title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_TweenSolvent2h_IndividualTree_Hyb4

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

institute: University of British Columbia

description: Gene expression.

hyb_protocol: Following pooling of the appropriate cDNAs, samples were precipitated with linear acrylamide and resuspended in a 45 µL hybridization solution consisting of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, 1 mM EDTA, 4.0 µL LNA d(T) blocker, 2 µg sheared salmon testes DNA (Invitrogen) and 0.75 µL of Cy5-labeled GFP cDNA (Cy5-dUTP and Ready-To-Go labeling beads, Amersham Pharmacia Biotech). Immediately prior to use, arrays were pre-washed 3´ in 0.1% SDS at room temperature for 5 min each, followed by two washes in MilliQ-H2O for 2 min each, 3 min at 95°C in MilliQ-H2O, and dried by centrifugation (3 minutes at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat denatured at 80°C for 10 min, then maintained at 65°C prior to adding to a microarray slide heated to 55°C, covered with a 22 ´ 60 ´ 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 48°C. Arrays were washed in 2´ SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65°C in the same solution, then three washes of 5 min in 2´ SSC at room temperature, and three washes of 5 min in 0.2´ SSC at room temperature, and dried by centrifugation. The Cy3 and Cy5 3DNA capture reagent (Genisphere) were then hybridized to the bound cDNA on the microarray in a 45 µL volume consisting of 25% formamide, 4x SSC, 0.5% SDS, 2x Denhardt’s solution, 1 mM EDTA,, 2.5 µL Cy3 capture reagent and 2.5 µL Cy5 capture reagent. The 3DNA capture reagent is bound to its complementary cDNA capture sequence on the Cy3 or Cy5 oligo d(T) primers. The second hybridization was performed for 3 h at 48°C, then washed and dried as before.

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

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104). For the herbivory (24 hours), mechanical wounding (6 hours), oral secretion (2 hours), and methyl jasmonate (2 hours) treatments, total RNA from leaves of four individual treated trees and four individual control trees was compared using four hybridizations for each treatment, with dye balance, using a total of 16 hybridizations. To assess the transcriptional response to stress treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of each experiment using 16 microarray slides. The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point. Expression variance was obtained from a combination of technical and biological variance. Next, the ratio of the treatment minus untreated or tween control parameter estimate to the standard error was used to calculate a t statistic and P value. The Q value for each effect and gene was calculated for each of the models to adjust for the false discovery rate (Storey and Tibshirani et al., 2003). All statistical analyses were performed within the R statistical package (version 2.5.1; http://www.r-project.org/).

organism: Populus trichocarpa x Populus deltoides

source_name: Hybrid poplar leaves, tween solvent control for 2 hours

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

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

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

treatment_protocol: For tween solvent control treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves. Uncovered leaves were sprayed with 25 mL of 0.1% v/v Tween 20 solvent. Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour. Leaves were harvested 2 hours after the initiation of treatment.

tag: Genotype

tag: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from a single tree (four biological replicate trees per treatment). Harvested leaves had a surface area of approximately 425 cm2.

source_name: Hybrid poplar leaves, methyl jasmonate treatment for 2 hours

treatment_protocol: For methyl jasmonate treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves. Uncovered leaves were sprayed with 25 mL of a 0.01% v/v solution of methyl jasmonate dissolved in 0.1% v/v Tween 20 solvent. Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour. Leaves were harvested 2 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_TweenSolvent2h_IndividualTree_Hyb1

status: Public on Dec 31 2008

type: RNA

country: Canada

description: Gene expression.

molecule: total RNA

label_protocol: Hybridizations were performed using the Genisphere Array350 kit (Genisphere) following manufacturer’s instructions. Forty µg total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen) and oligo d(T18) primers with a 5’ unique sequence overhang specific to either the Cy3 or Cy5 labeling reactions. The RNA strand of the resulting cDNA:RNA hybrid was hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65°C for


title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_TweenSolvent2h_IndividualTree_Hyb3

description: Gene expression.


title: WT_Gal_AntimycinA_Air_Gen013_rep3

city: Urbana

first: Kurt

middle: E

last: Kwast

state: IL

address: 407 S. Goodwin Ave.

department: Molecular & Integrative Physiology

country: USA

institute: University of Illinois at Urbana-Champaign

description: Sparged, fermentor cultures of a wild-type yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA) for six generations of preconditioning.  When cell density was ≈1 Klett unit, Antimycin A (1 μM) was added into medium.  Samples were harvested after 0 (control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, and 3 generations of aerobic growth in the presence of Antimycin A.  Total RNA was reverse transcribed (Cy3) and hybridized against a reference (Cy5).

data_processing: GenePix Pro software (v4.1) was used for spot identification and fluorescence intensity quantification.  After manually flagging and removing spots with aberrant measurements, background fluorescence was subtracted from the median Cy3 and median Cy5 fluorescence intensity values.  Any resulting negative intensity values were set to zero and a constant of one fluorescent unit was then added to all intensity values.  Outliers were identified and removed using SAS, and the log2Cy3 intensity (query cDNA) for all remaining observations on a slide was normalized against that of the log2Cy5 intensity (reference cDNA) using locally weighted linear regression (Loess).  The log2(Cy3/Cy5) ratio for each spot was calculated, and the mean log2(Cy3/Cy5) ratio across all observations on a slide was normalized to a value of zero.  The mean of the normalized log2(Cy3/Cy5) ratio for each gene was then calculated by averaging the duplicate observations on each slide and pooling replicate slides by sampling time.

organism: Saccharomyces cerevisiae

tag: Strain

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.13 generations, Replication:Rep3

value: JM43 (wild-type), Medium:SSG-TEA, Condition:a pool of RNA collected from both anaerobic and aerobic cultures


title: WT_Gal_AntimycinA_Air_Gen013_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.13 generations, Replication:Rep1


title: WT_Gal_AntimycinA_Air_Gen013_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.13 generations, Replication:Rep2


title: WT_Gal_AntimycinA_Air_Gen004_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.04 generations, Replication:Rep1


title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_TweenSolvent2h_IndividualTree_Hyb2

description: Gene expression.


title: WT_Gal_AntimycinA_Air_Gen008_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.08 generations, Replication:Rep1


title: WT_Gal_AntimycinA_Air_Gen019_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.19 generations, Replication:Rep1


title: WT_Gal_AntimycinA_Air_Gen008_rep4

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.08 generations, Replication:Rep4


title: WT_Gal_AntimycinA_Air_Gen004_rep4

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.04 generations, Replication:Rep4


title: WT_Gal_AntimycinA_Air_Gen004_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.04 generations, Replication:Rep3


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_FTCherbivory24h_IndividualTree_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, forest tent caterpillar herbivory treatment for 24 hours

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem. Larvae were first starved for 40 hours on moist filter paper. Leaves were harvested 24 hours after the initiation of the experiment.

source_name: Hybrid poplar leaves, untreated control for 24 hours

treatment_protocol: Five leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Leaves were harvested 24 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_FTCherbivory24h_IndividualTree_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_IndividualTree_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, untreated control for 2 hours

treatment_protocol: Five leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Leaves were harvested 2 hours after the initiation of the experiment.

source_name: Hybrid poplar leaves, oral secretion treatment for 2 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. The oral secretion treatment was identical to mechanical wounding except that 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Leaves were harvested 2 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_IndividualTree_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_IndividualTree_Hyb3

description: Gene expression.

source_name: Hybrid poplar leaves, mechanical wounding treatment for 6 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. Leaves were harvested 6 hours after the initiation of treatment.

source_name: Hybrid poplar leaves, untreated control for 6 hours

treatment_protocol: Five leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Leaves were harvested 6 hours after the initiation of the experiment.


title: WT_Gal_AntimycinA_Air_Gen008_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.08 generations, Replication:Rep3


title: WT_Gal_AntimycinA_Air_Gen0_rep3

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0 generation (control), Replication:Rep3


title: WT_Gal_AntimycinA_Air_Gen0_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0 generation (control), Replication:Rep2


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_IndividualTree_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_FTCherbivory24h_IndividualTree_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_IndividualTree_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_IndividualTree_Hyb4

description: Gene expression.


title: WT_Gal_AntimycinA_Air_Gen0_rep1

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0 generation (control),

value: JM43 (wild-type), Medium:SSG-TEA,

tag: Condition

value: a pool of RNA collected from both anaerobic and aerobic cultures


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_IndividualTree_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_IndividualTree_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_FTCherbivory24h_IndividualTree_Hyb1

description: Gene expression.


title: WT_Gal_AntimycinA_Air_Gen019_rep2

value: JM43 (wild-type), Medium:SSG-TEA + Antimycin A, Condition:Air, Generation:0.19 generations, Replication:Rep2


title: CD8+CD122+vs.CD8+CD122- second trial

city: Nagoya

first: Haruhiko

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: Immunology

country: Japan

institute: Nagoya University Graduate School of Medicine

description: To compare the gene expression profile of murine CD8+CD122+ cells and CD8+CD122- cells.

hyb_protocol: Performed by Hokkaido System Science according to the Agilent standard method

data_processing: Performed with Agilent's Feature Extraction software.

molecule: polyA RNA

organism: Mus musculus

source_name: mouse CD8+CD122-

label_protocol: Performed by Hokkaido System Science

extract_protocol: Performed by Hokkaido System Science

tag: CD8+CD122- cells derived from spleen of C57BL/6

source_name: mouse CD8+CD122+

tag: CD8+CD122+ cells derived from spleen of C57BL/6


title: HybridPoplar_H11-11_Leaves_MethylJasmonate6h_vs_MethylJasmonate24h_Hyb2

description: Gene expression.

