title: slide2_35dpc: Pre- and postnatal hepatic expression profiles of two pig breeds

tag: 2nd pool of RNAs derived from liver of animals of the breed Pietrain (Pi) at 35 dpc

tag: 2nd pool of RNAs derived from liver of animals of the breed German Landrace (DL) at 35 dpc


title: genotype A81 developing seed at 5 days after anthesis, biological rep2

status: Public on Mar 25 2007

type: RNA

city: Winnipeg

first: Mark

last: Jordan

state: Manitoba

address: 195 Dafoe Rd.

department: Cereal research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

description: Gene expression data from field grown developing seeds 5 days after anthesis

hyb_protocol: Following fragmentation, the labelled samples were mixed with 0.1 mg/ml sonicated herring sperm DNA in hybridization buffer (100mM 2-N-morpholino-ethane-sulphonic acid (MES), 1 M NaCL, 20mM EDTA, 0.01% Tween 20, 0.5 mg/ml BSA, 10% DMSO), denatured at 99°C for 5 min then added to GeneChip Wheat Genome Array (Affymetrix) according to manufacturer instructions and hybridized for 16 h at 45°C in a rotisserie oven at 60 rpm. Following hybridization the arrays were washed and stained in the Affymetrix fluidics station 450 according to standard protocol (Section 2.3.3 of the Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000.

data_processing: The raw data in the Affymetrix CEL files of all 78 arrays representing two biological replicates of each of 39 genotypes were subjected to quantile normalization using Robust Multi-Array Average (RMA) (Bolstad, B.M., Irizarry, R.A., Astrand, M., Speed, T.P. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193) followed by normalization to the median.

label: biotin

molecule: polyA RNA

organism: Triticum aestivum

source_name: developing seed collected from field grown material 5 days after anthesis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix). mRNA was used for first and second strand cDNA synthesis using the One Cycle cDNA Synthesis Kit (Affymetrix, http://www.affymetrix.com) following the manufacturers instructions. The resulting cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) according to instructions and then used to make purified biotin labelled cRNA using the GeneChip IVT labelling kit and the GeneChip Sample Cleanup Module (Affymetrix). The resulting labelled cRNA was quantified and the yield and size distribution of labelled fragments checked by electrophoresis using the Agilent Bioanalyzer. The labelled cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and stored at -20°C.

growth_protocol: The 39 lines and parental lines were grown as 1.47 m rows in three replications in a 7x7 (49 entry) lattice design at Winnipeg, Manitoba in 2004. Each replicate had a unique randomization

extract_protocol: Total RNA was extracted from frozen seed using a modification of the protocol described at http://plantsciences.montana.edu/wheat-transformation/molecular.htm. The content of a 2 mL tube full of frozen seeds was ground to a fine powder in liquid nitrogen using a mortar and pestle. Ground seed was transferred to 50 mL Oak Ridge tubes and 7.5 mL of extraction buffer was added. [50 mL Extraction Buffer contained 35 mL nuclease-free water, 2.5 mL 1M Tris, pH 9.0. 5 mL 2M NaCl, 5 mL 10% Sarcosyl, 2 mL 0.5M EDTA,  pH 8.0, 250 ?L 1M DTT]. After vortexing well, 3.75 mL phenol and 3.75 mL chloroform/isoamyl alcohol (49:2) were added and samples vortexed again. Samples were centrifuged 10 min at 13,000 rpm in a Sorvall model RC5C at 4 using an SS-34 rotor. A total of 7.5 mL of the upper aqueous phase was transferred to a clean Oak Ridge tube, 15 mL Trizol was added and the sample was vortexed. A volume of 3 mL of choloroform was added and the sample was vortexed again. Samples were centrifuged 10 min at 13,000 rpm in the Sorvall at 4. A volume of 15 mL of the upper aqueous phase was transferred to a fresh Oak Ridge tube and 10 mL of chloroform was added and the sample was vortexed. Samples were centrifuged again in the Sorvall at 13,000 rpm for 10 min at 4. A volume of 12 mL of the upper phase was transferred to a fresh Oak Ridge tube and the RNA precipitated by adding 1,200 uL of 3M sodium acetate and 24 mL of absolute ethanol. Samples were left at -80 overnight then centrifuged at 14,000 rpm at 4 in the Sorvall for 20-30 minutes to precipitate the RNA. The pellet was rinsed with 70% ethanol, lightly dried and re-suspended in 1 mL of nuclease-free water. RNA concentration was quantified using a spectrophotometer. All solutions and equipment used in this procedure were RNAse-free. Messenger RNA was enriched from total RNA using the Poly(A) Purist MAG kit  (Ambion, http://www.ambion.com) according to the protocol provided by the manufacturer. Messenger RNA was checked for quality and quantified by micro-chromatography using an Agilent 2000 Bioanalyzer and the RNA 6000 Nano Assay Kit both purchased from Agilent Technologies (http://www.agilent.com). Quantification was carried out according to the instructions provided with the kit.

treatment_protocol: spikes were tagged when anthers were visible, enough developing seeds to fill a 2mL tube were isolated from each spike 5 days after tagging and flash frozen in liquid nitrogen

