSlipTM (Erie Company, Portsmouth, NH).  The hybridization chamber was laid on a three-phase tiling agitator to prompt the microfluidic circulation under the coverslip.  The array was hybridizaed at 42 ℃ overnight and washed with two consecutive washing solutions.

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner (CapitalBio. Corp.), and obtained images were analyzed with SpotDataTM software (CapitalBio. Corp.).

data_processing:
normalization method:Lowess method;
significance analysis: SAM

organism: Escherichia coli

source_name: bacteria, chicken infection

label_protocol: The purified cDNA was labeled with Cy5-dCTP (Amersham Pharmacia Biotech, Inc., Piscataway, NJ, USA).  The hybridization was performed under LifterSlipTM (Erie Company, Portsmouth, NH).

extract_protocol: An E. coli infection model using 1-day-old SPF chicks was used.  Briefly, 10 chickens (1 days old) were infected with a 1010 CFU of UPEC U17 and APEC E058 by air sac route, respectively.  Four hours following challenge with the E. coli strains, chickens were euthanized.  Blood was collected directly into 15 ml centrifuge tube containing 1 ml anticoagulant (0.5% sodium citrate).  Tube containing the anticoagulating blood was centrifuged (5 min, 500×g, 4°C), the bacteria-containing supernatant was collected into another tube.  The supernatants were centrifuged (10 min, 2,500×g, 4°C), and the bacterial pellet was frozen at –70°C until RNA extraction.

tag: strain:E.coli strain UPEC U17, station

value: during chicken infection

source_name: bacteria, LB

label_protocol: The purified cDNA was labeled with Cy3-dCTP (Amersham Pharmacia Biotech, Inc., Piscataway, NJ, USA).  The hybridization was performed under LifterSlipTM (Erie Company, Portsmouth, NH).

extract_protocol: RNA was extracted from the collected bacterial grown in LB broth using an RNeasy Mini kit with a 1 h on-column DNase digestion (QIAGEN) according to the RNeasy Mini kit handbook. Multiple RNA preparations of the same sample were pooled prior to cDNA synthesis.  Up to 20 µg of RNA was mixed with 750 ng of random hexamers for each cDNA synthesis reaction according to a previously described protocol.  SuperScript II reverse transcriptase (1,500 U; Invitrogen) was added to these reactions, along with First Strand buffer, dithiothreitol, and deoxyribonucleotides at concentrations recommended by the manufacturer (Invitrogen).  The reactions were incubated at 25 °C for 10 min, 37 °C for 60 min, 42 °C for 60 min, and 70 °C for 10 min.  cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany).

value: grown in LB


title: RH RRE2 WT B VS QW231 B 6D 3

city: Austin

first: Rasika

last: Harshey

state: TX

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

description: No

hyb_protocol: 42 degree overnight

scan_protocol: Genepix 400B

data_processing: Genepix Pro 4.0, normalized so that the mean of the ratio of medians of all the features was equal to one

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: WILDTYPE 14028

label_protocol: reverse transcription

extract_protocol: BioRad Aquapure RNA isolation kit

tag: FROM LB CULTURE AT LOG PHASE

value: igaA(T191P), wza::kan, RcsAB box mutation in flhD promoter


title: Expression of genes from APEC E058 during chicken infection relative to that in vitro

source_name: bactria, LB

extract_protocol: RNA was extracted using an RNeasy Mini kit with a 1 h on-column DNase digestion (QIAGEN) according to the RNeasy Mini kit handbook. Multiple RNA preparations of the same sample were pooled prior to cDNA synthesis.  Up to 20 µg of RNA was mixed with 750 ng of random hexamers for each cDNA synthesis reaction according to a previously described protocol.  SuperScript II reverse transcriptase (1,500 U; Invitrogen) was added to these reactions, along with First Strand buffer, dithiothreitol, and deoxyribonucleotides at concentrations recommended by the manufacturer (Invitrogen).  The reactions were incubated at 25 °C for 10 min, 37 °C for 60 min, 42 °C for 60 min, and 70 °C for 10 min.  cDNA was purified with PCR Clean-up NucleoSpin Extract Ⅱ kits (Macherey-Nagel, Germany).

tag: Strain

value: E.coli APEC E058,Station:grown in LB

value: E.coli APEC E058,Station:during chicken infection


title: Expression of genes from APEC E058 during murine UTI infection relative to that in vitro

description: RNAs from urine of 40 BALB/c mice transurethrally inoculated with APEC E058 and that grown in LB were extracted.

value: E.coli strain APEC E058, station:grown in LB

extract_protocol: Urine was collected for 15 days after 18 h following the inoculations every time.  On average, 50 µl of urine was collected from each mouse every 45 min during an 8 h period. Urine was collected directly into 1.5-ml microcentrifuge tubes containing 650 µl of RNA Protect Bacterial Reagent purchased from QIAGEN (Santa Clarita, CA) and was pooled until the total volume reached approximately 1 ml. The RNA Protect Bacterial Reagent-treated sample remained on ice until all samples had been collected for that day.  A crystalline precipitate was allowed to settle before pipetting off the bacteria-containing supernatant into a 15-ml centrifuge tube for collection. Tubes were centrifuged (15 min, 2,500×g, 4°C), the supernatant was decanted, and the bacterial pellet was frozen at –70°C until RNA extraction.

value: E.coli strain APEC E058, station:during murine UTI infection


title: Expression of genes from UPEC U17 during murine UTI infection relative to that in vitro

description: RNAs from urine of 40 BALB/c mice transurethrally inoculated with UPEC U17 and that grown in LB were extracted.

source_name: UPEC U17, LB

growth_protocol: UPEC U17 were grown statically to mid-exponential phase at 37 °C in LB.

treatment_protocol: UPEC U17 were grown statically to mid-exponential phase at 37 °C in LB, and the bacterial RNA were extracted.

value: E.coli strain UPEC U17, Grown station:in LB.

source_name: UPEC U17, urine

value: E.coli strain UPEC U17, Grown station:during murine UTI infection.


title: RH RRE2 WT B VS QW434 B 6D 1

description: No

scan_protocol: Genepix 4000B

source_name: Wildtype 14028

extract_protocol: Biorad Auapure RNA Isolation Kit

tag: from LB at log phase

value: delta rcsB


title: RH RRE2 WT P vs QW226 B 6D 2

description: No

tag: LB at log phase

value: igaA(T191P), carrying RcsAB box mutation in flhD promoter


title: RH RRE2 WT B VS QW231 B 6D 2

description: No


title: RH RRE2 WT B VS QW226 6D 3

description: No


title: RH RRE2 WT B VS QW231 B 6D 1

description: No


title: RH RRE2 WT B VS QW434 B 6D 2

description: No


title: C.elegans exposed to Rhine sediment, replicate 5

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

description: Rhine sediment exposed nematodes: Biological replicate 5 of 5.

hyb_protocol: The cDNA was applied to the pre-blocked surface (5X SSC, 0.1 % SDS, 1 % BSA at 42 0C for 45 min. ; rinsed 4X with deionized water ; rinsed 1X with iso-propanol for a few seconds and dried with compressed air) of the array slide and allowed to hybridize to the oligonucleotides. The hybridization reaction was performed in 50 % formamide, 10X SSC, 0.2 % SDS at 42 0C for 24 hr in an air tight box with a 9 cm diameter petri dish containing 20 ml of water in the base. After hybridization, the arrays were washed (with 2X SSC, 0.2 % SDS for 5 min. at 42 0C ; 0.2X SSC, 0.2 % SDS for 3 min. at RT ; 0.2X SSC for 2 min. at RT, rinsed 2X with 0.1 % SSC for 1 min. each) and dried with compressed air.

scan_protocol: Slides were scanned using a Scan Array Express Microarray Scanner (Perkin Elmer).

data_processing: The VALUE data was derived following normalization (background correction and Print-Tip-Lowess algorithm) using the R-Package, then imported in to GeneSpring 7.3.1 & Log transformed using “per chip” and “per gene” median polishing. The log2 values ranging between 0.71 and 1.4 of normal distribution were used for “Fold Change” and “1way ANOVA” analysis.

organism: Caenorhabditis elegans

label_protocol: Indirect labelling method was used to produce fluorescently labelled cDNA. 10 µg of total RNA was reverse transcribed using both anchored oligo(dT) and random hexamer primers, aa-dUTP/dNTP, and reverse transcriptase m-MULV(ABgene) at 42 0C for 3 hr. The sample was precipitated using sodium acetate/ethanol and resuspended in 9 µl of sodium bi-carbonate (0.1M). NHS dye Cy5 (Amersham Biosciences) was first dissolved in 3 µl of DMSO, subsequently added to the cDNA in NaHCO3 solution, incubated in the dark at room temperature for 2.5 hr and quenched using hydroxylamine. Following a precipitation step, the Cy labelled cDNA was purified via GFX DNA purification columns (Amersham Biosciences). All experimental procedures followed the instructions of the suppliers and essentially as described in the ULTRAGAPS activated slide processing protocol.

