title: Col-98-3|15

value: Colon


title: D.rerio_adult_CR_vs_Mma20_6dpi_6

status: Public on Jul 31 2009

type: RNA

city: Leiden

first: Anna

middle: Magdalena

last: Zakrzewska

address: Wassenaarseweg 64

department: IBL

country: Netherlands

institute: University of Leiden

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) according to Agilent protocol G4140-90050 v.5.7 (www.Agilent.com) for Two-Color Microarray-Based Gene Expression Analysis.

scan_protocol: Microarray data were processed from raw data image files with Feature Extraction Software 9.5.3 (Agilent Technologies).

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of UniGene clusters (UniGene build #105). The significance cut-off for ratios of infected versus control was set at P ≤ 10-4. For adult infection studies, where triplicate individuals are tested, an absolute fold change cut-off (≥ 1.5) was applied additionally.

molecule: total RNA

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 dye(GE Healthcare) and column purified.

extract_protocol: Adult fish were homogenized in liquid nitrogen using a mortar and pestle and portions of 50 -100 μg of powdered tissue were used for extraction of total RNA with 1 ml of TRIZOL® Reagent (Invitrogen) according to the manufacturer’s instructions. Embryos were directly homogenized in TRIZOL® Reagent. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). Samples used for microarray analysis had an average RIN value of 9 and a minimum RIN value of 8.

treatment_protocol: This sample is a mixture of all RNA samples from early adult infection study (1 and 6 dpi infection with Mma20 and E11 strains and PBS-injected controls)

tag: reference

value: CR (common reference) is a mixture of all RNA samples from healthy and infected adult zebrafish used in this microarray study

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 μg of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy5 dye(GE Healthcare) and column purified.

growth_protocol:
Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org).
Infection experiments with adult fish were performed on young males selected from a wild type laboratory-breeding colony and acclimated to their new environment for one week in a quarantine area. These fish were kept at 28˚C on a 12:12 h light/dark rhythm throughout the experiment. Groups of 30 fish, infected with the same dose and strain of mycobacteria, were kept in small fish tanks (10 l) with their own separate filtering system (Eheim Ecco).

treatment_protocol: Zebrafish were inoculated intraperitoneally as previously described (Meijer et al., 2004) with approximately 10000 bacteria or with phosphate-buffered saline (PBS) as a control.

tag: tissue

value: adult zebrafish

tag: infection

value: 10000 bacteria of M.marinum Mma20 strain

tag: time

value: 6 dpi (day post infection)


title: D.rerio_adult_CR_vs_Mma20_6dpi_4

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org).


title: D.rerio_adult_CR_vs_PBS_1dpi_1

growth_protocol: Infection experiments with adult fish were performed on young males selected from a wild type laboratory-breeding colony and acclimated to their new environment for one week in a quarantine area. These fish were kept at 28˚C on a 12:12 h light/dark rhythm throughout the experiment.

treatment_protocol: Zebrafish were inoculated intraperitoneally as previously described (Meijer et al., 2004) with phosphate-buffered saline (PBS) as a control.

tag: agent

value: PBS and harvested

value: 1 dpi (day post injection)


title: Col-92-2|14

city: Mukilteo

first: Michael

middle: Joseph

last: Lodes

state: WA

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

country: USA

institute: CombiMatrix Corp

hyb_protocol: Sectored array chambers (4 chambers per array) (CombiMatrix 4×2K arrays™) were each filled with 30 μl of Pre-Hybridization Solution (CombiMatrix Corp) and incubated for 10 min at 45°C.  MicroRNA was mixed with 9 μl 20× SSPE (Ambion), 4.8 μl BSA at 50 mg/ml (Ambion), 3.6 μl deionized formamide (Sigma) and 7.5 μl of 10% SDS (Ambion) and heated to 95°C for 3 min.  30 μl of each sample were added to sectored hybridization chambers, sealed with aluminum tape, and incubated at 45°C for 16 hr with rotation.  After hybridization, arrays were washed 2 × with 2 × SSC with 0.1% SDS at room temperature (RT) for 10 sec (CombiMatrix Corp), 2 × with 2× SSC at RT for 10 sec and then washed 1 × with 0.2 × SSC at RT for 10 sec each.  Arrays were blocked with 5× PBS/Casein Blocking Buffer at RT for 10 min and then labeled with streptavidin-Cy5 labeling solution for fluorescence scanning and incubated for 30 min at RT.  Arrays were then washed 2 × with Biotin Wash Solution (2× PBST) for 30 sec each at room temp and again washed 2 × with 2 × PBS followed by scanning with an Axon instrument.

scan_protocol: Arrays were scanned with an Axon Instruments GenePix 4000B scanner

data_processing: Data were extracted from scanned images with the CombiMatrix software Microarray Imager.  For each miRNA mature region, two controls were written on the chip: a sense wild-type probe (s), an anti-sense wild-type (PM) form and a double mutant control (MM). This probe set was used to evaluate significance as well as intensity of each miRNA mature form. For each hybridization, the raw signal was extracted and probes were grouped by the miRNA that they were designed for. PM signal was log2 transformed, and Z-normalized. For the classifier and for the focused cancer versus normal hierarchical clustering, we used a simple heuristic to determine if a probe was indeed present. For each miRNA that was evaluated, we counted a signal significant if the signal for PM/MM >1.0. If so, then the Z-normalized log2 (signal) was used for that miRNA, otherwise the probe data for that particular probe was not used. Normalization was thus performed over anti-sense wild-type probes across the chip; however, only data from significant probes were used for clustering and classification.   Data Mining was performed using the WEKA package. Normalized probe intensity data was converted into ARFF format and input into the WEKA program. Hybridizations were grouped into two classes, ‘cancer’ and ‘normal’. We used the CfsSubsetEval routine to choose miRNA’s (attributes). This method gave the best classification of the data into the two classes. This routine assesses the predictive ability of each attribute as well as the degree of redundancy among each miRNA. It prefers attributes that are highly correlated within each class, but that have low inter-correlation. The choice of attributes was performed using 10-fold cross-validation, and selection of the 28 best attributes was based upon their being selected at least 30% of the time.    We next extracted signal from each hybridization for just this selected set of miRNA’s. Two different classifiers were used to distinguish cancer vs. normal samples. A Bayesian network and an instance-based method called K* were able to clearly differentiate the two classes within 36 samples. Clustering was next performed using the Cluster program from Eisen et al. Average linkage was used as the tree-building criteria and Spearman rank correlation was used as the distance function.

organism: Homo sapiens

source_name: Serum,RNA

label_protocol: Approximately one μg of isolated RNA was labeled with a Mirus miRNA Biotin labeling kit (MIR8450) following manufacturers directions.  Briefly, 1 μg RNA was diluted to 86 μl with water and 10 μl of 10 × buffer was added followed by 4 μl LabelIT biotin labeling reagent and incubation at 37°C for 1 hr.  The reaction was stopped with 10 μl stop reagent and the sample precipitated as described above.  The dried pellet was resuspended in 5.1 μl water.

extract_protocol: An aliquot of 400 μl of each serum sample was mixed with 500 μl lysis buffer (RLT, Qiagen, Valencia, CA) and 800 μl acid phenol: Chloroform (Ambion, Foster City, CA), vortexed for 30 seconds and centrifuged at 16000 rcf for 10 min at 25°C.  The aqueous phase was extracted 2 × with an equal volume of acid phenol:chloroform and centrifuged at 16000 rcf for 10 min at 25°C.  The resulting aqueous phase was then precipitated with 0.1 vol 5 M NaCl, 2 μl precipitation enhancer (Mirus, Madison, WI), 2 μl GlycoBlue (Ambion) and 2.5 vol 100% ethanol at –20ºC for at least 1 hr.  After centrifugation at 4ºC for 30 min, the pellets were washed 2 × with 75% ethanol and then air-dried.  Precipitated RNA was resuspended in 50 μl molecular grade water (Ambion) and quantified with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: Human serum samples were purchased from Bioreclamation, Inc, Hicksville, NY and include: stages 2 to 4 prostate, stages 1 to 4 colon, stage 4 ovarian, stage 4 breast, and stages 3 and 4 lung cancer sera; and sera from normal male and female donors. Samples were stored at minus 80ºC until use.

tag: gender

value: female

tag: tumor stage

tag: tumor site


title: D.rerio_adult_CR_vs_Mma20_6dpi_5


title: D.rerio_adult_CR_vs_Mma20_1dpi_3

value: 1 dpi (day post infection)


title: D.rerio_adult_CR_vs_Mma20_1dpi_2


title: RP58+/+

city: Setagaya

first: Hiroshi

last: Asahara

state: Tokyo

department: Department of Systems BioMedicine

country: Japan

institute: National Research Institute for Child Health and Development

description: Gene expression data from WT mouse.

hyb_protocol: Hybridization of 10 ug cRNA to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols.

scan_protocol: GeneChips® were scanned using GeneChip Scanner 3000.

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Command Console using default parameters. We used the Expression Console Version 1.1 software for data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation.

label: biotin

organism: Mus musculus

source_name: muscle in diaphragm

label_protocol: Biotinylated cRNA were prepared from total RNA following standard Affymetrix® protocols.

extract_protocol: RNA of the culture was extracted using ISOGEN (NIPPONGENE).

tag: strain

value: skeletal muscle

tag: developmental stage

tag: genotype


title: D.rerio_adult_CR_vs_Mma20_1dpi_1


title: D.rerio_adult_CR_vs_E11_6dpi_6

value: 10000 bacteria of M.marinum E11 strain


title: Col-798-3|19


title: D.rerio_adult_CR_vs_E11_6dpi_5


title: D.rerio_adult_CR_vs_E11_6dpi_4


title: Col-796-3|10

value: male


title: Col-792-2|18


title: Col-123-2|39


title: Col-122-2|38


title: Col-121-1|37


title: Bre-157-4|32

value: Breast


title: Col-120-3|36


title: D.rerio_adult_CR_vs_E11_1dpi_2


title: D.rerio_adult_CR_vs_E11_1dpi_1


title: D.rerio_adult_CR_vs_E11_1dpi_3


title: D.rerio_adult_chronic (i4) vs control (c4)

description: D.rerio_adult_M.marinum_infected vs control replica_4

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3 (Agilent Technologies). The XDR function was used to extend the dynamic range. Samples from control fish (c1-c4) were labelled with Cy3 dye and samples from infected fish (i1-i4) with Cy5 dye. After feature extraction, data were imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modeling.  Ratio results from four control fish versus four infected fish (c1 vs. i1, c2 vs. i2, c3 vs. i3, c4 vs. i4) were combined using the default ratio experiment builder.

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 dye (GE Healthcare) and column purified.

extract_protocol: Fish were snap frozen in liquid nitrogen, stored at -80°C, and homogenized in liquid nitrogen using a mortar and pestle. Portions of 50 -100 μg of powdered tissue were used for extraction of total RNA with 1 ml of TRIZOL® Reagent (Invitrogen) according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to clean up using RNeasy columns (Qiagen). The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). The samples used had an average RIN value of 9.5 and a minimum RIN value of 8.9.

tag: disease state

value: healthy

value: whole organism

tag: age

value: adult

source_name: M.marinum_chronic_infected fish_i4

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy5 dye (GE Healthcare) and column purified.

treatment_protocol: Adult male zebrafish were infected by intraperitoneal inoculation with approximately 1x 10-3 M. marinum bacteria

value: M. marinum infected fish showing overt signs of fish tuberculosis


title: Rice mutant dst, biological rep1

status: Public on Jul 30 2009

city: Shanghai

first: Hong-Xuan

last: Lin

address: 300 Fenglin Road

country: China

institute: Shanghai Institute of Plant Physiology and Ecology

description: mutant plant dst,replicate1

hyb_protocol: standard Affymetrix procedures

scan_protocol: GeneChips were scanned using the Gene array Scanner3000.

organism: Oryza sativa

source_name: mutant plant dst,replicate1

label_protocol: standard Affymetrix procedures

growth_protocol: Seedlings were grown in a growth chamber with an 11h light (26°C)/13h dark(22°C) photoperiod for 25 days.