tag: Genotype

value: A81 from RL4452 x AC Domain mapping population

tag: Age

value: developing seed 5 days after anthesis


title: genotype H10 developing seed at 5 days after anthesis, biological rep1

value: H10 from RL4452 x AC Domain mapping population


title: genotype B33 developing seed at 5 days after anthesis, biological rep1

value: B33 from RL4452 x AC Domain mapping population


title: genotype F44 developing seed at 5 days after anthesis, biological rep1

value: F44 from RL4452 x AC Domain mapping population


title: genotype A81 developing seed at 5 days after anthesis, biological rep1


title: genotype F44 developing seed at 5 days after anthesis, biological rep2


title: genotype G13 developing seed at 5 days after anthesis, biological rep1

value: G13 from RL4452 x AC Domain mapping population


title: genotype H10 developing seed at 5 days after anthesis, biological rep2


title: genotype F82 developing seed at 5 days after anthesis, biological rep2

value: F82 from RL4452 x AC Domain mapping population


title: genotype B65 developing seed at 5 days after anthesis, biological rep2

value: B65 from RL4452 x AC Domain mapping population


title: genotype B65 developing seed at 5 days after anthesis, biological rep1


title: genotype F48 developing seed at 5 days after anthesis, biological rep1

value: F48 from RL4452 x AC Domain mapping population


title: genotype H5 developing seed at 5 days after anthesis, biological rep2

value: H5 from RL4452 x AC Domain mapping population


title: genotype C58 developing seed at 5 days after anthesis, biological rep2

value: C58 from RL4452 x AC Domain mapping population


title: genotype H23 developing seed at 5 days after anthesis, biological rep1

value: H23 from RL4452 x AC Domain mapping population


title: genotype B11 developing seed at 5 days after anthesis, biological rep1

value: B11 from RL4452 x AC Domain mapping population


title: genotype H5 developing seed at 5 days after anthesis, biological rep1


title: genotype H23 developing seed at 5 days after anthesis, biological rep2


title: genotype F29 developing seed at 5 days after anthesis, biological rep2

value: F29 from RL4452 x AC Domain mapping population


title: genotype DH91 developing seed at 5 days after anthesis, biological rep2

value: DH91 from RL4452 x AC Domain mapping population


title: genotype C58 developing seed at 5 days after anthesis, biological rep1


title: genotype A88 developing seed at 5 days after anthesis, biological rep2

value: A88 from RL4452 x AC Domain mapping population


title: genotype B11 developing seed at 5 days after anthesis, biological rep2


title: genotype D15 developing seed at 5 days after anthesis, biological rep2

value: D15 from RL4452 x AC Domain mapping population


title: genotype DH91 developing seed at 5 days after anthesis, biological rep1


title: genotype B10 developing seed at 5 days after anthesis, biological rep2

value: B10 from RL4452 x AC Domain mapping population


title: genotype A77 developing seed at 5 days after anthesis, biological rep2

value: A77 from RL4452 x AC Domain mapping population

value: developing seed 5 days after anthesis


title: genotype F36 developing seed at 5 days after anthesis, biological rep2

value: F36 from RL4452 x AC Domain mapping population


title: genotype A10 developing seed at 5 days after anthesis, biological rep1

value: A10 from RL4452 x AC Domain mapping population


title: genotype F29 developing seed at 5 days after anthesis, biological rep1


title: genotype D15 developing seed at 5 days after anthesis, biological rep1


title: genotype B10 developing seed at 5 days after anthesis, biological rep1


title: genotype A77 developing seed at 5 days after anthesis, biological rep1


title: genotype A10 developing seed at 5 days after anthesis, biological rep2


title: genotype D39 developing seed at 5 days after anthesis, biological rep1

value: D39 from RL4452 x AC Domain mapping population


title: genotype D39 developing seed at 5 days after anthesis, biological rep2


title: genotype J15 developing seed at 5 days after anthesis, biological rep2

value: J15 from RL4452 x AC Domain mapping population


title: genotype F36 developing seed at 5 days after anthesis, biological rep1


title: genotype J15 developing seed at 5 days after anthesis, biological rep1


title: genotype C25 developing seed at 5 days after anthesis, biological rep2

value: C25 from RL4452 x AC Domain mapping population


title: genotype A88 developing seed at 5 days after anthesis, biological rep1


title: genotype G32 developing seed at 5 days after anthesis, biological rep1

value: G32 from RL4452 x AC Domain mapping population


title: genotype F38a developing seed at 5 days after anthesis, biological rep1

value: F38a from RL4452 x AC Domain mapping population


title: genotype B68 developing seed at 5 days after anthesis, biological rep2

value: B68 from RL4452 x AC Domain mapping population


title: genotype C25 developing seed at 5 days after anthesis, biological rep1


title: genotype C22 developing seed at 5 days after anthesis, biological rep2

value: C22 from RL4452 x AC Domain mapping population


title: genotype H9 developing seed at 5 days after anthesis, biological rep2

value: H9 from RL4452 x AC Domain mapping population


title: genotype G32 developing seed at 5 days after anthesis, biological rep2


title: genotype H9 developing seed at 5 days after anthesis, biological rep1


title: genotype C31 developing seed at 5 days after anthesis, biological rep2

value: C31 from RL4452 x AC Domain mapping population


title: genotype C22 developing seed at 5 days after anthesis, biological rep1


title: genotype C31 developing seed at 5 days after anthesis, biological rep1


title: genotype A40 developing seed at 5 days after anthesis, biological rep2

value: A40 from RL4452 x AC Domain mapping population


title: genotype A40 developing seed at 5 days after anthesis, biological rep1


title: genotype DH95 developing seed at 5 days after anthesis, biological rep1

value: DH95 from RL4452 x AC Domain mapping population


title: genotype DH95 developing seed at 5 days after anthesis, biological rep2


title: genotype E5 developing seed at 5 days after anthesis, biological rep2

value: E5 from RL4452 x AC Domain mapping population


title: genotype RL4452 developing seed at 5 days after anthesis, biological rep2

description: Replicate 2

data_processing: RMA-calculated, normalized to median signal intensity

extract_protocol: Total RNA was extracted from frozen seed using a modification of the protocol described at http://plantsciences.montana.edu/wheat-transformation/molecular.htm. The content of a 2 mL tube full of frozen seeds was ground to a fine powder in liquid nitrogen using a mortar and pestle. Ground seed was transferred to 50 mL Oak Ridge tubes and 7.5 mL of extraction buffer was added. [50 mL Extraction Buffer contained 35 mL nuclease-free water, 2.5 mL 1M Tris, pH 9.0. 5 mL 2M NaCl, 5 mL 10% Sarcosyl, 2 mL 0.5M EDTA,  pH 8.0, 250 μL 1M DTT]. After vortexing well, 3.75 mL phenol and 3.75 mL chloroform/isoamyl alcohol (49:2) were added and samples vortexed again. Samples were centrifuged 10 min at 13,000 rpm in a Sorvall model RC5C at 4°C using an SS-34 rotor. A total of 7.5 mL of the upper aqueous phase was transferred to a clean Oak Ridge tube, 15 mL Trizol was added and the sample was vortexed. A volume of 3 mL of choloroform was added and the sample was vortexed again. Samples were centrifuged 10 min at 13,000 rpm in the Sorvall at 4°C. A volume of 15 mL of the upper aqueous phase was transferred to a fresh Oak Ridge tube and 10 mL of chloroform was added and the sample was vortexed. Samples were centrifuged again in the Sorvall at 13,000 rpm for 10 min at 4°C. A volume of 12 mL of the upper phase was transferred to a fresh Oak Ridge tube and the RNA precipitated by adding 1,200 uL of 3M sodium acetate and 24 mL of absolute ethanol. Samples were left at -80°C overnight then centrifuged at 14,000 rpm at 4°C in the Sorvall for 20-30 minutes to precipitate the RNA. The pellet was rinsed with 70% ethanol, lightly dried and re-suspended in 1 mL of nuclease-free water. RNA concentration was quantified using a spectrophotometer. All solutions and equipment used in this procedure were RNAse-free. Messenger RNA was enriched from total RNA using the Poly(A) Purist MAG kit  (Ambion, http://www.ambion.com) according to the protocol provided by the manufacturer. Messenger RNA was checked for quality and quantified by micro-chromatography using an Agilent 2000 Bioanalyzer and the RNA 6000 Nano Assay Kit both purchased from Agilent Technologies (http://www.agilent.com). Quantification was carried out according to the instructions provided with the kit.

value: RL4452, Age:developing seed 5 days after anthesis


title: genotype RL4452 developing seed at 5 days after anthesis, biological rep1

description: Replicate 1

tag: Genotype:RL4452, Age


title: genotype AC Domain developing seed at 5 days after anthesis, biological rep2

description: Replicate 2

value: AC Domain, Age:developing seed 5 days after anthesis


title: genotype F38a developing seed at 5 days after anthesis, biological rep2

value: developing seed 5 days after anthesis


title: brownfat_KO4_day3

status: Public on Mar 11 2007

city: Los Angeles

first: Lola

last: Rahib

state: CA

address: 695 Charles E young Drive south Gonda 5335

department: Human Genetics

country: USA

institute: UCLA

data_processing: The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

molecule: total RNA

organism: Mus musculus

source_name: brownfat

extract_protocol: Trizol reagents

tag: Strain

tag: Gender

value: male

value: KO

tag: Tissue

value: brown fat


title: genotype AC Domain developing seed at 5 days after anthesis, biological rep1

description: Replicate 1

tag: Genotype:AC Domain, Age

value: developing seed 5 days after anthesis,


title: genotype G30 developing seed at 5 days after anthesis, biological rep1

value: G30 from RL4452 x AC Domain mapping population


title: genotype G30 developing seed at 5 days after anthesis, biological rep2


title: genotype F48 developing seed at 5 days after anthesis, biological rep2

value: F48 from RL4452 x AC Domain mapping population


title: brownfat_WT1_day3

value: WT


title: brownfat_WT4_day3


title: brownfat_KO2_day3


title: brownfat_KO3_day3


title: brownfat_KO1_day3

value: Male

tag: age

tag: tissue


title: genotype E5 developing seed at 5 days after anthesis, biological rep1


title: brownfat_wt3_day3


title: genotype B68 developing seed at 5 days after anthesis, biological rep1

value: B68 from RL4452 x AC Domain mapping population


title: RhoAQ63L transformed cells treated with Y27632_A Y5

status: Public on Jan 03 2007

city: Salamanca

first: Xose

middle: Garcia

last: Bustelo

state: Salamanca

address: Campus Unamuno

country: Spain

institute: Centro de Investigacion del Cancer

description: Gene expression data from RhoAQ63L transformed cells treated with Y27632 for 24 h, grown in the presence of serum until confluency levels lower than 70%

hyb_protocol: Following fragmentation, cRNAs were hybridized on GeneChip MGU75Av2 Genome Array using standard Affymetrix protocols at the CIC Genomics and Proteomics Facility (www.cicancer.org). 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: Normalization, filtering and analysis of the raw data obtained from the microarrays was carried out with the Bioconductor software (www.bioconductor.com) using de ReadAffy package and the RMA application. The RMA algorithm was selected over the standard Affymetrix software because it provides a better precision in signal detection to achieve adequate normalization of multiple microarray hybridizations, especially in cases of low levels of gene expression (Bolstad et al., 2004; Gautier et al., 2004; Gentleman et al., 2004; Parrish and Spencer, 2004)

source_name: RhoAQ63L transformed after 24 h to treatment with Y27632 (10uM), grown in the presence of serum until confluency levels lower than 70%.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 microg total RNA (Expression Analysis Technical Manual, 2002, Affymetrix).

extract_protocol: three 10-cm diameter plates containing exponentially growing cultures of RhoAQ63L transformed cells treated with Y27632 (10uM) for 24 h, were washed with PBS and their total cellular RNAs isolated using the RNeasy kit (Qiagen) according to the supplier’s specifications.The quantity and quality of the total RNAs obtained was determined using 6000 Nano Chips (Agilent Technologies)

tag: A Y1 to A Y5 (RNA isolated from 5 independent cell cultures).


title: RhoAQ63L transformed cells treated with Y27632_A Y3


title: RhoAQ63L transformed cells treated with Y27632_A Y1


title: RhoAQ63L transformed cells treated with Y27632_A Y2


title: RhoAQ63L transformed cells treated with Y27632_A Y4


title: Mt-Gi vs Mt-root, rep1

status: Public on Mar 08 2007

city: Ithaca

first: Maria

middle: J.

last: Harrison

state: NY

address: Tower Road, Cornell Campus

institute: Boyce Thompson Institute for Plant Research

description: Gene expression data of Mt/Gi vs Mt root samples

hyb_protocol: Equivalent quantity of Cy3TM labeled cDNA and Cy5TM labeled cDNA probes were combined and evaporated to dryness in a speedvac at darkness. The combined dried cDNA targets were then suspended in 58 μl of hybridization solution containing 46 μl of 1.25x formamide based HybIt2™ hybridization solution (Telechem international, USA: catalog no. HHS2), 1 μl Poly (dA) (Invitrogen: catalog no. POLYA.GF) and 11 μl of H2O. The re-suspended cDNA probes were then incubated at 95°C for 5min and applied to a pre-warmed (50°C) slide, and covered with a clean glass LifterSlip (Erie Scientific company, USA: catalog no. 22X50I-2-4711). The slides were then sealed in Corning hybridization chambers (Corning Inc., USA: catalog no. 2551) and maintained at 43°C H2O bath with gentle shaking at 40 rpm for 16-20 hrs in the dark.

scan_protocol: Slides were scanned using a two-channel confocal microarray scanner (ScanArray5000, GSI Lumonics, MA, USA) and the associated ScanArray software (version3.1, Packard BioChip Technologies, MA, USA).

data_processing: Normalization and analysis of microarray data were performed using Genespring® software (version 6.2, Silicon Genetics, CA, USA). For each experiment, data from six slides were imported into Genespring® software and values for all spots on the arrays were normalized with per spot and per chip intensity dependent (Lowess) normalization, using 20% of the data to calculate the Lowess fit at each point.

organism: Medicago truncatula

source_name: Mt-root, Cy5

label_protocol: 25μg total RNA was used to generate fluorescently labeled cDNA probes using SuperScriptTM Indirect cDNA Labeling System (Invitrogen: catalog no. L1014-02).

growth_protocol: Medicago truncatula cv Jemalong, line A17 plants were grown in growth rooms under a 16-h-light (25 °C ) / 8-h-dark (22 °C ) regime.

extract_protocol: Total RNA was isolated with Trizol Reagent® (Invitrogen) with an extra phenol-chloroform purification step, treated with RNase-free DNase (Promega) at 37°C for 20 minutes, and then purified using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 2-week old M. truncatula seedlings were transplanted to 11-cm pot containing sterile Turface (eight plants per pot) and were mock-inoculated with the final distilled-water wash from the spore purification procedure. The plants were fertilized with half-strength Hoagland’s solution containing 0.02mM KH2PO4 twice weekly and harvested at 30 days post inoculation (dpi).

tag: G. intraradices mock-inoculated root tissues

organism:
Medicago truncatula
Rhizophagus intraradices

source_name: Mt/Gi-root, Cy3

tag: G. intraradices inoculated root tissues


title: Control non transformed NIH3T3 cells treated with Y27632_N Y4

description: Gene expression data from NIH3T3 cells treated with Y27632 for 24 h, grown in the presence of serum until confluency levels lower than 70%

source_name: NIH3T3 cells after 24 h to treatment with Y27632 (10uM), grown in the presence of serum until confluency levels lower than 70%.