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104). For the methyl jasmonate experiment, a total of 18 hybridizations were performed to directly compare total RNA from methyl jasmonate-treated and tween solvent control leaves at each time point, as well as among methyl jasmonate-treated leaves across time points, with dye balance. To assess the transcriptional response to stress treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of each experiment using 18 (pooled biological replicates) microarray slides. The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point. Expression variance was obtained from technical variance among slides. Next, the ratio of the treatment minus untreated or tween control parameter estimate to the standard error was used to calculate a t statistic and P value. The Q value for each effect and gene was calculated for each of the models to adjust for the false discovery rate (Storey and Tibshirani et al., 2003). All statistical analyses were performed within the R statistical package (version 2.5.1; http://www.r-project.org/).

source_name: Hybrid poplar leaves, methyl jasmonate treatment for 24 hours

treatment_protocol: For methyl jasmonate treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves. Uncovered leaves were sprayed with 25 mL of a 0.01% v/v solution of methyl jasmonate dissolved in 0.1% v/v Tween 20 solvent. Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour. Leaves were harvested 24 hours after the initiation of treatment.

tag: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Harvested leaves had a surface area of approximately 425 cm2. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar leaves, methyl jasmonate treatment for 6 hours

treatment_protocol: For methyl jasmonate treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves. Uncovered leaves were sprayed with 25 mL of a 0.01% v/v solution of methyl jasmonate dissolved in 0.1% v/v Tween 20 solvent. Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour. Leaves were harvested 6 hours after the initiation of treatment.


title: CD8+CD122+vs.CD8+CD122-

scan_protocol: Performed by Hokkaido System Science according to the Agilent standard method


title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_TweenSolvent2h_Hyb4

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate6h_vs_TweenSolvent6h_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, tween solvent control for 6 hours

treatment_protocol: For tween solvent control treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves. Uncovered leaves were sprayed with 25 mL of 0.1% v/v Tween 20 solvent. Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour. Leaves were harvested 6 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_TweenSolvent6h_vs_MethylJasmonate6h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_TweenSolvent24h_vs_MethylJasmonate24h_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, tween solvent control for 24 hours

treatment_protocol: For tween solvent control treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves. Uncovered leaves were sprayed with 25 mL of 0.1% v/v Tween 20 solvent. Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour. Leaves were harvested 24 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_TweenSolvent2h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate24h_vs_MethylJasmonate6h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_TweenSolvent2h_vs_MethylJasmonate2h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_MethylJasmonate24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate2h_vs_MethylJasmonate6h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_TweenSolvent2h_vs_MethylJasmonate2h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate24h_vs_TweenSolvent24h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate6h_vs_MethylJasmonate2h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_FTCherbivory2h_vs_FTCherbivory6h_Hyb2

description: Gene expression.

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104). For the herbivory, mechanical wounding and oral secretion treatments using pooled biological replicates, total RNA from treated and untreated control leaves was compared using a balanced loop consisting of direct and indirect comparisons across treatments and time points, with dye balance, using a total of 54 hybridizations. To assess the transcriptional response to stress treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of each experiment using 54 (pooled biological replicates; herbivory, mechanical wounding and OS treatments) microarray slides. The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point. Expression variance was obtained from technical variance among slides. Next, the ratio of the treatment minus untreated or tween control parameter estimate to the standard error was used to calculate a t statistic and P value. The Q value for each effect and gene was calculated for each of the models to adjust for the false discovery rate (Storey and Tibshirani et al., 2003). All statistical analyses were performed within the R statistical package (version 2.5.1; http://www.r-project.org/).

source_name: Hybrid poplar leaves, forest tent caterpillar herbivory treatment for 2 hours

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem. Larvae were first starved for 40 hours on moist filter paper. Leaves were harvested 2 hours after the initiation of the experiment.

source_name: Hybrid poplar leaves, forest tent caterpillar herbivory treatment for 6 hours

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem. Larvae were first starved for 40 hours on moist filter paper. Leaves were harvested 6 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate24h_vs_MethylJasmonate2h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate24h_vs_TweenSolvent24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_FTCherbivory24h_Hyb4

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_OralSecretion24h_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, oral secretion treatment for 24 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. The oral secretion treatment was identical to mechanical wounding except that 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Leaves were harvested 24 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_Wounding24h_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, mechanical wounding treatment for 24 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. Leaves were harvested 24 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_FTCherbivory2h_Hyb4

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_OralSecretion2h_vs_OralSecretion24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_TweenSolvent6h_vs_MethylJasmonate6h_Hyb1

description: Gene expression.

treatment_protocol: For methyl jasmonate treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves.  Uncovered leaves were sprayed with 25 mL of a 0.01% v/v solution of methyl jasmonate dissolved in 0.1% v/v Tween 20 solvent.  Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour.  Leaves were harvested 6 hours after the initiation of treatment.

treatment_protocol: For tween solvent control treatments, a light-weight plastic bag was used to cover all leaves on each tree except for the five lowest, fully-expanded, healthy leaves.  Uncovered leaves were sprayed with 25 mL of 0.1% v/v Tween 20 solvent.  Plants were sprayed in a room separate from other treatments, and the plastic bags were removed after 1 hour.  Leaves were harvested 6 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_Wounding2h_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, mechanical wounding treatment for 2 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. Leaves were harvested 2 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_FTCherbivory2h_vs_FTCherbivory24h_Hyb2

description: Gene expression.

source_name: Hybrid poplar leaves, forest tent caterpillar herbivory treatment for 24 hours

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem. Larvae were first starved for 40 hours on moist filter paper. Leaves were harvested 24 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_TweenSolvent24h_vs_MethylJasmonate24h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_MethylJasmonate6h_vs_TweenSolvent6h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_Wounding6h_vs_Wounding24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_OralSecretion6h_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, oral secretion treatment for 6 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. The oral secretion treatment was identical to mechanical wounding except that 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Leaves were harvested 6 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_FTCherbivory2h_Hyb3

description: Gene expression.

source_name: Hybrid poplar leaves, untreated control for 2 hours

treatment_protocol: Five leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Leaves were harvested 2 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_Wounding6h_vs_Wounding24h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_FTCherbivory6h_Hyb4

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_Hyb4

description: Gene expression.

source_name: Hybrid poplar leaves, oral secretion treatment for 2 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. The oral secretion treatment was identical to mechanical wounding except that 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites. Leaves were harvested 2 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_FTCherbivory6h_vs_FTCherbivory24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_Wounding2h_vs_Wounding24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_FTCherbivory2h_Hyb2

description: Gene expression.

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104). For the herbivory, mechanical wounding and oral secrection treatments using pooled biological replicates, total RNA from treated and untreated control leaves was compared using a balanced loop consisting of direct and indirect comparisons across treatments and time points, with dye balance, using a total of 54 hybridizations. To assess the transcriptional response to stress treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of each experiment using 54 (pooled biological replicates; herbivory, mechanical wounding and OS treatments) microarray slides. The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point. Expression variance was obtained from technical variance among slides. Next, the ratio of the treatment minus untreated or tween control parameter estimate to the standard error was used to calculate a t statistic and P value. The Q value for each effect and gene was calculated for each of the models to adjust for the false discovery rate (Storey and Tibshirani et al., 2003). All statistical analyses were performed within the R statistical package (version 2.5.1; http://www.r-project.org/).


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_FTCherbivory6h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_Wounding2h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_OralSecretion24h_vs_OralSecretion2h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_FTCherbivory24h_Hyb3

description: Gene expression.

source_name: Hybrid poplar leaves, untreated control for 24 hours

treatment_protocol: Five leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Leaves were harvested 24 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_OralSecretion6h_vs_OralSecretion24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_Wounding24h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_OralSecretion2h_vs_OralSecretion6h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_FTCherbivory6h_Hyb2

description: Gene expression.

source_name: Hybrid poplar leaves, untreated control for 6 hours

treatment_protocol: Five leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated. Leaves were harvested 6 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_OralSecretion6h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_Wounding24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_Wounding24h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_OralSecretion24h_Hyb3

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_OralSecretion24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_Hyb3

description: Gene expression.

source_name: Hybrid poplar leaves, mechanical wounding treatment for 6 hours

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel. Leaves were harvested 6 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_Wounding2h_vs_Wounding6h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_Hyb4

description: Gene expression.


title: normal male Wistar rat - replicate1

city: shanghai

first: huang

last: bing

state: shanghai

address: yueyang road 320

department: chemistry

country: China

institute: Chinese Academy of Sciences

description: analysis of rat microRNAs expression under diabetic condition.