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

tag: Strain

value: Oryza sativa L.dst mutant,Tissue:shoots

tag: Age

value: 25 days


title: D.rerio_adult_chronic (i3) vs control (c3)

description: D.rerio_adult_M.marinum_infected vs control replica_3

source_name: M.marinum_chronic_infected fish_i3


title: D.rerio_adult_chronic (i1) vs control (c1)

description: D.rerio_adult_M.marinum_infected vs control replica_1

source_name: M.marinum_chronic_infected fish_i1


title: D.rerio_adult_chronic (i2) vs control (c2)

description: D.rerio_adult_M.marinum_infected vs control replica_2

source_name: M.marinum_chronic_infected fish_i2


title: Rice mutant dst, biological rep3

description: mutant plant dst,replicate3

source_name: mutant plant dst,replicate3


title: Bre-158-4|11


title: H2030-BrM3 replicate 2

status: Public on Jul 10 2009

city: New York

first: Don

middle: X

last: Nguyen

state: NY

address: 1275 York Box 116

department: Cancer Biology and Genetics

institute: MSKCC

hyb_protocol: standard

scan_protocol: standard

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Subconfluent, in RPMI

extract_protocol: Rneasy qiagen kit.

treatment_protocol: 0.2% serum overnight, +/- Wnt3A for 3 hours


title: Rice Zhonghua11, biological rep2

description: wild-type plant Zhonghua11,biological replicate2

source_name: wild-type plant Zhonghua11,replicate2

value: Oryza sativa L. Japonica cv. Zhonghua 11,Tissue:shoots


title: Rice Zhonghua11, biological rep3

description: wild-type plant Zhonghua11,biological replicate3

source_name: wild-type plant Zhonghua11,replicate3


title: D.rerio_embryo_CR_vs_E11_embryo_2hpiB

data_processing: Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. Data were analyzed at the level of UniGene clusters (UniGene build #105). The significance cut-off for ratios of infected versus control was set at P ≤ 10-4.

growth_protocol: Embryos were grown at 28,5 -30 °C in egg water (60µg/ml Instant Ocean see salts).

extract_protocol: Embryos were directly homogenized in TRIZOL® Reagent. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies). Samples used for microarray analysis had an average RIN value of 9 and a minimum RIN value of 8.

treatment_protocol: For the duration of bacterial injections embryos were kept under anaesthesia in egg water containing 0.02% buffered 3-aminobenzoic acid ethyl ester (tricaine, Sigma). Embryos were staged at 28 hours post fertilization (hpf) by morphological critera (Kimmel et al.) and approximately 50 cfu of E11 bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Infection experiments were carried out in triplicate on separate days and pools of 15-20 embryos were taken at 2, 24 and 120 hours post infection (hpi).

value: Common reference (CR) consisting of a mixture of samples from embryo infections

value: 15-20 embryos

value: 2 hours post infection

value: 50 cfu of E11 M. marinum strain


title: H2030-BrM3 replicate 1


title: Parental H2030+wnt3A  replicate 2

source_name: parental H2030+wnt3A

tag: parental H2030+wnt3A


title: Rice Zhonghua11, biological rep1

description: wild-type plant Zhonghua11,biological replicate1

source_name: wild-type plant Zhonghua11,replicate1


title: H2030-BrM3+wnt3A replicate 2


title: H2030-BrM3+wnt3A replicate 1


title: Parental H2030+wnt3A replicate 1


title: Parental H2030 replicate 2

source_name: parental H2030

tag: parental H2030


title: Rice mutant dst, biological rep2

description: mutant plant dst,replicate2

source_name: mutant plant dst,replicate2


title: Parental H2030 replicate 1


title: D.rerio_adult_CR_vs_PBS_1dpi_3

tag: reference

value: CR (common reference) is a mixture of all RNA samples from healthy and infected adult zebrafish used in this microarray study

value: adult zebrafish

value: PBS and harvested

value: 1 dpi (day post injection)


title: PC9-BrM3+wnt3A replicate 2


title: PC9-BrM3+wnt3A replicate 1


title: parental PC9+wnt3A  replicate 1

source_name: Parental PC9+wnt3A

tag: Parental PC9+wnt3A


title: parental PC9+Wnt3A replicate 2


title: PC9-BrM3 replicate 2


title: PC9-BrM3 replicate 1


title: parental PC9 replicate 2

source_name: Parental PC9

tag: Parental PC9


title: parental PC9 replicate 1


title: Lin-UCB culture d 12 Lin+ 2

status: Public on Jul 01 2009

city: Toronto

first: Daniel

last: Kirouac

state: Ontario

department: Biomaterials and Biomedical Engineering

country: Canada

institute: University of Toronto

description: Lin+ UCB cells, cultured 12 days

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

source_name: Lin+ UCB cells, cultured 12 days

label_protocol: Affymetrix protocol

extract_protocol: RNEasy kit

tag: cell type

value: Lin+ UCB cells


title: Endometrial stromal cell - Jag1 retrovirus infected 3

city: Stony Brook

first: Anatoly

last: Mikhailik

address: HSC-T8, Rm 053

department: OB/GYN/Pathology

institute: SUNY at Stony Brook

scan_protocol: Standard Affymetrix protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY),

data_processing: MAS 5 protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY),

source_name: endometrial stromal cell - Jag1 retrovirus infected3, 3 days post infection

growth_protocol: cultured in RPMI 1640 with 10% FBS as described previously (Liu and Tseng, 1979), harvested for mRNAs analysis on day-3 post-infection

extract_protocol: DNA-free total RNA was isolated from cell cultures (day-3 post-infection) using RNAqueous-4PCR Kit (Ambion)

treatment_protocol: cultured in RPMI 1640 with 10% FBS as described previously (Liu and Tseng, 1979), infected with Jag1 nonreplicative retrovirus

value: endometrial stromal cells

tag: growth phase

value: early passage


title: Endometrial stromal cell - control/vector 3

description: Standard Affymetrix protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY)

source_name: endometrial stromal cell - control/vector1, 3 days post infection

treatment_protocol: cultured in RPMI 1640 with 10% FBS as described previously (Liu and Tseng, 1979), infected with control nonreplicative retrovirus (vector)


title: Endometrial stromal cell - Jag1 retrovirus infected 1

hyb_protocol: Standard Affymetrix protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY)

source_name: endometrial stromal cell - Jag1 retrovirus infected1, 3 days post infection


title: Lin-UCB culture d 8 NSNE Lin+ 2

description: Lin+ UCB cells, cultured 8 days, NS/NE at day 4

source_name: Lin+ UCB cells, cultured 8 days, NS/NE at day4


title: Lin-UCB culture d 8 NSNE Lin- 2

description: Lin- UCB cells, cultured 8 days, NS/NE at day 4

value: Lin- UCB cells


title: Endometrial stromal cell - control/vector 1

label_protocol: Standard Affymetrix protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY)


title: Lin-UCB culture d 12 Lin- 2

description: Lin- UCB cells, cultured 12 days

source_name: Lin- UCB cells, cultured 12 days


title: MCL 7466/02

status: Public on Jun 03 2010

city: Heidelberg

first: Alexandra

last: Farfsing

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: Labeled, amplified material (700 to 1250 ng per array) was hybridized to the Illumina Human whole genome Sentrix-6 V2 BeadChip® array according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Raw data extraction was done using the beadarray R package (svn release 1.7.0) from bioconductor.org. Bead outliers were removed when their expression value dropped below a threshold: the imaging system background, non-specific binding and cross hybridization signal. Individual bead types were flagged as filtered when their bead replicate count dropped below 17. All data was used for the mean expression value calculation within beadarray. Finally, we excluded a bead type when the bead type’s filter flag was set across all samples. Data analysis was done by variance stabilizing and spline normalizing the signals using the algorithms from the lumi R package (release 1.1.0) from bioconductor.org.

source_name: Primary MCL

label_protocol: Labeling was achieved by use of the incorporation of biotin-16-UTP.

growth_protocol: B-cells of MCL and CLL patients were isolated from peripheral blood using ficoll gradient protocoll.

extract_protocol: RNA  was isolated from the freshly islolated B-cells using the RNeasy kit (Qiagen, Hilden, Germany). RNA quality and concentration were assessed with the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: B lymphocytes

tag: disease

value: mantle cell lymphoma

value: Primary MCL

tag: isolate

value: MCL patient 1


title: Endometrial stromal cell - control/vector 2

source_name: endometrial stromal cell - control/vector2, 3 days post infection


title: Lin-UCB culture d 12 Lin+ 1

description: Lin+ UCB cells, cultured 12 days


title: Lin-UCB culture d 12 Lin- 1

description: Lin- UCB cells, cultured 12 days


title: Endometrial stromal cell - Jag1 retrovirus infected 2

source_name: endometrial stromal cell - Jag1 retrovirus infected2, 3 days post infection


title: Lin-UCB culture d 8 SE Lin+ 2

description: Lin+ UCB cells, cultured 8 days, S/E at day 4


title: Lin-UCB culture d 8 NSNE Lin+ 1


title: CLL.12q.1

source_name: Primary CLL

value: chronic lymphocytic leukemia

value: Primary CLL

value: CLL patient 22


title: Lin-UCB culture d 8 SE Lin- 2

description: Lin- UCB cells, cultured 8 days, S/E at day 4

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

label_protocol: Standard Affymetrix protocol


title: Lin-UCB culture d 4 Lin- 1

description: Lin- UCB cells, cultured 4 days

source_name: Lin- UCB cells, cultured 4 days


title: Lin-UCB culture d 4 Lin+ 1

description: Lin+ UCB cells, cultured 4 days

source_name: Lin+ UCB cells, cultured 4 days


title: Immature WEEV infected biological replicate 2 (WEEV)

city: Ann Arbor

first: David

last: Miller

state: MI

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Fragmented cRNAs were hybridized to Affymetrix Human Genome Array U133 Plus 2.0 array chips for 16 h at 45C, washed, and stained using an Affymetrix microfluids station.

scan_protocol: Chips were scanned with an Affymetrix Scanner 3000.

data_processing: The data were analyzed using the Affymetrix package of Bioconductor - expression values were calculated using a robust multi-array average (RMA).

source_name: BE(2)-C cell line

label_protocol: Biotinylated cRNAs were prepared from 5-10 ug total RNA using standard Affymetix protocol.  Processing and chip analyses done at the University of Michigan Affymetrix Core.

growth_protocol: Cells cultured at 37C in 5% CO2 in DMEM supplemented with 5% bovine growth serum, 10 U/ml penicillin, and 10 ug/ml streptomycin.  For differentiation, 10 uM all-trans retinoic acid added and cell incubated for additional 3 weeks.

extract_protocol: Trizol extraction of total RNA done per the manufacturer's instruction.  Total RNA digested with RQ1 DNAse and reisolated with RNAsy columns per the manufacturer's instructions.  Quality and quantity analyzed with Agilent 2100 BioAnalyzer.

treatment_protocol: Cells infected with WEEV at an MOI=10 for 6 h - mock cells were incubated with media alone for same time period.