extract_protocol: three 10-cm diameter plates containing exponentially growing cultures of NIH3T3 cells treated with Y27632 (10uM) for 24 h, were washed with PBS and their total cellular RNAs isolated using the RNeasy kit (Qiagen) according to the supplier’s specifications.The quantity and quality of the total RNAs obtained was determined using 6000 Nano Chips (Agilent Technologies)

tag: N Y1 to N Y5 (RNA isolated from 5 independent cell cultures).


title: Control non transformed NIH3T3 cells treated with Y27632_N Y3


title: Control non transformed NIH3T3 cells treated with Y27632_N Y2


title: TAR syndrome female TAR_587

status: Public on Jan 07 2007

type: genomic

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: TAR syndrome

hyb_protocol: Hybridization was done for 24h at 42°C on a slide booster (Advalytix, Brunnthal, Germany).

scan_protocol: Slides were scanned using an Axon 4100A scanner (Axon Instruments, Union City, CA)

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen et al., 2005). Background intensities were not subtracted. Signal intensities were normalized by subgrid LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants ( version Dec 2005)

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA isolated from blood

label_protocol: labeled by random priming

extract_protocol: chloroform extraction

tag: DNA isolated from blood of a TAR syndrome patient

value: female

source_name: female reference DNA

tag: DNA isolated from peripheral blood of a pool of healthy female donors


title: Sh-Mt-Gi vs Mt-shoot, rep1

description: Gene expression data of Sh-Mt-Gi vs Mt shoot samples

hyb_protocol: Equivalent quantity of Cy3 labeled cDNA and Cy5 labeled cDNA probes were combined and evaporated to dryness in a speedvac at darkness. The combined dried cDNA targets were then suspended in 58 μl of hybridization solution containing 46 μl of 1.25x formamide based HybIt2™ hybridization solution (Telechem international, USA: catalog no. HHS2), 1 μl Poly (dA) (Invitrogen: catalog no. POLYA.GF) and 11 μl of H2O. The re-suspended cDNA probes were then incubated at 95°C for 5min and applied to a pre-warmed (50°C) slide, and covered with a clean glass LifterSlip (Erie Scientific company, USA: catalog no. 22X50I-2-4711). The slides were then sealed in Corning hybridization chambers (Corning Inc., USA: catalog no. 2551) and maintained at 43°C H2O bath with gentle shaking at 40 rpm for 16-20 hrs in the dark.

data_processing: Normalization and analysis of microarray data were performed using Genespring? software (version 6.2, Silicon Genetics, CA, USA). For each experiment, data from six slides were imported into Genespring? software and values for all spots on the arrays were normalized with per spot and per chip intensity dependent (Lowess) normalization, using 20% of the data to calculate the Lowess fit at each point.

source_name: Mt-shoot, Cy3

tag: Shoot tissues from Glomus intraradices mock-inoculated Medicago truncatula plants

source_name: Sh-Mt-Gi, Cy5

treatment_protocol: 2-week old M. truncatula seedlings were transplanted to 11-cm pot containing sterile Turface (eight plants per pot) and about 8,000 G. intraradices spores were evenly inoculated onto the root of the seedlings. The plants were fertilized with half-strength Hoagland’s solution containing 0.02mM KH2PO4 twice weekly and harvested at 30 days post inoculation (dpi).

tag: Shoot tissues from Glomus intraradices inoculated Medicago truncatula plants


title: Control non transformed NIH3T3 cells treated with Y27632_N Y1


title: TAR syndrome female TAR_521

description: TAR syndrome

tag: gender

source_name: male reference DNA

tag: DNA isolated from peripheral blood blood of a pool of healthy male donors


title: Control non transformed NIH3T3 cells treated with Y27632_N Y5


title: RhoCQ63L transformed cells_C5

description: Gene expression data from RhoCQ63L transformed cells grown in the presence of serum until confluency levels lower than 70%

data_processing: Normalization, filtering and analysis of the raw data obtained from the microarrays was carried out with the Bioconductor software (www.bioconductor.com) using de ReadAffy package and the RMA function. The RMA function was selected over the standard Affymetrix software because it provides a better precision in signal detection to achieve adequate normalization of multiple microarray hybridizations, especially in cases of low levels of gene expression (Bolstad et al., 2004; Gautier et al., 2004; Gentleman et al., 2004; Parrish and Spencer, 2004)

source_name: NIH3T3 cells stably expressing RhoCQ63L cells grown in the presence of serum until confluency levels lower than 70%.

extract_protocol: three 10-cm diameter plates containing exponentially growing cultures of RhoCQ63L transformed cells were washed with PBS and their total cellular RNAs isolated using the RNeasy kit (Qiagen) according to the supplier’s specifications.The quantity and quality of the total RNAs obtained was determined using 6000 Nano Chips (Agilent Technologies)

tag: C1 to C6 (RNA isolated from 6 independent cell cultures).


title: Mt-Gigi vs Mt-root, rep1

description: Gene expression data of Mt/Gigi vs Mt root samples

source_name: Mt-root, Cy3

treatment_protocol: About 3-day old seedlings were transplanted into small cones (3x15cm) containing sterile Turface and were mock-inoculated with the final distilled-water wash from the spore purification procedure. The plants were fertilized with half-strength Hoagland’s solution containing 0.02mM KH2PO4 twice weekly and harvested at 28 days post inoculation (dpi).

tag: Gigaspora gigantea mock-inoculated M. truncatula root tissues

organism:
Medicago truncatula
Gigaspora gigantea

source_name: Mt/Gigi-root, Cy5

treatment_protocol: About 3-day old seedlings were transplanted into small cones (3x15cm). Each cone contains ten seedlings and  50 spores were evenly inoculated onto the root of the seedlings. The plants were fertilized with half-strength Hoagland’s solution containing 0.02mM KH2PO4 twice weekly and harvested at 28 days post inoculation (dpi).

tag: Gigaspora gigantea inoculated Medicago root tissues


title: RhoCQ63L transformed cells_C4


title: RhoCQ63L transformed cells_C6


title: TAR syndrome female TAR 453

description: TAR syndrome

tag: Gender


title: RhoCQ63L transformed cells_C2


title: TAR syndrome male TAR_584

description: TAR syndrome

tag: DNA isolated from peripheral blood of a pool of healthy male donors


title: RhoCQ63L transformed cells_C3


title: RhoBQ63L transformed cells_B3

description: Gene expression data from RhoBQ63L transformed cells grown in the presence of serum until confluency levels lower than 70%

source_name: NIH3T3 cells stably expressing RhoBQ63L cells grown in the presence of serum until confluency levels lower than 70%.

extract_protocol: three 10-cm diameter plates containing exponentially growing cultures of RhoBQ63L transformed cells were washed with PBS and their total cellular RNAs isolated using the RNeasy kit (Qiagen) according to the supplier’s specifications.The quantity and quality of the total RNAs obtained was determined using 6000 Nano Chips (Agilent Technologies)

tag: B1 to B6 (RNA isolated from 6 independent cell cultures).


title: RhoBQ63L transformed cells_B4


title: RhoCQ63L transformed cells_C1


title: RhoBQ63L transformed cells_B5


title: RhoBQ63L transformed cells_B2


title: RhoAQ63L transformed cells_A7

description: Gene expression data from RhoAQ63L transformed cells grown in the presence of serum until confluency levels lower than 70%

source_name: NIH3T3 cells stably expressing RhoAQ63L cells grown in the presence of serum until confluency levels lower than 70%.

extract_protocol: three 10-cm diameter plates containing exponentially growing cultures of RhoAQ63L transformed  cells were washed with PBS and their total cellular RNAs isolated using the RNeasy kit (Qiagen) according to the supplier’s specifications.The quantity and quality of the total RNAs obtained was determined using 6000 Nano Chips (Agilent Technologies)

tag: A1 to A7 (RNA isolated from 7 independent cell cultures).


title: RhoAQ63L transformed cells_A5


title: RhoAQ63L transformed cells_A6


title: RhoBQ63L transformed cells_B1


title: RhoAQ63L transformed cells_A4


title: RhoAQ63L transformed cells_A2


title: RhoBQ63L transformed cells_B6


title: RhoAQ63L transformed cells_A1


title: Control non transformed NIH3T3 cells_N7

description: Gene expression data from NIH3T3 cells grown in the presence of serum until confluency levels lower than 70%

source_name: NIH3T3 cells grown in the presence of serum until confluency levels lower than 70%.

extract_protocol: three 10-cm diameter plates containing exponentially growing cultures of NIH3T3 cells were washed with PBS and their total cellular RNAs isolated using the RNeasy kit (Qiagen) according to the supplier’s specifications.The quantity and quality of the total RNAs obtained was determined using 6000 Nano Chips (Agilent Technologies)

tag: N1 to N8 (RNA isolated from 8 independent cell cultures).


title: Control non transformed NIH3T3 cells_N6


title: Control non transformed NIH3T3 cells_N8


title: RhoAQ63L transformed cells_A3


title: Control non transformed NIH3T3 cells_N5


title: Control non transformed NIH3T3 cells_N4


title: Control non transformed NIH3T3 cells_N3


title: Control non transformed NIH3T3 cells_N1


title: Control non transformed NIH3T3 cells_N2


title: Spo11 DSB exp 2

status: Public on Jan 01 2007

city: Paris

first: Valerie

last: Borde

address: 26, rue d'Ulm

country: France

institute: Institut Curie

description: Experiment to map Spo11 DSB sites.

hyb_protocol: hybridization: overnight at 63C in 3X SSC, 0.75 mg/ml polyA, 25mM HEPES pH7.0, 0.25% SDS. washes: 3mn each at room temperature, once in 1X SSC, 0.03% SDS, then once in 0.2X SSC, then 3 times in 0.05X SSC.