hyb_protocol: Microscope glass slides were activated as described.The antisense sequences of microRNAs were used for probes. The melting temperatures of all probes were adjusted to 55 ± 3 °C as described.In addition, each probe contains a 5′ C6-amino modified 10 deoxyadenosines spacer at the 5′ end of the probe.The probes were dissolved in printing buffer (2× SSC/1 M betaine hydrochloride/5% formamide/0.01% SDS, pH 8.5) at the concentration of 20 μM, and then printed onto the epoxy coated slides with PixSys 5500 spotting robot in quadruplicate under 60% humidity. The printed microarrays were further chemically covalently coupled under 60% humidity overnight. Before hybridization, printed microarrays were quenched by quenching buffer (0.1 M Tris–HCl/50 mM ethanolamine, pH 8.0). Small RNA cDNA libraries of samples were amplified and labeled by PCR using the 5′primer (5′-Cy5-CTGGAATTCTGACGATCTGC) and the 3′primer (5′-ACCGAATTCACAGTCAGACC) as described [11]. The PCR product was precipitated, washed, resuspended in 10 μl ddH2O, and cleaned up by a Sephadex G-50 column. Heat the PCR product at 95 °C for 3 min to denature and chill on ice immediately. Combine the PCR product with equal volume of 2× hybridization buffer (8× SSC/0.2% SDS, pH 7.0) that has been heated to 48 °C and mix thoroughly. Immediately, inject the mixture into the hybridization chamber. Hybridization was carried out at 45 °C for 16 h. After hybridization, slides were washed (2× SSC/0.03% SDS, 2 min; 0.2× SSC, 2 min; 0.1× SSC, 1 min) at 25 °C.

scan_protocol: Images were quantified by GenePix Pro6.0 (Axon) using the fixed circle quantification methods.

data_processing: Signal intensities for each spot were calculated by subtracting local background from total intensities. No further process was performed.

organism: Rattus norvegicus

source_name: normal male Wistar rat

label_protocol: labeled by PCR using a Cy5 labeled primer

extract_protocol: The total RNAs were extracted with the RNarose reagent (Watson and Sangon).

treatment_protocol: All animal experiments were performed according to “The Animal Care & Welfare Committee’’ of PUMC. In this study we used male GK rats, which were established by selectively breeding of normal Wistar rats with signs of impaired glucose tolerance, as type 2 diabetes model and male Wistar rats as control. Rats were housed in a temperature-controlled room and were given free access to water and standard laboratory chow during the 14 weeks. The blood glucose levels of the rats were measured each other day up to 4 times before being killed.

tag: normal male Wistar rat as control


title: normal male Wistar rat - replicate2


title: male diabetic GK rat - replicate2

source_name: male GK rat

tag: male diabetic GK rat


title: HybridPoplar_H11-11_Leaves_FTCherbivory2h_vs_UntreatedControl2h_Hyb1

description: Gene expression.


title: male diabetic GK rat - replicate1


title: HybridPoplar_H11-11_Leaves_UntreatedControl24h_vs_FTCherbivory24h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_Wounding2h_vs_Wounding24h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_OralSecretion2h_Hyb1

description: Gene expression.

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104).  For the herbivory, mechanical wounding and oral secrection treatments using pooled biological replicates, total RNA from treated and untreated control leaves was compared using a balanced loop consisting of direct and indirect comparisons across treatments and time points, with dye balance, using a total of 54 hybridizations.  To assess the transcriptional response to stress treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of each experiment using 54 (pooled biological replicates; herbivory, mechanical wounding and OS treatments) microarray slides.  The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point.  Expression variance was obtained from technical variance among slides.  Next, the ratio of the treatment minus untreated or tween control parameter estimate to the standard error was used to calculate a t statistic and P value.  The Q value for each effect and gene was calculated for each of the models to adjust for the false discovery rate (Storey and Tibshirani et al., 2003).  All statistical analyses were performed within the R statistical package (version 2.5.1; http://www.r-project.org/).

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


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_OralSecretion6h_Hyb2

description: Gene expression.

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct for background intensity. After quantification of the signal intensities, data were normalized to compensate for non-linearity of intensity distributions using the vsn method (Huber et al., 2002 Bioinformatics 18: S96-S104).  For the herbivory, mechanical wounding and oral secretion treatments using pooled biological replicates, total RNA from treated and untreated control leaves was compared using a balanced loop consisting of direct and indirect comparisons across treatments and time points, with dye balance, using a total of 54 hybridizations.  To assess the transcriptional response to stress treatments, a linear mixed-effects model was fitted to the normalized intensities in the Cy3 and Cy5 channels of each experiment using 54 (pooled biological replicates; herbivory, mechanical wounding and OS treatments) microarray slides.  The model contained an adjustment for dye effect, an array effect indicating which Cy5/Cy3 pair was on each array, and a treatment effect indicating treatment and time point.  Expression variance was obtained from technical variance among slides.  Next, the ratio of the treatment minus untreated or tween control parameter estimate to the standard error was used to calculate a t statistic and P value.  The Q value for each effect and gene was calculated for each of the models to adjust for the false discovery rate (Storey and Tibshirani et al., 2003).  All statistical analyses were performed within the R statistical package (version 2.5.1; http://www.r-project.org/).


title: HybridPoplar_H11-11_Leaves_UntreatedControl2h_vs_Wounding2h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_OralSecretion24h_vs_UntreatedControl24h_Hyb1

description: Gene expression.

treatment_protocol: Five leaves were caged on each tree using nylon mesh bags, but were otherwise left untreated.  Leaves were harvested 24 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_FTCherbivory2h_vs_FTCherbivory24h_Hyb1

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_Wounding2h_vs_UntreatedControl2h_Hyb2

description: Gene expression.


title: HybridPoplar_H11-11_Leaves_FTCherbivory6h_vs_FTCherbivory24h_Hyb1

description: Gene expression.

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem.  Larvae were first starved for 40 hours on moist filter paper.  Leaves were harvested 6 hours after the initiation of the experiment.

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem.  Larvae were first starved for 40 hours on moist filter paper.  Leaves were harvested 24 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_OralSecretion2h_vs_OralSecretion6h_Hyb1

description: Gene expression.


title: polyamine_chemo_SP1

type: other

city: Kent

first: Xiaozhen

last: Mou

state: OH

address: 41 cunningham Hall, P. O. box 5190

department: Biological Sciences

institute: Kent State University

description: One of the four replicates

hyb_protocol: Protocol developed by Protocol developed Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755

scan_protocol: Axon Genpix GenPix 4000B microarray scanner (Molecular Devices Corporation, Sunnyvale, CA) at 5 µm resolution

data_processing: Background corrected expression data from each array were globally normalized by trimmed means (2% from each side) and log2 transformed prior to being imported into the Acuity 4.0 software (Molecular Devices Corporation, Sunnyvale, CA). Analysis datasets were created using the conditions (SNR>3 and Circularity >80 and F635% <2 and B635 CV< 50) to exclude probes that with features close to background, saturated, with bad circularity or with highly non-uniform intensities or background

label: AlexaFluor dye 647

molecule: other

organism: Ruegeria pomeroyi

source_name: S. pomeroyi DSS3 cells incubated in chemostat with spermidine at 3 mM carbon concentration

label_protocol: Protocol developed by Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755

tag: DSS-3 cells incubated in chemostat with spermidine


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_OralSecretion6h_Hyb1

description: Gene expression.


title: polyamine_chemo_SP3

description: One of the four replicates

growth_protocol: S. pomeroyi DSS3 cells incubated in chemostat with spermidine at 3 mM carbon concentration

extract_protocol: Protocol developed by Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755


title: polyamine_chemo_SE3

description: One of the four replicates

source_name: S. pomeroyi DSS3 cells incubated in chemostat with serine at 3 mM carbon concentration

tag: DSS-3 cells incubated in chemostat with serine


title: polyamine_chemo_SP4

description: One of the four replicates

treatment_protocol: S. pomeroyi DSS3 cells incubated in chemostat with spermidine at 3 mM carbon concentration


title: polyamine_chemo_SP2

description: One of the four replicates


title: HybridPoplar_H11-11_Leaves_Wounding2h_vs_Wounding6h_Hyb1

description: Gene expression.

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel.  Leaves were harvested 2 hours after the initiation of treatment.

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel.      Leaves were harvested 6 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_OralSecretion6h_vs_OralSecretion24h_Hyb1

description: Gene expression.

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel.  The oral secretion treatment was identical to mechanical wounding except that 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites.  Leaves were harvested 24 hours after the initiation of treatment.

tag: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Harvested leaves had a surface area of approximately 425 cm2.  RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

treatment_protocol: For mechanical wounding treatments, four 10 cm strips were punctured parallel to the midrib on each of the five caged leaves with a pattern wheel.  The oral secretion treatment was identical to mechanical wounding except that 20 microL of forest tent caterpillar oral secretion was also applied to the wound sites.  Leaves were harvested 6 hours after the initiation of treatment.


title: HybridPoplar_H11-11_Leaves_FTCherbivory24h_vs_UntreatedControl24h_Hyb1

description: Gene expression.


title: polyamine_chemo_SE1

description: One of the four replicates

scan_protocol: GenPix 4000B microarray scanner (Molecular Devices Corporation, Sunnyvale, CA) at 5 µm resolution

data_processing: Background corrected expression data from each array were globally normalized by trimmed means (2% from each side) and log2 transformed prior to being imported into the Acuity 4.0 software (Molecular Devices Corporation, Sunnyvale, CA). Analysis datasets were created using the conditions (SNR>3 and Circularity >80 and F635% <2 and B635 CV< 50) to exclude probes that with features close to background, saturated, with bad circularity or with highly non-uniform intensities or background.

growth_protocol: S. pomeroyi DSS3 cells incubated in chemostat with serine at 3 mM carbon concentration


title: HybridPoplar_H11-11_Leaves_FTCherbivory2h_vs_FTCherbivory6h_Hyb1

description: Gene expression.

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem.  Larvae were first starved for 40 hours on moist filter paper.  Leaves were harvested 2 hours after the initiation of the experiment.