tag: differentiation

value: immature

tag: treatment

value: WEEV 6h

tag: cell line


title: Lin-UCB culture d 8 NSNE Lin- 1

source_name: Lin- UCB cells, cultured 8 days, NS/NE at day 4


title: Mature WEEV infected biological replicate 1 (WEEV)

source_name: RA-differentiated BE(2)-C cell line

value: mature


title: Mature IFN 12h biological replicate 2 (IFN)

scan_protocol: Chips were scanned with an Affymetrix GCS3000.

data_processing: The data were analyzed by Seqwright - expression values were calculated using a robust multi-array average (RMA).

label_protocol: Biotinylated cRNAs were prepared from 5-10 ug total RNA using NuGen Ovation Biotin labeling system per the manufacturer's instructions.  Processing and chip analyses done by SeqWright.

treatment_protocol: For IFN treatment, cells incubated with 50 U/ml recombinant human IFNa-A/D for 6 or 12 h.  Control cells incubated with media alone for same time period.

value: IFN 12h


title: Mature unstimulated biological replicate 2 (WEEV)


title: Mature IFN 12h biological replicate 3 (IFN)


title: Mature unstimulated biological replicate 1 (WEEV)


title: Immature unstimulated biological replicate 2 (WEEV)


title: Mature IFN 12h biological replicate 1 (IFN)


title: Lin-UCB culture d 0 Lin+ 1

description: Lin+ UCB cells, freshly isolated

source_name: Lin+ UCB cells, freshly isolated


title: Lin-UCB culture d 0 Lin+ 2

description: Lin+ UCB cells, freshly isolated


title: Lin-UCB culture d 8 SE Lin- 1

source_name: Lin- UCB cells, cultured 8 days, S/E at day4


title: Lin-UCB culture d 0 Lin- 2

description: Lin- UCB cells, freshly isolated

source_name: Lin- UCB cells, freshly isolated


title: Lin-UCB culture d 4 Lin+ 2

description: Lin+ UCB cells, cultured 4 days


title: Lin-UCB culture d 0 Lin- 1

description: Lin- UCB cells, freshly isolated


title: Lin-UCB culture d 4 Lin- 2

description: Lin- UCB cells, cultured 4 days


title: Mature WEEV infected biological replicate 2 (WEEV)


title: Immature unstimulated biological replicate 1 (WEEV)


title: Immature WEEV infected biological replicate 1 (WEEV)


title: Mature IFN 6h biological replicate 3 (IFN)

value: IFN 6h


title: Mature IFN 6h biological replicate 1 (IFN)


title: Mature unstimulated biological replicate 3 (IFN)


title: Mature IFN 6h biological replicate 2 (IFN)


title: Immature IFN 12h biological replicate 3 (IFN)


title: Immature IFN 12h biological replicate 1 (IFN)


title: Mature unstimulated biological replicate 1 (IFN)


title: Immature IFN 12h biological replicate 2 (IFN)


title: Immature unstimulated biological replicate 1 (IFN)


title: Immature unstimulated biological replicate 2 (IFN)


title: Immature IFN 6h biological replicate 3 (IFN)


title: Immature IFN 6h biological replicate 1 (IFN)


title: Immature IFN 6h biological replicate 2 (IFN)


title: Fungiform taste buds, sample 4

city: San Diego

first: Bryan

last: Moyer

state: CA

address: 4767 Nexus Centre Drive

institute: Senomyx, Inc.

description: Material collected from ~5,000 cells by laser capture microdissection

hyb_protocol: Following fragmentation, approximately 2.0 ug of single stranded cDNA were hybridized for 18-20 hr at 45C on Affymetrix GeneChip Rhesus Macaque Genome Arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 with Autoloader.

data_processing: The data were analyzed with Agilent Technologies GeneSpring GX software.  Raw data were processed using GC-RMA normalization.

organism: Macaca fascicularis

source_name: FG taste buds

label_protocol: Total RNA was amplified to generate cDNA using the NuGEN Ovation Biotin RNA Amplification (v1).  Labelled cDNA was prepared according to NuGEN Ovation Biotin RNA Amplification and Labeling System kit (v1).  Material was labeled with Biotin.

extract_protocol: Extraction of total RNA was performed using a Qiagen microRNeasy kit according to the manufacturer's instructions.

tag: animal id number

tag: gender

value: Male

tag: age (years)

tag: tissue

value: Fungiform taste buds


title: Lingual epithelium, sample 7

source_name: Lingual epithelium surrounding CV taste buds

value: Female

value: Lingual epithelium surrounding Circumvallate taste buds


title: Circumvallate taste buds, sample 4

source_name: CV taste buds

value: Circumvallate taste buds


title: Lingual epithelium, sample 1

source_name: Lingual epithelium surrounding FG taste buds

value: Lingual epithelium surrounding Fungiform taste buds


title: Lingual epithelium, sample 10


title: Circumvallate taste buds, sample 1


title: Lingual epithelium, sample 6


title: Fungiform taste buds, sample 6


title: Immature unstimulated biological replicate 3 (IFN)


title: Lingual epithelium, sample 4


title: Circumvallate taste buds, top portion, sample 1

source_name: Top portion of CV taste buds

value: Top portion of Circumvallate taste buds


title: Circumvallate taste buds, bottom portion, sample 1

source_name: Bottom portion of CV taste buds

value: Bottom portion of Circumvallate taste buds


title: Circumvallate taste buds, top portion, sample 4


title: Circumvallate taste buds, bottom portion, sample 4


title: Circumvallate taste buds, bottom portion, sample 2


title: Circumvallate taste buds, top portion, sample 2


title: Circumvallate taste buds, sample 3


title: Lingual epithelium, sample 3


title: Fungiform taste buds, sample 3


title: Circumvallate taste buds, sample 2


title: Gene Expression profiling of M. bovis BCG strain under extended stationary phase compared to Resuscitation phase

city: Lucknow

first: Ranjana

last: Srivatsava

address: Chattar Manzil Palace

country: India

institute: Central Drug Research Institute

description: Slides were scanned at 5 micron resolution using Agilent scanner.Automated feature extraction was done using Agilent’s Feature Extraction Software.

hyb_protocol: 825ng each of labeled control cRNA was mixed with 825ng of treated labelled cRNA, mixed with appropriate amount of blocking buffer and hybridization buffer (Agilent Technologies). The hybridization mix was applied on to the backings and hybridized to custom designed 60mer Mycobacterium tuberculosis microarray using sure hyb chambers at 65degC for 17 hours. Slides were washed with gene expression wash buffer 1 and 2 (Agilent Technologies) followed by Acetonitrile.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Analysis of feature extracted data was done using Agilent’s GeneSpring GX V 7.3.1 software. Pre-processing of the replicate experiment data was done to flag the outliers. Normalization of the data was done using per spot per chip intensity dependant lowess normalization and dye swap experiment was data transformed. Genes with log2 ratio of 1.29 and above in replicate experiments were considered as up regulated and 0.81 and below was considered down regulated. p-value was calculated by GeneSpring GX for each gene on the basis of replicate probes to indicate statistical significance. Biological significance of differentials were analyzed using Genotypics Biointerpreter - Web based tool for biological interpretation of given genelist.

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: Mycobacterium bovis BCG Resuscitation phase

label_protocol: Total RNA (500ng) of Mycobacterium under Resuscitation phase was labelled with Cy5 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

extract_protocol: Qiagen’s bacterial RNA kit

value: Resuscitation phase

source_name: Mycobacterium bovis BCG extended stationary phase culture

label_protocol: Total RNA (500ng) of Mycobacterium under extended stationary phase was labelled with Cy3 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

value: Stationary phase culture


title: Lingual epithelium, sample 9


title: Fungiform taste buds, sample 5


title: Lingual epithelium, sample 8


title: Lingual epithelium, sample 5


title: Gene Expression profiling of M. bovis BCG strain under extended stationary phase compared to Log Phase culture

label_protocol: Total RNA (500ng) of Mycobacterium under extended stationary phase was labelled with Cy5 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

source_name: Mycobacterium bovis BCG log phase culture

label_protocol: Total RNA (500ng) of Mycobacterium under log phase was labelled with Cy3 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

value: Log phase culture


title: Circumvallate taste buds, top portion, sample 3


title: Fungiform taste buds, sample 2


title: Lingual epithelium, sample 2


title: Circumvallate taste buds, bottom portion, sample 3


title: Gene Expression profiling of M. bovis BCG strain under extended stationary phase compared to Log Phase culture DyeSwap

label_protocol: Total RNA (500ng) of Mycobacterium under log phase was labelled with Cy5 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.


title: Week 2

city: La Jolla

first: Martina

last: Spehlmann

address: 9500 Gilman Drive

institute: UCSD

description: Total genomic DNA was spotted for positive and negative controls. These spot data were already eliminated from the whole 34,790 spot data on the array.

hyb_protocol: RNA was hybridized to arrays in 6xSSPE/30% formamide at 25oC for 18h. Hybridized slides are washed post-hybridization and signals on slides were detected using indirect ditection of Streptavidin-Alexa 647.

scan_protocol: Processed slides are scanned by using Axon 4000B Scanner (Molecular Devices).

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. Normalization Method: Median-Normalization

label: Steptavidin Alexa 647

source_name: Whole colon

label_protocol: 2.5 to 5mg of total RNA were labeled with first-strand biotin-cDNA.

growth_protocol: All mice were obtained from The Jackson Laboratory and were at least 8 weeks old for experiments. For infections, C. rodentium was grown overnight in LB broth, harvested by centrifugation, and resuspendend in fresh broth at 2.5x10^9/ml.

extract_protocol: RNA was isolated from whole colon tissue using Trizol reagent (Invitrogen). RNA quality was assessed with an Agilent Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were infected by oral gavage with 0.2ml (5x10^8 bacteria) of the suspension.

tag: time point

value: Week 2 after C. rodentium infection


title: Week 3

value: Week 3 after C. rodentium infection


title: Week 0

value: Before C. rodentium infection (week 0)


title: Week 1

value: Week 1 after C. rodentium infection


title: OAD11_mammary_high_loss_rep6

city: Auckland

first: Matt

middle: D

last: Littlejohn

address: PO Box 109-185 Newmarket

country: New Zealand

institute: DairyNZ

description: 'Signal' and 'Control' values in sheet represent normalised values for experimental probes only. 'Control probes' are un-normalised (including dye swaps) in these tables.

hyb_protocol: Microarray hybridization was performed using the Agilent Gene Expression Hybridisation Kit in accordance with the Agilent 60-mer oligo microarray processing protocol, version 2.0 (Agilent Technologies). Fragmented, dye-labelled aRNA was added to each Agilent 22K 60-mer oligonucleotide microarray, hybridized overnight (17 hrs), and washed and dried the following day according to the same protocol guidelines.

scan_protocol: Arrays were scanned immediately after drying step using an Agilent DNA microarray scanner, using Agilent Scan Control software v7.0.3. Scans were performed at 10 micron resolution with laser power set at 50%. Data was extracted from the image files using Agilent Feature Extraction software v9.5.3 with all options set at default values. Data output was a tab delimited text file.

data_processing: Data analyses were performed with Genespring GX 7.3.1. (Agilent Technologies). Array data were imported into Genespring using Agilent’s two-colour ‘Enhanced FE’ import scenario which included ‘Per Spot: Divide by control channel’ and ‘Per Chip: Normalize to 50th percentile’ normalization steps. A dye swap normalization was also carried out on the six arrays that used reverse signal and control channel dye labelling.

organism: Bos taurus

source_name: mammary, twice daily milked, cow 450, high loss, dye swapped

label_protocol: 5ug of modified aRNA was vacuum dried and labelled with Cy3 or Cy5 NHS ester dyes (Amersham Cy3 and Cy5 Mono-Reactive Dye Packs, GE Healthcare UK Ltd., Little Chalfont, Buckinghamshire, UK). Purified, dye-incorporated aRNA was then quantified and assessed for dye coupling efficiency using the Nanodrop (Nanodrop Technologies, Wilmington, DE, USA) instrument.