scan_protocol: Axon 4000B scanner. GenePix5.0 software

data_processing: Log2Ratios of background-corrected Intensities, spatial bias normalized with MANOR (Neuvial et al. 2006 Bioinformatics) median fitted to 0, and weighted average of the 3 replicates

organism: Saccharomyces cerevisiae

source_name: Spo11-Myc ChIP

label_protocol: indirect aa-dUTP

growth_protocol: 1% potassium acetate

extract_protocol: chromatin immunoprecipitation without prior crosslinking, with anti-Myc antibody

tag: rad50S Spo11-Myc

tag: Strain ORD8127

tag: t=6h after meiosis induction

source_name: Spo11-Myc input chromatin


title: pADH1Spo11 DSB exp 3

description: Experiment to map Gal4BD-Spo11 binding sites.

source_name: pADH1Spo11-Myc ChIP

tag: Strain ORD8257

source_name: pADH1Spo11-Myc input chromatin


title: Spo11 DSB exp 1

description: Experiment to map Spo11 DSB sites.


title: B. longum mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9135

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

description: Laser captured cecal epithelium from B. longum mono-associated (10d) NMRI adult mice on a standard polysaccharide-rich diet

data_processing: MAS5; scaling = 500


title: Spo11 DSB exp 3

description: Experiment to map Spo11 DSB sites.


title: Gal4BD-Spo11 DSB exp 3

description: Experiment to map Gal4BD-Spo11 DSB sites.

source_name: Gal4BD-Spo11-Myc ChIP

tag: rad50S Gal4BD-Spo11-Myc

tag: Strain ORD7392

source_name: Gal4BD-Spo11-Myc input chromatin


title: Gal4BD-Spo11 DSB exp 2


title: pADH1Spo11 DSB exp 1


title: Gal4BD-Spo11 DSB exp 1


title: pADH1Spo11 DSB exp 2


title: B. thetatiotaomicron-B. longum bi-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9132

description: Laser captured cecal epithelium from B. thetatiotaomicron-B. longum bi-associated (10d) NMRI adult mice on a standard polysaccharide-rich diet


title: B. thetatiotaomicron-B. longum bi-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9133


title: Gal4BD-alone Spo11-Myc DSB exp 2

data_processing: Log2Ratios of background-corrected Intensities, spatial bias normalized with MANOR (Neuvial et al. 2006 Bioinformatics) median fitted to 0, and weighted average of the 2 replicates

source_name: Gal4BD-alone Spo11-Myc ChIP

tag: Strain ORD8270

source_name: Gal4BD-alone Spo11-Myc input chromatin


title: Gal4BD-alone Spo11-Myc DSB exp 1


title: Gal4BD-Spo11 binding exp 1

source_name: Gal4BD-Spo11 ChIP

extract_protocol: chromatin immunoprecipitation after prior crosslinking, with anti-Gal4BD antibody

tag: rad50S Gal4BD-Spo11

tag: Strain ORD7366

tag: t=0h after meiosis induction

source_name: Gal4BD-Spo11 input chromatin


title: Gal4BD-Spo11 binding exp 3


title: B. thetatiotaomicron-B. longum bi-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9180


title: B. longum mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9181


title: B. longum mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9134


title: B. thetatiotaomicron mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9130

description: Laser captured cecal epithelium from B. thetatiotaomicron mono-associated (10d) NMRI adult mice on a standard polysaccharide-rich diet


title: Gal4BD-Spo11 binding exp 2


title: B. thetatiotaomicron mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9443


title: GF NMRI mice LCM cecal epithelium (pool of 4 animals)_#9129

description: Laser captured cecal epithelium from GF NMRI adult mice on a standard polysaccharide-rich diet


title: B. thetatiotaomicron-B. longum bi-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9179


title: B. thetatiotaomicron mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9568


title: B. thetatiotaomicron mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9177


title: GF NMRI mice LCM cecal epithelium (pool of 4 animals)_#9128


title: GF NMRI mice LCM cecal epithelium (pool of 4 animals)_#9176


title: GF NMRI mice LCM cecal epithelium (pool of 4 animals)_#9175


title: B. longum mono-associated (10d) gnotobiotic NMRI mice LCM cecal epithelium (pool of 4 animals)_#9182


title: 00022416 Clone #1 replicate 2 basal Cy5/Dox Cy3

type: other

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

institute: IPMC

description: 2005/02/11 - 00022416

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software.

data_processing: Normalized log2 ratio of means defined by CH1/CH2

molecule: other


title: 00022447 Clone #2 replicate 2 basal Cy5/Dox Cy3

description: 2005/02/11 - 00022447


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_20d_#8967

description: Bacteroides thetaiotaomicron in gnotobiotic C57BL/6J mice on a standard polysaccharide-rich diet, harvested from the cecum after 20 days.

organism: Bacteroides thetaiotaomicron

source_name: Bacteroides thetaiotaomicron, cecum C57BL/6J mice, 20days


title: 00022354 Clone #1 replicate 1 basal Cy3/Dox Cy5

description: 2005/02/11 - 00022354

data_processing: Normalized log2 ratio of means defined by CH2/CH1


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_20d_#8592

tag: Bacteroides thetaiotaomicron, cecum C57BL/6J mice, 20days


title: 016518 4 months F 2 WT transgenic

description: 2006/07/11 - 016518


title: Bthetaiotaomicron/Lcasei_C57BL/6Jcecum_Stdchow_20d/10d_#8964

description: Bacteroides thetaiotaomicron in gnotobiotic C57BL/6J mice on a standard polysaccharide-rich diet, harvested from the cecum after 20 days; final 10 days L. casei administration

source_name: Bacteroides thetaiotaomicron  and Lactobacillus casei, cecum C57BL/6J mice; 20days Bt; final 10days Lc


title: Bthetaiotaomicron/Lcasei_C57BL/6Jcecum_Stdchow_20d/10d_#8962

tag: Bacteroides thetaiotaomicron  and Lactobacillus casei, cecum C57BL/6J mice; 20days Bt; final 10days Lc


title: Bthetaiotaomicron/Blongum_C57BL/6Jcecum_Stdchow_10d_#8595

description: Bacteroides thetaiotaomicron and Bifidobacterium longum bi-associated in gnotobiotic C57BL/6J mice on a standard polysaccharide-rich diet, harvested from the cecum after 10 days.

organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

source_name: Bacteroides thetaiotaomicron and Bifidobacterium longum bi-association, cecum C57BL/6J mice, 10days

tag: Bacteroides thetaiotaomicron  and Bifdobacterium longum bi-association, cecum C57BL/6J mice, 10days


title: 00022446 Clone #2 replicate 1 basal Cy3/Dox Cy5

description: 2005/02/11 - 00022446


title: Bthetaiotaomicron/Banimalis_C57BL/6Jcecum_Stdchow_20d/10d_#8958

description: Bacteroides thetaiotaomicron in gnotobiotic C57BL/6J mice on a standard polysaccharide-rich diet, harvested from the cecum after 20 days; final 10 days B. animalis administration

source_name: Bacteroides thetaiotaomicron  and Bifidobacterium animalis, cecum C57BL/6J mice; 20days Bt; final 10days Ba


title: Bthetaiotaomicron/Banimalis_C57BL/6Jcecum_Stdchow_20d/10d_#8960

tag: Bacteroides thetaiotaomicron  and Bifidobacterium animalis, cecum C57BL/6J mice; 20days Bt; final 10days Ba


title: 016685 10 days F 1 WT transgenic

description: 2006/07/11 - 016685


title: 016516 4 months M 2 WT transgenic

description: 2006/07/11 - 016516


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_20d_#8968


title: 016682 10 days M 1 WT transgenic

description: 2006/07/11 - 016682


title: 016680 10 days F 1 transgenic WT

description: 2006/07/07 - 016680


title: 016683 10 days M 1 WT transgenic

description: 2006/07/11 - 016683


title: 016517 4 months M 2 WT transgenic

description: 2006/07/11 - 016517


title: Bthetaiotaomicron/Blongum_C57BL/6Jcecum_Stdchow_10d_#8592


title: Bthetaiotaomicron/Blongum_C57BL/6Jcecum_Stdchow_10d_#8593


title: Bthetaiotaomicron/Blongum_C57BL/6Jcecum_Stdchow_10d_#8594


title: 016452 4 months M 2 transgenic WT

description: 2006/07/07 - 016452


title: 016625 10 days M 1 transgenic WT

description: 2006/07/07 - 016625


title: 016453 4 months M 2 transgenic WT

description: 2006/07/07 - 016453


title: 016479 10 days M 1 transgenic WT

description: 2006/07/07 - 016479


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_10d_#8589

description: Bacteroides thetaiotaomicron monoassociated in gnotobiotic C57BL/6J mice on a standard polysaccharide-rich diet, harvested from the cecum after 10 days.

source_name: Bacteroides thetaiotaomicron, monoassociation, cecum C57BL/6J mice, 10days


title: Bthetaiotaomicron/Blongum_C57BL/6Jcecum_Stdchow_10d_#8591


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_10d_#8590

tag: Bacteroides thetaiotaomicron, monoassociation, cecum C57BL/6J mice, 10days


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_10d_#8587


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_10d_#8586


title: Bthetaiotaomicron/Blongum_NMRIcecum_Stdchow_10d_#8438

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

source_name: Bacteroides thetaiotaomicron and Bifidobacterium longum bi-association, cecum NMRI mice, 10days

tag: Bacteroides thetaiotaomicron  and Bifdobacterium longum bi-association, cecum NMRI mice, 10days


title: Blongum_NMRIcecum_Stdchow_10d_#8441

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

organism: Bifidobacterium longum

source_name: Bifidobacterium longum, monoassociation, cecum NMRI mice, 10days


title: Bthetaiotaomicron/Blongum_NMRIcecum_Stdchow_10d_#8435


title: 016475 4 months F 2 transgenic WT

description: 2006/07/07 - 016475


title: Blongum_NMRIcecum_Stdchow_10d_#8439

tag: Bifidobacterium longum, monoassociation, cecum NMRI mice, 10days


title: Blongum_NMRIcecum_Stdchow_10d_#8443


title: Bthetaiotaomicron/Lcasei_C57BL/6Jcecum_Stdchow_20d/10d_#8961


title: Blongum_NMRIcecum_Stdchow_10d_#8442


title: Bthetaiotaomicron/Blongum_NMRIcecum_Stdchow_10d_#8434


title: Bthetaiotaomicron_NMRIcecum_Stdchow_10d_#8433

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

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


title: Bthetaiotaomicron_C57BL/6Jcecum_Stdchow_10d_#8588


title: Bthetaiotaomicron/Blongum_NMRIcecum_Stdchow_10d_#8436


title: Bthetaiotaomicron/Blongum_NMRIcecum_Stdchow_10d_#8437


title: Bthetaiotaomicron_NMRIcecum_Stdchow_10d_#8431

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


title: MUT1.1

status: Public on Aug 22 2007

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

institute: Institute for Medical Microbiology

description: blood samples were collected on admission to the ICU (that is 12 hours after trauma) in PAXgene Blood RNA System tubes (PreAnalytiX, Heidelberg, Germany) and stored at -80?C according to the   manufacturer?s recommendations (PreAnalytiX)

hyb_protocol: Purified cRNA were fragmented in fragmentation buffer (40 mM Tris-acetate pH 7.9, 100 mM KOAc, 31.5 mM MgOAc) at 94?C for 20 minutes. For hybridization on CodeLink bioarrays, 10 ug of fragmented cRNA in 260 ul of hybridization solution was added to each bioarray via the Flex Chamber port and incubated for 18 hours in a Minitron shaker incubator (Infors AG, Germany) at 37?C, 300 rpm. cRNA was hybridized onto microarrays at least in duplicate (technical replicates).

