title: Array 1-16-26 (GR#2 vs WT(A+B))

city: Wageningen

first: Paul

last: Passarinho

address: Bornsesteeg 65

department: Business Unit Bioscience

institute: Plant Research International BV

description: Hybridizations were performed using four slides with Cy3-labeled wild-type RNA (WT DC) versus Cy5-labeled 35S:BBM GR RNA from the replicated samples of each of the two transgenic lines (GR#1A DC, GR #1B DC, GR #2A DC and GR #2B DC). The target labeling was reversed for one technical replicate from each transgenic line on two additional slides (GR#1A DC and GR #2A DC versus WT DC). Cy3-labeled WT DC RNA was hybridized in duplicate with Cy5-labeled wild-type RNA from untreated biological replicates (WTA and WTB) on two slides in a control experiment designed to rule out nonspecific induction due to DEX+CHX treatment as opposed to BBM activation. An additional control hybridization was performed in duplicate with RNA from untreated samples of both GR lines (GR#1 and GR#2) labeled with Cy3 and wild-type biological replicates pooled before labeling with Cy5 to identify background expression solely due to the 35S:BBM-GR transgene.

hyb_protocol: Labeled target samples were hybridized to 26,000 element Arabidopsis Oligonucleotide Microarrays (Qiagen-Operon Arabidopsis Genome Oligo Set Version 1.0,Qiagen Operon, Alameda, CA, USA), which were printed and provided by the University of Arizona. Immobilization of the oligonucleotide array elements was performed as described at http://ag.arizona.edu/microarray/protocol1.doc. Slides were pre-hybridized at 50C in 120 µl SlideHyb Glass Array Hybridization Buffer #1 (Ambion) using the HybArray hybridization station (Perkin Elmer Life and Analytical Sciences, Boston, MA, USA). The pre-hybridization mixture was replaced after 2 hours by 120 µl pre-warmed SlideHyb Glass Array Hybridization Buffer #1 (Ambion) containing heat-denatured labeled target (2.5 µg Cy3-labeled aRNA and 1.25 µg Cy5-labeled aRNA) and incubated overnight at 50C. The slides were then washed at room temperature down to 0.1x SSC in the hybridization station.

scan_protocol: Slides were scanned separately for the two fluorescent dyes with a GenePix 4000B scanner (Axon Instruments, Union City, CA, USA). The integrated optical density of each probe was measured using the AIS software (Imaging Research Inc., St Catharines, Ontario, Canada).

data_processing: Normalization was performed using the median of the background corrected ratios for all spots excluding negative controls and blanks. Differential expression in each hybridization experiment, expressed as the 2Log value of the normalized signal ratios, was tested for statistical significance using a simple t-test per clone, an Analysis Of Variance (Anova) and SAM (Significance Analysis of Microarrays; Tusher et al., 2000).

label_protocol: For target labeling, 1 µg of seedling total RNA was linearly amplified in the presence of 5-(3-aminoallyl)-UTP (Sigma-Aldrich) using the MessageAmp aRNA Kit (Ambion Ltd., Huntingdon, UK). Cy3 and Cy5 mono-Reactive Dyes (Amersham Biosciences, Rosendaal, The Netherlands) were coupled to the amplified RNA (aRNA) in freshly made 0.1M sodium carbonate buffer, pH 9.3 for 30 min at room temperature. Labeled aRNA was fragmented prior to hybridization using RNA Fragmentation Reagents (Ambion). RNA amplification, labeling and fragmentation efficiencies were monitored by agarose gel electrophoresis and by measurement of the Cy5 and Cy3 fluorescence emissions at 635 and 532 nm, respectively, using a Molecular Imager FX Pro Plus scanner (BioRad Laboratories Inc. Veenendaal, The Netherlands).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Plant Mini kit (Qiagen, Hilden, Germany). RNA quality was monitored by agarose gel electrophoresis and spectrophotometry. 35S:BBM GR lines were grown in duplicate and RNA was isolated for each sample. The RNA from wild-type seedlings treated with DEX+CHX was isolated from 4 different plates and pooled after assessing RNA quality.