extract_protocol:
Mammary tissue biopsies were homogenized in Qiagen buffer RLT (QIAGEN GmbH, Hilden, Germany) using Fastprep Lysing Matrix D tubes in a FastPrep instrument (MP Biomedicals, Solon, OH, USA). Total RNA was extracted using a Qiagen RNeasy kit (Qiagen). RNA quantity was determined by spectrophotometry in a Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE, USA). RNA integrity was checked with the Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA, USA).
Amplified RNA (aRNA) for microarray hybridization was prepared using the Amino Allyl MessageAmp ™ aRNA Kit (Ambion, Austin TX, USA) in accordance with the protocol provided with the kit. One ug of total RNA was used to generate the amino allyl modified aRNA.

tag: cow

tag: milking frequency

value: twice per day

tag: yield loss group

value: high

source_name: mammary, once daily milked, cow 450, high loss, dye swapped

value: once per day


title: OAD09_mammary_low_loss_rep5

source_name: mammary, twice daily milked, cow 269, low loss, dye swapped

value: low

source_name: mammary, once daily milked, cow 269, low loss, dye swapped


title: OAD10_mammary_high_loss_rep5

source_name: mammary, twice daily milked, cow 332, high loss, dye swapped


title: OAD12_mammary_high_loss_rep7

source_name: mammary, twice daily milked, cow 452, high loss, dye swapped

source_name: mammary, once daily milked, cow 452, high loss, dye swapped


title: Lin-UCB culture d 8 SE Lin+ 1

source_name: Lin+ UCB cells, cultured 8 days, S/E at day 4

value: Lin+ UCB cells


title: OAD03_mammary_low_loss_rep2

source_name: mammary, once daily milked, cow 108, low loss

source_name: mammary, twice daily milked, cow 108, low loss


title: OAD01_mammary_low_loss_rep1

source_name: mammary, once daily milked, cow 270, low loss

source_name: mammary, twice daily milked, cow 270, low loss


title: OAD07_mammary_low_loss_rep3

source_name: mammary, twice daily milked, cow 372, low loss, dye swapped

source_name: mammary, once daily milked, cow 372, low loss, dye swapped


title: WH8102_13049627_pCu11-shock_rep6

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

country: Australia

institute: Macquarie University

description: This slide measures gene expression of Synechococcus sp. WH8102 exposed to copper shock compared to a non-shocked control.

hyb_protocol: Combine Cy3 and Cy5 samples and 1 microliter cy-labeled arabidopsis 70-mer positional controls (This is a pool of 4 70-mers labeled with Cy3 and Cy5 for a total of 8 70-mers at 2 ng/microliter each.  The sequences are:  At2g14610a_219_rev - AAAAAAATATATCAACAATGGCAAAGCTACCGATACGAAACAATATTAGGAAAAATGTGTGTAAGGACAA; At2g14610b_265_rev - AATTTAAACTGCGTATTAGTGTTTGGAAAAAAAAAACAAAGTGTATACAATGTCAATCGGTGATCTTTTT; At2g14610c_305_rev - TTAATAACATATAATATTGAATAGGATATCATAGGATATTATTACGTAATAATATCCTATGGTGTCATTT; At2g14610d_298_rev - CGACTTTTCTTGCTTAGAAGTCTTTGCATTGTTAATAGATTGTTGAAAAGGTTTATTCATTACTTTCATG). Dry using a speed vac. Make pre-hybridization buffer by combining: 0.5 g BSA; 37 mL DEPC water; 12.5 mL 20X SSC; 0.5 mL 10% SDS. Incubate pre-hybridization buffer for 20 minutes at 42 degrees C. Filter using a 0.45 micrometer cellulose acetate filter into a coplin jar. Incubate for 20 minutes at 42 degrees C. Make hybridization buffer by combining: 500 microliters fomamide; 250 microliters 20X SSC; 10 microliters 10% SDS; 240 microliters DEPC water. Filter hybridization buffer through a 0.45 micrometer cellulose acetate filter. Add 50 uL sheared salmon sperm DNA (Ambion) to hybridization buffer. Add 60 microliters hybridization buffer to speed vac-dried probes. Put slide into pre-hybridization buffer in coplin jar. Incubate for 45 minutes at 42 degrees C. Wash slide 4 times in water and 3 times in isopropanol for 2 minutes per wash with gentle shaking by hand. Dry slide by spinning. Clean 25 mm x 60 mm lifterslip (Erie Scientific Company) by dipping in MilliQ water for 5 minutes at room temperature. Dip in 100% EtOH and dry with a Chem Wipe. Heat probes for 15 minutes at 95 degrees C with occassional "flicking" to resuspend probes. Remove probes from heat block and centrifuge for 2 minutes at 15,000g. Place lifterslip onto slide and add probes by allowing capillary action to pull the probes under the lifterslip. Hybridize overnight at 42 degrees C. Wash slide 2 times in glass staining dish with 1X SSC, 0.2% SDS for 5 minutes at 42 degrees C. Wash slide in 0.1X SSC, 0.1% SDS for 5 minutes at room temperature. Wash slide 3 times in 0.1X SSC for 5 minutes at room temperature. Dry slide by spinning.

scan_protocol: Slide were scanned at 10 micrometer resolution using an Axon 4000B scanner with GenePix 4.0 software.

data_processing: Tiff images were processed using TIGR-Spotfinder (www.tigr.org/software) with Otsu thresholding, a minimum spot size of 10 and a maximum spot size of 15, and applying the default quality control filter options.  The data were normalized ignoring controls with the LOWESS algorithm in block mode with a smooth parameter of 0.33 by using TIGR-MIDAS (www.tigr.org/software).

organism: Parasynechococcus marenigrum WH 8102

source_name: RS8102r3-pCu11 shock, Rep B Control

label_protocol:
Make spike-in control pools from RNA amplified from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) using the MegaScript Kit (Ambion) by combining for Cy5 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
4.7 microliters 13.279 ng/microliter ltp6 RNA;
11.8 microliters 21.313 ng/microliter rcp1 RNA;
40.7 microliters 23.23 ng/microliter nac RNA;
4.6 microliters 18.177 ng/microliter xcp2 RNA;
14.7 microliters 11.436 ng/microliter prk RNA;
18.9 microliters 11.084 ng/microliter tim RNA;
826.5 microliters water.
And for Cy3 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
1.6 microliters 13.279 ng/microliter ltp6 RNA;
3.9 microliters 21.313 ng/microliter rcp1 RNA;
13.6 microliters 23.23 ng/microliter nac RNA;
13.9 microliters 18.177 ng/microliter xcp2 RNA;
44.1 microliters 11.436 ng/microliter prk RNA;
56.8 microliters 11.084 ng/microliter tim RNA;
788.1 microliters water.
To label RNA sample combine:
4 micrograms RNA;
2 microliters 3 mg/mL random hexamers (Invitrogen);
2 microliters arabidopsis spike-in control RNA;
DEPC water to a final volume to 17.5 microliters.
Mix and incubated at 70 degrees C for 10 minutes.
Snap-freeze in dry ice/ethanol for 30 seconds and centrifuged for 1 minute at approximately 16,000g.
Add:
6 microliters 5X Superscript II buffer (Invitrogen);
3 microliters 0.1 M dithiothreitol;
1.2 microliters aminoallyl-dNTP mix containing 12.5 mM dATP, 12.5 mM dCTP, 12.5 mM dGTP, 4.16 mM dTTP, and 8.33 mM aadUTP;
2 microliters SuperScript II (Invitrogen).
Mix and incubated overnight at 42 degrees C.
Add:
10 microliters 1 M NaOH;
10 microliters 0.5 M EDTA.
Incubate for 15 minutes at 65 degrees C.
Add:
25 microliters 1 M Tris pH 7.4;
400 microliters PB buffer (Qiagen).
Apply sample to QIAquick column (Qiagen).
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters phosphate wash buffer (84.25 mL 95% EtOH + 15.25 mL water + 0.5 mL 1 M KPO4 pH 8.5 solution made by combining 0.5 mL 1M KH2PO4 with 9.5 mL 1M K2HPO4).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters phosphate elution buffer (4 mM KPO4 solution made by diluting 1 M KPO4 pH 8.5 solution).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Dry sample using a speed vac.
Resuspend cDNA in 4.5 microliters 0.1 M carbonate buffer (1 M Na2CO3 buffer pH 9.0 diluted 1:10 with water).
Allow the sample to resuspend for 15 minutes at room temperature.
Add 4.5 microliters NHS-Cy (Amersham) resuspended in 73 microliters DMSO.
Incubate for 1 hour at room temperature in the dark.
Add 4.5 microliters 4 M hydroxylamine.
Incubate for 15 minutes at room temperature in the dark.
Add:
35 microliters 100 mM NaOAc pH 5.2;
500 microliters PB buffer.
Apply to Qiaquick column.
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters PE buffer (Qiagen).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters EB buffer (Qiagen).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Check quality of probes spectrophotometrically from 200nm to 700nm.
Store at -80 degrees C.

growth_protocol: Batch cultures of Synechococcus sp. strains WH8102 were grown in chelexed SOW media, as previously described by Dupont et al. (1) with the exception that copper was not added to the media in the trace metal mix and nickel was added at final concentration of 0.5 nM.  The cultures were grown at 24C under constant light at approximately 80 M photons m-2 s-1 in trace metal clean polycarbonate or glass and until in mid-exponential phase, as measured by fluorescence-based growth curve and validated later with flow cytometry.

extract_protocol:
Half the batch culture was spun down at room temperature at 10,400  g, resuspended in Trizol and frozen at -80C for eventual RNA extraction, taking care that the harvesting time stayed under 30 minutes.  Cu/EDTA was added to the other half for Cu2+ levels of pCu 11.1 (as determined using a MINEQL (2) calculation). After a two-hour incubation, these cells were harvested as outlined above. All samples were then thawed at room temperature, incubated for 60 minutes at 65C.  Chloroform at 0.2X was then added to the Trizol cell mixture and tubes were shaken vigorously by hand for 30 seconds.  The samples were then incubated at room temperature for 10 minutes, spun down at 4C at 12,0000  g for 15 minutes and the aqueous layer was carefully removed.  1X volume of cold isopropanol was then added, incubated on ice for 12 minutes, and spun down at 4C at 12,000  g for 15 minutes.  The supernatant was removed and the pellet was washed with 1X volume cold 75% ethanol and stored at -20C overnight.  The samples were then spun down again at 4C at 12,000  g for 15 minutes, resuspended in smaller tubes and spun down once more in the same conditions.  The supernatant was then removed, and the pellet given at least 30 minutes to dry before resuspension in 100 µl DEPC-treated water.  Concentrations were then assessed using a NanoDrop spectrophotometer and if greater than 100 µg were split and diluted before proceeding.  The RNA was then cleaned using a Qiagen RNeasy kit with two additional RNase-free DNase treatments on column according to the manufacturer’s specifications.
1.	Dupont, C. L., K. Barbeau, and B. Palenik. 2008. Ni uptake and limitation in marine Synechococcus strains. Applied and Environmental Microbiology 74:23-31.
2.	Westall, J. C., J. L. Zachary, and F. M. M. Morel. 1976. MINEQL-General algorithm for computation of chemical –equilibrium in aqueous systems. Abstracts of Papers of the American Chemical Society 172:8-8.