growth_protocol: Age-synchronized populations were generated by rinsing nematodes (maintained on NGM plates) over a 45 µm-gauze using K-medium. The juveniles were split and spread over a further 100 plates with a fresh lawn of E. coli. After two days at 20°C, L1 and L2 developed to juveniles of the fourth stage (L4) and young adults. Nematodes were rinsed off using K-medium and the density of the nematode suspension was adjusted to 40,000 individuals per ml.

extract_protocol: The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen), however modified to include a homogenization step with 0.5 mm glass beads (Sigma) to maximize cell breakage. RNA was subsequently purified using an RNeasy kit (Qiagen) followed by a DNase digestion (Qiagen).

treatment_protocol: Sediment (0.5g, wet weight) and 0.25 ml of bacterial suspension (approximately 1.0E+10 E. coli cells/ml suspended in K-medium) were mixed and transferred to 24 test vials (2x 12-well polystyrene multi dishes). Nematode-suspension (0.5 ml, 20,000 age synchronized individuals) was transferred to each test vial and the test organisms exposed for 48 h to the respective treatment. To recover the nematodes, the content of the vials were transferred into 50 ml centrifuge tubes using a suspension of colloidal silica in deionized water (density: 1.15 g cm-³) and centrifuged for 5 min at 800 x g. The supernatant, containing the majority of nematodes, was filtered over a 45 µm-gauze, rinsed back in the falcon tubes and centrifuged for 15 min at 800 x g. Trizol (Invitrogen, Germany) was added to the nematode pellet and stored at -20°C.

tag: Age

value: L4 and young adult (48 h post staged L1)

tag: Tissue

value: whole animal

value: N2 (Bristol)

source_name: C.elegans universal reference for control

tag: The sample is an equi-molar fractional representation of all samples/replicates generated for this experiment


title: C.elegans exposed to Rhine sediment, replicate 4

description: Rhine sediment exposed nematodes: Biological replicate 4 of 5.


title: RH RRE2 WT P vs QW119 P 6D 1

description: No

scan_protocol: GenePix 400B

extract_protocol: Biorad Aquapure

tag: from swarming plate at 3.0hr


title: RH RRE2 WT B vs QW226 B 6D 1

description: No

value: igaA(T191P), carrying RcsAB-box mutation in flhD promoter


title: RH RRE2 WT B vs QW119 B 6D-2

description: No

label_protocol: Reverse transcription

extract_protocol: BioRad Aquapure RNA Isolation Kit

tag: QW119 is an igaA point mutation


title: C.elegans exposed to Rhine sediment, replicate 3

description: Rhine sediment exposed nematodes: Biological replicate 3 of 5.


title: C.elegans exposed to Rhine sediment, replicate 2

description: Rhine sediment exposed nematodes: Biological replicate 2 of 5.


title: RH RRE2 WT B vs QW119 B 6D 3

description: No


title: RH RRE2 WT B vs QW119 B 6D 1

description: No

tag: total RNA from LB at log phase


title: C.elegans exposed to Elbe sediment, replicate 5

description: Elbe sediment exposed nematodes: Biological replicate 5 of 5.


title: RH RRE2 WT P vs QW119 P 6D 3

description: No


title: RH RRE2 WT P vs QW119 P 6D 2

description: No


title: C.elegans exposed to Elbe sediment, replicate 3

description: Elbe sediment exposed nematodes: Biological replicate 3 of 5.


title: C.elegans exposed to Rhine sediment, replicate 1

description: Rhine sediment exposed nematodes: Biological replicate 1 of 5.


title: C.elegans exposed to Elbe sediment, replicate 4

description: Elbe sediment exposed nematodes: Biological replicate 4 of 5.


title: C.elegans exposed to Elbe sediment, replicate 2

description: Elbe sediment exposed nematodes: Biological replicate 2 of 5.


title: RH RRE2 WT B stnry vs QW434 B stnry 7D 4

description: No

tag: from LB at stationary phase


title: RH RRE2 WT B stnry vs QW434 B stnry 7D 3

description: No


title: RH RRE2 WT B stnry vs QW434 B stnry 7D 6

description: No


title: RH RRE2 WT B stnry vs QW434 B stnry 7D 5

description: No


title: C.elegans exposed to Danube sediment, replicate 5

description: Danube sediment exposed nematodes: Biological replicate 5 of 5.


title: RH RRE2 WT B stnry vs QW434 B stnry 7D 1

description: No


title: C.elegans exposed to Danube sediment, replicate 2

description: Danube sediment exposed nematodes: Biological replicate 2 of 5.

hyb_protocol: The cDNA was applied to the pre-blocked surface (5X SSC, 0.1 % SDS, 1 % BSA at 42 0C for 45 min. ; rinsed  4X with deionized water ; rinsed  1X with iso-propanol for a few seconds  and dried with compressed air) of the array slide and allowed to hybridize to the oligonucleotides.  The hybridization  reaction was performed in 50 % formamide, 10X SSC, 0.2 % SDS at 42 0C  for 24 hr in an air tight box with a 9 cm diameter petri dish containing 20 ml of water in the base.  After hybridization, the arrays were washed (with 2X SSC, 0.2 % SDS for 5 min. at 42 0C ;   0.2X SSC, 0.2 % SDS for 3 min. at  RT ;  0.2X SSC  for 2  min. at  RT, rinsed 2X with 0.1 % SSC for 1 min. each) and dried with compressed air.

data_processing: The VALUE data was derived following normalization (background correction and Print-Tip-Lowess algorithm) using the R-Package, then imported in to GeneSpring 7.3.1 & Log transformed using “per chip” and “per gene” median polishing.  The log2 values ranging between 0.71 and1.4 of normal distribution were used for “Fold Change” and “1way ANOVA” analysis.

label_protocol: Indirect labelling method was used to produce fluorescently labelled cDNA.  10 µg of total RNA was reverse transcribed using both anchored oligo(dT)  and random hexamer primers, aa-dUTP/dNTP, and reverse transcriptase m-MULV(ABgene) at 42 0C for 3 hr.  The sample was precipitated using sodium acetate/ethanol and resuspended in 9 µl of sodium bi-carbonate (0.1M). NHS dye Cy5 (Amersham Biosciences)  was first dissolved in 3 µl of DMSO,  subsequently added to the cDNA in NaHCO3  solution,  incubated in the dark at room temperature for  2.5 hr  and  quenched using hydroxylamine.  Following a precipitation step, the Cy labelled cDNA was purified via GFX  DNA purification columns (Amersham Biosciences).  All experimental procedures followed the instructions of the suppliers and essentially as described in the ULTRAGAPS activated slide processing protocol.

treatment_protocol: Sediment (0.5g, wet weight) and 0.25 ml of bacterial suspension (approximately 1.0E+10 E. coli cells/ml suspended in K-medium) were mixed and transferred to 24 test vials (2x 12-well polystyrene multi dishes). Nematode-suspension (0.5 ml, 20,000 age synchronized individuals) was transferred to each test vial and the test organisms exposed for 48 h to the respective treatment. To recover the nematodes, the content of the vials were transferred into 50 ml centrifuge tubes using a suspension of colloidal silica  in deionized water (density: 1.15 g cm-³) and centrifuged for 5 min at 800 x g. The supernatant, containing the majority of nematodes, was filtered over a 45 µm-gauze, rinsed back in the falcon tubes and centrifuged for 15 min at 800 x g. Trizol (Invitrogen, Germany) was added to the nematode pellet and stored at -20°C.


title: Time=0 (n=1)

status: Public on Jun 24 2008

city: Pacific Grove

first: Tyler

middle: G

last: Evans

state: CA

address: 120 Oceanview Blvd

institute: Stanford University

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample Time=0-individual 1

hyb_protocol: cDNAs were coupled to a monoreactive fluorescent (either Cy3 or Cy5; Amersham) dye and hybridized to the array for 15h at 65 degrees C; lowering hybridization temperature can increase detection of features with low sequence homology, so the use of a single, high hybridization temperature were used to reduce non-specific binding of probes to the array. Control or osmotic stress samples were competitively hybridized against a reference sample of total RNA from the same species.

scan_protocol: Slides were scanned on an Axon 4.0 scanner

data_processing: GeneSpring software was used to convert raw data values into ratios of Cy5 to Cy3. These ratios were Lowess normalized and then each value was normalized to the average of the control slides

organism: Gillichthys mirabilis

label_protocol: Total RNAs were reverse transcribed to cDNA and covalently linked via a amino-allyl UTP to Cy3 or Cy5 monoreactive dye prepared in 100 microliters DMSO by incubating at room temp for 2 hours.