treatment_protocol: Dexamethasone (DEX) and cycloheximide (CHX; Sigma-Aldrich, Zwijndrecht, The Netherlands) were dissolved in 70% (v/v) ethanol as 10 mM stocks and used at a final concentration of 10 µM for both liquid and solid media. Wild-type and 35S:BBM GR seeds were germinated on a 150 micron nylon mesh placed on top of 0.5X MS-10 agar plates. Four days later, the nylon mesh with the germinated seedlings was transferred to a 9 cm Petri dish containing 5 ml water supplemented with either 10 µM DEX and 10 µM CHX or the corresponding amount of 70% ethanol. Seedlings were incubated in either solution with gentle rotation for 8 hours, and then frozen in liquid nitrogen and stored at 80C. To ensure the DEX responsiveness of the 35S:BBM GR transgenic lines, the same seed batch was germinated directly on solid 0.5X MS-10 medium containing 10 µM DEX and then scored for somatic embryo formation.

tag: 4 day old 35S:BBM-GR seedlings (line 2), 8h mock treatment

source_name: WT(A+B)

tag: 4 day old wild-type seedlings (pooled samples), 8h mock treatment


title: zincsulfate-Ctrl4-heart

status: Public on Sep 22 2008

type: RNA

city: Research Triangle Park

first: beena

last: vallanat

address: 109 Tw Alexanser Dr

country: USA

institute: EPA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000G

data_processing: The data were analyzed with Rosetta Resolver 6.0  using Affymetrix default profile builder analysis settings.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat whole heart-16 weeks

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

extract_protocol: Target RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) and further purified using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA).

tag: Healthy male Wistar Kyoto (WKY) rats, 12 weeks old, were purchased from Charles River Laboratories Inc., Raleigh, NC.  Animals were double housed in polycarbonate cages with beta chips bedding and acclimatized for at least one week in an AAALAC-approved animal facility (21 ± 1OC, 50 ± 5% relative humidity, 12:12 h light/dark cycle) prior to the experimental period. All animals received standard Purina rat chow (Brentwood, MO) and water ad libitum, except during exposures.Rats were randomly assigned to four groups (n = 15 per group) according to body weight, and exposed by nose-only inhalation (Ledbetter et al., 1998) to either filtered air or aerosolized zinc sulfate (10, 30 or 100 ug Zn/m3) for 5 h/day, 3 days/week for 16 weeks.  The aerosol was generated by aerosolizing solutions of zinc sulfate heptahydrate (Sigma Aldrich Chemicals), mixed at different starting concentrations with a TSI Model 3076 atomizer operating at 30 PSIG.  The output was mixed with dry air and directed to the exposure chamber (air flow of 98-105 liters/minute).  Chamber concentration data was determined by gravimetric analysis, with Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) to determine zinc concentration.


title: Array 1-16-25 (GR#1 vs. WT(A+B))

country: Netherlands

organism: Arabidopsis thaliana

tag: 4 day old 35S:BBM-GR seedlings (Line 1), 8h mock treatment


title: Nipponbare, 2 days after infection with S. hermonthica, biological replicate #2

city: Sheffield

first: Julie

last: Scholes

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from Oryza sativa (cultivar Nipponbare) roots infected with Striga hermonthica at 2 days post-inoculation

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using an Affymetrix GeneChip scanner 3000 7G

data_processing: Data were analysed using Affymetrix GCOS, with global scaling to a target of 100

organism: Oryza sativa Japonica Group

source_name: Oryza sativa roots infected with Striga hermonthica at 2 days post-inoculation

label_protocol: 3'IVT Affymetrix protocol using 5 ug total RNA

growth_protocol: Seedlings of the rice cultivars Nipponbare and IAC 165 (Oryza sativa subspecies japonica) were grown for three weeks in a controlled environment growth room under a 14 hour photoperiod with an irradiance of 400 μmol m-2 s-1, a daytime and night-time temperature of 27 oC and 23 oC respectively and 60% relative humidity.

extract_protocol: RNA was isolated using TRI reagent (Ambion) and then purified using an RNA purification column kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Twenty one day-old seedlings were infected with 25 mg of preconditioned and pre-germinated Striga hermonthica seeds by aligning them along the roots.  Control plants were treated in a similar manner (mock-inoculated).