scan_protocol: Bioarrays were scanned using the GenePix 4000 B scanner and the GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA).

data_processing: A total of 22 patient samples were subjected to microarrays with at least two technical replicates per sample (total 58 arrays). Spot signals of CodeLink bioarrays were quantified using CodeLink System Software ? Batch Submission (V2.2.27) and ? Expression Analysis (V2.2.25) (GE Healthcare) as outlined in the user's manual. CodeLink Expression Software 1.21 generated background corrected raw as well as median centered intra-slide normalized data. The intra-slide normalized data were used for further analysis. The software automatically calculated thresholds for intra-slide normalized intensities for each array and flagged genes as TRUE when the gene intensity was higher than the threshold or FALSE when the intensity was lower than the threshold. Furthermore, the software flagged each gene value as GOOD, EMPTY, POOR, NEG or MSR defining quality measures. Only gene values flagged as GOOD or EMPTY were used for the analysis. Patients (arrays) were separated in two groups: A) 12 patients without the TNF rs1800629 A variant and B) 10 patients carrying the TNF rs1800629 A variant. Genes with missing values >= 50% of all arrays in a group were excluded from the analysis. Genes that were flagged as FALSE in > 50% of arrays in each group were also excluded from the analysis. These procedures revealed a filtered set of 8551 genes (Set1). Missing values in this filtered set were imputed using sequential K-nearest neighbor (SKNN) imputation (Kim et al. 2004). To detect outlier values for a particular gene in a group, all gene values > median + 3 standard deviations (SD) or < median -3 SD were flagged as BLANK. Exempted from this rule were those gene values being consistently > median + 3 SD or < median -3 SD in all technical replicates of a patient since the consistency of these values in all technical replicates of the same sample was considered as a biological feature rather than a technical outlier. All gene values that were flagged as BLANK were removed in Set1 which was then subjected to SKNN imputation. Finally, this set of 8551 genes was normalized using quantiles normalization in R (Bolstad et al. 2003) and logged (base 2).

source_name: peripheral blood

label_protocol: Total RNA were subjected to cDNA synthesis using a poly-A binding primer containing the T7-polymerase promoter (CodeLink Expression Assay Kit). Double-stranded DNA fragments were purified using the QIAquickTM PCR Purification Kit (Qiagen, Germany). For target labeling, the cDNA was in-vitro transcribed (IVT) by partially substituting UTP with bio-16-UTP in the reaction mixture. Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Germany). The eluted cRNA was quantified with the NanoDrop (NanoDrop Technologies) and quality was assesed with the Agilent 2100 bioanalyser (Agilent Technologies GmbH).

extract_protocol: Total RNA was extracted from the PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany) using the  manufacturer?s recommendations (PreAnalytiX). Total RNA was quantified with Nanodrop (NanoDrop Technologies, Rockland DE, USA) and the quality of RNA was assessed using the Agilent 2100 Bioanalyzer Bioanalyzer (Agilent Technologies GmbH, Boeblingen, Germany)

tag: Human peripheral blood collected in PAXgene Blood RNA System (PreAnalytiX, Heidelberg, Germany)


title: Bthetaiotaomicron_NMRIcecum_Stdchow_10d_#8429


title: 15wk_E2_AFB1_rep2_Cy3

status: Public on Dec 31 2006

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 5 ppm E2 for 15 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. For each sample, equal amounts of RNA (ug) were pooled from three fish per tank for every treatment (n=2 biological replicates).  Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 - 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from one of the two biological replicates was dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt's solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier.

scan_protocol: Scanned images (5 um) were acquired with ScanArray Express (PerkinElmer, Boston, MA) at an excitation of 543 nm for Cy3 and 633 nm for Cy5 and at 90% power. The photomultiplier tube (PMT) settings for each fluor were set based on intensity of spiked internal alien controls to normalize among all slides in the experiment. Image files were quantified in QuantArray (PerkinElmer) and raw mean signal and background values were exported to BioArray Software Environment (BASE; Saal et al. 2002) for analysis.

data_processing: Raw mean signal and background values are included. For experiment, data were background subtracted and normalized by LOWESS. Stringent criteria were used to filter for genes that were regulated at least 1.8-fold consistently in all features from biological replicates (n=2 per treatment) and had a p-value <0.05 by Welch's t-test.

organism: Oncorhynchus mykiss

source_name: Liver

label_protocol: Labeled using Genisphere Array 350 kit adapted from manufacturer protocol

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb AFB1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 5 ppm E2 in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of fish at 3-week and 15-week timepoints on promotional diets for microarray analysis.  Gene expression was correlated with tumorigenesis measured at 13 months of age.

tag: Strain

value: Mt. Shasta

tag: Timepoint

tag: Tissue

value: liver

tag: Initiation

value: aflatoxin B1

source_name: Reference

treatment_protocol: Trout embryos were sham initiated with aqueous 0.01% ethanol for 30 min.  At 3 months of age, fish were fed 0.1% DMSO vehicle in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of fish at 3-week and 15-week timepoints for microarray analysis.  Reference sample RNA was isolated from individual livers of ten sham-initiated trout at both timpeoints and aliquots were pooled in equal amounts (ug).

value: 3- and 15-week combined

value: sham


title: 15wk_E2_AFB1_rep2_Cy5

extract_protocol: Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol


title: 15wk_E2_AFB1_rep1_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 5 ppm E2 for 15 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: Bthetaiotaomicron_NMRIcecum_Stdchow_10d_#8430


title: 3wk_E2_AFB1_rep2_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 5 ppm E2 for 3 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: Bthetaiotaomicron/Banimalis_C57BL/6Jcecum_Stdchow_20d/10d_#8957


title: Blongum_NMRIcecum_Stdchow_10d_#8440


title: 3wk_E2_AFB1_rep2_Cy3


title: 3wk_E2_AFB1_rep1_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 5 ppm E2 for 3 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 15wk_DIM_AFB1_rep2_Cy3

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 15 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb AFB1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 400 ppm DIM in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of fish at 3-week and 15-week timepoints on promotional diets for microarray analysis.  Gene expression was correlated with tumorigenesis measured at 13 months of age.


title: 15wk_DIM_AFB1_rep2_Cy5


title: 15wk_DIM_sham_rep2_Cy3

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 15 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Trout embryos were initiated with aqueous 0.01% ethanol for 30 min. At 3 months of age, fish were fed 400 ppm DIM in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of fish at 3-week and 15-week timepoints on promotional diets for microarray analysis.  Gene expression was correlated with tumorigenesis measured at 13 months of age.


title: 3wk_DIM_AFB1_rep2_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 3 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 3wk_DIM_sham_rep2_Cy5

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 3 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 3wk_DIM_sham_rep2_Cy3


title: 15wk_DIM_sham_rep1_Cy5

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 15 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 15wk_DIM_sham_rep2_Cy5


title: 15wk_CON_sham_rep1_Cy5

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 0.1% DMSO vehicle for 15 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Trout embryos were initiated with aqueous 0.01% ethanol for 30 min. At 3 months of age, fish were fed 0.1% DMSO vehicle in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of fish at 3-week and 15-week timepoints on promotional diets for microarray analysis.  Gene expression was correlated with tumorigenesis measured at 13 months of age.


title: 3wk_DIM_AFB1_rep2_Cy3


title: 15wk_CON_sham_rep2_Cy3

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 0.1% DMSO vehicle for 15 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

source_name: References


title: 3wk_CON_sham_rep2_Cy5

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 0.1% DMSO vehicle for 3 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 15wk_CON_sham_rep2_Cy5


title: 3wk_CON_sham_rep1_Cy5

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 0.1% DMSO vehicle for 3 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 15wk_CON_AFB1_rep2_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 0.1% DMSO vehicle for 15 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb AFB1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 0.1% DMSO vehicle in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of fish at 3-week and 15-week timepoints on promotional diets for microarray analysis.  Gene expression was correlated with tumorigenesis measured at 13 months of age.


title: 3wk_CON_AFB1_rep2_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 and the fed promotional diet of 0.1% DMSO vehicle for 3 weeks - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 0.1% DMSO vehicle in the diet 5 days/week for 18 weeks.  Liver samples were collected from a subset of fish at 3-week and 15-week timepoints on promotional diets for microarray analysis.  Gene expression was correlated with tumorigenesis measured at 13 months of age.


title: 3wk_DIM_sham_rep1_Cy5

description:
Liver from trout initiated with 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 3 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 15wk_DIM_AFB1_rep1_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 15 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 15wk_CON_AFB1_rep2_Cy3


title: 3wk_DIM_AFB1_rep1_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 400 ppm DIM for 3 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 15wk_CON_AFB1_rep1_Cy5

description:
Liver from trout initiated with 50 ppb AFB1 in 0.01% ethanol and the fed promotional diet of 0.1% DMSO vehicle for 15 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 3wk_CON_AFB1_rep1_Cy3

description:
Liver from trout initiated with 50 ppb AFB1 and the fed promotional diet of 0.1% DMSO vehicle for 3 weeks - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. For each sample, equal amounts of RNA (µg) were pooled from three fish per tank for every treatment (n=2 biological replicates).  Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 - 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from one of the two biological replicates was dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier.