growth_protocol: Fish were maintained in recirculating seawater and fed trout pellets daily

extract_protocol: Trizol extraction of total RNA and cleaned using Ambion filter catridges

treatment_protocol: Fish were acclimated to 31 ppt and sacrificed directly

tag: Gill tissue cDNAs from control Time=0 fish

source_name: Reference

extract_protocol: Trizol extraction of total RNA and cleaned using Ambion filter cartridges. Following reverse transcription, cDNAs from several individuals were pooled to create the reference sample used throughout these experiments.

tag: Gill tissue cDNAs from reference fish


title: RH RRE2 WT B vs QW434 B 7D 2

description: No


title: RH RRE2 WT B VS QW226 B 7D 3

description: No

hyb_protocol: 42 degree for overnight

extract_protocol: Biorad Aquapure RNA isolation kit


title: RH RRE2 WT B stnry vs QW434 B stnry 7D 2

description: No


title: Time=0 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample Time=0-individual 3


title: RH RRE2 WT b VS QW226 B 7D 1

description: No

tag: from LB culture at log phase

value: igaA(T191P), RcsAB box mutation in flhD promoter

source_name: Wild type 14028


title: C.elegans exposed to Danube sediment, replicate 1

description: Danube sediment exposed nematodes: Biological replicate 1 of 5.


title: Low Salt Water Time=12 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=12-individual 2

source_name: Low Salt Water Time=12

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 10 ppt and sacrificed after 12 hours

tag: Gill tissue cDNAs from hypoosmotic stressed fish


title: Low Salt Water Time=12 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=12-individual 1


title: RH RRE2 WT B vs QW119 B 5D 2

description: no

tag: QW119 (also called QW117) is an igaA point mutant

source_name: wildtype 14028

extract_protocol: biorad Aquapure RNA isolation kit


title: C.elegans exposed to Danube sediment, replicate 4

description: Danube sediment exposed nematodes: Biological replicate 4 of 5.

data_processing: The VALUE data was derived following normalization (background correction and Print-Tip-Lowess algorithm) using the R-Package, then imported in to GeneSpring 7.3.1 & Log transformed using “per chip” and “per gene” median polishing. The log2 values ranging between 0.71 and1.4 of normal distribution were used for “Fold Change” and “1way ANOVA” analysis.


title: Low Salt Water Time=12 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=12-individual 3


title: Time=0 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample Time=0-individual 2


title: RH RRE2 WT B vs QW119 B 5D 3

description: no


title: C.elegans exposed to Elbe sediment, replicate 1

description: Elbe sediment exposed nematodes: Biological replicate 1 of 5.


title: RH RRE2 WT B VS QW226 B 7D 2

description: No

tag: FROM LB AT LOG PHASE


title: RH RRE2 WT B VS QW434 B 7D 1

description: No

tag: From LB culture at log phase


title: RH RRE2 WT B vs QW434 B 7D 3

description: No


title: Low Salt Water Time=4 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=4-individual 3

source_name: Low Salt Water Time=4

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 10 ppt and sacrificed after 4 hours


title: Low Salt Water Time=4 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=4-individual 2


title: RH RRE2 WT B vs QW119 B 5D 1

description: no

source_name: QW119 RNA from LB broth at log phase

tag: total RNA labled with Cy5

tag: QW119 (also called qw117) is a igaA point mutation

source_name: wild type RNA from LB broth at log phase

tag: total RNA labled with Cy3


title: Low Salt Water Time=2 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=2-individual 3

source_name: Low Salt Water Time=2

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 10 ppt and sacrificed after 2 hours


title: Low Salt Water Time=4 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=4-individual 1

tag: Gill tissue cDNAs from hypoosmotic strssed fish


title: C.elegans exposed to Danube sediment, replicate 3

description: Danube sediment exposed nematodes: Biological replicate 3 of 5.

tag: Age

tag: Tissue

tag: Strain


title: Low Salt Water Time=2 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=2-individual 2


title: Low Salt Water Time=1 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=1-individual 3

source_name: Low Salt Water Time=1

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 10 ppt and sacrificed after 1 hour


title: Low Salt Water Time=2 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=2-individual 1


title: Low Salt Water Time=1 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=1-individual 1


title: Low Salt Water Time=1 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Low Salt sample-Time=1-individual 2


title: High Salt Water Time=12 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=12-individual 1

source_name: High Salt Water Time=12

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 70 ppt and sacrificed after 12 hours

tag: Gill tissue cDNAs from hyperosmotic stressed fish


title: High Salt Water Time=4 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=4-individual 3

source_name: High Salt Water Time=4

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 70 ppt and sacrificed after 4 hours


title: High Salt Water Time=12 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=12-individual 2

tag: Gill tissue cDNAs form hyperosmotic stressed fish


title: High Salt Water Time=12 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=12-individual 3


title: High Salt Water Time=4 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=4-individual 1


title: High Salt Water Time=1 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=1-individual 2

source_name: High Salt Water Time=1

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 70 ppt and sacrificed after 1 hour

extract_protocol: Trizol extraction of total RNA and cleaned using Ambion filter cartridges. Following reverse transcription, cDNAs from serveral individuals were pooled to create the reference sample used throughout these experiments.


title: High Salt Water Time=2 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=2-individual 2

source_name: High Salt Water Time=2

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks at 70 ppt and sacrificed after 2 hours

tag: Gill tissue cDNAs from hyperosmotic stress fish


title: High Salt Water Time=2 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=2-individual 1

tag: Gill tissue from hyperosmotic stressed fish


title: High Salt Water Time=2 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=2-individual 3

tag: Gill tissue cDNAs from reference fish


title: Control Time=12 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=12-individual 2

source_name: Control Time=12

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks also at 31 ppt and sacrificed after 12 hours

tag: Gill tissue cDNAs from control fish


title: Control Time=4 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=4-individual 1

source_name: Control Time=4

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks also at 31 ppt and sacrificed after 4 hours


title: Control Time=4 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=4-individual 3


title: High Salt Water Time=1 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=1-individual 3


title: Control Time=4 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=4-individual 2


title: Control Time=12 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=12-individual 3


title: High Salt Water Time=4 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=4-individual 2

tag: Gill tissie cDNAs from hyperosmotic stressed fish


title: Control Time=12 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=12-individual 1


title: Control Time=2 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=2-individual 2

source_name: Control Time=2

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks also at 31 ppt and sacrificed after 2 hours


title: Control Time=2 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=2-individual 3


title: Control Time=2 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=2-individual 1


title: Control Time=1 (n=2)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=1-individual 2

hyb_protocol: cDNAs were coupled to a monoreactive fluorescent (either Cy3 or Cy5; Amersham) dye and hybridized to the array for 15h at 65 degrees C; lowering hybridization temperature can increase detection of features with low sequence homology, so the use of a single, high hybridization temperature were used to reduce non-specific binding of probes to the array. Control or osmotic stress gill samples were competitively hybridized against a reference sample of total RNA from the same species.

scan_protocol: Slides were scanned on an Axon Pro 4.0 scanner

data_processing: GeneSpring software was used to convert raw data values into ratios of Cy5 to Cy3. These ratios were Lowess normalized and then each value was normalized to the average of the control slides.

source_name: Control Time=1

label_protocol: Total RNAs were reverse transcribed to cDNA and covalently linked via a amino-allyl UTP to Cy3 or Cy5 cyanine monoreactive dye prepared in 100 microliters of DMSO by incubating at room temp for 2 hours

growth_protocol: Fish were maintained in recirculating seawater aquaria and fed trout pellets daily

extract_protocol: Trizol extraction of total RNA and cleaned using Ambion filter cartridges

treatment_protocol: Fish were acclimated to 31 ppt and transfered into tanks also at 31 ppt and sacrificed after 1 hour.

treatment_protocol: Fish were acclimated to 31 ppt and sacrificed directly.


title: Control Time=1 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=1-individual 1

source_name: Reference


title: High Salt Water Time=1 (n=1)

description: Gillichthys mirabilis osmotic stress gill tissue-High Salt sample-Time=1-individual 1


title: Control Time=1 (n=3)

description: Gillichthys mirabilis osmotic stress gill tissue-Control sample-Time=1-individual 3


title: OAW_42_02.CEL

city: Budapest

first: Balazs

last: Györffy

address: Bókay 53

country: Hungary

institute: Hungarian Academy of Sciences

description: total RNA extracted from different cancer cell lines

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite version 5.0

label: standard Affymetrix procedure

organism: Homo sapiens

source_name: cancer cell line

label_protocol: standard Affymetrix procedure

extract_protocol: Qiagen Rneasy

tag: cell line


title: 257P_17.CEL


title: TEV-At17 infected Replicate 2

status: Public on Jun 23 2008

city: Valencia

first: Miguel

last: Perez-Amador

state: Valencia

address: Avda. de los Naranjos s/n

country: Spain

institute: Inst. Biologia Molecular y Celular de Plantas (IBMCP-CSIC)

description: TEV At17-infected plant, replica 2, labelled with Cy5, compared with reference mix, labelled with Cy3