tag: synonym

value: Oryza sativa subsp. japonica

tag: cultivar

value: Nipponbare

tag: Age

value: 23 days


title: multi-v-ko-4

city: Parkville

first: Matthew

middle: J

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

description: no additional information

hyb_protocol: Hybridization was conducted as per Agilent 2 color microarray-based gene expression analysis manual (version 5.7) with the modification 4 microg of labeled total RNA was used per hybridization.

scan_protocol: Images were quantified using Agilent Feature Extraction Software.

data_processing:
Data was normalized within arrays using loess normalization in limma.  DE was analyzed in limma with design <- cbind(dye=c(1,1,1,1,1,1,1,1), UnstimKOvMC=c(0,-1,0,-1,0,1,0,1), StimKOvMC=c(-1,0,-1,0,1,0,1,0))
VALUE column below reports normalized log2 (ko/ref) ratios.

organism: Citrobacter rodentium

source_name: ko

label_protocol: 5microg of total RNA was labeled with Cy3-ULS or Cy5-ULS (Kreatech) as per manufacturers instructions

growth_protocol: overnight cultures of Citrobacter rodentium were inoculated into LB medium to obtain an OD600 of 0.1 and grown until the OD600 was 0.88

extract_protocol: 10mL of a culture was incubated with 20mL of RNAprotect solution (Qiagen) at room temperature for 15min.  Cells were pelleted and RNA was purified using a FastRNA Pro Blue kit (Qbiogene).  RNA samples were Dnase treated (Qiagen) and further purified using an RNeasy MiniElute kit (Qiagen).

treatment_protocol: Bicarbonate was added to a final concentration of 45mM

tag: RegA Knockout

source_name: multi

tag: RegA multicopy transgene


title: IAC165, 11 days after infection with S. hermonthica, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar IAC165) roots infected with Striga hermonthica at 11 days post-inoculation

source_name: Oryza sativa roots infected with Striga hermonthica at 11 days post-inoculation

value: 32 days


title: zincsulfate-Ctrl1-heart


title: IAC165, 11 days after mock-infection, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar IAC165) uninfected roots, 11 days after mock-inoculation

source_name: Oryza sativa uninfected roots, 11 days after mock-inoculation


title: Array 1-16-24 (WT DC vs. GR#2B DC)

source_name: WT DC

tag: 4 day old wild-type seedlings, 8h DEX+CHX treatment

source_name: GR#2B DC

tag: 4 day old 35S:BBM-GR seedlings (line 2, samle B), 8h DEX+CHX treatment


title: multi-bicarb-v-ko-bicarb-4

description: no additional information

source_name: ko-bicarb

tag: agent

value: bicarbonate

source_name: multi-bicarb


title: IAC165, 11 days after infection with S. hermonthica, biological replicate #1


title: IAC165, 4 days after infection with S. hermonthica, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar IAC165) roots infected with Striga hermonthica at 4 days post-inoculation

source_name: Oryza sativa roots infected with Striga hermonthica at 4 days post-inoculation

value: 25 days


title: multi-v-ko-3

description: no additional information


title: multi-bicarb-v-ko-bicarb-3

description: no additional information


title: Nipponbare, 2 days after infection with S. hermonthica, biological replicate #1


title: IAC165, 4 days after mock-infection, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar IAC165) uninfected roots, 4 days after mock-inoculation

source_name: Oryza sativa uninfected roots, 4 days after mock-inoculation


title: IAC165, 4 days after infection with S. hermonthica, biological replicate #1


title: Nipponbare, 2 days after mock-infection, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar Nipponbare) uninfected roots, 2 days after mock-inoculation

source_name: Oryza sativa uninfected roots, 2 days after mock-inoculation


title: Array 1-16-21 (WT DC vs. WTA)

source_name: WTA

tag: 4 day old wild-type seedlings (sample A), 8h mock treatment


title: IAC165, 11 days after mock-infection, biological replicate #1


title: Array 1-16-23 (WT DC vs. GR#2A DC)