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_FTCherbivory6h_Hyb1

description: Gene expression.

treatment_protocol: For insect treatments, groups of five 3rd to 5th instar Malacosoma disstria larvae were caged on leaves using mesh bags secured at the stem. Larvae were first starved for 40 hours on moist filter paper. Leaves were harvested 6 hours after the initiation of the experiment.


title: polyamine_chemo_SE4

description: One of the four replicates

treatment_protocol: S. pomeroyi DSS3 cells incubated in chemostat with serine at 3 mM carbon concentration


title: polyamine_chemo_SE2

description: One of the four replicates


title: Yeast Protein Array Ubr1 control 2

status: Public on Dec 30 2008

type: protein

city: Baltimore

first: Eitan

last: Halper-Stromberg

state: MD

address: 733 N Broadway

institute: Johns Hopkins

description: GST-fusion protein expressed and purified from yeast

hyb_protocol: Not provided

scan_protocol: Fluorescent array images were collected for Cy5 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software

data_processing: Each protein is printed in duplicate on the array; for each protein, the values of F635_MEAN - B635_MEAN and F532 - B532 are used to create log intensity ratios and log intensity averages to be used in lowess normalization.

molecule: protein

source_name: Ubr1 Signal Detection

label_protocol: 3000 fold dilution anti Ub antibodies labeled with Cy5

extract_protocol: Cy3 labeled secondary Antibody detection of Anti-Ub antibodies

tag: Ubr1 protein treated

source_name: GST Signal detection

label_protocol: 5000 fold dilution anti GST antibodies labeled with Cy5

extract_protocol: Cy5 labeled secondary antibody detection of Anti GST antibodies

tag: Anti GST antibody


title: Yeast Protein Array Rsp5 treated 1

data_processing: Each protein is printed in duplicate on the array; for each protein, the values of F635_MEAN - B635_MEAN and F532 - B532 are used to create log intensity ratios and log intensity averages to be used in lowess normalization

source_name: Rsp5 Signal Detection

label_protocol: 5000 fold dilution anti GST antibodies labeled with Cy3

extract_protocol: Cy3 labeled secondary Antibody detection of Anti-GST antibodies

tag: Rsp5-GST fusion protein treated


title: Yeast Protein Array control 2

data_processing: Each protein is printed in duplicate on the array; for each protein, the values of F635_MEAN - B635_MEAN and F532 - B532 are used to create log intensity ratios and  log intensity averages to be used in lowess normalization

source_name: Negative Control

tag: E3 enzyme left out


title: Yeast Protein Array Ubr1 control 1


title: E11.5 liver endoderm 2

city: Cambridge

first: Richard

last: Sherwood

state: MA

address: 7 Divinity Ave

department: Department of Molecular and Cellular Biology

institute: Harvard University

hyb_protocol: Illumina BeadStation (Illumina)

scan_protocol: Illumina BeadStation (Illumina)

data_processing: Illumina BeadStudio (Illumina); rank invariant normalization, background subtraction using Illumina BeadStudio (Illumina)

label: biotin

source_name: E11.5 mouse embryo

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

extract_protocol: Trizol (Invitrogen)

tag: ICR


title: Yeast Protein Array Rsp5 treated 2


title: E11.5 pancreatic endoderm 4

description: Illumina TotalPrep RNA Amplification kit


title: E11.5 pancreatic endoderm 3


title: E11.5 pancreatic endoderm 2


title: E11.5 intestinal endoderm 1


title: Yeast Protein Array control 1

data_processing: Each protein is printed in duplicate on the array; for each protein, the values of F635_MEAN - B635_MEAN and F532-B532 were used to produce log intensity ratios and average log intensities to be used in lowess normalization for each protein.


title: E11.5 pancreatic endoderm 1


title: E11.5 liver endoderm 1


title: E11.5 stomach endoderm 3


title: E11.5 lung endoderm 3


title: Strain M22-cys4::N123I, YPD media, replicate 3

city: Dallas

first: Hyun Seok

last: Kim

state: TX

address: Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Overnight cultures of M22-CYS4::N123I were diluted in fresh YPD to 10% v/v and grown for 3 hours at 30'C. Total RNA was isolated using an RNeasy mini kit (Qiagen), reverse transcribed, labeled, and hybridized to epoxy-coated slides (MWG Biotech).

hyb_protocol: Hybridization was performed in the microarray core facility in Washington University in St. Louis. http://www.genisphere.com/pdf/Array350_10-02-06.pdf

scan_protocol: Arrays were scanned using a ScanArray Express laser scanner (Perkin Elmer).

data_processing: Individual array is normalized using the LOWESS algorithm.

source_name: Reference, YPD media, replicate 3

label_protocol: Genisphere Array 350 Expression Array Detection Kit, http://www.genisphere.com/array_detection_protocols.html

extract_protocol: RNeasy mini kit (Qiagen)

tag: A pool of RNA from all samples

tag: Allele replacement strain of M22 (CYS4-N123I)


title: E11.5 stomach endoderm 1


title: Strain M22-cys4::N123I, YPD media, replicate 2

source_name: Reference, YPD media, replicate 2


title: E11.5 liver endoderm 3


title: E11.5 intestinal endoderm 2


title: Strain M22-cys4-, YPD media, replicate 3

description: Overnight cultures of M22 with CYS4 deletion were diluted in fresh YPD to 10% v/v and grown for 3 hours at 30'C. Total RNA was isolated using an RNeasy mini kit (Qiagen), reverse transcribed, labeled, and hybridized to epoxy-coated slides (MWG Biotech).

source_name: Strain M22 with CYS4 deletion, YPD media, replicate 3

tag: S. cerevisiae M22 with CYS4 deletion.


title: E11.5 lung endoderm 2


title: E11.5 intestinal endoderm 3


title: E11.5 stomach endoderm 2


title: E11.5 lung endoderm 1


title: Strain M22-cys4::N123I, YPD media, replicate 1

source_name: Reference, YPD media, replicate 1


title: hrp36-1.b KD

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

description: Hrp36 knock-down from dsRNA B sample 1

hyb_protocol: A custom protocol, see Blanchette et al. (2005) Genes Dev, PMID: 15937219 as well as Castle et al. (2003) Genome Biology, PMID: 14519201

scan_protocol: Feature Extractor version 7.5.1. Scanner settings can be found in the raw data file.

data_processing: Detail description of the data processing can be found in Blanchette et al. (2005). Genes and Dev. PMID: 15937219

organism: Drosophila melanogaster

source_name: Non-specific RNAi control

label_protocol: A custom labeling protocol described in Blanchette et al. (2005) Genes Dev., PMID: 15937219

growth_protocol: 2x10e6 S2 cells exponentially growing in Schneider's media were seeded in 6 well plates

extract_protocol: At day 4, total RNA is extracted using the RNAeasy mini kit and the QiaShredder (Qiagen) following the manufacturor protocol.

treatment_protocol: 10 µg of dsRNA at day 0 and repeated at day 2

tag: Schneider SL2 cells

source_name: treated with hrp36 dsRNA for 4 days


title: hrp36-2.b KD

description: Hrp36 knock-down from dsRNA B sample 2


title: hrp36-2.a KD

description: Hrp36 knock-down from dsRNA A sample 2


title: hrp36-1.a KD

description: Hrp36 knock-down from dsRNA A sample 1


title: Strain M22-cys4-, YPD media, replicate 2

source_name: Strain M22 with CYS4 deletion, YPD media, replicate 2


title: E11.5 esophagus endoderm 3


title: Total RNA

description: Total RNA extracted from RNP extract (2 replicates)

hyb_protocol: Recommended Affymetrix protocol

scan_protocol: The microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to the manual

data_processing: The processed sgr data files were generated from the Affymetrix cel files using the TiMAT programs developed by the Berkeley Drosophila Transcription Network Project (http://bdtnp.lbl.gov/TiMAT/TiMAT2/index.html). The probe intensities for all immunoprecipitation and control (input and/or mock) cel files in each hybridization set (each sample is a hybridization set) were normalized using median scaling and assigned to a genome position using a tpmap file based on the April 2004 release of the Drosophila melangaster genome sequence (Berkeley Drosophila Genome Project). The relative immunoprecipitation and control sample normalized intensities were used to generate scores for the microarray features.

label_protocol: GeneChip® WT Double-Stranded cDNA Synthesis Kit (Affymetrix)

growth_protocol: Exponentiaolly growing SL2 cells in Schneider's media supplemented with 10% FBS where used to prepare nuclear RNP extract (Olson et al., 2007, NSMB. PMID: 18059285)

extract_protocol: A description of the immuno-purification can be found in Olson et al., 2007, NSMB. PMID: 18059285. The RNA was purified using Quiagen RNAeasy kit following manufacturer protocol (Qiagen)

treatment_protocol: The extracts used for the immunopurification come from nuclear enriched RNP fraction.

tag: Nuclear RNP enriched extract from SL2 cells

tag: Nuclear extract from cell culture


title: E11.5 esophagus endoderm 2


title: Strain M22-cys4-, YPD media, replicate 1

source_name: Strain M22 with CYS4 deletion, YPD media, replicate 1


title: HybridPoplar_H11-11_Leaves_UntreatedControl6h_vs_Wounding6h_Hyb1

description: Gene expression.

source_name: Hybrid poplar leaves, mechanical wounding treatment for 6 hours

tag: Genotype

tag: Six month old clonal trees grown under greenhouse conditions. The five lowest, fully-expanded, healthy leaves with petioles removed were harvested from five trees subjected to the same treatment. Harvested leaves had a surface area of approximately 425 cm2. RNA was isolated individually from each of the five trees and then pooled prior to cDNA synthesis.