tag: axenic Synechococcus sp. WH8102

source_name: RS8102r4-pCu11 shock, Rep B 2 hrs


title: OAD05_mammary_high_loss_rep3

source_name: mammary, once daily milked, cow 12, high loss

source_name: mammary, twice daily milked, cow 12, high loss


title: OAD08_mammary_low_loss_rep4

source_name: mammary, twice daily milked, cow 419, low loss, dye swapped

source_name: mammary, once daily milked, cow 419, low loss, dye swapped


title: OAD02_mammary_high_loss_rep1

source_name: mammary, once daily milked, cow 99, high loss

source_name: mammary, twice daily milked, cow 99, high loss


title: OAD04_mammary_high_loss_rep2

source_name: mammary, once daily milked, cow 61, high loss

source_name: mammary, twice daily milked, cow 61, high loss


title: WH8102_13049626_pCu11-shock_rep5


title: WH8102_13049625_pCu11-shock_rep4


title: WH8102_13049624_pCu11-shock_rep3

source_name: RS8102r1-pCu11 shock, Rep A Control

source_name: RS8102r2-pCu11 shock, Rep A 2 hrs


title: WH8102_bsy89280d0057_copper-shock_rep6

source_name: CD43r(2)-WH8102 in normal SOW-Control of CD44r(2)

extract_protocol:
Half the batch culture was spun down at room temperature at 10,400  g, resuspended in Trizol and frozen at -80C for eventual RNA extraction, taking care that the harvesting time stayed under 30 minutes.  Cu/EDTA was added to the other half for Cu2+ levels of pCu 10.1 (as determined using a MINEQL (2) calculation). After a two-hour incubation, these cells were harvested as outlined above. All samples were then thawed at room temperature, incubated for 60 minutes at 65C.  Chloroform at 0.2X was then added to the Trizol cell mixture and tubes were shaken vigorously by hand for 30 seconds.  The samples were then incubated at room temperature for 10 minutes, spun down at 4C at 12,0000  g for 15 minutes and the aqueous layer was carefully removed.  1X volume of cold isopropanol was then added, incubated on ice for 12 minutes, and spun down at 4C at 12,000  g for 15 minutes.  The supernatant was removed and the pellet was washed with 1X volume cold 75% ethanol and stored at -20C overnight.  The samples were then spun down again at 4C at 12,000  g for 15 minutes, resuspended in smaller tubes and spun down once more in the same conditions.  The supernatant was then removed, and the pellet given at least 30 minutes to dry before resuspension in 100 µl DEPC-treated water.  Concentrations were then assessed using a NanoDrop spectrophotometer and if greater than 100 µg were split and diluted before proceeding.  The RNA was then cleaned using a Qiagen RNeasy kit with two additional RNase-free DNase treatments on column according to the manufacturer’s specifications.
1.	Dupont, C. L., K. Barbeau, and B. Palenik. 2008. Ni uptake and limitation in marine Synechococcus strains. Applied and Environmental Microbiology 74:23-31.
2.	Westall, J. C., J. L. Zachary, and F. M. M. Morel. 1976. MINEQL-General algorithm for computation of chemical –equilibrium in aqueous systems. Abstracts of Papers of the American Chemical Society 172:8-8.

source_name: CD44r(2)-WH8102 in normal SOW-CuEDTA shock


title: OAD06_mammary_high_loss_rep4

source_name: mammary, once daily milked, cow 277, high loss

source_name: mammary, twice daily milked, cow 277, high loss


title: WH8102_13049622_pCu11-shock_rep1


title: Mature unstimulated biological replicate 2 (IFN)

source_name: RA-differentiated BE(2)-C cell line

value: mature


title: WH8102_bsy89280d0047_copper-shock_rep3

source_name: CD38r-WH8102 in normal SOW-Control of CD37r

source_name: CD37r-WH8102 in normal SOW-CuEDTA shock


title: WH8102_bsy89280d0056_copper-shock_rep5


title: WH8102_13049623_pCu11-shock_rep2


title: Mouse E17.5 placental labyrinth

status: Public on Jun 30 2009

type: protein

first: Brian

last: Cox

address: 1 King's College Circle, Rm 3360

department: Physiology

description: The placental labyrinth was microdissected away from the spongio trophoblast layer

data_processing: Raw files were converted to m/zXML using ReAdW and searched by X!Tandem against a mouse (v3.28) or human (v3.28) IPI (International Protein Index; http://www.ebi.ac.uk/IPI) protein sequence database. To estimate and minimize our false positive rate the protein sequence database also contained every IPI protein sequence in its reversed amino acid orientation (target-decoy strategy) (Gortzak-Uzan et al., 2008; Sodek et al., 2008). A conservative false discovery rate was set to 0.5% on the peptide level, as recently described (Gortzak-Uzan et al., 2008; Sodek et al., 2008). Only fully tryptic peptides matching these criteria were accepted to generate the final list of identified proteins. We only accepted proteins identified either with two unique peptides or one unique, unambigious peptide found in greater that or equal to 2 MudPIT runs per analyzed organelle fraction. To minimize protein inference, we developed a database grouping scheme and only report proteins with substantial peptide information, as recently reported (Gortzak-Uzan et al., 2008; Sodek et al., 2008).

molecule: protein

source_name: E17.5 placental labyrinth

extract_protocol:
EXTRACTION: Placentas from naturally-mated crosses of C57Bl/6J mice on embryonic day 17.5 were cut into thick slices. A scalpel blade was used to isolate the blood-red labyrinth tissue from the more poorly vascularized, and hence paler, spongiotrophoblast tissue, and to remove the superficial chorionic vasculature.  From each litter, a quarter of the collected labyrinth tissues were set aside for RNA extraction and microarray analysis and ¾ for cellular fractionation and proteomic analysis, as recently described (Kislinger et al., 2006).

SEPARATION: The preparation of tissue organelle fractions was previously described (Kislinger et al., 2006). Briefly, tissue was quickly excised, collected and washed several times in ice-cold phosphate-buffered saline to remove blood, and homogenized in ice-cold lysis buffer (250 mM sucrose, 50 mM HEPES (pH 7.4), 25 mM KCl, 5 mM MgCl2, 1 mM dithiothreitol (DTT), and 1 mM phenylmethylsulfonyl fluoride (PMSF) using a tight fitting glass pestle homogenizer. All subsequent steps were performed at 4C or on ice. The lysate was centrifuged in a benchtop centrifuge at 800g for 10 min, with the supernatant serving as the source of cytosol, mitochondria and microsomes. The nuclear pellet was re-homogenized in lysis buffer, recentrifuged, solubilized in 5 ml of lysis buffer, and over-layered onto 4 ml of 0.9 M sucrose cushion buffer and centrifuged at 1000g for 10 min in a swing-bucket rotor. The pellet was then re-solubilized in 5 ml of 1.9 M sucrose cushion buffer (1.9 M sucrose, 50 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 1 mM DTT, and 1 mM PMSF). After over-laying onto 4 ml of 1.9 M cushion buffer, the nuclei were pelleted by ultracentrifugation at 150,000g for 1 h (Beckman SW 40Ti rotor). The mitochondria were isolated from the crude cytoplasm by centrifugation at 8,000g for 15 min, with the resulting pellet washed twice in lysis buffer. Mixed membranes were isolated by centrifugation of the post-mitochondrial cytoplasmic fraction at 150,000g for 1 h (Beckman SW 40Ti rotor), while the supernatant served as the cytosolic fraction. Nuclear proteins were extracted by re-suspending the nuclei in 5 volumes of nuclear extraction (NE) buffer (25 mM HEPES, pH 7.4, 400 mM NaCl), followed by 30 min incubation with gentle shaking at 4ÂºC. The nuclei were then lysed by 10 passages through an 18-gauge needle. The debris was removed by microcentrifugation at 20,000g for 30 min and the supernatant saved (NUC1 fraction). The pellet was resuspended in 5 volumes NET buffer (NE with addition of 1% Triton-X-100), gently shaken for 30 minutes 4C, and the nuclei lysed by 10 passages through an 18-gauge needle. Debris was removed by microcentrifugation at 20,000g for 30 minutes, with the supernatant saved (NUC2 fraction). Mitochondrial proteins were isolated by incubating the isolated mitochondria in hypotonic lysis buffer (10 mM HEPES, pH 7.4, 1 mM DTT, 1 mM PMSF) for 30 min on ice. The suspension was briefly sonicated, shaken at 4ÂºC for 1 h, and debris removed by microcentrifugation at 20,000g for 30 min. The supernatant was saved (MITO fraction). Membrane proteins were extracted by re-suspending the microsomes in 5 volumes of NET buffer. The suspension was incubated with gentle shaking for 1 h. Insoluble membranes were removed by microcentrifugation at 20,000g for 30 min, while the supernatant was saved (MEMB fraction).

DIGESTION: An aliquot of 150 micrograms of protein from each sample was precipitated overnight at -20C with 5-volumes of ice-cold acetone, followed by centrifugation at 20,000 g for 15 min. The protein pellet was solubilized in 8M urea, 2 mM DTT, 50 mM Tris-HCl, pH 8.5 at 37C for 1 hour, followed by carboxyamidomethylation with 10mM iodoacetamide for 1 hour at 37C in the dark. The samples were then diluted with 100 mM Tris-HCl, pH 8.5 to ~1.5 M urea. Calcium chloride was added to a final concentration of 1mM and digested with a 1:25 molar ratio of recombinant, proteomics grade trypsin (Roche Diagnostics, Laval, QC) at 37C overnight. The resulting peptide mixtures were solid phase-extracted with Varian OMIX cartridges (Mississauga, ON, Canada) according to the manufacturers instructions and stored at -80C until further use.

SET-UP: A fully automated 9-cycle, 18-h MudPIT procedure was set up similar as previously described (Kislinger et al., 2006; Washburn et al., 2001). A quaternary HPLC-pump was interfaced with a LTQ linear ion-trap mass spectrometer (Thermo Fisher Scientific, San Jose, CA) equipped with a nano-electrospray source (Proxeon Biosystems, Odense, Denmark). A 100 micrometer inner diameter fused silica capillary (InnovaQuartz, Phoenix, AZ) was pulled to a fine tip using a P-2000 laser puller (Sutter Instruments, Novato, CA) and packed with ~ 7cm of JupiterTM 4 micron Proteo 90Ã… C12 reverse phase resin (Phenomenex, Torrance, CA), followed by ~ 5cm of Luna 5 micron SCX 100… strong cation exchange resin (Phenomenex, Torrance, CA). Samples were loaded manually on separate columns using an in-house pressure vessel. As peptides eluted from the microcapillary columns, they were electrosprayed directly into the MS. A distal 2.3 kV spray voltage was applied to the microsplitter tee (Proxeon Biosystems). The MS operated in a cycle of one full-scan mass spectrum (400-1400 m/z), followed by 6 data-dependent MS/MS spectra at 35% normalized collision energy, which was continuously repeated throughout the entire MudPIT separation. The MS functions and the HPLC solvent gradients were controlled by the Xcalibur data system (Thermo Fisher Scientific, San Jose, CA).

tag: Tissue

value: placental labyrinth

tag: Strain

tag: Stage


title: Human 38 week placental villous tree

description: The placental villous tree was microdissected and inspected to assure normal pathology

source_name: 38 week placental villous tree

extract_protocol:
EXTRACTION: Human villous trees from a normal placenta delivered by cesarean section at term (~38 weeks) were dissected and washed in PBS. A quarter of the collected labyrinth tissues were set aside for RNA extraction and microarray analysis and ¾ for cellular fractionation and proteomic analysis, as recently described (Kislinger et al., 2006).