source_name: GR#2A DC

tag: 4 day old 35S:BBM-GR seedlings (Line 2, sample A), 8h DEX+CHX treatment


title: IAC165, 4 days after mock-infection, biological replicate #1


title: Array 1-16-22 (WT DC vs. WTB)

hyb_protocol: Labeled target samples were hybridized to 26,000 element Arabidopsis Oligonucleotide Microarrays (Qiagen-Operon Arabidopsis Genome Oligo Set Version 1.0,Qiagen Operon, Alameda, CA, USA), which were printed and provided by the University of Arizona. Immobilization of the oligonucleotide array elements was performed as described at http://ag.arizona.edu/microarray/protocol1.doc. Slides were pre-hybridized at 50C in 120 ?l SlideHyb Glass Array Hybridization Buffer #1 (Ambion) using the HybArray hybridization station (Perkin Elmer Life and Analytical Sciences, Boston, MA, USA). The pre-hybridization mixture was replaced after 2 hours by 120 ?l pre-warmed SlideHyb Glass Array Hybridization Buffer #1 (Ambion) containing heat-denatured labeled target (2.5 ?g Cy3-labeled aRNA and 1.25 ?g Cy5-labeled aRNA) and incubated overnight at 50C. The slides were then washed at room temperature down to 0.1x SSC in the hybridization station.

label_protocol: For target labeling, 1 ?g of seedling total RNA was linearly amplified in the presence of 5-(3-aminoallyl)-UTP (Sigma-Aldrich) using the MessageAmp aRNA Kit (Ambion Ltd., Huntingdon, UK). Cy3 and Cy5 mono-Reactive Dyes (Amersham Biosciences, Rosendaal, The Netherlands) were coupled to the amplified RNA (aRNA) in freshly made 0.1M sodium carbonate buffer, pH 9.3 for 30 min at room temperature. Labeled aRNA was fragmented prior to hybridization using RNA Fragmentation Reagents (Ambion). RNA amplification, labeling and fragmentation efficiencies were monitored by agarose gel electrophoresis and by measurement of the Cy5 and Cy3 fluorescence emissions at 635 and 532 nm, respectively, using a Molecular Imager FX Pro Plus scanner (BioRad Laboratories Inc. Veenendaal, The Netherlands).

source_name: WTB

treatment_protocol: Dexamethasone (DEX) and cycloheximide (CHX; Sigma-Aldrich, Zwijndrecht, The Netherlands) were dissolved in 70% (v/v) ethanol as 10 mM stocks and used at a final concentration of 10 ?M for both liquid and solid media. Wild-type and 35S:BBM GR seeds were germinated on a 150 micron nylon mesh placed on top of 0.5X MS-10 agar plates. Four days later, the nylon mesh with the germinated seedlings was transferred to a 9 cm Petri dish containing 5 ml water supplemented with either 10 ?M DEX and 10 ?M CHX or the corresponding amount of 70% ethanol. Seedlings were incubated in either solution with gentle rotation for 8 hours, and then frozen in liquid nitrogen and stored at 80C. To ensure the DEX responsiveness of the 35S:BBM GR transgenic lines, the same seed batch was germinated directly on solid 0.5X MS-10 medium containing 10 ?M DEX and then scored for somatic embryo formation.

tag: 4 day old wild-type seedlings (sample B), 8h mock treatment


title: IAC165, 2 days after infection with S. hermonthica, biological replicate #2

description: Gene expression data from Oryza sativa (cultivar IAC165) roots infected with Striga hermonthica at 2 days post-inoculation

source_name: Oryza sativa  roots infected with Striga hermonthica at 2 days post-inoculation


title: Liver_SampleN3_rep1

status: Public on Sep 21 2008

city: Guangzhou

first: Jian-Rong

last: Yang

address: No. 74, Zhongshan 2nd Road

country: China

institute: Sun Yat-sen University

description: MiRNA isolation, labeling, hybridization and scanning were performed by CapitalBio Corp.