source_name: Hybrid poplar leaves, untreated control for 6 hours


title: Strain M22, YPD media, replicate 2

description: Overnight cultures of M22 were diluted in fresh YPD to 10% v/v and grown for 3 hours at 30'C. Total RNA was isolated using an RNeasy mini kit (Qiagen), reverse transcribed, labeled, and hybridized to epoxy-coated slides (MWG Biotech).

source_name: Strain M22, YPD media, replicate 2

tag: S. cerevisiae M22 (wine, Italy).


title: E8.25 4-6s mesoderm 3

source_name: E8.25 mouse embryo


title: hrp40-2 KD

description: Hrp40 knock-down sample 2

treatment_protocol: 10 µg of dsRNA at day 0 and day 2

source_name: treated with hrp40 dsRNA for 4 days


title: hrp40-1 KD

description: Hrp40 knock-down sample 1


title: E8.25 4-6s mesoderm 1


title: E11.5 esophagus endoderm 1


title: Strain M22, YPD media, replicate 1

source_name: Strain M22, YPD media, replicate 1


title: hrp48-2 KD

description: Hrp48 knock-down sample 2

source_name: treated with hrp48 dsRNA for 4 days


title: hrp38-3 KD

description: Hrp38 knock-down sample 3

source_name: treated with hrp38 dsRNA for 4 days


title: Strain M22, YPD media, replicate 3

source_name: Strain M22, YPD media, replicate 3


title: Mock IgG IP

description: Mock IP used to control FDR in TiMAT analysis (3 replicates)


title: hrp38-1 KD

description: Hrp38 knock-down sample 1


title: E8.25 4-6s ectoderm 3


title: hrp40-3 KD

description: Hrp40 knock-down sample 3


title: E8.25 4-6s mesoderm 2


title: hrp48-1 KD

description: Hrp48 knock-down sample 1


title: hrp38-2 KD

description: Hrp38 knock-down sample 2


title: hrp48-3 KD

description: Hrp48 knock-down sample 3


title: hrp48 bound RNA

description:
Sample arrays:
H48_IP_L2-1.CEL
H48_IP_L2-2.CEL
H48_IP_L2-3.CEL
Control arrays:
Total_L2_RNP-1.CEL
Total_L2_RNP-2.CEL
FDR evaluation arrays:
IgG_IP_L2-1.CEL
IgG_IP_L2-2.CEL
IgG_IP_L2-3.CEL

source_name: hrp48 nuclear RNPs (3 replicates)


title: E8.25 4-6s ectoderm 2


title: hrp36-3 KD

description: Hrp36 knock-down sample 3


title: hrp36-2 KD

description: Hrp36 knock-down sample 2


title: hrp40 bound RNA

description:
Sample arrays:
H40_IP_L2-1.CEL
H40_IP_L2-2.CEL
H40_IP_L2-3.CEL
Control arrays:
Total_L2_RNP-1.CEL
Total_L2_RNP-2.CEL
FDR evaluation arrays:
IgG_IP_L2-1.CEL
IgG_IP_L2-2.CEL
IgG_IP_L2-3.CEL

source_name: hrp40 nuclear RNPs (3 replicates)


title: hrp38 bound RNA

description:
Sample arrays:
H38_IP_L2-1.CEL
H38_IP_L2-2.CEL
H38_IP_L2-3.CEL
Control arrays:
Total_L2_RNP-1.CEL
Total_L2_RNP-2.CEL
FDR evaluation arrays:
IgG_IP_L2-1.CEL
IgG_IP_L2-2.CEL
IgG_IP_L2-3.CEL

source_name: hrp38 nuclear RNPs (3 replicates)


title: hrp36-1 KD

description: Hrp36 knock-down sample 1


title: E8.25 4-6s ectoderm 1


title: E8.25 4-6s definitive endoderm 3


title: hrp36 bound RNA

description:
Sample arrays:
H36_IP_L2-1.CEL
H36_IP_L2-2.CEL
H36_IP_L2-3.CEL
Control arrays:
Total_L2_RNP-1.CEL
Total_L2_RNP-2.CEL
FDR evaluation arrays:
IgG_IP_L2-1.CEL
IgG_IP_L2-2.CEL
IgG_IP_L2-3.CEL

source_name: hrp36 nuclear RNPs (3 replicates)


title: E8.25 4-6s definitive endoderm 1


title: NCI-N87 Cell Line(32K_B)

status: Public on Dec 29 2008

type: genomic

city: Singapore

first: Wu

last: Yonghui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Center of Singapore

description:
NCI-N87 Cell Line(32K_B)
aCGH profiling for Gastric Cell Lines

hyb_protocol: Hybridizations were performed using a MAUI hybridization station, and hybridized onto microarrays containing 32,000 DOP-PCR amplified BAC clones covering the human genome (Children’s Hospital Oakland Research Institute, BACPAC resources)

scan_protocol: GeneChips were scanned using the GenePix 4000B scanner (Axon Instruments).

data_processing: The data were analyzed Genedata software for normalization and expression estimation

molecule: genomic DNA

organism: Homo sapiens

source_name: NCI-N87 Cell Line(32K_B)

label_protocol: 2 µg of cell line and reference genomic DNA (unrelated pooled male lymophocyte DNA from healthy donors) were labeled with Cy3-dCTP or Cy5-dCTP respectively (Amersham Biosciences) using the Bioprime Labelling system (Invitrogen)

extract_protocol: Qiagen Blood and Cell Culture DNA extraction kit.

tag: Gastric Cell Line (NCI-N87)

source_name: reference genomic DNA


title: NCI-N87 Cell Line(Hind)

description:
NCI-N87 Cell Line(Hind)
SNP profiling for Gastric Cell Lines

hyb_protocol: Following Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000

data_processing: The data were analyzed dChip software for normalization and expression estimation

source_name: NCI-N87 Cell Line(Hind)

label_protocol: biotinylated dideoxy ATP is terminal deoxynucleotidyl transferased

extract_protocol: Qiagen DNA extraction kit was used according to the manufacturer's instructions.


title: E8.25 4-6s definitive endoderm 2


title: SNU-16 Cell Line(Hind)

description:
SNU-16 Cell Line(Hind)
SNP profiling for Gastric Cell Lines

source_name: SNU-16 Cell Line(Hind)

tag: Gastric Cell Line (SNU-16)


title: SNU-5 Cell Line(Hind)

description:
SNU-5 Cell Line(Hind)
SNP profiling for Gastric Cell Lines

source_name: SNU-5 Cell Line(Hind)

tag: Gastric Cell Line (SNU-5)


title: SNU-16 Cell Line(32K_B)

description:
SNU-16 Cell Line(32K_B)
aCGH profiling for Gastric Cell Lines

source_name: SNU-16 Cell Line(32K_B)

tag: unrelated pooled male lymophocyte DNA from healthy donors


title: SNU-1 Cell Line(32K_B)

description:
SNU-1 Cell Line(32K_B)
aCGH profiling for Gastric Cell Lines

source_name: SNU-1 Cell Line(32K_B)

tag: Gastric Cell Line (SNU-1)


title: SNU-5 Cell Line(32K_B)

description:
SNU-5 Cell Line(32K_B)
aCGH profiling for Gastric Cell Lines

source_name: SNU-5 Cell Line(32K_B)


title: KATO III Cell Line(Hind)

description:
KATO III Cell Line(Hind)
SNP profiling for Gastric Cell Lines

source_name: KATO III Cell Line(Hind)

tag: Gastric Cell Line (KATO III)


title: SNU-1 Cell Line(32K_A)

description:
SNU-1 Cell Line(32K_A)
aCGH profiling for Gastric Cell Lines

source_name: SNU-1 Cell Line(32K_A)


title: Hs 746T Cell Line(Hind)

description:
Hs 746T Cell Line(Hind)
SNP profiling for Gastric Cell Lines

source_name: Hs 746T Cell Line(Hind)

tag: Gastric Cell Line (Hs 746T)


title: NCI-N87 Cell Line(32K_A)

description:
NCI-N87 Cell Line(32K_A)
aCGH profiling for Gastric Cell Lines

source_name: NCI-N87 Cell Line(32K_A)


title: SNU-1 Cell Line(Hind)

description:
SNU-1 Cell Line(Hind)
SNP profiling for Gastric Cell Lines

source_name: SNU-1 Cell Line(Hind)


title: NCI-N87 Cell Line(Xba)

description:
NCI-N87 Cell Line(Xba)
SNP profiling for Gastric Cell Lines

source_name: NCI-N87 Cell Line(Xba)


title: SNU-5 Cell Line(32K_A)

description:
SNU-5 Cell Line(32K_A)
aCGH profiling for Gastric Cell Lines

source_name: SNU-5 Cell Line(32K_A)


title: SNU-16 Cell Line(Xba)

description:
SNU-16 Cell Line(Xba)
SNP profiling for Gastric Cell Lines

source_name: SNU-16 Cell Line(Xba)


title: SNU-1 Cell Line(Xba)

description:
SNU-1 Cell Line(Xba)
SNP profiling for Gastric Cell Lines

source_name: SNU-1 Cell Line(Xba)


title: KATO III Cell Line(Xba)

description:
KATO III Cell Line(Xba)
SNP profiling for Gastric Cell Lines

source_name: KATO III Cell Line(Xba)


title: AGS Cell Line(Hind)

description:
AGS Cell Line(Hind)
SNP profiling for Gastric Cell Lines

source_name: AGS Cell Line(Hind)

tag: Gastric Cell Line (AGS)


title: KATO III Cell Line(32K_B)

description:
KATO III Cell Line(32K_B)
aCGH profiling for Gastric Cell Lines

source_name: KATO III Cell Line(32K_B)

source_name: reference genomic DNA


title: Hs 746T Cell Line(Xba)

description:
Hs 746T Cell Line(Xba)
SNP profiling for Gastric Cell Lines

source_name: Hs 746T Cell Line(Xba)


title: Hs 746T Cell Line(32K_B)

description:
Hs 746T Cell Line(32K_B)
aCGH profiling for Gastric Cell Lines

source_name: Hs 746T Cell Line(32K_B)


title: SNU-5 Cell Line(Xba)

description:
SNU-5 Cell Line(Xba)
SNP profiling for Gastric Cell Lines

source_name: SNU-5 Cell Line(Xba)


title: SNU-16 Cell Line(32K_A)

description:
SNU-16 Cell Line(32K_A)
aCGH profiling for Gastric Cell Lines

source_name: SNU-16 Cell Line(32K_A)


title: IPS-MEF-Ng-38C-2 #1 (251508710503 Array1_3)

status: Public on Dec 28 2008

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

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

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 50ul of DEPC dH2O.