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains of 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillary between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-nm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.

organism: Arabidopsis thaliana

source_name: TEV At17-infected resette and cauline leaves

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Seeds were sown in standard Arabidopsis media and kept at 25°C in a 16h light/8h dark photoperiod.

extract_protocol: Total RNA was extracted from frozen rossete and cauline leaves, using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Four-week-old (stages 3.5-3.7 in the Boyes scale (Boyes et al. 2001, Plant Cell 13: 1499-1510) were inoculated with mock, TEV and TEV-At17, and were harvested two weeks later.

tag: 6-week-old resette and cauline leaves TEV At17-infected

source_name: reference mix

tag: reference mix


title: TEV-At17 infected Replicate 3

description: TEV At17-infected plant, replica 3, labelled with Cy3, compared with reference mix, labelled with Cy5


title: 181P_07.CEL

source_name: pancreas cancer cell line


title: TEV infected Replicate 5

description: TEV-infected plant, replica 5, labelled with Cy5, compared with reference mix, labelled with Cy3

source_name: TEV-infected resette and cauline leaves

tag: 6-week-old resette and cauline leaves TEV-infected


title: TEV-At17 infected Replicate 4

description: TEV At17-infected plant, replica 4, labelled with Cy3, compared with reference mix, labelled with Cy5


title: TEV-At17 infected Replicate 1

description: TEV At17-infected plant, replica 1, labelled with Cy5, compared with reference mix, labelled with Cy3


title: Mutant histone H4R45H- replicate3

city: Pullman

first: Michael

middle: J.

last: Smerdon

state: WA

department: School of Molecular Biosciences

institute: Washington State University

description: Mutant yeast strain H4 R45H

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0.

label: Biotin

source_name: Yeast RNA, H4 R45H (Arginine 45 of histone H4 mutated to Histidine)

label_protocol: Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Cells were grown in YPD media until mid log phase and harvested at OD600 of 0.5-0.7.

extract_protocol: Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

treatment_protocol: Cells were fixed in liquid nitrogen


title: Mock Infected Replicate 3

description: Control Mock-infected plant, replica 3, labelled with Cy3, compared with reference mix, labelled with Cy5

source_name: Mock-infected resette and cauline leaves

tag: 6-week-old resette and cauline leaves Mock-infected


title: TEV Infected Replicate 1

description: TEV-infected plant, replica 1, labelled with Cy5, compared with reference mix, labelled with Cy3


title: TEV-At17 infected Replicate 5

description: TEV At17-infected plant, replica 5, labelled with Cy5, compared with reference mix, labelled with Cy3


title: TEV infected Replicate 4

description: TEV-infected plant, replica 4, labelled with Cy3, compared with reference mix, labelled with Cy5


title: Mock Infected Replicate 1

description: Control Mock-infected plant, replica 1, labelled with Cy5, compared with reference mix, labelled with Cy3


title: Mutant histone H4R45H- replicate2

description: Mutant yeast strain H4 R45H

tag: H4 R45H (Arginine 45 of histone H4 mutated to Histidine)


title: TEV infected Replicate 2

description: TEV-infected plant, replica 2, labelled with Cy5, compared with reference mix, labelled with Cy3


title: Mutant histone H4R45H- replicate1

description: Mutant yeast strain H4 R45H


title: Wild type for H4 R45H-replicate2

description: Wild type yeast strain

source_name: Yeast RNA, WY139 (wild-type histone H4)

tag: WY139 (wild-type histone H4)


title: Wild type for H4 R45H-replicate3

description: Wild type yeast strain


title: TEV infected Replicate 3

description: TEV-infected plant, replica 3, labelled with Cy3, compared with reference mix, labelled with Cy5


title: Mock Infected Replicate 4

description: Control Mock-infected plant, replica 4, labelled with Cy5, compared with reference mix, labelled with Cy3


title: Mock Infected Replicate 2

description: Control Mock-infected plant, replica 2, labelled with Cy3, compared with reference mix, labelled with Cy5


title: Mock Infected Replicate 5

description: Control Mock-infected plant, replica 5, labelled with Cy5, compared with reference mix, labelled with Cy3


title: Saccharomyces cerevisiae oligo microarray_rep2_allicin

city: Changchun

first: Xuming

last: Deng

address: Xi'an Street 5333#

institute: College of Animal Science and Veterinary Medicine, Jilin University

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in  hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.hybridization solution was denatured at 95? for 3 min prior to loading onto a microarray.then,hybridizing at a rotation speed of 8 rpm and a temperature of 42? overnight and washed with two consecutive solutions.

scan_protocol: LuxScanTM 3.0 software

data_processing: A space- and intensity-dependent normalization based on a LOWESS program,For further statistical analyses, The Significance Analysis of Microarrays (SAM ) add-in to Microsoft Excel was used to  compare the replicate arrays experiments.

source_name: Saccharomyces cerevisiae_allicin

label_protocol: cDNA products subjected to transcription reactions .Klenow enzyme labeling strategy was adopted after reverse transcription.

growth_protocol: S. cerevisiae strain L1190 was incubated in a rotary shaker. Subsequently, allicin stock solution, prepared in dimethyl sulfoxide (DMSO), was added to the culture. Then, the yeast cells were further incubated for a certain time.

extract_protocol: Total RNA was extracted by a hot acidic phenol method. Collart,M.A. & Oliviero, S. (1995). Preparation of yeast RNA.In Short Protocols in Molecular Biology, 3rd edn, (Ausubel F., Brent R., Kingston, R. T., Moode, D. D, Seidman, J. G., Smith, J. A. et al., Eds), pp. 13-46-13-47. John Wiley and Sons, Inc., New York, NY.

treatment_protocol: plant medicine allicin

tag: strain L1190 refer to the previous study done by liang zhang et al 2002 JAC

source_name: Saccharomyces cerevisiae_DMSO

growth_protocol: S. cerevisiae strain L1190 was incubated in a rotary shaker. Subsequently,DMSO was added to the culture. Then, the yeast cells  were further incubated for a certain time.

treatment_protocol: DMSO


title: Wild type for H4 R45H-replicate1

description: Wild type yeast strain


title: 2 hr IL-3 stimulated BaF3 cells + ctrl SiRNA_U74B

city: Regensburg

first: Anne

last: Rascle

address: Universitaetsstrasse

country: Germany

institute: University of Regensburg

hyb_protocol: Affymetrix Protocol

scan_protocol: Affymetrix Protocol

label: biotinylation

organism: Mus musculus

source_name: 2 hr IL-3 stimulated BaF3 cells

label_protocol: Affymetrix Protocol

extract_protocol: RNeasy Maxi kit, including an on-column DNase I treatment (Qiagen)


title: 2 hr IL-3 stimulated BaF3 cells + Stat5 SiRNA_U74B


title: Saccharomyces cerevisiae oligo microarray_rep3_allicin

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in  hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.hybridization solution was denatured at 95C for 3 min prior to loading onto a microarray.then,hybridizing at a rotation speed of 8 rpm and a temperature of 42C overnight and washed with two consecutive solutions.


title: Saccharomyces cerevisiae oligo microarray_rep1_allicin

hyb_protocol: Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in  hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide.Hybridization solution was denatured at 95? for 3 min prior to loading onto a microarray.then,hybridizing at a rotation speed of 8 rpm and a temperature of 42? overnight and washed with two consecutive solutions.


title: 30 min IL-3 stimulated BaF3 cells + Stat5 SiRNA_U74B

source_name: 30 min IL-3 stimulated BaF3 cells


title: unstimulated BaF3 cells + ctrl SiRNA_U74B

source_name: BaF3 cells + ctrl SiRNA

tag: unstimulated BaF3 cells + ctrl SiRNA


title: unstimulated BaF3 cells + ctrl SiRNA_U74C

source_name: unstimulated BaF3 cells


title: CHC562N-dChip-U133A

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description: Detailed procedure is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, PMID: 17379603].

hyb_protocol: Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).

data_processing: Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].

label_protocol: For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.

tag: Sample

tag: Gender

value: female;

tag: Age at onset

value: 33 years;

tag: Disease

value: hepatocellular adenoma;

tag: Tissue

value: non tumoral liver.


title: CHC357N-dChip-U133A

value: 28 years;


title: 30 min IL-3 stimulated BaF3 cells + ctrl SiRNA_U74C


title: 2 hr IL-3 stimulated BaF3 cells + ctrl SiRNA_U74C


title: Kidney_High-dose_Rep3

city: Osaka

first: Masatomo

last: Rokushima

state: Osaka

address: 12-4, Sagisu 5-chome, Fukushima-ku

department: Discovery Research Laboratories

institute: SHIONOGI & CO., LTD.