SEPARATION: The preparation of tissue organelle fractions was previously described (Kislinger et al., 2006). Briefly, tissue was quickly excised, collected and washed several times in ice-cold phosphate-buffered saline to remove blood, and homogenized in ice-cold lysis buffer (250 mM sucrose, 50 mM HEPES (pH 7.4), 25 mM KCl, 5 mM MgCl2, 1 mM dithiothreitol (DTT), and 1 mM phenylmethylsulfonyl fluoride (PMSF) using a tight fitting glass pestle homogenizer. All subsequent steps were performed at 4C or on ice. The lysate was centrifuged in a benchtop centrifuge at 800g for 10 min, with the supernatant serving as the source of cytosol, mitochondria and microsomes. The nuclear pellet was re-homogenized in lysis buffer, recentrifuged, solubilized in 5 ml of lysis buffer, and over-layered onto 4 ml of 0.9 M sucrose cushion buffer and centrifuged at 1000g for 10 min in a swing-bucket rotor. The pellet was then re-solubilized in 5 ml of 1.9 M sucrose cushion buffer (1.9 M sucrose, 50 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 1 mM DTT, and 1 mM PMSF). After over-laying onto 4 ml of 1.9 M cushion buffer, the nuclei were pelleted by ultracentrifugation at 150,000g for 1 h (Beckman SW 40Ti rotor). The mitochondria were isolated from the crude cytoplasm by centrifugation at 8,000g for 15 min, with the resulting pellet washed twice in lysis buffer. Mixed membranes were isolated by centrifugation of the post-mitochondrial cytoplasmic fraction at 150,000g for 1 h (Beckman SW 40Ti rotor), while the supernatant served as the cytosolic fraction. Nuclear proteins were extracted by re-suspending the nuclei in 5 volumes of nuclear extraction (NE) buffer (25 mM HEPES, pH 7.4, 400 mM NaCl), followed by 30 min incubation with gentle shaking at 4ÂºC. The nuclei were then lysed by 10 passages through an 18-gauge needle. The debris was removed by microcentrifugation at 20,000g for 30 min and the supernatant saved (NUC1 fraction). The pellet was resuspended in 5 volumes NET buffer (NE with addition of 1% Triton-X-100), gently shaken for 30 minutes 4C, and the nuclei lysed by 10 passages through an 18-gauge needle. Debris was removed by microcentrifugation at 20,000g for 30 minutes, with the supernatant saved (NUC2 fraction). Mitochondrial proteins were isolated by incubating the isolated mitochondria in hypotonic lysis buffer (10 mM HEPES, pH 7.4, 1 mM DTT, 1 mM PMSF) for 30 min on ice. The suspension was briefly sonicated, shaken at 4ÂºC for 1 h, and debris removed by microcentrifugation at 20,000g for 30 min. The supernatant was saved (MITO fraction). Membrane proteins were extracted by re-suspending the microsomes in 5 volumes of NET buffer. The suspension was incubated with gentle shaking for 1 h. Insoluble membranes were removed by microcentrifugation at 20,000g for 30 min, while the supernatant was saved (MEMB fraction).

DIGESTION: An aliquot of 150 micrograms of protein from each sample was precipitated overnight at -20C with 5-volumes of ice-cold acetone, followed by centrifugation at 20,000 g for 15 min. The protein pellet was solubilized in 8M urea, 2 mM DTT, 50 mM Tris-HCl, pH 8.5 at 37C for 1 hour, followed by carboxyamidomethylation with 10mM iodoacetamide for 1 hour at 37C in the dark. The samples were then diluted with 100 mM Tris-HCl, pH 8.5 to ~1.5 M urea. Calcium chloride was added to a final concentration of 1mM and digested with a 1:25 molar ratio of recombinant, proteomics grade trypsin (Roche Diagnostics, Laval, QC) at 37C overnight. The resulting peptide mixtures were solid phase-extracted with Varian OMIX cartridges (Mississauga, ON, Canada) according to the manufacturers instructions and stored at -80C until further use.

SET-UP: A fully automated 9-cycle, 18-h MudPIT procedure was set up similar as previously described (Kislinger et al., 2006; Washburn et al., 2001). A quaternary HPLC-pump was interfaced with a LTQ linear ion-trap mass spectrometer (Thermo Fisher Scientific, San Jose, CA) equipped with a nano-electrospray source (Proxeon Biosystems, Odense, Denmark). A 100 micrometer inner diameter fused silica capillary (InnovaQuartz, Phoenix, AZ) was pulled to a fine tip using a P-2000 laser puller (Sutter Instruments, Novato, CA) and packed with ~ 7cm of JupiterTM 4 micron Proteo 90Ã… C12 reverse phase resin (Phenomenex, Torrance, CA), followed by ~ 5cm of Luna 5 micron SCX 100… strong cation exchange resin (Phenomenex, Torrance, CA). Samples were loaded manually on separate columns using an in-house pressure vessel. As peptides eluted from the microcapillary columns, they were electrosprayed directly into the MS. A distal 2.3 kV spray voltage was applied to the microsplitter tee (Proxeon Biosystems). The MS operated in a cycle of one full-scan mass spectrum (400-1400 m/z), followed by 6 data-dependent MS/MS spectra at 35% normalized collision energy, which was continuously repeated throughout the entire MudPIT separation. The MS functions and the HPLC solvent gradients were controlled by the Xcalibur data system (Thermo Fisher Scientific, San Jose, CA).

value: placental villous tree

value: 38 week


title: WH8102_bsy89280d0046_copper-shock_rep2


title: WH8102_bsy89255d0025_copper-shock_rep4

source_name: CD43r(2)-WH8102 in normal SOW- Control of CD44r(2)


title: Fungiform taste buds, sample 1

source_name: FG taste buds

value: Female

value: Fungiform taste buds


title: CC9311_13532133_pCu9-shock_rep5

description: This slide measures gene expression of Synechococcus sp. CC9311 exposed to copper-shock compared to a no-shock control.

organism: Synechococcus sp. CC9311

source_name: RS9311r8-pCu9 Shock, Rep B, 2 hrs

growth_protocol: Batch cultures of Synechococcus sp. strains CC9311 were grown in chelexed SOW media, as previously described by Dupont et al. (1) with the exception that copper was not added to the media in the trace metal mix and nickel was added at final concentration of 0.5 nM.  The cultures were grown at 24C under constant light at approximately 80 M photons m-2 s-1 in trace metal clean polycarbonate or glass and until in mid-exponential phase, as measured by fluorescence-based growth curve and validated later with flow cytometry.

extract_protocol:
Half the batch culture was spun down at room temperature at 10,400  g, resuspended in Trizol and frozen at -80C for eventual RNA extraction, taking care that the harvesting time stayed under 30 minutes.  Cu/EDTA was added to the other half for Cu2+ levels of pCu 9.1 (as determined using a MINEQL (2) calculation). After a two-hour incubation, these cells were harvested as outlined above. All samples were then thawed at room temperature, incubated for 60 minutes at 65C.  Chloroform at 0.2X was then added to the Trizol cell mixture and tubes were shaken vigorously by hand for 30 seconds.  The samples were then incubated at room temperature for 10 minutes, spun down at 4C at 12,0000  g for 15 minutes and the aqueous layer was carefully removed.  1X volume of cold isopropanol was then added, incubated on ice for 12 minutes, and spun down at 4C at 12,000  g for 15 minutes.  The supernatant was removed and the pellet was washed with 1X volume cold 75% ethanol and stored at -20C overnight.  The samples were then spun down again at 4C at 12,000  g for 15 minutes, resuspended in smaller tubes and spun down once more in the same conditions.  The supernatant was then removed, and the pellet given at least 30 minutes to dry before resuspension in 100 µl DEPC-treated water.  Concentrations were then assessed using a NanoDrop spectrophotometer and if greater than 100 µg were split and diluted before proceeding.  The RNA was then cleaned using a Qiagen RNeasy kit with two additional RNase-free DNase treatments on column according to the manufacturer’s specifications.
1.	Dupont, C. L., K. Barbeau, and B. Palenik. 2008. Ni uptake and limitation in marine Synechococcus strains. Applied and Environmental Microbiology 74:23-31.
2.	Westall, J. C., J. L. Zachary, and F. M. M. Morel. 1976. MINEQL-General algorithm for computation of chemical –equilibrium in aqueous systems. Abstracts of Papers of the American Chemical Society 172:8-8.

tag: axenic Synechococcus sp. CC9311

source_name: RS9311r7-pCu9 Shock, Rep B, Control


title: CC9311_13532144_copper-shock_rep8

source_name: RS9311r4-Cu Shock, Rep B, 2 hrs

source_name: RS9311r3-Cu Shock, Rep B, Control


title: WH8102_bsy89255d0020_copper-shock_rep1


title: CC9311_13532135_pCu9-shock_rep6


title: CC9311_13532130_pCu9-shock_rep2

source_name: RS9311r6-pCu9 Shock, Rep A, 2 hrs

source_name: RS9311r5-pCu9 Shock, Rep A, Control


title: CC9311_13532132_pCu9-shock_rep4


title: CC9311_13532131_pCu9-shock_rep3


title: CC9311_13531524_copper-shock_rep5

description: This slide measures gene expression of copper-shocked wild-type cells to that of cells not exposed to copper-shock.


title: CC9311_13532129_pCu9-shock_rep1


title: CC9311_13531529_copper-shock_rep7

label_protocol:
Make spike-in control pools from RNA amplified from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) using the MegaScript Kit (Ambion) by combining for Cy5 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
4.7 microliters 13.279 ng/microliter ltp6 RNA;
11.8 microliters 21.313 ng/microliter rcp1 RNA;
40.7 microliters 23.23 ng/microliter nac RNA;
4.6 microliters 18.177 ng/microliter xcp2 RNA;
14.7 microliters 11.436 ng/microliter prk RNA;
18.9 microliters 11.084 ng/microliter tim RNA;
826.5 microliters water.
And for Cy3 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
1.6 microliters 13.279 ng/microliter ltp6 RNA;
3.9 microliters 21.313 ng/microliter rcp1 RNA;
13.6 microliters 23.23 ng/microliter nac RNA;
13.9 microliters 18.177 ng/microliter xcp2 RNA;
44.1 microliters 11.436 ng/microliter prk RNA;
56.8 microliters 11.084 ng/microliter tim RNA;
788.1 microliters water.
To label Synechococcus sp. CC9311 RNA sample combine:
4 micrograms RNA;
2 microliters 3 mg/mL random hexamers (Invitrogen);
2 microliters arabidopsis spike-in control RNA;
DEPC water to a final volume to 17.5 microliters.
Mix and incubated at 70 degrees C for 10 minutes.
Snap-freeze in dry ice/ethanol for 30 seconds and centrifuged for 1 minute at approximately 16,000g.
Add:
6 microliters 5X Superscript II buffer (Invitrogen);
3 microliters 0.1 M dithiothreitol;
1.2 microliters aminoallyl-dNTP mix containing 12.5 mM dATP, 12.5 mM dCTP, 12.5 mM dGTP, 4.16 mM dTTP, and 8.33 mM aadUTP;
2 microliters SuperScript II (Invitrogen).
Mix and incubated overnight at 42 degrees C.
Add:
10 microliters 1 M NaOH;
10 microliters 0.5 M EDTA.
Incubate for 15 minutes at 65 degrees C.
Add:
25 microliters 1 M Tris pH 7.4;
400 microliters PB buffer (Qiagen).
Apply sample to QIAquick column (Qiagen).
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters phosphate wash buffer (84.25 mL 95% EtOH + 15.25 mL water + 0.5 mL 1 M KPO4 pH 8.5 solution made by combining 0.5 mL 1M KH2PO4 with 9.5 mL 1M K2HPO4).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters phosphate elution buffer (4 mM KPO4 solution made by diluting 1 M KPO4 pH 8.5 solution).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Dry sample using a speed vac.
Resuspend cDNA in 4.5 microliters 0.1 M carbonate buffer (1 M Na2CO3 buffer pH 9.0 diluted 1:10 with water).
Allow the sample to resuspend for 15 minutes at room temperature.
Add 4.5 microliters NHS-Cy (Amersham) resuspended in 73 microliters DMSO.
Incubate for 1 hour at room temperature in the dark.
Add 4.5 microliters 4 M hydroxylamine.
Incubate for 15 minutes at room temperature in the dark.
Add:
35 microliters 100 mM NaOAc pH 5.2;
500 microliters PB buffer.
Apply to Qiaquick column.
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters PE buffer (Qiagen).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters EB buffer (Qiagen).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Check quality of probes spectrophotometrically from 200nm to 700nm.
Store at -80 degrees C.