tag: Strain

tag: Gender

value: unknown sex

tag: Individual Identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

tag: Universale Mouse Reference


title: AGS Cell Line(32K_A)

description:
AGS Cell Line(32K_A)
aCGH profiling for Gastric Cell Lines

source_name: AGS Cell Line(32K_A)


title: AGS Cell Line(32K_B)

description:
AGS Cell Line(32K_B)
aCGH profiling for Gastric Cell Lines

source_name: AGS Cell Line(32K_B)


title: KATO III Cell Line(32K_A)

description:
KATO III Cell Line(32K_A)
aCGH profiling for Gastric Cell Lines

source_name: KATO III Cell Line(32K_A)


title: Hs 746T Cell Line(32K_A)

description:
Hs 746T Cell Line(32K_A)
aCGH profiling for Gastric Cell Lines

source_name: Hs 746T Cell Line(32K_A)


title: AGS Cell Line(Xba)

description:
AGS Cell Line(Xba)
SNP profiling for Gastric Cell Lines

source_name: AGS Cell Line(Xba)


title: ES-C57BL6.9  Lif+ (251508710500 Array1_3)

description: Embryonic stem cells

source_name: Embryonic stem cells

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 10 ul of DEPC dH2O.

tag: Embryonic stem cells

value: male


title: ES-D3-GL   Lif+ (251508710502 Array1_4)

description: Embryonic stem cells

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 20 ul of DEPC dH2O.


title: IPS-MEF-FB-20A-10 #1 (251508710503 Array1_1)

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30ul of DEPC dH2O.


title: TGC 8.5-5 passage36 Lif+ (251508710501 Array1_3)

description: TGC(Embryonic germ cells)

source_name: TGC(Embryonic germ cells)

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

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 40 ul of DEPC dH2O.

tag: embryonic germ cell


title: MEF-DR4 #1 (251508710493 Array1_3)

description: fibroblasts

source_name: fibroblasts

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 20ul of DEPC dH2O.

tag: fibroblasts

value: mixed


title: ES -D3-GL Passage13  LIF+ (251508710502 Array1_3)

description: ES

source_name: ES

extract_protocol: One ml of TrizolTM (Invitrogen) was added to 1 well. Total RNA was extracted using Phase lock gelTM (Eppendorf) columns according to manufacturer protocol. RNA was precipitated with isopropanol, washed with 70% ethanol and dissolved in 30 ul of DEPC dH2O.

tag: embryonic stem cell


title: EBRTcH3   Lif+ (251508710502 Array1_2)

description: Embryonic stem cells


title: ES-129.3  Lif+ (251508710500 Array1_2)

description: Embryonic stem cells


title: MEF-BL6 #1 (251508710493 Array1_1)

description: fibroblasts


title: ES-C57BL6.9  Lif+ (251508710500 Array1_4)

description: Embryonic stem cells


title: TGC 8.5-5  Lif+ (251508710501 Array1_4)

description: (TGC)Embryonic germ cells

source_name: (TGC)Embryonic germ cells

tag: Embryonic Germ cells


title: ES-129.3  Lif+ (251508710500 Array1_1)

description: Embryonic stem cells


title: IPS-MEF-FB-20A-10 #2 (251508710503 Array1_2)


title: EBRTcH3  Passage5  LIF+ (251508710502 Array1_1)

description: ES


title: EG-1 passage 8 Lif+ (251508710501 Array1_1)

description: TGC(Embryonic germ cells)


title: MEF-BL6 #2 (251508710493 Array1_2)

description: fibroblasts


title: MEF-DR4 #2 (251508710493 Array1_4)

description: fibroblasts


title: 3T3 replication 2 (251508710492 Array1_4)

tag: cell line


title: 3T3 replication 1 (251508710492 Array1_3)


title: EG-1  Lif+ (251508710501 Array1_2)

description: (TGC)Embryonic germ cells


title: E12.5 Placenta2, 5 pooled (251508710476 Array1_4)

description: E12.5 Placenta

source_name: E12.5 Placenta

extract_protocol: TROZOL standard extraction method. The full protocol can be found in the Life Technologies CAT 15596. The following are the steps we used. 1.Homogenize tissue samples in 1 mL of TRIZOL Reagent per 50-100 mg of tissue using a glass-Teflon? or power homogenizer (Polytron, or Tekmar's TISSUMIZER? or equivalent). The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization.  3.PHASE SEPARATION Incubate the homogenized samples for 5 minutes at 15 to 30?C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30?C for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 2 to 8?C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. 4. RNA PRECIPITATION Transfer the aqueous phase to a fresh tube, and save the organic phase if isolation of DNA or protein is desired. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at 15 to 30?C for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 2 to 8?C. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 5. RNA WASH Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 2 to 8?C. 6. REDISSOLVING THE RNA At the end of the procedure, briefly dry the RNA pellet (air-dry or vacuum-dry for 5-10 minutes). Do not dry the RNA by centrifugation under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Partially dissolved RNA samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water or 0.5% SDS solution by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60?C. (Avoid SDS when RNA will be used in subsequent enzymatic reactions.) RNA can also be redissolved in 100% formamide (deionized) and stored at -70?C. (See Bracete, et.al. (1998) Focus 20:3 p 82).

treatment_protocol: Pregnant female mice from timed matings were sacrificed by cervical dislocation at 12.5 days post-coitus.  Decidua were removed to 1x PBS on ice, and embryos/placentas were dissected and transferred to iced PBS.  For each litter, embryos were combined in one tube, while placentas were combined in another.  Tubes were snap frozen on dry ice and stored at -80?C.

tag: placenta

value: mixed sex

tag: Age

value: 12.5 days

tag: Development stage

value: embryo


title: E12.5 Placenta1, 5 pooled (251508710476 Array1_3)

description: E12.5 Placenta


title: SNL-STO replication 2 (251508710492 Array1_2)

description: SNL-STO

source_name: SNL-STO


title: N2_d6 #2 (251508710476 Array1_2)

description: N2 day6

source_name: N2 day6

extract_protocol: Total RNA extracted with TRIzol reagent (Invitrogen) according to the manufacturers instructions.

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 6 days.

value: TBE


title: N2_d6 #1 (251508710474 Array1_3)

description: N2 day6


title: N2_d4 #1 (251508710474 Array1_1)

description: N2 day4

source_name: N2 day4

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 4 days.


title: ES_129b #2 (251508710474 Array1_4)

treatment_protocol: Undifferentiated 129 ES cells (2.5 x 106 cells) were cultured in gelatin-coated T25 flasks in ES standard medium with LIF for 24h.


title: IPS-MEF-Ng-38C-2 #2 (251508710503 Array1_4)


title: N2_d1 #2 (251508710475 Array1_1)

description: N2 day1

source_name: N2 day1

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 1 day.


title: N2_d3 #2 (251508710475 Array1_3)

description: N2 day3

source_name: N2 day3

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 3 days.


title: N2_d2 #2 (251508710475 Array1_2)

description: N2 day2

source_name: N2 day2

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 2 days.

source_name: Universal Mouse Reference 129ES Cell


title: N2_d4 #2 (251508710475 Array1_4)

description: N2 day4


title: ES_129a #2 (251508710471 Array1_4)

treatment_protocol: Undifferentiated embryonic stem cells, 129.3 (129/SvEv) was cultivated on gelatin-coated 100 mm-dishes in DMEM supplemented with 15% FBS, 2 mM glutamine, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, Penicillin-Streptomycin and 103 unit/ml of LIF.


title: N2_d2 #1 (251508710472 Array1_3)

description: N2 day2


title: SNL-STO replication 1 (251508710492 Array1_1)

description: SNL-STO


title: ES_129b #1 (251508710472 Array1_1)


title: N2_d3 #1 (251508710472 Array1_4)

description: N2 day3


title: P19 3-1 (251508710470 Array1_4)

treatment_protocol: grown on gelatin in DMEM (GIBCO 11965-092) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin.

tag: embryonic carcinomal cell


title: N2_d5 #2 (251508710476 Array1_1)

description: N2 day5

source_name: N2 day5

treatment_protocol: ES cells were plated at 1 x104 cells/cm2 onto gelatin-coated 60 mm-dishes and were cultured as a monolayer in N2B27, which is a 1:1 mixture of DMEM/F12 supplement with modified N2 and Neurobasal medium supplement with B27 without vitamin A (GIBCO) for 5 days.