description: Raw data file contains a variety of information.  The raw signals used for analysis are located in the column Q, which is entitled gProcessedSignal in the spreadsheet.

hyb_protocol: Cyanine 3-labeled cRNA targets were hybridized to Whole Rat Genome Oligo Microarray at 65°C for 17 h following the procedures recommended by the manufacturer (Agilent Technologies).  After hybridization, the microarray slide was washed and dried according to the protocol provided by the manufacturer.

scan_protocol: The microarray slide was scanned on an Agilent DNA microarray scanner (Agilent Technologies).  The scan resolution was 5 micrometer and the eXtended Dynamic Range feature (XDR Hi 100%, XDR Low 10%) was used to scan the array twice at two different PMT levels.  Hybridization images were quantified using Feature Extraction Software 9.1 (Agilent Technologies), and background-subtracted signal values were utilized for following analyses.

data_processing: Raw microarray data were processed and analyzed with GeneSpring GX 7.3.1 (Agilent Technologies).  For per array normalization, the 50th percentile of the signal values taken from each microarray was used as the normalizing reference.  Per gene normalization was based on calculating fold expression levels relative to the median of the control animals (n = 3).

organism: Rattus norvegicus

source_name: kidney cortex, high-dose of CER, 24 h

label_protocol: Labeled cRNA targets were prepared using Low RNA Input Linear Amplification Kit according to the “One-Color Microarray-Based Gene Expression Analysis” protocol provided by the manufacturer (Agilent Technologies).  Briefly, 500 ng of total RNA was reverse-transcribed using a primer containing oligo-dT and a T7 promoter.  Using the resultant cDNAs as templates, cRNA targets were synthesized by in vitro transcription in the presence of cyanine 3-CTP.  The resultant labeled cRNAs were purified using RNeasy Mini Kit and quantified by absorbance at 260 nm.

growth_protocol: Male Fisher 344 rats (7-week-old) were purchased from Charles River Laboratories Japan (Kanagawa, Japan) and housed in plastic cages in an environmentally controlled room (12 h light-dark cycle, 23 ± 3°C and 50 ± 20% relative humidity).  The animals had ad libitum access to certified rodent chow (Oriental Yeast, Tokyo, Japan) and water, and were acclimatized under these conditions for a week before experimentation.

extract_protocol: The kidney cortex was disrupted and homogenized in QIAzol Lysis Reagent with TissueLyser (Qiagen).  Total RNA was isolated from the homogenates using a BioRobot® M48 Workstation (Qiagen) in combination with MagAttract® RNA Cell Mini M48 Kit following the manufacturer’s instructions, including a DNase digestion step.

treatment_protocol: CER was dissolved in saline and intravenously administered as a single dose of 0 (vehicle only), 150, 300 or 600 mg/kg.  The animals were sacrificed 24 h after the administration.

tag: Strain

value: Fisher 344

value: male

tag: Age

value: 8 weeks

value: kidney cortex


title: CHC573N-dChip-U133A


title: 30 min IL-3 stimulated BaF3 cells + Stat5 SiRNA_U74C


title: 2 hr IL-3 stimulated BaF3 cells + Stat5 SiRNA_U74C

source_name: BaF3 cells + Stat5 SiRNA


title: CHC535N-dChip-U133A

value: 30 years;


title: Kidney_High-dose_Rep1


title: Kidney_High-dose_Rep2


title: Kidney_Low-dose_Rep1

source_name: kidney cortex, low-dose of CER, 24 h


title: 2 hr IL-3 stimulated BaF3 cells + Stat5 SiRNA_U74A


title: Kidney_Middle-dose_Rep1

source_name: kidney cortex, middle-dose of CER, 24 h


title: Kidney_Low-dose_Rep2


title: Kidney_Control_Rep2

source_name: kidney cortex, saline, 24 h


title: Kidney_Middle-dose_Rep2


title: 30 min IL-3 stimulated BaF3 cells + ctrl SiRNA_U74A

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

source_name: BaF3 cells

label_protocol: Affymetrix protocol

tag: BaF3 cells + ctrl SiRNA stimulated with IL-3


title: Kidney_Low-dose_Rep3


title: 2 hr IL-3 stimulated BaF3 cells + ctrl SiRNA_U74A

tag: BaF3 cells stimulated with IL-3


title: 30 min IL-3 stimulated BaF3 cells + Stat5 SiRNA_U74A


title: Kidney_Control_Rep3


title: Kidney_Middle-dose_Rep3


title: Kidney_Control_Rep1


title: unstimulated BaF3 cells + ctrl SiRNA_U74A

tag: BaF3 cells + ctrl SiRNA


title: Control GFPi-122 siRNA vs Reference (Replicate 1)

status: Public on Jun 21 2008

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

description: 10-condition, two-color hybridization experiment employing a common reference design (Stratagene Universal Human Reference RNA), Scrambled vs. GLUTi-1356 siRNA vs. GLUTi-774 siRNA vs. KERi-1084 siRNA vs. KERi-660 siRNA vs. DEADi-1261 siRNA vs. RPL32i-378 siRNA vs. TFDPi-1196 siRNA vs. TFDPi-680 siRNA vs. Control GFPi-122 siRNA.

hyb_protocol: Printed arrays were pre-hybridized in a prehybridization buffer (5x SSC; 0.1% SDS; 1% BSA) for 45 minutes at 42C. Labeled cDNA samples (one labeled with Cy3 and a second with Cy5) were combined and lyophilized. The lyophilized pellet was resuspended in a hybridization buffer (50% formamide; 5x SSC; 0.1% SDS) and heated to 95C for 5 minutes and immediately snap-cooled. The labeled cDNA was then applied to the pre-hybridzed array under glass coverslip. The array was sealed in a hyb chamber and incubated overnight at 42C. The array was subsequently washed three times in buffers of increasing stringency (Low: 1.0x SSC, 0.2% SDS; Medium: 0.1x SSC, 0.2% SDS; High: 0.1x SSC). The arrays were quickly dried and immediately scanned.

scan_protocol: The hybridized microarray chips were scanned on an Axon GenePix 4000B scanner under the two-color mode for Cy3 and Cy5 fluorophores.

data_processing: The Cy3 and Cy5 images were analyzed through GenePix Pro 4.0 to calculate spot intensities and exported obtaining a .gpr file. The .gpr file was processed through TIGR Express Converter to generate a .mev file. The .mev file was then taken through the TIGR MIDAS to perform lowess normalization.

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: Control GFPi-122

label_protocol: Single-stranded cDNA was generated through reverse transcription of total RNA by Superscript III (Invitrogen) and random primers. Amino-allyl dUTP (in a ratio of 2:3 with dTTP) was incorporated during the reverse transcription. The RNA was then degraded by hydrolysis under alkaline conditions and the amino-allyl cDNA was subsequently purified with PCR Purification columns (Qiagen) substituting a phosphate wash buffer and phosphate elution buffer for the Tris-containing buffers in the kit. The purified sample was lyophilized and resuspended in sodium carbonate buffer and allowed to couple to the Cy3 fluorophore for an hour at room temperature. The reaction was stopped by sodium acetate and then the labeled cDNA was purified to remove uncoupled dye with PCR Purification columns (Qiagen) as per manufacturer's protocol.

growth_protocol: Cells were cultured in 100 mm dishes containing RPMI medium supplemented with 10% fetal bovine serum and grown at 37C and 5% CO2

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) and subsequently puried using Rneasy columns (Qiagen) according to manufacturer's protocols.

treatment_protocol: Cells were cultured for 24 hours to 50% confluence before transfection with the small interfering RNA (siRNA) duplex using LipofectAMINE (Invitrogen), following the manufacturer's protocol. Briefly, the siRNA duplex mixed with 50 ul OptiMEM and LipofectAMINE mixed with 50 ul of OptiMEM were simultaneously incubated at room temperature for 5 minutes. Subsequently, the two mixtures were combined and incubated at room temperature for 20 minutes. The siRNA:LipofectAMINE complex was added to the cells (at a final siRNA duplex concentration of 100 pmol per milliliter of culture medium) and left in the plate for 48 hours after which the cells were harvested for RNA extraction.

tag: HT29 cells were transfected with siRNA (according to treatment protocol). siRNA

value: Control GFPi-122. Sense sequence:GCAAGCUGACCCUGAAGUUCAU. Antisense sequence:GAACUUCAGGGUCAGCUUGCCG.

source_name: Stratagene Universal Human Reference RNA (Catalog # 740000)

tag: Stratagene's Universal Human Reference RNA is composed of total RNA from 10 human cells lines. Cell line derivations include

value: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, marcophage, histocyte; Lymphoblastic leukemia, T lymphoblast; and Plasmacytoma, myeloma, B lymphocyte.