title: Plasmodium berghei_sporozoites_PbeIK2KO (biological replicate)

first: Elizabeth

middle: Ann

last: Winzeler

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

data_processing: RMA normalization

organism: Plasmodium berghei

source_name: Plasmodium berghei eIK2KO sporozoites

label_protocol: Affymetrix two-cycle target labeling

extract_protocol: total RNA extraction with Qiagen RNeasy miniKit

tag: genotype/variation

value: PbeIK2 knockout


title: Plasmodium berghei_sporozoites_WT

source_name: Plasmodium berghei sporozoites WT

value: wildtype


title: CC9311_13531526_copper-shock_rep6


title: CC9311_13531519_copper-shock_rep1

source_name: RS9311r1-Cu Shock, Rep A, Control

source_name: CD3RS9311r2-Cu Shock, Rep A, 2 hrs


title: Plasmodium berghei_sporozoites_WT (biological replicate)


title: CC9311_13532143_copper-shock_rep4

source_name: RS9311r2-Cu Shock, Rep A, 2 hrs


title: CC9311_13531522_copper-shock_rep2

source_name: RS9311r2-Cu Shock, Rep A, 2hrs


title: CLL.13.36

source_name: Primary CLL

tag: cell type

value: B lymphocytes

tag: disease

value: chronic lymphocytic leukemia

value: Primary CLL

tag: isolate

value: CLL patient 13


title: Plasmodium berghei_sporozoites_PbeIK2KO


title: CC9311_13531523_copper-shock_rep3


city: Ibaraki

first: Naoki

last: Osada

state: Osaka

address: 7-6-8 Saito-Asagi

department: Division of Biomedical Research Resources

institute: National Institute of Biomedical Innovation

description: Gene expression comparison between CBA/J and DBA/2 mice after CAWS injection.

hyb_protocol: Probes were hybridized at 60C for 16-20 hours.

scan_protocol: Signals were scanned using GenePix.

data_processing: VALUE is log2-ratio of test (Cy3) to control (Cy5) signal intensity after normalization.

source_name: CBA/J mouse splenocytes

label_protocol: cDNA was label by Cy3 using FluoroLink (Amersham).

extract_protocol: RNA was extracted using Trizol.

tag: strain

value: CBA/J

value: splenocytes

tag: treatment

value: CAWS (Candida albicans water-soluble fraction) injection

tag: post-treatment time

value: 21 days

source_name: DBA/2 mouse splenocytes

label_protocol: cDNA was labeled by Cy5 using FluoroLink (Amersham).


title: Gene Expression profiling of M. bovis BCG strain under extended stationary phase compared to Resuscitation phase DyeSwap

source_name: Mycobacterium bovis BCG Resuscitation phase

label_protocol: Total RNA (500ng) of Mycobacterium under Resuscitation phase was labelled with Cy3 (Perkin Elmer) dyes respectively using Ambion Message AmpII bacteria kit as per manufacturer recommended protocol.

tag: growth phase

value: Resuscitation phase

source_name: Mycobacterium bovis BCG extended stationary phase culture

value: Stationary phase culture


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 8

first: Vera

last: Huang

address: 3855 Health Science Drive, Room 4317

department: Medicine

institute: UCSD-Moores Cancer Center

description: Four biological repeats were performed for each condition (-HU or +HU), with two technical repeats (dye swap) per biological sample.

hyb_protocol: standard hybridization procedure

scan_protocol: After hybridization, the slides were scanned with Axon 4000B, and the raw data were generated by Genepix 6.0.

data_processing: The data was normalized with quantile normalization of DNAMR (http://www.rci.rutgers.edu/~cabrera/DNAMR), and fitted with the linear model from the R package Limma (Smyth, 2004).

source_name: Human HCT116-3(6) cells p53 and p73 siRNA transfected, untreated

label_protocol: Total RNA were converted to cRNA, labeled with Cy3 dUTP using Agilent Low Input Linear RNA Amplification, and hybridized to the Phalanx Human One array

extract_protocol: Total RNA from HCT116-3(6) cells transiently transfected with p53 and p73 siRNA oligos without treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.

source_name: Human HCT116-3(6) cells p53 and p73 siRNA transfected, HU treated

label_protocol: Total RNA were converted to cRNA, labeled with Cy5 dUTP using Agilent Low Input Linear RNA Amplification, and hybridized to the Phalanx Human One array

extract_protocol: Total RNA from HCT116-3(6) cells transiently transfected with p53 and p73 siRNA oligos with treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.


title: lacZ transfected HCT116-3(6), replicate 5

source_name: Human HCT116-3(6) cells lacZ transfected, HU treated

extract_protocol: Total RNA from HCT116-3(6) cells transiently transfected with lacZ siRNA oligo with treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.

source_name: Human HCT116-3(6) cells lacZ transfected, untreated

extract_protocol: Total RNA from HCT116-3(6) cells transiently transfected with lacZ siRNA oligo without treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 6

tag: Human HCT116-3(6) cells p53 and p73 siRNA transfected, untreated

tag: Human HCT116-3(6) cells p53 and p73 siRNA transfected, HU treated


title: lacZ transfected HCT116-3(6), replicate 6

tag: Human HCT116-3(6) cells lacZ transfected, untreated

tag: Human HCT116-3(6) cells lacZ transfected, HU treated


title: lacZ transfected HCT116-3(6), replicate 4


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 2

source_name: Human HCT116-3(6) cells p53 siRNA and p73 siRNA transfected, untreated

source_name: Human HCT116-3(6) cells p53 siRNA and p73 siRNA transfected, HU treated

tag: Human HCT116-3(6) cells p53siRNA and p73 siRNA transfected, HU treated


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 4


title: lacZ transfected HCT116-3(6), replicate 8


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 1

extract_protocol: Total RNA from HCT116-3(6) cells transiently transfected with p53 and p73 siRNA oligo with treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.

extract_protocol: Total RNA from HCT116-3(6) cells transiently transfected with p53 and p73 siRNA oligo without treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 5


title: lacZ transfected HCT116-3(6), replicate 3


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 3


title: Arabidopsis: C24 vs rst1 Replicate 1

city: West Lafayette

first: Dong-Ha

last: Oh

state: IN

address: 625 Agriculture Mall Dr

department: HLA

institute: Purdue Univ.

description: Biological replicate 1 of 3

hyb_protocol: as described in Gong Q, Li P, Ma S, Indu Rupassara S, Bohnert HJ (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J 44: 826-839

organism: Arabidopsis thaliana

tag: genotype

value: wild type


title: Arabidopsis: C24 vs rst1 Replicate 2 (with dye swap)

description: Biological replicate 2 of 3 (with dye swap)

scan_protocol: as described in Gong Q, Li P, Ma S, Indu Rupassara S, Bohnert HJ (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J 44: 826-839


title: 22RV1 cells treated with actinomycin D only after treatment with caffeine

city: Buffalo

first: Yurij

last: Ionov

address: Elm and Carlton streets

department: Cancer Genetics

institute: Roswell Park Cancer Institute

description: Affymetrix gene expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Convolution background correction, quantile normalization and a summarization of probe intensity were processed using an adaptation of the Robust Multi-Chip Average (gcRMA).  To compute GCRMA expression values, we used a gcrma function of the Bioconductor package, publicly available at the www.bioconductor.org.

source_name: 22Rv1 cell line

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

growth_protocol: Cells were grown in the RPMI medium complemented with 10% fetal bovine and antibiotics

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

treatment_protocol: Caffeine (10mM ) was added to tissue culture medium to inhibit NMD. Actinomycin (2mkg/ml) was added to inhibit transcription

tag: cell line

value: prostate cancer cell line 22Rv1

tag: treatment protocol

value: treated with actinomycin D alone after treatment with caffeine


title: LNCaP cells treated with caffeine

description: Affymetrix gene expression

source_name: LNCaP cell line

value: prostate cancer cell line LNCaP

value: treated with caffeine


title: Arabidopsis: C24 vs rst1 Replicate 3

description: Biological replicate 3 of 3

data_processing: as described in Gong Q, Li P, Ma S, Indu Rupassara S, Bohnert HJ (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J 44: 826-839


title: lacZ siRNA transfected HCT116-3(6), replicate 1


title: 22Rv1 cells treated with caffeine

description: Affymetrix gene expression


title: 22Rv1 untreated cells

description: Affymetrix gene expression

value: prostate cancer cell line 22RV1

value: untreated (control)


title: p53 and p73 siRNA transfected HCT116-3(6), replicate 7


title: LNCaP untreated cells

description: Affymetrix gene expression


title: 22Rv1 cells treated with both actinomycin D and caffeine after treatment with caffeine

description: Affymetrix gene expression

value: treated with both caffeine and actinomycin D after treatment with caffeine


title: lacZ transfected HCT116-3(6), replicate 7


title: LNCaP cells treated with actinomycin D only after treatment with caffeine

description: Affymetrix gene expression


title: lacZ siRNA transfected HCT116-3(6), replicate 2


title: LNCaP cells treated with both actinomycin D and caffeine after treatment with caffeine

description: Affymetrix gene expression


title: C57BL6 3860mJ/cm2 ssUV vs C57BL6 unirradiated control, rep5

status: Public on Jun 29 2009

first: Michael

middle: Peter

last: Stapelberg

address: The University of Sydney

institute: The University of Sydney

description: Analysis used RNA from unirradiated control C57BL/6 mouse.

hyb_protocol: Prior to hybridisation, 4.25 ml of 20 SSC and 0.75 ml of 10% SDS was added to each labelled probe to make a final volume of 25 ml. Each labelled probe was then denatured through incubation in the thermal cycler at 99 ºC for 2 min. Immediately after denaturation, the denatured probe was added directly to the center of a glass compugen 22k mouse oligonucleotide microarray slide (The Clive and Vera Ramaciotti Centre for Gene Function Analysis, Sydney Australia) and covered with a 24 x 50 mm glass cover slip (Chase Scientific Glass, Rockwood, TN, USA) taking care not to trap any air bubbles. Each microarray slide was then placed in a 50 ml falcon tube containing a folded sheet of kimwipe (Kimberly-Clark, Erie, PA, USA) saturated with 2x SCC to maintain a humid hybridisation environment. Each hybridisation chamber was then placed in an incubation oven at 65 ºC for 16 h. Following incubation, microarray slides were removed from their hybridisation chambers and washed in a solution containing 2x SSC and 0.1% SDS for 1 min, followed by 1x SSC for a further 1 min and finally in 0.2x SSC for 1 min. All washing steps were performed at room temperature with gentle agitation and at no point were the microarray slides allowed to dry. After washing, each microarray slide was placed in a 50 ml falcon tube and centrifuged at 800x g at room temperature for 5 min.

scan_protocol: Each microarray was scanned immediately after washing using an axon scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA) with GenePix Pro 5.0 microarray image acquisition and image analysis software (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA). For each microarray scan the laser power was set to 100% and the pixel resolution at 5 mm.