hyb_protocol: Hybridization was performed under LifterSlipTM (Erie Company), which allows for even dispersal of hybridization solutions between the microarray and coverslip.  The hybridization chamber was laid on a three-phase tiling agitator BioMixerTM II (CapitalBio Corp.) to prompt the microfluidic circulation under the coverslip. The hybridization was performed in water bath under 42℃ overnight. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner (CapitalBio Corp.). The scanning setting was adjusted to obtain a visualized equal intensity of U6 spots across arrays.Data was extracted from the TIFF images using GenePix software.

data_processing: Signal intensity from each spot was log-transformed and normalized among arrays using quantile normalization method in the BIOCONDUCTOR package.

organism: Homo sapiens

source_name: Liver

label_protocol: We adopted the T4 RNA ligase labeling method according to Thomson' protocol. In brief, 4 ug of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 h. Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15 ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide.

extract_protocol: Total RNAs were isolated using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s recommendations. ~60 ug of total RNAs were used to extract miRNA using miRNA Isolation Kit (Ambion Inc. Texas)

tag: Gender

value: Female

tag: Tissue

value: Liver

tag: HBS-Ag

value: negative

tag: pathology

value: Cavernous hemangioma of the liver


title: GSE_Dox_2

city: Rehovot

first: reut

last: shalgi

address: Weizmann Institute of Science

country: Israel

institute: Weizmann Institute of Science

description: miRNA expression profiles in WI38 cells (normal fibroblasts) +/- p53 inactivation with GSE56, +/-DNA damage by Doxorubicin, +/-grown to senescence

hyb_protocol: Exiqon's protocol

scan_protocol: Exiqon's protocol

data_processing: Median of replicated probes for each miRNA, Global Lowess normalization and Log2 transformation of Cy5/Cy3 Ratios.

source_name: Primary WI38 cells, Young, p53 inactivation by overexpression of GSE56, treated with Doxorubicin 0.2 microgram/ml for 24 hours

label_protocol: Exiqon's protocol

growth_protocol: WI-38 cells were cultured in MEM with 10% FCS (Fetal Calf Serum), 1mM sodium pyruvate, 2mM L-glutamine, and antibiotics.

extract_protocol: Tri-Reagent

source_name: Reference sample (Cy3) was a mix of all samples.


title: GSE_Dox_1

tag: Primary WI38 cells, Young, p53 inactivation by overexpression of GSE56, treated with Doxorubicin 0.2 microgram/ml for 24 hours

tag: Reference sample (Cy3) was a mix of all samples.


title: Con_Old_1

source_name: Primary WI38 cells, Senescent

tag: Primary WI38 cells, Senescent


title: Con_Old_2


title: GSE_Old_1

source_name: Primary WI38 cells, Senescent, p53 inactivation by overexpression of GSE56


title: GSE_Old_2

tag: Primary WI38 cells, Senescent, p53 inactivation by overexpression of GSE56


title: multi-v-ko-2

description: no additional information

source_name: multi

source_name: ko


title: Liver_SampleN2_rep2

extract_protocol: Total RNAs were isolated using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s recommendations. ~60 μg of total RNAs were used to extract miRNA using miRNA Isolation Kit (Ambion Inc. Texas)

tag: Age

value: positive


title: Liver_SampleN2_rep1


title: Liver_SampleN3_rep2


title: Liver_SampleN1_rep2


title: Con_Dox_1

source_name: Primary WI38 cells, Young, treated with Doxorubicin 0.2 microgram/ml for 24 hours


title: GSE_Young_2

source_name: Primary WI38 cells, Young, p53 inactivation by overexpression of GSE56


title: multi-v-ko-1

description: no additional information

tag: RegA Knockout


title: HCC_SampleT4_rep2

source_name: Hepatocellular carcinoma from Southeast China

value: Male

value: hepatocellular carcinoma

value: moderate differenciated HCC


title: IAC165, 2 days after infection with S. hermonthica, biological replicate #1

source_name: Oryza sativa roots infected with Striga hermonthica at 2 days post-inoculation