title: TFDPi-680 siRNA vs Reference (Replicate 2)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: TFDPi-680 (NM_007111)

value: TFDPi-680 (NM_007111). Sense sequence:CGAGUCAGCUUAUGACCAGdTdT. Antisense sequence:CUGGUCAUAAGCUGACUCGdTdT.


title: Control GFPi-122 siRNA vs Reference (Replicate 2)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: ControlGFPi-122


title: TFDPi-680 siRNA vs Reference (Replicate 1)


title: TFDPi-1196 siRNA vs Reference (Replicate 1)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: TFDPi-1196 (NM_007111)

value: TFDPi-1196 (NM_007111). Sense sequence:GGCUCUGGAGCCAUACGUGdTdT. Antisense sequence:CACGUAUGGCUCCAGAGCCdTdT.


title: RPL32i-378 siRNA vs Reference (Replicate 2)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: RPL32i-378 (NM_001007074)

value: RPL32i-378 (NM_001007074). Sense sequence:GCCAUCGUGGAAAGAGCUGdTdT. Antisense sequence:CAGCUCUUUCCACGAUGGCdTdT.


title: 30 min IL-3 stimulated BaF3 cells + ctrl SiRNA_U74B


title: DEADi-1261 siRNA vs Reference (Replicate 2)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: DEADi-1261 (NM_018180)

value: DEADi-1261 (NM_018180). Sense sequence:GACAUGACGCCACUGAAGCdTdT. Antisense sequence:GCUUCAGUGGCGUCAUGUCdTdT.


title: KERi-660 siRNA vs Reference (Replicate 2)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: KERi-660 (NM_09010)

value: KERi-660 (NM_09010). Sense sequence:GGAGCAUCAGGAGGAAGUCdTdT. Antisense sequence:GACUUCCUCCUGAUGCUCCdTdT.


title: KERi-660 siRNA vs Reference (Replicate 1)


title: TFDPi-1196 siRNA vs Reference (Replicate 2)


title: KERi-1084 siRNA vs Reference (Replicate 2)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: KERi-1084 (NM_09010)

value: KERi-1084 (NM_09010). Sense sequence:CGCCAGAACAACGAAUACCdTdT. Antisense sequence:GGUAUUCGUUGUUCUGGCGdTdT.


title: DEADi-1261 siRNA vs Reference (Replicate 1)


title: RPL32i-378 siRNA vs Reference (Replicate 1)


title: GLUTi-1356 siRNA vs Reference (Replicate 2)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: GLUTi-1356 (NM_014905)

value: GLUTi-1356 (NM_014905). Sense sequence:GAGUACUGAGCCCUGAAGCdTdT. Antisense sequence:GCUUCAGGGCUCAGUACUCdTdT.


title: KERi-1084 siRNA vs Reference (Replicate 1)


title: GLUTi-774 siRNA vs Reference (Replicate 1)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: GLUTi-774 (NM_014905)

value: GLUTi-774 (NM_014905). Sense sequence:CUGGCCAAAUUCAGUCCCGdTdT. Antisense sequence:CGGGACUGAAUUUGGCCAGdTdT.


title: GLUTi-774 siRNA vs Reference (Replicate 2)


title: GLUTi-1356 siRNA vs Reference (Replicate 1)


title: Scrambled Control 1 vs Reference (Replicate 1)

source_name: HT29 (human colon adenocarcinoma) cell line transfected with siRNA: Scrambled Control 1 (sequence-scrambled version of CCR9i-436)

value: Scrambled Control 1 (sequence-scrambled version of CCR9i-436). Sense sequence:GUAGGCAAGCAUCUGAGCUdTdT. Antisense sequence:AGCUCAGAUGCUUGCCUACdTdT.


title: F3-Vinclozolin Ventral Prostate, replica 1

status: Public on Jun 20 2008

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data for ventral prostate of F3 Vinclozolin treated 180-day-old rats

scan_protocol: chips were scanned using Affymetrix GeneArray Scanner G2500A

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software using default normalization method. Target signal was set to 125. MAS-5 preprocessing was used.

source_name: whole ventral prostate from vinclozolin treated F3 generation, 180-day-old male rat

label_protocol: standard Affymetrix procedures

extract_protocol: Several ventral prostates from animals with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).

treatment_protocol: Sprague-Dawley pregnant rats were given intraperitoneal injections of vehicle (DMSO) from pregnancy day E8 to E14. Offsprings from above (F0 generation animals)  were used for sequential breeding to obtain generations F1, F2, and F3. Tissue from F3 rats was used in the experiment.


title: Scrambled Control 1 vs Reference (Replicate 2)


title: F3-Control Prostate Epithelium, replica 2

description: Gene expression data for epithelium cells of ventral prostate of F3 control 45-day-old rats

source_name: epithelium cells of ventral prostate from control F3 generation, 45-day-old male rat

extract_protocol: Epithelium of ventral prostates from 11 animals with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).


title: F3-Vinclozolin Prostate Epithelium, replica 1

description: Gene expression data for epithelium cells of ventral prostate of F3 Vinclozolin treated 45-day-old rats

source_name: epithelium cells of ventral prostate from Vinclozolin treated F3 generation, 45-day-old male rat


title: F3-Vinclozolin Ventral Prostate, replica 2

tag: whole ventral prostate from vinclozolin treated F3 generation, 180-day-old male rat


title: F3-Control Ventral Prostate, replica 2

description: Gene expression data for ventral prostate of F3 control 180-day-old rats

source_name: whole ventral prostate from control F3 generation, 180-day-old male rat

tag: whole ventral prostate from control F3 generation1, 180-day-old male rat


title: F3-Control Prostate Epithelium, replica 1

tag: epithelium cells of ventral prostate from control F3 generation, 45-day-old male rat


title: F3-Vinclozolin Prostate Epithelium, replica 2

tag: epithelium cells of ventral prostate from Vinclozolin treated F3 generation, 45-day-old male rat


title: F3-Control Ventral Prostate, replica 1

scan_protocol: chips were scanned using Affimetrix Gene Chip Scanner 3000

tag: whole ventral prostate from control F3 generation, 180-day-old male rat


title: V6_WILDTY_24_YA0403#20_074

city: Birmingham

first: Nicklas

last: Bonander

address: Aston University

department: LHS -Life and Health Science

institute: Aston university

hyb_protocol: Wistar Institute Hybridization protocol

scan_protocol: Wistar Institute scan protocol

data_processing: Wistar Institute nMD: normalized Median Density method

source_name: Wild-type V5 strain media glucose concentration 7.4 g/L

label_protocol: Wistar Institute label protocol

extract_protocol: Wistar Institute extract protocol

treatment_protocol: Transformants were selected by growth on glucose. The resulting ura3 strain is referred to as V5.TM6*. The auxotrophic V5 wild type and V5.TM6* used in this study were made prototrophic by integration of URA3 [3] and are referred to as the V5 wild-type strain and V5.TM6*P, respectively. The growth media in the bioreactor was 5 × defined minimal medium [4], stirring was 1000rpm; Temp  30C; Aeriation 0.5 vvm; pH 5.

tag: Compare a wild type Saccaromyces cerevisise strain V5 strain (=V), with a mutant strain where glucose transport has been reduced by at least 30% in the strain V5.TM6*P (=T), mutant is lacking 7 hexose transporters HXT1, HXT2, HXT3, HXT4, HXT5, HXT6, HXT7, the plasma membrane contains a HXT1-HXT7 fusion protein. This construct is a combination of a low and high affinity glucose transporters. The glucose concentration in the culture media of each array is the parameter that can be how the arrays are sorted.

tag: Yeast cells grown in bioreactors monitoring, pH (=5) temp (=30ºC) and pO2>50% as well as O2 and CO2 in outlet gas. Growth media is YNB-CSM starting at 5% glucose. No detectable or small levels of glycerol (0g/g-starting glucose concentration) and ethanol (<2.5g/g-starting glucose concentration) after glucose depletion in the V5.TM6*P supporting the claim that V5.TM6*P grows fully respiratory on glucose. Result 1

value: V5 to V5.TM6*P RNA transition induce genes typical for respiratory growth. Result 2:There is a glucose dependence in the array signal of 20 genes (e.g HXT1, RGS2, ADH7, CHA4 and GLK1) in wild type V5 strain is not seen in the V5.TM6*P strain, this is an evidence for that glucose sensing occurs inside the yeast cell. That is, an intact glucose plasma membrane transport system is required for responding to a change in glucose concentration in the range 40 to 5g/L glucose. Last three letters of title is glucose concentration in media, in units g/L if divided by 10 (e.g. T1_MUTANT_13_YA0403#22_365, the residual glucose concentration of this sample is 36.5g/L).