data_processing: Raw mean signal and background values are included. For experiment, data were background subtracted and normalized by LOWESS. Stringent criteria were used to filter for genes that were regulated at least 1.8-fold consistently in all features from biological replicates (n=2 per treatment) and had a p-value <0.05 by Welch’s t-test.


title: ES2_rep2_Cy3

description:
HCC from trout treated with 5 ppm E2 - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 - 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt?s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier.

data_processing: Raw mean signal and background values are included. For experiment, data were background subtracted and normalized by LOWESS. Stringent criteria were used to filter for genes that were regulated at least 1.8-fold consistently in all features from biological replicates (n=3 per treatment) and had a p-value <0.05 by Welch?s t-test.

source_name: Hepatocellular carcinoma

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 5 ppm E2 in the diet 5 days/week for 18 weeks.  At 13 months, trout were sampled for tumors. Tumors were isolated under a dissection microscope and placed separately in TRIzol Reagent (Invitogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis. Only HCC tumors (determined by histopathology) were used for microarray analysis.

tag: Age

value: 13 months

value: hepatocellular carcinoma

treatment_protocol: Trout embryos were sham initiated with aqueous 0.01% ethanol for 30 min. At 13 months, trout were sampled for tumors. Sham-initiated trout had no tumors. Reference sample RNA was isolated from individual livers of ten sham-initiated trout and aliquots were pooled in equal amounts (ug).


title: ES2_rep3_Cy5

description:
HCC from trout treated with 5 ppm E2 - rep3
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 3wk_CON_sham_rep1_Cy3


title: ES2_rep2_Cy5

extract_protocol: Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: ES2_rep1_Cy5

description:
HCC from trout treated with 5 ppm E2 - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: 3wk_CON_AFB1_rep1_Cy5


title: DIM_rep2_Cy3

description:
HCC from trout treated with 400 ppm DIM - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 400 ppm DIM in the diet 5 days/week for 18 weeks.  At 13 months, trout were sampled for tumors. Tumors were isolated under a dissection microscope and placed separately in TRIzol Reagent (Invitogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis. Only HCC tumors (determined by histopathology) were used for microarray analysis.


title: DIM_rep3_Cy5

description:
HCC from trout treated with 400 ppm DIM - rep3
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: ES2_rep1_Cy3


title: CON_rep1_Cy3

description:
HCC from trout treated with 0.1% DMSO - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.

hyb_protocol: Hybridizations were performed with the Genisphere Array 350 kit and instructions (Hatfield, PA) using standard reference design with dye-swapping. Briefly, 7 ug total RNA were reverse-transcribed with Superscript II (Invitrogen) using the Genisphere oligo d(T) primer containing a capture sequence for the Cy3 or Cy5 labelling reagents. Each reaction was spiked with a range of concentrations (0.0049 – 2.5 ng/ul) of the ten SpotReport Alien Oligo controls (Stratagene). Each cDNA sample containing the capture sequence for the Cy3 or Cy5 label was combined with equal amounts of reference cDNA (pooled from sham-initiated controls) containing the capture sequence for the opposite label. cDNA from two of the three biological replicates were dye-swapped and hybridized to two slides as technical replicates. cDNA from the reference sample was also hybridized to dye-swapped slides (against itself) following the same protocol as experimental samples for use as a negative control. Prior to hybridization, microarrays were processed post-printing by washing twice in 0.1% SDS for 5 min, 2X SSC, 0.1% SDS at 47C for 20 min, 0.1X SSC for 5 min, water for 3 min, then dried by centrifugation. The cDNAs (25 ul) were hybridized to arrays in formamide buffer [50% formamide, 8X SSC, 1% SDS, 4X Denhardt’s solution] for 16 h at 47C with 22x25 mm Lifterslips (Erie Scientific, Portsmouth, NH). Arrays were then washed once in 2X SSC, 0.1% SDS at 47C for 10 min, twice in 2X SSC, 0.1% SDS for 5 min, twice in 1X SSC for 5 min, twice in 0.1X SSC for 5 min and dried by centrifugation. Shaded from light, the Cy3 and Cy5 fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized in formamide buffer for 3 h at 49C to the corresponding capture sequences on cDNAs bound to the arrays. Arrays were washed in the dark with SSC containing 0.1 M DTT and dried as described earlier.

data_processing: Raw mean signal and background values are included. For experiment, data were background subtracted and normalized by LOWESS. Stringent criteria were used to filter for genes that were regulated at least 1.8-fold consistently in all features from biological replicates (n=3 per treatment) and had a p-value <0.05 by Welch’s t-test.

label_protocol: Labeled using Genisphere Array 350 kit adapted from manufacturer protocol.

treatment_protocol: Trout embryos were initiated with aqueous 50 ppb aflatoxin B1 in 0.01% ethanol for 30 min. At 3 months of age, fish were fed 0.1% DMSO vehicle in the diet 5 days/week for 18 weeks.  At 13 months, trout were sampled for tumors. Tumors were isolated under a dissection microscope and placed separately in TRIzol Reagent (Invitogen, Carlsbad, CA) and quick frozen in liquid nitrogen for gene expression analysis. Only HCC tumors (determined by histopathology) were used for microarray analysis.


title: CON_rep3_Cy5

description:
HCC from trout treated with 0.1% DMSO - rep3
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: DIM_rep1_Cy3

description:
HCC from trout treated with 400 ppm DIM - rep1
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: DIM_rep1_Cy5


title: BST2

city: Columbus

first: Brian

last: Trainor

state: OH

address: 1835 Neil Ave.

department: Psychology

institute: Ohio State University

description: bed nucleus of the stria terminalis RNA sample2 from long day

hyb_protocol: http//www.dnaarrays.org/CNP.php. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: The data was analyzed with ArrayAssist Lite RMA version 3.4.

organism: Peromyscus polionotus

source_name: micropunch sample of bed nucleus of the stria terminalis

extract_protocol: RNaqueous (Ambion, Austin, TX).

tag: Male, housed in  16 light:8 dark. The punch sample was taken from a 2 mm slice of brain tissue and includes the bed nucleus of the stria terminalis.


title: CON_rep1_Cy5


title: BST4

description: bed nucleus of the stria terminalis RNA sample4 from short day

tag: Male, housed in  8 light:16 dark. The punch sample was taken from a 2 mm slice of brain tissue and includes the bed nucleus of the stria terminalis.


title: DIM_rep2_Cy5


title: CON_rep2_Cy5

description:
HCC from trout treated with 0.1% DMSO - rep2
Hybridized with reference sample.
Packard ScanArray Model 4000
QuantArray
Genisphere labeling and hybridization kit.
Invitrogen TRIzol extraction followed by cleanup with Qiagen RNeasy according to vendor protocol.


title: CON_rep2_Cy3


title: BST3

description: bed nucleus of the stria terminalis RNA sample3 from long day

tag: Male, housed in 16 light:8 dark. The punch sample was taken from a 2 mm slice of brain tissue and includes the bed nucleus of the stria terminalis.


title: POA5

description: medial preoptic RNA sample5 from short day

source_name: micropunch sample of medial preoptic area

tag: Male, housed in  8 light:16 dark. The punch sample was taken from a 2 mm slice of brain tissue and includes the medial preoptic area.


title: BST1

description: bed nucleus of the stria terminalis RNA sample1 from long day


title: BST5

description: bed nucleus of the stria terminalis RNA sample5 from short day


title: POA6

description: medial preoptic RNA sample6 from short day


title: POA2

description: medial preoptic RNA sample2 from long day

tag: Male, housed in 16 light:8 dark. The punch sample was taken from a 2 mm slice of brain tissue and includes the medial preoptic area.


title: POA1

description: medial preoptic RNA sample1 from long day


title: Ssn6HA-ts/WT @ 36 Deg J290Dsl17

status: Public on Nov 15 2006

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: Gene expression profiling experiment

hyb_protocol: Xue et al, 2004

scan_protocol: Scanexpress Laser scanner TIGR spotfinder Quantification

data_processing: Gene Spring Silicon genetics

organism: Schizosaccharomyces pombe

label_protocol: Xue et al, 2004

growth_protocol: Xue et al, 2004

extract_protocol: Xue et al, 2004

treatment_protocol: Xue et al, 2004

tag: CY3=Ssn6HA-ts @36 Deg

source_name: WT

tag: CY5=WT @36 Deg


title: Hst4 vs WT Expression 2nd Array

status: Public on Dec 15 2006

description: Expression data for Hst4 vs WT

data_processing: Genespring software Silicon Genetics

tag: YES 30 Deg


title: POA3

description: medial preoptic RNA sample3 from long day


title: POA4

description: medial preoptic RNA sample4 from short day


title: Ssn6HA-ts/WT @ 36 Deg J290Dsl16

description: Gene expression profiling experiment

tag: CY3=WT @36 Deg

tag: CY5=Ssn6HA-ts @36 Deg


title: P4XB2 Mutant (1994) in Arginine

status: Public on Nov 01 2006

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: no additional information

hyb_protocol: A minimum of 1mg fragmented probe was resuspended in 80 ml hybridization buffer containing 3nM of control oligo B2 (Affymetrix, UK). Hybridization was performed in a rotisserie oven at 45°C for 16 hours. The chips were washed and stained in a GeneChip® Fluidics Station 400™ (Affymetrix, UK) using the Mini_prok2v1 protocol

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 (Affymetrix, UK).

data_processing: Initial data analysis was performed using the GeneChip® Operating Software. Microarray quality control parameters were as follow: noise (RawQ) less than 5, background signal less than 40 (100 target intensity for array scaling), consistent numbers of genes detected as present across arrays.

label: Biotin

organism: Escherichia coli

source_name: E.Coli, strain P4XB2 mutant, grown in presence of arginine(100 ug/ml)

label_protocol: Total RNA was controlled for its integrity and purity using a Bioanalyzer 2100 (Agilent) and a Nanodrop spectrophotometer. Total RNA (10µg) showing no signs of degradation or impurities, was supplemented with Poly-A RNA controls and reverse transcribed to cDNA using random primers. After RNA degradation with NaOH, cDNA was purified (MinElute PCR Purification Kit®, QIAGEN), analyzed for yield (30-120µg) and purity (260nm/280nm and 260nm/230nm absorption ratios >1.8), then fragmented using DNase-I (Amersham Pharmacia Biosciences) and labelled terminally with biotinylated GeneChipÒ DNA Labeling Reagent (Affymetrix, UK).