tag: synonym

tag: cultivar


title: HCC_SampleT5_rep1

value: Edmondson grade II, trabecular type


title: HCC_SampleT5_rep2


title: Liver_SampleN1_rep1

tag: Pathology


title: B6 brain rep1

city: Davis

first: Kyoungmi

last: Kim

state: CA

address: One Shields Avenue

department: Rowe Program in Human Genetics

institute: University of California-Davis

description: We previously constructed a congenic mouse, B6.S-D2Mit194-D2Mit311 (B6.S-2) with SPRET/Ei donor DNA on distal chromosome 2 in a C57BL/6J background that captured an obesity quantitative trait locus (QTL). Mice homozygous for SPRET/Ei alleles at the donor region had decreased body weight and obesity related phenotypes. The B6.S-2 congenic donor region spanned a minimum of 26 Mb. In this study, we constructed five overlapping subcongenics with smaller SPRET/Ei donor regions to fine map the underlying gene(s). One of the five subcongenic lines derived from the B6.S-2 founding congenic, B6.S-2A, captures most of the body weight and adiposity phenotypes in a donor region with a maximum size of 7.4 Mb. Homozygous SPRET/Ei donor alleles in both the founding congenic and the derived B6.S-2A subcongenic exhibit significant decreases in body weight, multiple fat pad weights with the greatest decrease in mesenteric fat pad weight, and Adiposity Index (total fat pad weight divided by body weight). Interval specific microarray analysis in four tissues for donor region genes from the founding B6.S-2 congenic identified several differentially expressed genes mapping to the B6.S-2A subcongenic donor region, including prohormone convertase 2 (PC2). Quantitative real-time PCR confirmed a modest decrease of PC2 expression in whole brains of mice homozygous for SPRET/Ei donor alleles. Analysis of the relative levels of mRNA for B6 and SPRET/Ei in heterozygous congenic mice showed differentially higher expression of the C57BL/6J allele over the SPRET/Ei allele indicating a cis regulation of differential expression. Using subcongenic mapping, we have successfully narrowed a body weight and obesity QTL interval and identified PC2 as a positional candidate gene.

hyb_protocol: cRNA was then hybridized according to the NimbleGen protocol

scan_protocol: Maskless Array Synthesizer (MAS) technology (Nuwaysir, Huang et al. 2002)

data_processing: RMA

organism: Mus musculus

source_name: B6 brain rep1

label_protocol: cDNA was transcribed into cRNA using the MEGAscript T7 Kit (Ambion, Austin, TX) with biotin labeled CTP and UTP followed by purification with RNeasy (QIAGEN, Valencia, CA).

growth_protocol: At weaning, F2 mice were group housed with ad libitum access to water and a standard chow diet (Purina Rodent Chow 5001, Dean’s Animal Feed) with approximately 12% energy from fat (Research Diets D12492, Research Diets, New Brunswick, NJ). One group of male B6.S-2 congenic mice were also fed a purified high fat diet with 60% energy from fat.

extract_protocol: Total RNA from whole brain, epididymal white adipose tissue, gastrocnemius skeletal muscle, and liver were isolated using TRIzol reagent (Gibco/BRl, Grand Island, NY) followed by further purification with QIAGEN RNeasy kit (QIAGEN Inc., Valencia, CA) using the RNA cleanup protocol. cRNA was then hybridized to a custom NimbleScreen 12-well array platform.

treatment_protocol: congenic mouse

tag: B6 brain rep1


title: multi-bicarb-v-ko-bicarb-1

description: no additional information

source_name: multi-bicarb

tag: RegA multicopy transgene

tag: agent

source_name: ko-bicarb


title: Array 1-16-16 (WT DC vs. GR#1B DC)

source_name: WT DC

tag: 4 day old wild-type seedlings, 8h DEX+CHX treatment

source_name: GR#1B DC

tag: 4 day old 35S:BBM-GR seedlings (line 1, sample B), 8h DEX+CHX treatment


title: Array 1-16-18 (GR#2A DC vs. WT DC)

source_name: GR#2A DC

tag: 4 day old 35S:BBM-GR seedlings(Line 2 sample A), 8h DEX+CHX treatment


title: Array 1-16-17 (GR#1A DC vs. WT DC)

source_name: GR#1A DC

tag: 4 day old 35S:BBM-GR seedlings (line 1, sample A), 8h DEX+CHX treatment


title: Array 1-16-15 (WT DC vs. GR#1A DC)