title: V5_WILDTY_23_YA0403#18_105

source_name: Wild-type V5 strain media glucose concentration 10.5 g/L


title: V4_WILDTY_22_YA0403#16_244

source_name: Wild-type V5 strain media glucose concentration 24.4 g/L


title: V6_WILDTY_24_YA0403#21_074


title: T5_MUTANT_17_YA0403#06_135

source_name: Mutant V5.TM6*P strain media glucose concentration 13.5 g/L


title: V1_WILDTY_19_YA0403#10_384

source_name: Wild-type V5 strain media glucose concentration 38.4 g/L


title: T4_MUTANT_16_YA0403#05_251

source_name: Mutant V5.TM6*P strain media glucose concentration 25.1 g/L


title: T6_MUTANT_18_YA0403#09_056

source_name: Mutant V5.TM6*P strain media glucose concentration 5.6 g/L


title: V5_WILDTY_23_YA0403#19_105


title: V1_WILDTY_19_YA0403#11_384


title: V4_WILDTY_22_YA0403#17_244


title: T4_MUTANT_16_YA0403#04_251


title: T6_MUTANT_18_YA0403#08_056


title: V2_WILDTY_20_YA0403#12_350

source_name: Wild-type V5 strain media glucose concentration 35.0 g/L


title: T5_MUTANT_17_YA0403#07_135


title: V2_WILDTY_20_YA0403#13_350


title: V3_WILDTY_21_YA0403#14_255

source_name: Wild-type V5 strain media glucose concentration 25.5 g/L


title: T2_MUTANT_14_YA0403#24_348

source_name: Mutant V5.TM6*P strain media glucose concentration 34.8 g/L


title: V3_WILDTY_21_YA0403#15_255


title: T3_MUTANT_15_YA0403#02_263

source_name: Mutant V5.TM6*P strain media glucose concentration 26.3 g/L


title: T2_MUTANT_14_YA0403#01_348


title: T1_MUTANT_13_YA0403#23_365

source_name: Mutant V5.TM6*P strain media glucose concentration 36.5 g/L


title: T1_MUTANT_13_YA0403#22_365


title: uninf_1

city: Frederick

first: Shalini

last: Oberdoerffer

address: 1050 Boyles Street

institute: National Cancer Institute

description: FileNumber: 4

hyb_protocol: microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450

scan_protocol: Genechip scanner 3000 7G

data_processing: The input files were normalized with full quantile normalization (Irizarry et al 2003).  For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points.  Next, the 6,553,590 probes were manipulated into the analysis values as follows.  Probes with GC count less than 6 and greater than 17 were excluded from the analysis.  Probe scores were then transformed by taking the Natural Logarithm of 0.1 plus the probe score.  Background CorrectionExon arrays do not use individual mis-match probes.  Background is established from a pool of probes designed for that purpose.  Background probes are stratified by CG content and are defined in the Human Exon 1.0 ST_antigenomic.bgp file.  BGP files can also be downloaded from www.affymetrix.com.  Each probe score was corrected for background by subtracting the median expression score of background probes with similar GC content.    The Human Exon 1.0 ST array contains 1,404,693 probe-sets (typically, but not always, groups of four probes).  Probe-set Expression Scores and Annotation FilteringThe expression score for a probe-set was defined to be the median of its probe expression scores and probe-sets with fewer than 1 probes (that pass all of the tests defined above) are excluded from further analysis.  Exon Array Probes are designed off of genomic sequence and hence the reliability of probes and probe-sets correspond to the quality of their parent genomic annotations.  Probe-set reliability is ranked from more to less reliable as Core, Extended, or Full.  For example 'Core' probe-sets include probe-sets that correspond to high quality genomic features like RefSeq (www.ncbi.nlm.nih.gov) or Ensembl (www.ensembl.org) transcripts while 'full' and 'extended' probe-sets match less reliable annotations like EST hits and gene prediction algorithms.  For this analysis, only 'Core' probe-sets were analyzed.

source_name: uninfected

label_protocol: labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual

growth_protocol: Human primary CD4+ T cells were isolated from peripheral blood and cultured in IL-2 containing medium.

extract_protocol: RNA was isolated with RNeasy columns (Qiagen)

treatment_protocol: The cells were activated with plate bound anti-CD3 and anti-CD28 for 48 hours.

tag: uninfected


title: 00032903

status: Public on Jun 19 2008

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

description:
Human primary myotubes culture 2 infected with SREBP1c for 48hours vs Human primary myotubes culture 2 infected with Renilla for 48hours
Date:2006/05/04

hyb_protocol: Agilent : 3000.0 ng at 60 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: No normalization performed

label_protocol: Custom

extract_protocol: Trizol

tag: subject #2

value: Human primary myotubes


title: Larvae b 1st instar cy3 vs pooled adult +egg cy 5

city: Lubbock

first: Scot

last: Dowd

address: 4321 Marsha Sharp Fwy

department: MBRI

institute: MBRI

scan_protocol: Microarray images were captured using a Genepix 4000B (Molecular Devices Corporation, Union City, CA) laser scanner and images processed using Genepix 6.0 software (Molecular Devices Corporation). Microarray data analyses were performed using Acuity 4.0 software. Slides were normalized using standard ratio-based methods. Data were analyzed based upon Log ratio (635/532) values. Genes were included in the final dataset that exhibit significance based upon a very conservative FDR less than 2.5% [27] and at least 2.0-fold comparative regulation.

organism: Haematobia irritans

source_name: 1st instar larvae hornfly cy3

label_protocol: In short, RNA from female horn flies was labeled and hybridized against labeled RNA from male horn flies in a dyeswap design. Similarly, RNA from first instar larvae was labeled and hybridized against labeled a 50:50 mix of RNA from adult male and female flies. All labeling, hybridization and washing procedures were performed according to respective manufacturer protocols. For each sample, 10 ug of total RNA and 50-fold dilution of Agilent two color spike-in control RNA kit (Agilent Technologies Inc.) were labeled with either CyDye3-dCTP or CyDye5-dCTP (Amersham Biosciences, Piscataway, NJ) using the LabelStar kit (Qiagen Inc., Valencia, CA) and oligo-dT and Random nonamers (Sigma-Aldrich Inc., St. Louis, MO). Labeled cDNA was hybridized to the Agilent microarrays using the Gene Expression Hybridization kit (Agilent Technologies Inc.) following manufacturer’s protocols. Arrays were washed with Gene Expression Wash Buffer kit (Agilent Technologies Inc.)

tag: 1st instar larvae hornfly cy3

source_name: pooled adult + egg cy 5

extract_protocol: All procedures were performed according to respective manufacturer protocols. RNA was extracted from approximately 1 g of adult flies and 0.1 g larvae using the TotallyRNA Kit (Ambion, Inc., Austin, TX). DNA was removed using Turbo DNA Free Kit (Ambion, Inc.). Two RNA preparations were made from independent samplings of the fly materials. RNA was quantified using a NanoDrop ND-1000 device (NanoDrop Technologies, Wilmington, DE) and quality confirmed by electrophoresis.

tag: pooled adult + egg cy 5


title: GFP_1

description: FileNumber: 5

source_name: shGFP

tag: shGFP


title: 1st instar larvae cy3 vs pooled adult + egg cy5

data_processing: Microarray images were captured using a Genepix 4000B (Molecular Devices Corporation, Union City, CA) laser scanner and images processed using Genepix 6.0 software (Molecular Devices Corporation). Microarray data analyses were performed using Acuity 4.0 software. Slides were normalized using standard ratio-based methods. Data were analyzed based upon Log ratio (635/532) values. Genes were included in the final dataset that exhibit significance based upon a very conservative FDR less than 2.5% [27] and at least 2.0-fold comparative regulation.

extract_protocol: In short, RNA from female horn flies was labeled and hybridized against labeled RNA from male horn flies in a dyeswap design. Similarly, RNA from first instar larvae was labeled and hybridized against labeled a 50:50 mix of RNA from adult male and female flies. All labeling, hybridization and washing procedures were performed according to respective manufacturer protocols. For each sample, 10 ug of total RNA and 50-fold dilution of Agilent two color spike-in control RNA kit (Agilent Technologies Inc.) were labeled with either CyDye3-dCTP or CyDye5-dCTP (Amersham Biosciences, Piscataway, NJ) using the LabelStar kit (Qiagen Inc., Valencia, CA) and oligo-dT and Random nonamers (Sigma-Aldrich Inc., St. Louis, MO). Labeled cDNA was hybridized to the Agilent microarrays using the Gene Expression Hybridization kit (Agilent Technologies Inc.) following manufacturer’s protocols. Arrays were washed with Gene Expression Wash Buffer kit (Agilent Technologies Inc.)