growth_protocol: Cells used for expression analysis were grown in minimal medium (Glansdorff, 1965) supplemented with 0.5% glucose (w/v), L-methionine (100ug ml-1) and with L-arginine (100ug ml-1). For expression analysis, cells were grown in a rotary shaker at 37°C and harvested by centrifugation at mid-log phase ( (OD) 660nm = 0.5) and the metabolism was quenched in liquid nitrogen.

extract_protocol: Total RNA was isolated using a RNeasy® RNA isolation kit, according to the manufacturer’s specifications (QIAGEN, Germany) and stored in RNase-free water at –80°C. RNA concentration was determined by UV-spectrometry and its quality controlled by agarose gel electrophoresis.


title: P4XB2 Mutant (1993) in Arginine

description: no additional information

tag: E.Coli, strain P4XB2 mutant, grown in presence of arginine(100 ug/ml)


title: Hst4 vs WT Expression

description: Expression data for Hst4 vs WT


title: P4XB2 Mutant (1992) in Arginine

description: no additional information


title: P4X Wild Type (1766) in Arginine

description: no additional information

source_name: E.Coli, strain P4X, grown in presence of arginine(100 ug/ml)


title: P4X Wild Type (1989) Reference

description: no additional information

source_name: E.Coli, strain P4X, grown on minimal medium, reference sample

growth_protocol: Cells used for expression analysis were grown in minimal medium (Glansdorff, 1965) supplemented with 0.5% glucose (w/v), L-methionine (100ug ml-1). For expression analysis, cells were grown in a rotary shaker at 37°C and harvested by centrifugation at mid-log phase ( (OD) 660nm = 0.5) and the metabolism was quenched in liquid nitrogen.


title: P4X Wild Type (1754) in Arginine

description: no additional information

growth_protocol: Cells used for expression analysis were grown in minimal medium (Glansdorff, 1965) supplemented with 0.5% glucose (w/v), L-methionine (100mg ml-1) and with L-arginine (100ug ml-1). For expression analysis, cells were grown in a rotary shaker at 37°C and harvested by centrifugation at mid-log phase ( (OD) 660nm = 0.5) and the metabolism was quenched in liquid nitrogen.

tag: E.Coli, strain P4X, grown in presence of arginine(100 ug/ml)


title: P4X Wild Type (1753) Reference

description: no additional information

hyb_protocol: A minimum of 1mg fragmented probe was resuspended in 80 ml hybridization buffer containing 3nM of control oligo B2 (Affymetrix, UK). Hybridization was performed in a rotisserie oven at 45°C for 16 hours. The chips were washed and stained in a GeneChip® Fluidics Station 400™ (Affymetrix, UK) using the Mini_prok2v1 protocol.

source_name: Strain P4X, grown on minimal medium, reference sample

tag: E.Coli, strain P4X, grown on minimal medium, reference sample


title: P4X Wild Type (1990) in Arginine

description: no additional information


title: MHS+MG, 480 min, replica C

status: Public on Oct 31 2006

first: Helmy

last: Rachman

address: Schumannstrasse 21-22

institute: MPIIB

description: third biological replica/sample

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Affymetrix scan protocol

data_processing: MAS 5.0

label: Affymetrix labeling protocol

source_name: MH-S cell line

label_protocol: Affymetrix labeling protocol

growth_protocol: RPMI complete medium

extract_protocol: Trizol extraction, purified by RNeasy column from Qiagen

treatment_protocol: 0.8 mM methylglyoxal for 480 minutes

tag: murine alveolar macrophages


title: MHS+MG, 30 min, replica C

description: third biological replica/sample

treatment_protocol: 0.8 mM methylglyoxal for 30 minutes


title: P4X Wild Type (1765) Reference

description: no additional information


title: MHS+MG, 480 min, replica A

description: first biological replica/sample


title: MHS+MG, 240 min, replica C

description: third biological replica/sample

treatment_protocol: 0.8 mM methylglyoxal for 240 minutes


title: MHS+MG, 240 min, replica B

description: second biological replica/sample


title: MHS+MG, 480 min, replica B

description: second biological replica/sample


title: MHS+MG, 0 min, replica C

description: third biological replica/sample

treatment_protocol: without methylglyoxal


title: MHS+MG, 30 min, replica B

description: second biological replica/sample


title: PU.1 KD HSC 1

status: Public on Oct 15 2006

city: Boston

first: Ulrich

last: Steidl

state: MA

address: 77 Avenue Louis Pasteur

department: Hematology/Oncology

institute: Harvard Institutes of Medicine

description: Total RNA from FACS-sorted HSC was amplified by two rounds of RT and T7 promoter-based in-vitro transcription and the resultant biotinylated cRNA was then hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

data_processing: Array data were analyzed with the dChip software. After smoothing spline normalization, expression values were calculated applying the perfect-match/mismatch difference model algorithm (dChip).

label: biotin/SAPE

source_name: Bone marrow HSC

label_protocol: Amplification of RNA by two rounds of reverse transcription followed by T7 promoter-dependent in-vitro transcription. Then standard labeling according to Affymetrix protocols.

extract_protocol: RNeasy Micro

tag: FACS-sorted Lin-, c-kit+, Sca-1+ HSC from the bone marrow of PU.1 knockdown mice with targeted disruption of the distal enhancer (URE) –14kb upstream of the PU.1 gene.


title: MHS+MG, 30 min, replica A

description: first biological replica/sample


title: WT HSC 2


title: WT HSC 3


title: nst1-1 nst3-1 #2 vs wild type

status: Public on Oct 28 2006

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: nst1-1 nst3-1 cannot produce secondary xylem in inflorescence stem and hypocotyl.

data_processing: Agilent Feature-extraction software version A.6.1.1

organism: Arabidopsis thaliana

source_name: Stem of nst1-1 nst3-1 #2

growth_protocol: 8hr light / 16hr dark

treatment_protocol: No treatment

tag: RNA was extracted from the base 4cm part of inflorescence stem whose height was 15 cm.

source_name: Stem of wild type

tag: RNA was extracted from the base 4cm part of inflorescence stems whose heights were between 12 and 17 cm.


title: nst1-1 nst3-1 #1 vs wild type

source_name: Stem of nst1-1 nst3-1 #1


title: MHS+MG, 240 min, replica A

description: first biological replica/sample


title: WT HSC 1


title: PU.1 KD HSC 2


title: MHS+MG, 0 min, replica B

description: second biological replica/sample

data_processing: MSA 5.0


title: MHS+MG, 0 min, replica A

description: first biological replica/sample


title: H157 siDJ-1 #1

status: Public on Oct 01 2006

city: Chapel Hill

first: Casey

middle: M

last: Clements

state: NC

department: Lineberger Cancer Center

institute: UNC Chapel Hill

description: Gene expression data from H157 cells  transfected siRNA oligomers targeting DJ-1

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridizd onto arrays for 16 hours at 45oC in the GeneChip Hybridization Oven 640

scan_protocol: Arrays were scanned with the Hewlett Packard GeneArray Scanner

data_processing: Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.

label_protocol: Biotinylated cRNA were prepared using BioArray High Yield RNA Transcript Kit

extract_protocol: Promega SV Total RNA; DNAse I treated

treatment_protocol: H157 cells grown in RPMI w/ 10% FCS transfected 3 consecutive days annd GITC lysed 96 hours after first transfection.  RNA isolated by column (Promega).  Then cRNA made and labeled, hybridized to Affy U133A array

tag: NSCLC cell line H157. Transfected with siRNA oligomers targeting DJ-1 - #1


title: H157 siDJ-1 #2

tag: NSCLC cell line H157. Transfected with siRNA oligomers targeting DJ-1 - #2


title: nst1-1 nst3-1 #3 vs wild type

source_name: Stem of nst1-1 nst3-1 #3


title: PU.1 KD HSC 3


title: H157 siCTL1

description: Gene expression data from H157 cells  transfected with non-targetting scrambeled control siRNA oligomers

source_name: H157 siCTL1

tag: NSCLC cell line H157. Transfected with scrambeled control non-targetting oligomer siRNA - #1


title: H157 siMOCK

description: Gene expression data from H157 cells Mock transfected with transfection reagent alone.

source_name: H157 siMOCK

tag: NSCLC cell line H157. Transfected with Oligofectamine (Invitrogen) without RNA


title: H157 siCTL2

source_name: H157 siCTL2

tag: NSCLC cell line H157. Transfected with scrambeled control non-targetting oligomer siRNA - #2


title: N6_Cy5

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

description: Labeling, hybridization, and scanning done using Agilent reagents, hardware, and protocols

data_processing: Lowess normalization in Feature Extraction

source_name: Universal Human Reference RNA (UHRR)

tag: Manufacturer

value: Stratagene;

tag: Catalog number

source_name: Lung, Normal Tissue

tag: Tissue

value: Lung


title: N8_Cy3


title: Anaerobic pH 8.5 rep3

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

description: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH during growth without aeration.  The experiment was designed for direct comparison with the pH profile under aerobic conditions reported previously (GSE4511). Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5.  Tubes were incubated at37°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2.    For each of the three pH conditions, RNA was isolated from five independent cultures.

hyb_protocol: Affymetrix standard procedures

data_processing: Affymetrix GCOS software

source_name: Escherichia coli K-12 W3110

label_protocol: Labeled cDNA was prepared and hybridized to Affymetrix Antisense E. coli arrays by standard procedures.

growth_protocol: Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5.  Tubes were incubated at37°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2. Five replicate cultures were grown at each pH.

extract_protocol: RNA was isolated using RNAprotect (Qiagen) and the RNeasy Kit.