title: P19 RA 3-1 (251508710471 Array1_2)

description: P19 RA

source_name: P19 RA

treatment_protocol: To induce neural differentiation of P19 cells, they were aggregated in presence of 1μM all-trans-retinoic acid (RA, Sigma) in 100 mm bacteriological dishes (Fisher). The RA stock solution (10mM) was made with anhydrous ethanol. Cultures were fed with fresh media containing RA after 2 days. P19 cell aggregates were cultured for following 2days.


title: N2_d1 #1 (251508710472 Array1_2)

description: N2 day1


title: ES_129a #1 (251508710471 Array1_3)


title: P19 1-1 (251508710470 Array1_3)


title: N2_d5 #1 (251508710474 Array1_2)

description: N2 day5


title: P19 RA 1-1 (251508710471 Array1_1)

description: P19 RA


title: NS1 #2 (251508710469 Array1_4)

description: doublet cells

source_name: doublet cells

treatment_protocol: Cells isolated from the forebrain periventricular zone were cultured to form neurospheres. The neurospheres were dissociated into single cells and passaged to a new culture dish. After one day in culture (1DIV), cells that divided and formed doublets were harvested as NS1.

tag: neural stem/progenitor cells

value: doublet cells #2 251508710469 Array1_4


title: F9 1-1 (251508710470 Array1_1)


title: F9 3-1 (251508710470 Array1_2)


title: TS #2 (251508710468 Array1_4)

description: GFP-Exe TS cells

source_name: GFP-Exe TS cells

treatment_protocol: grown on TC plastic, 70cond+Fgf4+Heparin, p28, DNA/GFP sort, p4

tag: trophoblast stem cell

tag: Genetic modification

value: GFP transgenic

value: GFP-Exe TS cells #2 on plastic, 70cond+Fgf4+Heparin, p28 251508710468 Array1_4


title: NS1 #1 (251508710469 Array1_3)

description: doublet cells

tag: Strain

value: doublet cells #1 251508710469 Array1_3


title: DC #1 (251508710469 Array1_1)

description: differentiated cells

source_name: differentiated cells

treatment_protocol: By culturing in differentiation promoting conditions, NS5 cells were turned into differentiated neural cells (DC).

tag: Gender

value: Differentiated neural cells #1 251508710469 Array1_1


title: TS #1 (251508710468 Array1_3)

description: GFP-Exe TS cells

tag: Individual Identifier

value: GFP-Exe TS cells #1  251508710468 Array1_3


title: ZHBTc4(Tc+), 120hr, #1 (251508710468 Array1_1)

description: ZHBTc4(Tc+), 120hr

source_name: ZHBTc4(Tc+), 120hr

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

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

value: gene knock in

tag: Universale Mouse Reference


title: ZHBTc4(Tc+), 96hr, #2 (251508710467 Array1_4)

description: ZHBTc4(Tc+), 96hr

source_name: ZHBTc4(Tc+), 96hr


title: ZHBTc4(Tc+), 120hr, #2 (251508710468 Array1_2)

description: ZHBTc4(Tc+), 120hr


title: ZHBTc4(Tc+), 72hr, #1 (251508710467 Array1_1)

description: ZHBTc4(Tc+), 72hr

source_name: ZHBTc4(Tc+), 72hr


title: ZHBTc4(Tc+), 72hr, #2 (251508710467 Array1_2)

description: ZHBTc4(Tc+), 72hr


title: DC #2 (251508710469 Array1_2)

description: differentiated cells

value: Differentiated neural cells #2 251508710469 Array1_2


title: Muscle spaceflight 11

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

description: AEM animals were housed at Cape Canaveral Air Force Station’s Hangar L orbital environmental simulator for 11 days and 19 h with conditions mimicking the shuttle’s middeck temperature, humidity, and CO2 levels

hyb_protocol: Fragmented cRNA samples were hybridized overnight at 45oC in a GeneChip hybridization oven 640. Post hybridization washing and phycoerythrin-streptavidin staining were performed in an Affymetrix Fluidics Station 450 using established Affymetrix protocols.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip Scanner 3000, two passes

data_processing: Expression values were calculated using RMA; detection calls were calculated using MAS5

source_name: gastrocnemius, spaceflight, 11 days1 9hr

label_protocol: Synthesis of double stranded cDNA, in vitro transcription of biotin-labeled cRNA targets and fragmentation of target cRNA were performed as outlined by Affymetrix protocols.

extract_protocol: Total RNA was prepared from tissue samples by Trizol extraction followed by purification using RNeasy columns (Qiagen Inc., Valencia, CA). Quality and purity of the RNA preparations were assessed by spectrophotometric determination of A260:A280 ratios and by quantification of 28S:18S ribosomal RNA ratios using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: tissues were dissected and then snap frozen in liquid nitrogen.

value: C57BL/6J; Gender:female; Age:77 days


title: Muscle spaceflight 8


title: ZHBTc4(Tc+), 96hr, #1 (251508710467 Array1_3)

description: ZHBTc4(Tc+), 96hr


title: Muscle AEM 4

description: SF animals were flown on the middeck of the space shuttle Endeavour (STS-108/UF-1) for 11 days and 19 h beginning December 5, 2001

source_name: gastrocnemius, animal enclosure module on earth, 11 days 19hr


title: Muscle AEM 3


title: Muscle AEM 2


title: ZHBTc4(Tc+), 24hr, #1 (251508710466 Array1_1)

description: ZHBTc4(Tc+), 24hr

source_name: ZHBTc4(Tc+), 24hr


title: Muscle spaceflight 10


title: Muscle suspension 8

description: mice were suspended at approximately a 30° angle by taping the tail to a plastic dowel attached to a swivel apparatus

source_name: calf muscle, hindlimb suspension, 12 days


title: Muscle suspension 9


title: Muscle spaceflight 9


title: ZHBTc4(Tc+), 48hr, #1 (251508710466 Array1_3)

description: ZHBTc4(Tc+), 48hr

source_name: ZHBTc4(Tc+), 48hr


title: ZHBTc4(Tc+), 48hr, #2 (251508710466 Array1_4)

description: ZHBTc4(Tc+), 48hr


title: ZHBTc4(Tc+), 24hr, #2 (251508710466 Array1_2)

description: ZHBTc4(Tc+), 24hr


title: Muscle suspension 30


title: Muscle AEM 1


title: ZHBTc4(Tc+), 0hr, #3 (251508710465 Array1_4)

description: ZHBTc4(Tc+), 0hr

source_name: ZHBTc4(Tc+), 0hr


title: postnatal week 3.5-replicate3

city: Taipei

first: wencheng

last: chen

address: 128 Sec. 2, Academia Rd

department: Insititute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression in early phases of Autosomal Dominant Polycystic Kidney Disease

hyb_protocol: Fluorescent probes from wild-type and Pkd1L3/L3 groups were co-hybridized to oligonucleotides from a IMB mouse 32K oligonucleotide array (Qiagen Array-Ready Mouse Oligo Set, V3.0)

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalization was used to normalize data obtained from GeneSpring.

label: Alexa 647

source_name: postnatal week 3.5

label_protocol: Fluorescence-labeled cDNA probes were generated from 20 μg DNase-treated RNAs using 400 U of Superscript III (Invitrogen) with oligo-dT primers (PerkinElmer, Waltham, MA, USA), hydrolyzed in EDTA/NaOH mixture at 70°C for 15 min, and cleaned up using QIAquick columns (Qiagen).

extract_protocol: Total RNA was isolated from kidney tissue from Pkd1L3/L3 mice and age-matched control groups using TRIZOL reagent (Invitrogen).

tag: Pkd1L3/L3 mice

label: Alexa 555

source_name: Wt mice

value: C57BL6 (B6) mice


title: Muscle suspension 25


title: ZHBTc4(Tc+), 0hr, #1 (251508710465 Array1_3)

description: ZHBTc4(Tc+), 0hr

source_name: Universal Mouse Reference 129ES Cell


title: 5G6GR5(Dx+), Day5 replication 2 (251508710465 Array1_2)

description: 5G6GR5(Dx+), Day5

source_name: 5G6GR5(Dx+), Day5

extract_protocol: Total RNA extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions and further purified with PureLink Micro-to-Midi Total RNA purification System (Invitrogen). Total RNA were dissolved in 40 microL of water and stored at -80 degree.

treatment_protocol: The 5G6GR5 cells (1x10^5 cells) were plated on gelatin coated 10cm plate with DMEM containing Dexametasone(Dx) (100nM) in presence of LIF and cultured to 5 days.  Medium were changed every day until 24 hours before harvest.  Day 0 samples were same cells before plating.