data_processing: The first component of the microarray analysis was done using the R software package Linear Models for Microarray Data (LIMMA) (Wettenhall and Smyth, 2004) and involved no background correction, within-array print-tip loess normalisation, followed by scale normalisation for each unirradiated control and UV irradiated group.

source_name: skin from C57BL6 mouse irradiated with 3860mJ/cm2 ssUV

label_protocol: For the microarray study a direct incorporation of Cyanine 3-dCTP and Cyanine 5-dCTP fluorescent dyes (Perkin Elmer Life Sciences, Inc. Boston, MA, USA) was used for cDNA synthesis. For each UV dose, a reference design was used to compare an unirradiated control against an irradiated sample. A fluorescent dye swap was done for each alternate hybridisation to reduce systematic dye bias of incorporated fluorescent dyes.

extract_protocol: 24 hours after UVA, UVB and ssUV irradiation a 1 cm2 uniform section of skin was excised from the dorsal surface of irradiated and control mice. Total RNA was then extracted from the whole skin using TRIzol reagent (Gibco Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions, purified, DNase treated and reverse transcribed into cDNA.

treatment_protocol: Female C57BL/6 and Balb/c mice aged 8-9wks at the start of irradiations were used for these experiments (Animal Resource Centre, Perth, WA, Australia), which were conducted with the approval of the University of Sydney animal ethics committee. Prior to each irradiation the dorsal trunk was shaved and the mice were then allowed to rest for 24h. Mice to be irradiated were then placed in an animal-restraining cage covered with a quartz glass lid. All irradiation times were less than 2 min and air-conditioning was used to ensure that the mouse body temperature did not increase during irradiation. Single irradiations for microarray and RT-PCR experiments and 3 on consecutive days for contact sensitivity experiments were given to each mouse and all irradiations were always performed at the same time of day. A 1000 W xenon arc solar simulator (Oriel, Stratford, CT) with two dichroic mirrors that allow wavelengths between 200 nm and 400 nm to pass through were used with a filter that blocks UVB to produce a UVA spectrum. For ssUV and UVB filters were used to attenuate the visible and infrared wavelengths and remove UVC (< 290 nm) so that it simulated sunlight (ssUV), or comprised predominantly UVB. The spectra have previously been described (Byrne et al., 2002a). The intensity (mW per cm2) of the UVA, UVB and ssUV output was measured regularly using a radiometer (Solar Light Company, PA) which had been calibrated against the source with an OL-754 spectroradiometer (Optronics Laboratories, Orlando, FL), and the timing of UV exposure was adjusted using an automated timing device to deliver consistent UV doses. The spectral output was regularly measured using the OL-754 spectroradiometer calibrated against standard lamps. The UVA doses were 1750 and 3500 mJ/cm2 respectively and for simplicity will be referred to as the lower and higher UVA doses. The UVB and ssUV doses were 285 mJ/cm2 and 3860 mJ/cm2 respectively (comprising 285 mJ/cm2 UVB with 3575 mJ/cm2 UVA) and for simplicity will be referred to as the UVB and ssUV doses. The UV doses used in this study are physiological and representative of typical human sunlight exposure. The UVB and higher UVA doses are the amounts in sunlight that would cause barely detectable sunburn. The ssUV dose is the same amount of UVB combined with UVA to approximate the solar spectrum and give a barely detectable sunburn.

tag: gender

value: female

tag: tissue

value: skin

value: ssUV irradiation

source_name: skin from C57BL6 mouse not irradiated with UV

value: unirradiated


title: C57BL6 3860mJ/cm2 ssUV vs C57BL6 unirradiated control, rep3


title: Human HCT116-3(6) cells, untreated2

type: genomic

description: Human HCT116-3(6) cells, untreated

hyb_protocol: Probe labeling and hybridization were performed by NimbleGen (Reykjavik, Iceland).

scan_protocol: Slides were scanned by NimbleScan (NimbleGen)

data_processing: Data were processed by NimbleGen, Inc., log base 2 (immunoprecipitated DNA/input DNA) ratios were calculated after normalization.

molecule: genomic DNA

source_name: HCT116-3(6) cells, untreated; p73 Antibody

extract_protocol: standard chromatin immunoprecipitation procedure was carried out using home-made rabbit polyclonal anti-p73 antibody (827).

tag: p73 Antibody

source_name: HCT116-3(6) cells, untreated; total input DNA

extract_protocol: input chromatin without undergoing immunoprecipitation was decrosslinked by heating at 65°C overnight. Following treatment with Proteinase K, DNA fragments were extracted with phenol/chloroform 2X. DNA was treated with RNAse A and purified using Qiaquick PCR purification columns (Qiagen).

tag: control total input


title: C57BL6 3860mJ/cm2 ssUV vs C57BL6 unirradiated control, rep4


title: C57BL6 285mJ/cm2 UVB vs C57BL6 unirradiated control, rep6

source_name: skin from C57BL6 mouse irradiated with 285mJ/cm2 UVB

value: UVB irradiation


title: C57BL6 285mJ/cm2 UVB vs C57BL6 unirradiated control, rep5


title: Human HCT116-3(6) cells, HU treated

description: Human HCT116-3(6) cells, HU treated

source_name: HCT116-3(6) cells, HU treated; p53 Antibody

label_protocol: Probe labeling and hybridization were performed by NimbleGen (Reykjavik, Iceland).

extract_protocol: standard chromatin immunoprecipitation procedure was carried out using a mixture of anti-p53 antibodies (Ab1 and Ab12).

tag: p53 Antibody

source_name: HCT116-3(6) cells, HU treated; total input DNA


title: C57BL6 3860mJ/cm2 ssUV vs C57BL6 unirradiated control, rep6

tag: strain


title: Human HCT116-3(6) cells, HU treated2

description: Human HCT116-3(6) cells, HU treated2

scan_protocol: slides were scanned by NimbleScan (NimbleGen)

source_name: HCT116-3(6) cells, HU treated; p73 Antibody


title: C57BL6 285mJ/cm2 UVB vs C57BL6 unirradiated control, rep4

tag: treatment


title: C57BL6 285mJ/cm2 UVB vs C57BL6 unirradiated control, rep2


title: C57BL6 3860mJ/cm2 ssUV vs C57BL6 unirradiated control, rep2


title: C57BL6 3860mJ/cm2 ssUV vs C57BL6 unirradiated control, rep1


title: Balbc 3500mJ/cm2 UVA vs Balbc unirradiated control, rep4

description: Analysis used RNA from unirradiated control Balb/c mouse.

source_name: skin from Balbc mouse irradiated with 3500mJ/cm2 UVA

value: Balb/c

value: UVA irradiation

source_name: skin from Balbc mouse not irradiated with UV


title: C57BL6 3500mJ/cm2 UVA vs C57BL6 unirradiated control, rep6

source_name: skin from C57BL6 mouse irradiated with 3500mJ/cm2 UVA


title: Balbc 3500mJ/cm2 UVA vs Balbc unirradiated control, rep6


title: C57BL6 285mJ/cm2 UVB vs C57BL6 unirradiated control, rep1


title: Balbc 3500mJ/cm2 UVA vs Balbc unirradiated control, rep2


title: Balbc 3500mJ/cm2 UVA vs Balbc unirradiated control, rep1


title: Balbc 3500mJ/cm2 UVA vs Balbc unirradiated control, rep5


title: Balbc 3500mJ/cm2 UVA vs Balbc unirradiated control, rep3


title: C57BL6 285mJ/cm2 UVB vs C57BL6 unirradiated control, rep3


title: C57BL6 3500mJ/cm2 UVA vs C57BL6 unirradiated control, rep5


title: C57BL6 3500mJ/cm2 UVA vs C57BL6 unirradiated control, rep3


title: C57BL6 3500mJ/cm2 UVA vs C57BL6 unirradiated control, rep4


title: Balbc 1750mJ/cm2 UVA vs Balbc unirradiated control, rep4

source_name: skin from Balbc mouse irradiated with 1750mJ/cm2 UVA


title: Balbc 1750mJ/cm2 UVA vs Balbc unirradiated control, rep5


title: Balbc 1750mJ/cm2 UVA vs Balbc unirradiated control, rep1


title: C57BL6 1750mJ/cm2 UVA vs C57BL6 unirradiated control, rep6

source_name: skin from C57BL6 mouse irradiated with 1750mJ/cm2 UVA


title: Balbc 1750mJ/cm2 UVA vs Balbc unirradiated control, rep6


title: C57BL6 3500mJ/cm2 UVA vs C57BL6 unirradiated control, rep2


title: C57BL6 1750mJ/cm2 UVA vs C57BL6 unirradiated control, rep5


title: Balbc 1750mJ/cm2 UVA vs Balbc unirradiated control, rep3


title: Slide4_cellulose_3_cellobiose_5

city: Urbana

middle: A

last: White

state: IL

address: 1207 W. Gregory Drive

department: Animal Sciences

institute: University of Illinois

description: Biological replicate 4 of 4.

hyb_protocol: hybridized 3 d with Ambion slide hyb buffer at 42oC

scan_protocol: scanned with Axon GenePix 6.0

organism: Ruminococcus flavefaciens FD-1

source_name: R. flavefaciens FD-1 on cellulose

label_protocol: Indirect amino allyl labeling

growth_protocol: defined anaerobic media with cellulose as the carbohydrate substrate

extract_protocol: Cells were pelleted and RNA was extracted using the Qiagen RNeasy Kit – Yeast III Protocol

treatment_protocol: cellulose

tag: growth substrate

value: cellulose

source_name: R. flavefaciens FD-1 on cellobiose

growth_protocol: defined anaerobic media with cellobiose as the carbohydrate substrate

treatment_protocol: cellobiose

value: cellobiose


title: Slide1_cellulose_5_cellobiose_3

description: Biological replicate 1 of 4.


title: C57BL6 1750mJ/cm2 UVA vs C57BL6 unirradiated control, rep4


title: Balbc 1750mJ/cm2 UVA vs Balbc unirradiated control, rep2


title: NT_vs_NTwithNaB replicate 2

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

description: Biological replicate 2 of 3

hyb_protocol: Hybridization buffer (Genispere) were added, and microarray were applied to MAUI hybidization chamber

scan_protocol: scanned with a Genepix 4000B (Axon Instruments, USA)

data_processing: Analyzed with statistical R language and sma package in Bioconductor project (http://www.bioconductor.org/)

source_name: mRNA RNA from 14-d-old NT seedling roots treated with NaB labeled with Cy5

label_protocol: Performed as procedures provided by Genisphere 3DNA Array Detection Array 50 kit (v. 2, Genisphere, Hatfield, PA)

extract_protocol: TRI REAGENT (MRC, Inc., USA) as described in manufacturer's instructions

tag: NT seedling roots with NaB

tag: Age

source_name: mRNA RNA from 14-d-old NT seedling roots labeled with Cy3

tag: NT seedling roots


title: C57BL6 1750mJ/cm2 UVA vs C57BL6 unirradiated control, rep2


title: Slide3_cellulose_5_cellobiose_3

description: Biological replicate 3 of 4.


title: C57BL6 1750mJ/cm2 UVA vs C57BL6 unirradiated control, rep1


title: NT_vs_NTwithNaB replicate 3

description: Biological replicate 3 of 3

source_name: mRNA RNA from 14-d-old NT seedling roots labeled with Cy5

source_name: mRNA RNA from 14-d-old NT seedling roots treated with NaB labeled with Cy3


title: NT_vs_NTwithNaB replicate 1

description: Biological replicate 1 of 3


title: Slide2_cellulose_3_cellobiose_5

description: Biological replicate 2 of 4.