treatment_protocol: Growth at pH 8.5

tag: Escherichia coli K-12 W3110


title: N7_Cy5


title: N4_Cy5


title: N5_Cy3


title: Anaerobic pH 8.5 rep5


title: N6_Cy3


title: Anaerobic pH 8.5 rep2


title: N3_Cy5


title: Anaerobic pH 8.5 rep4


title: N8_Cy5


title: N9_Cy5


title: N5_Cy5


title: N2_Cy5


title: N3_Cy3


title: N9_Cy3


title: N1_Cy5


title: N7_Cy3


title: N4_Cy3


title: S-IIP(UIP)15_Cy5

source_name: Lung, Sporadic Idiopathic Interstitial Pneumonia (S-IIP), Usual Interstitial Pneumonia (UIP)

value: lung;

tag: Genetics

value: Sporadic IIP;

tag: Histology

value: Usual Interstitial Pneumonia


title: Bthetaiotaomicron_NMRIcecum_Stdchow_10d_#8432

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

data_processing: MAS5; scaling = 500

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


title: S-IIP(UIP)16_Cy3


title: N2_Cy3

value: lung


title: N1_Cy3


title: S-IIP(UIP)16_Cy5


title: S-IIP(UIP)14_Cy5


title: Anaerobic pH 8.5 rep1


title: S-IIP(UIP)14_Cy3


title: S-IIP(UIP)13_Cy3


title: S-IIP(UIP)13_Cy5


title: Anaerobic pH 7.0 rep3

treatment_protocol: Growth at pH 7.0


title: Anaerobic pH 7.0 rep4


title: Anaerobic pH 7.0 rep5


title: Anaerobic pH 7.0 rep1


title: Anaerobic pH 7.0 rep2


title: Anaerobic pH 5.7 rep5

treatment_protocol: Growth at pH 5.7


title: F-IIP(UIP)7_Cy5

source_name: Lung, Familial Idiopathic Interstitial Pneumonia (F-IIP), Usual Interstitial Pneumonia (UIP)

value: Familial IIP;


title: Anaerobic pH 5.7 rep4


title: F-IIP(UIP)9_Cy5


title: Anaerobic pH 5.7 rep3


title: F-IIP(NSIP)5_Cy5

source_name: Lung, Familial Idiopathic Interstitial Pneumonia (F-IIP), Nonspecific Interstitial Pneumonia (NSIP)

value: Nonspecific Interstitial Pneumonia


title: Anaerobic pH 5.7 rep2


title: S-IIP(NSIP)10_Cy5

source_name: Lung, Sporadic Idiopathic Interstitial Pneumonia (S-IIP), Nonspecific Interstitial Pneumonia (NSIP)


title: S-IIP(UIP)12_Cy5


title: F-IIP(UIP)10_Cy3


title: F-IIP(UIP)8_Cy3


title: F-IIP(UIP)8_Cy5


title: F-IIP(UIP)10_Cy5


title: F-IIP(UIP)9_Cy3


title: F-IIP(UIP)6_Cy3


title: F-IIP(UIP)7_Cy3


title: S-IIP(NSIP)10_Cy3


title: S-IIP(UIP)11_Cy3


title: F-IIP(NSIP)5_Cy3


title: S-IIP(UIP)11_Cy5


title: F-IIP(UIP)6_Cy5


title: MamGland_WildType_Lactating_replicate1

city: Davis

first: Juan

middle: F.

last: Medrano

address: One Shields Ave

department: Animal Science

institute: University of California

description: Wild type (C57BL/6J), whole mammary gland No4 from lactating female mouse.

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

label: ENZO biotin label

source_name: Mammary Gland

label_protocol: Approximately 10 micrograms of total RNA was processed to produce biotinylated cRNA targets. Fragmented cRNA was prepared (10 micrograms) and hybridized overnight to MG-U74AV2 chip.

treatment_protocol: Excised tissue was placed in RNAlater (Ambion Inc) and kept at –80oC.  RNA was isolated using Trizol (GibcoBRL).

tag: Whole mammary gland No4 (inguinal) harvested from lactating C57BL/6J female mouse at day 10 postpartum.


title: MamGland_WildType_Lactating_replicate2


title: MamGland_WildType_Virgin_replicate2

description: Wild type (C57BL/6J), Virgin whole mammary gland No4

tag: Virgin whole mammary gland No4 (inguinal) harvested from C57BL/6J female mouse at puberty (6 wks of age).


title: MamGland_WildType_Pregnant_replicate1

description: Wild type (C57BL/6J), whole mammary gland No4 from 14 day pregnant females

tag: Whole mammary gland No4 (inguinal) harvested from C57BL/6J female mouse at 14 days of pregnancy.


title: MamGland_WildType_Virgin_replicate3


title: S-IIP(UIP)9_Cy3


title: S-IIP(UIP)15_Cy3


title: S-IIP(UIP)12_Cy3


title: S-IIP(UIP)7_Cy5


title: Anaerobic pH 5.7 rep1


title: S-IIP(UIP)5_Cy5


title: MamGland_WildType_Pregnant_replicate2

description: Wild type (C57BL/6J), whole mammary gland No4 from 14 day pregnant females.


title: S-IIP(UIP)2_Cy5


title: S-IIP(UIP)6_Cy3


title: MamGland_WildType_Virgin_replicate1


title: S-IIP(UIP)9_Cy5


title: S-IIP(UIP)7_Cy3


title: MamGland_WildType_Involuting_replicate1

description: Wild type (C57BL/6J), whole mammary gland No4 from female mouse at postlactational involution.

tag: Whole mammary gland No4 (inguinal) harvested from C57BL/6J female mouse at postlactational involution (4 days post weaning of pups).


title: S-IIP(UIP)3_Cy5


title: IRF6 wt, biological rep1

city: St. Louis

first: David

middle: Michael

last: Alvarado

address: 4565 Scott Ave

department: Genetics

institute: Washington University in St. Louis

description: Gene expression data from E17.5 mouse skin, IRF6 wt

hyb_protocol: The resultant biotinylated cRNA was fragmented then hybridized to the GeneChip Mouse Genome 430 2.0 Array (45,000 probe sets used to analyze over 39,000 mouse transcripts and variants from over 34,000 well-characterized mouse genes; Affymetrix, Inc.).  The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station

scan_protocol: GeneChips were scanned using the Affymetrix Model 3000 scanner

data_processing: Expression values were generated using the microarray suite (MAS) v5.0 software (Affymetrix, Inc)

source_name: Skin from Irf6 wt

label_protocol: Five micrograms of total RNA was processed for use on the microarray by using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix, Inc., Santa Clara, CA) according to the manufacturer’s recommended protocols

extract_protocol: Total RNA was isolated as recommended (RNeasy, Qiagen, Valencia, CA), except that tissue was treated with proteinase K (20 mg/ml) for 20 minutes at 55°C.

treatment_protocol: Skin from E17.5 mice was removed and flash frozen.

tag: Background

value: mixed genetic backgroud of C57Bl/6 and 129/SvJ

tag: Genotype

value: IRF6 wt

tag: Age

value: Embryonic day 17.5


title: IRF6 knockout, biological rep1

description: Gene expression data from E17.5 mouse skin, IRF6 null

source_name: Skin from Irf6 null

value: IRF6 null


title: MamGland_WildType_Involuting_replicate2

treatment_protocol: Excised tissue was placed in RNAlater (Ambion Inc) and kept at –80oC. RNA was isolated using Trizol (GibcoBRL).


title: S-IIP(UIP)8_Cy5


title: S-IIP(UIP)3_Cy3


title: S-IIP(UIP)2_Cy3


title: S-IIP(UIP)4_Cy5


title: S-IIP(UIP)6_Cy5


title: F-IIP(UIP)4_Cy5


title: F-IIP(UIP)4_Cy3


title: short-term repopulating Hematopoietic Stem Cells (ST-HSC)

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1392 Storrs Rd. Unit 4243

department: Center for Regenerative Biology

institute: University of Connecticut

hyb_protocol: 10 ?g of labeled aRNA from each cell type was hybridized to an Affymetrix? Mouse 430-2 GeneChip. Fragmentation of aRNA, hybridization, staining, and scanning of the GeneChip was carried out according to the manufacturer's protocol.

data_processing: per chip per gene normalization

label: Aminoallyl-aRNA labeled wiht biotin-X-X-NHS (Epicentre Biotechnologies).

label_protocol: The isolated RNA immediately underwent linear amplification using the TargetAmp? 2-Round Aminoallyl-aRNA Amplification kit 1.0 (Epicentre Biotechnologies, Madison, WI). After amplification, the aminoallyl-aRNA was cleaned using an RNeasy kit (Qiagen, Venlo, The Netherlands) and concentration was determined by absorbance at 260 nm. Aminoallyl-aRNA was quick frozen in a dry ice ethanol bath and stored at -80 ?C until labeled with biotin-X-X-NHS (Epicentre Biotechnologies). The labeling reaction was cleaned using the Minelute cleanup kit (Qiagen) and the concentration was determined.

extract_protocol: Cells were thawed, selected based on morphology, and 50 or 100 were packed into empty, washed zonae pellucidae for ease with handling. Individual cell-packed zonae pellucidae were transferred to 1.5 ml microcentrifuge tubes and snap frozen on liquid nitrogen and then stored at -80 ?C. Total RNA was extracted from 50-200 cells from each cell type using TRIzol reagent (Invitrogen, Carlsbad, CA) with linear acrylamide (Ambion, Inc., Austin, TX) as a co-precipitant.

treatment_protocol: For HSC and HPC isolation, c-Kit positive cells were first enriched by immuno-selection with CD117 micromagnetic beads (Miltenyi Biotec, Auburn, CA). Cells were then stained with FITC-conjugated anti-CD34, PE-conjugated anti-Sca-1, allophycocyanin (APC)-conjugated anti-c-Kit, and a PE-Cy7-conjugated lineage marker cocktail consisting of anti-Gr-1, CD11b, B220, CD3, CD4, CD8, and Ter119 monoclonal antibodies (BD PharMingen, San Diego, CA, and eBioscience, San Diego, CA). 4?,6-Diamidino-2-phenylindole, dihydrochloride (DAPI) was added for dead cell discrimination. Based on multi-color flow cytometric analysis, LT-HSC (CD34-LKS), ST-HSC (CD34+LKS) and HPC (LKS-) were sorted by using a MoFlo High-Speed Cell Sorter (Dakocytomation, Fort Collins, CO).

tag: BDF1 9 week old female


title: S-IIP(UIP)4_Cy3


title: F-IIP(NSIP)3_Cy5


title: S-IIP(NSIP)1_Cy5