tag: ES cells

value: unknown sex

value: Transgenic and Knock down


title: 5G6GR5(Dx+), Day1 replication 2 (251508710463 Array1_2)

description: 5G6GR5(Dx+), Day1

source_name: 5G6GR5(Dx+), Day1


title: 5G6GR5(Dx+), Day4 replication 2 (251508710464 Array1_3)

description: 5G6GR5(Dx+), Day4

source_name: 5G6GR5(Dx+), Day4


title: 5G6GR5(Dx+), Day3 replication 2 (251508710464 Array1_2)

description: 5G6GR5(Dx+), Day3

source_name: 5G6GR5(Dx+), Day3


title: 5G6GR5(Dx+), Day1 replication 1 (251508710463 Array1_1)

description: 5G6GR5(Dx+), Day1


title: Muscle suspension 11


title: Muscle reloaded 33

description: mice were suspended at approximately a 30° angle by taping the tail to a plastic dowel attached to a swivel apparatus; at 12 days mice were unsuspended for 3.5 hours

source_name: calf muscle, hindlimb suspension, 12 days plus reloading for 3.5hr


title: postnatal week 3.5-replicate1


title: 5G6GR5(Dx+), Day0 replication 2 (251508710462 Array1_4)

description: 5G6GR5(Dx+), Day0

source_name: 5G6GR5(Dx+), Day0


title: 5G6GR5(Dx+), Day2 replication 2 (251508710463 Array1_4)

description: 5G6GR5(Dx+), Day2

source_name: 5G6GR5(Dx+), Day2


title: postnatal week 3-replicate3

source_name: postnatal week 3


title: postnatal week 3.5-replicate2


title: 5G6GR5(Dx+), Day0 replication 1 (251508710462 Array1_3)

description: 5G6GR5(Dx+), Day0


title: Muscle reloaded 15


title: 5G6GR5(Dx+), Day5 replication 2 (251508710465 Array1_1)

description: 5G6GR5(Dx+), Day5


title: 5G6GR5(Dx+), Day4 replication 2 (251508710464 Array1_4)

description: 5G6GR5(Dx+), Day4


title: postnatal week 3-replicate1


title: Muscle reloaded 18


title: postnatal week 2-replicate4

source_name: postnatal week 2


title: PrEn_d5 #2 (251508710462 Array1_2)

treatment_protocol: Grown on gelatin in DMEM (GIBCO 11965-092) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin. 5 days treatment with 100nM RA and 1mM dibutyryl cAMP.


title: postnatal week 3-replicate2


title: 5G6GR5(Dx+), Day2 replication 1 (251508710463 Array1_3)

description: 5G6GR5(Dx+), Day2


title: Muscle reloaded 16


title: 5G6GR5(Dx+), Day3 replication 2 (251508710464 Array1_1)

description: 5G6GR5(Dx+), Day3


title: PrEn_d4 #2 (251508710462 Array1_1)

treatment_protocol: grown on gelatin in DMEM (GIBCO 11965-092) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin. 4 days treatment with 100nM RA and 1mM dibutyryl cAMP.


title: Muscle reloaded 14


title: PrEn_d3 #2 (251508710461 Array1_4)

treatment_protocol: grown on gelatin in DMEM (GIBCO 11965-092) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin. 3 days treatment with 100nM RA and 1mM dibutyryl cAMP.


title: postnatal week 2-replicate3


title: PrEn_d5 #1 (251508710461 Array1_1)


title: PrEn_d2 #2 (251508710461 Array1_3)

treatment_protocol: grown on gelatin in DMEM (GIBCO 11965-092) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin. 2 days treatment with 100nM RA and 1mM dibutyryl cAMP.


title: PrEn_d4 #1 (251508710460 Array1_4)


title: postnatal week 2-replicate2


title: PrEn_d1 #2 (251508710461 Array1_2)

treatment_protocol: grown on gelatin in DMEM (GIBCO 11965-092) with 10%FCS, 2mM Glutamine and Penicillin-Streptomycin. 1 day treatment with 100nM RA and 1mM dibutyryl cAMP.


title: PrEn_d3 #1 (251508710460 Array1_3)


title: Muscle control 21

description: normally housed three per cage

source_name: calf muscle, no treatment, 12 days


title: postnatal week 1-replicate3

source_name: postnatal week 1


title: PrEn_d1 #1 (251508710460 Array1_1)


title: Muscle control 22

description: normally housed three per cage


title: Muscle control 2

description: normally housed three per cage


title: Muscle control 1

description: normally housed three per cage


title: Muscle control 19

description: normally housed three per cage


title: postnatal week 2-replicate1


title: postnatal week 1-replicate2


title: postnatal week 1-replicate1

scan_protocol: The microarrays were scanned for Alexa 555 and Alexa 647 fluorescent signals using a GenePix 4000B Microarray Scanner (Molecular Devices)


title: PrEn_d2 #1 (251508710460 Array1_2)


title: ZMS1_4493.1_ArrayA

status: Public on Dec 26 2008

city: Toronto

first: Lourdes

last: Pena-Castillo

state: Ontario

address: 160 College St. Room 1350

department: Banting and Best Department of Medical Research

institute: University of Toronto

description: Yeast ZMS1_4493.1_ArrayA

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) under LifterSlip cover slips (Erie Scientific) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 100 nM (unless otherwise specified) in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at 20°C. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. Slides were spun dry by centrifugation at 40 g for 5 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars at 20°C on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa488-conjugated antibody (488 nm ex, 522 nm em). Separately, slides were scanned after primer extension to quantify the amount of incorporated Cy3-conjugated dUTP (543 nm ex, 570 nm em). Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices)

data_processing: Every non-palindromic 8-mer occurs on at least 32 spots in each chamber of our universal PBM and we provide several scores for each 8-mer in each experiment: (1) Median Intensity, (2) Z-Score, and (3) Enrichment Score (E-Score). E-scores are a modified version of AUC, and describe how well each 8-mer ranks the intensities of the spots.

source_name: Baker's yeast ZMS1

label_protocol: T7-GST tagged proteins were not labelled after purification

extract_protocol: Protein open reading frames, consisting of the pfam-defined DNA-binding domain and 15 amino acids of flanking sequence (or to the end of the full open reading frame) were cloned into pMAGIC1  by either RT-PCR from pooled yeast mRNA or by gene synthesis (DNA 2.0).  We transferred the inserts into a T7-GST-tagged variant of pML280 following.  We expressed proteins by either (i) purification from E. coli C41 DE3 cells (Lucigen), or (ii) in vitro translation reactions (Ambion ActivePro Kit) without purification.

tag: Yeast ZMS1


title: YPR196W_2047.3_ArrayA.2

description: Yeast YPR196W_2047.3_ArrayA.2

source_name: Baker's yeast YPR196W

tag: Yeast YPR196W


title: YRM1_2064.3_ArrayA.2

description: Yeast YRM1_2064.3_ArrayA.2

source_name: Baker's yeast YRM1

tag: Yeast YRM1


title: YRM1_2064.2_ArrayA.1

description: Yeast YRM1_2064.2_ArrayA.1


title: YPR022C_4500.2_ArrayA

description: Yeast YPR022C_4500.2_ArrayA

source_name: Baker's yeast YPR022C

tag: Yeast YPR022C


title: YPR013C_2104.3_ArrayA.2

description: Yeast YPR013C_2104.3_ArrayA.2

source_name: Baker's yeast YPR013C

tag: Yeast YPR013C


title: YRR1_2114.2_ArrayA

description: Yeast YRR1_2114.2_ArrayA

source_name: Baker's yeast YRR1

tag: Yeast YRR1


title: YPR013C_2104.2_ArrayA.1

description: Yeast YPR013C_2104.2_ArrayA.1


title: YPR013C_2104.1_ArrayB

description: Yeast YPR013C_2104.1_ArrayB


title: YPL230W_2051.2_ArrayB

description: Yeast YPL230W_2051.2_ArrayB

source_name: Baker's yeast YPL230W

tag: Yeast YPL230W


title: YML081W_2152.1_ArrayB

description: Yeast YML081W_2152.1_ArrayB

source_name: Baker's yeast YML081W

tag: Yeast YML081W


title: YML081W_2152.3_ArrayA.2

description: Yeast YML081W_2152.3_ArrayA.2


title: YNR063W_2118.3_ArrayA.2

description: Yeast YNR063W_2118.3_ArrayA.2

source_name: Baker's yeast YNR063W

tag: Yeast YNR063W


title: YOX1_2073.3_ArrayB

description: Yeast YOX1_2073.3_ArrayB

source_name: Baker's yeast YOX1

tag: Yeast YOX1


title: YOX1_2073.5_ArrayA.2

description: Yeast YOX1_2073.5_ArrayA.2


title: YNR063W_2118.2_ArrayA.1

description: Yeast YNR063W_2118.2_ArrayA.1


title: YKL222C_2044.2_ArrayA

description: Yeast YKL222C_2044.2_ArrayA

source_name: Baker's yeast YKL222C

tag: Yeast YKL222C


title: YLR278C_2147.3_ArrayA.2

description: Yeast YLR278C_2147.3_ArrayA.2

source_name: Baker's yeast YLR278C

tag: Yeast YLR278C


title: YLL054C_2046.2_ArrayA

description: Yeast YLL054C_2046.2_ArrayA

source_name: Baker's yeast YLL054C

tag: Yeast YLL054C


title: YGR067C_2151.3_ArrayA.2

description: Yeast YGR067C_2151.3_ArrayA.2

source_name: Baker's yeast YGR067C

tag: Yeast YGR067C


title: YGR067C_2151.1_ArrayB

description: Yeast YGR067C_2151.1_ArrayB


title: YER130C_2103.2_ArrayA

description: Yeast YER130C_2103.2_ArrayA

source_name: Baker's yeast YER130C

tag: Yeast YER130C


title: YGR067C_2151.2_ArrayA.1

description: Yeast YGR067C_2151.2_ArrayA.1


title: YDR520c_2043.2_ArrayA

description: Yeast YDR520c_2043.2_ArrayA

source_name: Baker's yeast YDR520c

tag: Yeast YDR520c


title: YER184C_2108.3_ArrayA.2

description: Yeast YER184C_2108.3_ArrayA.2

source_name: Baker's yeast YER184C

tag: Yeast YER184C


title: YAP3_4535.2_ArrayA

description: Yeast YAP3_4535.2_ArrayA

source_name: Baker's yeast YAP3

tag: Yeast YAP3