source_name: pooled adult + egg hornfly cy 5

tag: pooled adult + egg hornfly cy 5


title: GFP_2

description: FileNumber: 6


title: 00032782

description:
Human primary myotubes culture 3 infected with SREBP1a for 48hours vs Human primary myotubes culture 3 infected with Renilla for 48hours
Date:2006/05/04

tag: subject #3

tag: Tissue


title: Act_48h_1

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: transcript (gene)-level data

hyb_protocol: Sample preparation, labeling and hybridization to Mouse Exon 1.0 ST Arrays (Affymetrix, CA) were performed according to manufacturer’s protocols by the Microarray Core Facility at the Dana Farber Cancer Institute.

data_processing: The raw intensity containing CEL files were processed using Affymetrix Power Tools (APT) (http://www.affymetrix.com/support/developer/powertools/index.affx). RMA was performed using updated probe annotations (custom CDFs, Version 8) mapping to Refseq transcripts.

source_name: Activated, 48h

growth_protocol: Freshly isolated spleens and lymph nodes were disaggregated into DMEM 10% FBS supplemented with L-glutamine, penicillin, streptomycin, sodium pyruvate, HEPES pH 7.4, non-essential amino acids, and β-mercapto-ethanol.  Following hypotonic lysis of erythrocytes, cell suspensions were incubated with 1:100 dilutions of biotinylated anti-CD8α, anti-CD11b, anti-CD19, anti-CD49b, anti-TER119, anti-GR-1, and anti-γδ (all BD Pharmingen).  Cells were washed once, incubated with anti-biotin magnetic microbeads (1:10, Miltenyi Biotec), washed once more, and purified on magnetic columns.  The eluate was stained with PE-labeled anti-CD4 and Cy-Chrome-labeled streptavidin (BD Pharmingen) and examined via flow cytometry to assess purity.

extract_protocol: Total RNA was isolated from resting and activated T-cells using RNEasy columns (Qiagen). The quality of the total RNA was verified using a BioAnalyzer (Agilent).

treatment_protocol: Purified T lymphocytes (1x106/ml) were stimulated with anti-CD3/anti-CD28 beads (Dynal) at a 1:1 ratio.  At six hours, an aliquot of harvested cells was stained with PE-labeled anti-CD4 and FITC-labeled anti-CD69 (BD Pharmingen) to monitor activation.

tag: aCD3/aCD28 beads


title: 00032880

description:
Human primary myotubes culture 3 infected with SREBP1c for 48hours vs Human primary myotubes culture 3 infected with Renilla for 48hours
Date:2006/05/04


title: 1st instar larvae cy5 vs pooled adult + egg cy3

hyb_protocol: Labeled cDNA was hybridized to the Agilent microarrays using the Gene Expression Hybridization kit (Agilent Technologies Inc.) following manufacturer’s protocols. Arrays were washed with Gene Expression Wash Buffer kit (Agilent Technologies Inc.)

source_name: 1st instar larvae hornfly cy 5

tag: 1st instar larvae hornfly cy 5

source_name: pooled adult + egg hornfly

tag: pooled adult + egg hornfly cy3


title: Act_48h_2

description: transcript (gene)-level data

scan_protocol: Sample preparation, labeling and hybridization to Mouse Exon 1.0 ST Arrays (Affymetrix, CA) were performed according to manufacturer’s protocols by the Microarray Core Facility at the Dana Farber Cancer Institute.


title: 00032858

description:
Human primary myotubes culture 1 infected with SREBP1c for 48hours vs Human primary myotubes culture 1 infected with renilla for 48hours
Date:2006/05/04

value: human primary myotubes

tag: subject #1


title: Act_6h_2

description: transcript (gene)-level data

source_name: Activated, 6h

label_protocol: Sample preparation, labeling and hybridization to Mouse Exon 1.0 ST Arrays (Affymetrix, CA) were performed according to manufacturer’s protocols by the Microarray Core Facility at the Dana Farber Cancer Institute.


title: Act_6h_1

description: transcript (gene)-level data


title: 00032808

description:
Human primary myotubes culture 2 infected with SREBP1A for 48hours vs Human primary myotubes culture 2 infected with Renilla for 48hours
Date:2006/05/04


title: Act_48h_X

description:
An additional 48h biological replicate only used for TLI analysis.
transcript (gene)-level data


title: Resting_2

description: transcript (gene)-level data

source_name: Resting


title: Nodal DLBCL 23N

city: Groningen

first: Marije

last: Booman

department: Pathology

country: Netherlands

institute: University Medical Center Groningen

description: Gender mismatch hybridisation

hyb_protocol: DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed by post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA).

scan_protocol: Slides were scanned on a GenePix 4100A scanner (Axon Instruments, Westburg BV).

data_processing: Scanned images were processed using GenePix Pro 4.1 software. Pixel intensities for each feature were integrated and median values were determined, and the local background was calculated. For each spot the intensities were corrected (pixel median values) by subtracting the local background (pixel median values) for both wavelengths. The median of the ratios of all spots was calculated and used to normalize all data points. As quality control, spots outside the 20% confidence interval of the average of the replicate were excluded. Only those targets presenting at least two spots within 20% confidence interval of their average were used. For each feature (3 spots), the log2 value of the average of the normalized ratios of the three spots was calculated.

source_name: Nodal DLBCL

label_protocol: 450 ng genomic DNA was labeled using Cy3- or Cy5-dCTP in an overnight random prime labeling reaction (BioPrime Random Prime labelling Kit, Invitrogen). Labeled test and reference samples were pooled and precipitated in the presence of Cot1 DNA.

extract_protocol: Genomic DNA was isolated using high salt after overnight SDS/proteinase K digestion.

value: Nodal diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:DNA, Gender:Female

source_name: Pooled reference DNA

tag: commercially available male DNAs (Promega, Leiden, the Netherlands) that represent DNA pools derived from at least seven individuals


title: 00032781

description:
Human primary myotubes culture 1 infected with SREBP1a for 48hours vs Human primary myotubes culture 1 infected with Renilla for 48hours
Date:2006/05/04


title: Resting_1

description: transcript (gene)-level data


title: LLsh4_1

description: FileNumber: 2


title: activated_1

description: FileNumber: 4

source_name: activated

label_protocol: labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual

growth_protocol: Naïve CD4+ T cells were collected from human cord blood and maintained in IL-2 containing medium.

extract_protocol: Total RNA was isolated from unstimulated cells or cells that had been stimulated for 24 hours with anti-CD3 and anti-CD28 antibodies with RNeasy columns (Qiagen).

treatment_protocol: Activation was accomplished by stimulating cells for 24 hours with anti-CD3 and anti-CD28 antibodies.

tag: activated


title: naïve_1

description: FileNumber: 2

source_name: naive

tag: naive


title: activated_2

description: FileNumber: 3


title: Larvae a cy5 vs pooled adult+egg cy3

source_name: 1st instar larvae hornfly

tag: 1st instar larvae hornfly cy5 labeled

source_name: Pooled hornfly from adult + egg cy3

tag: Pooled hornfly from adult + egg cy3


title: LLsh4_2

description: FileNumber: 1


title: uninf_2

description: FileNumber: 3

tag: uninfected


title: Nodal DLBCL 22N

description: Gender mismatch hybridisation

value: Nodal diffuse large B cell lymphoma, Sample origin:Whole frozen tissue sections, Sample type:DNA, Gender:Male

tag: commercially available female DNAs (Promega, Leiden, the Netherlands) that represent DNA pools derived from at least seven individuals


title: Nodal DLBCL 20N

description: Gender mismatch hybridisation


title: Nodal DLBCL 21N

description: Gender mismatch hybridisation


title: Female 3 cy5 vs male pool cy3

data_processing: Data VALUES were generated in Acuity 6.0 based upon Log ratio (635/532) values.

source_name: adult female hornfly cy5

label_protocol: In short, RNA from female horn flies was labeled and hybridized against labeled RNA from male horn flies in a dyeswap design. Similarly, RNA from first instar larvae was labeled and hybridized against labeled a 50:50 mix of RNA from adult male and female flies. All labeling, hybridization and washing procedures were performed according to respective manufacturer protocols. For each sample, 10 ug of total RNA and 50-fold dilution of Agilent two color spike-in control RNA kit (Agilent Technologies Inc.) were labeled with either CyDye3-dCTP or CyDye5-dCTP (Amersham Biosciences, Piscataway, NJ) using the LabelStar kit (Qiagen Inc., Valencia, CA) and oligo-dT and Random nonamers (Sigma-Aldrich Inc., St. Louis, MO).

tag: Adult female hornfly cy5

source_name: Male adult hornfly cy3

tag: male adult hornfly cy3


title: Hornfly Larvae cy5 vs hornfly adult+egg pool cy3

source_name: Hornfly 1st instar larvae cy5

tag: Hornfly 1st instar larvae cy5

source_name: hornfly adult + egg pooled control

tag: hornfly adult cy5 + egg pooled control