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Plant Mini kit (Qiagen, Hilden, Germany). RNA quality was monitored by agarose gel electrophoresis and spectrophotometry. 35S:BBM GR lines for the microarray experiments were grown in duplicate and RNA was isolated for each sample. The RNA from wild-type seedlings treated with DEX+CHX was isolated from 4 different plates and pooled after assessing RNA quality.

treatment_protocol:
Dexamethasone and cycloheximide treatments:
Dexamethasone (DEX) and cycloheximide (CHX; Sigma-Aldrich, Zwijndrecht, The Netherlands) were dissolved in 70% (v/v) ethanol as 10 mM stocks and used at a final concentration of 10 µM for both liquid and solid media. Wild-type and 35S:BBM GR seeds were germinated on a 150 micron nylon mesh placed on top of 0.5X MS-10 agar plates. Four days later, the nylon mesh with the germinated seedlings was transferred to a 9 cm Petri dish containing 5 ml water supplemented with either 10 µM DEX and 10 µM CHX or the corresponding amount of 70% ethanol. Seedlings were incubated in either solution with gentle rotation for 8 hours, and then frozen in liquid nitrogen and stored at 80C. To ensure the DEX responsiveness of the 35S:BBM GR transgenic lines, the same seed batch was germinated directly on solid 0.5X MS-10 medium containing 10 µM DEX and then scored for somatic embryo formation.

treatment_protocol:
Dexamethasone and cycloheximide treatments
Dexamethasone (DEX) and cycloheximide (CHX; Sigma-Aldrich, Zwijndrecht, The Netherlands) were dissolved in 70% (v/v) ethanol as 10 mM stocks and used at a final concentration of 10 µM for both liquid and solid media. Wild-type and 35S:BBM GR seeds were germinated on a 150 micron nylon mesh placed on top of 0.5X MS-10 agar plates. Four days later, the nylon mesh with the germinated seedlings was transferred to a 9 cm Petri dish containing 5 ml water supplemented with either 10 µM DEX and 10 µM CHX or the corresponding amount of 70% ethanol. Seedlings were incubated in either solution with gentle rotation for 8 hours, and then frozen in liquid nitrogen and stored at 80C. To ensure the DEX responsiveness of the 35S:BBM GR transgenic lines, the same seed batch was germinated directly on solid 0.5X MS-10 medium containing 10 µM DEX and then scored for somatic embryo formation.

tag: 4 day old 35S:BBM-GR seedlings (line 1, sampe A), 8h DEX+CHX treatment


title: IAC165, 2 days after mock-infection, biological replicate #1

description: Gene expression data from Oryza sativa (cultivar IAC165) uninfected roots, 2 days after mock-inoculation

source_name: Oryza sativa uninfected roots, 2 days after mock-inoculation


title: IAC165, 2 days after mock-infection, biological replicate #2


title: multi-bicarb-v-ko-bicarb-2

description: no additional information


title: Con_Dox_2

tag: Primary WI38 cells, Young, treated with Doxorubicin 0.2 microgram/ml for 24 hours

source_name: Reference sample (Cy3) was a mix of all samples.


title: Con_Young_1

source_name: Primary WI38 cells, Young

tag: Primary WI38 cells, Young

tag: Reference sample (Cy3) was a mix of all samples.


title: HCC_SampleT1_rep2

tag: Gender

tag: Tissue

tag: HBS-Ag

tag: pathology

value: Edmondson grade III, trabecular type


title: HCC_SampleT1_rep1

tag: Age


title: HCC_SampleT2_rep2


title: HCC_SampleT3_rep1


title: HCC_SampleT2_rep1

value: male


title: Con_Young_2


title: HCC_SampleT4_rep1


title: HCC_SampleT3_rep2


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T3_1

status: Public on Sep 20 2008

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: No additional information.

hyb_protocol: Labelled samples were combined (either an infected or a control sample combined with a CRR sample) and co-hybridized on the BOTL-5 microarrays using SlideHyb Glass Array Hybridization Buffer #3 (Ambion Ltd.). Microarray hybridizations were performed using a Tecan HS400 hybridisation station (Tecan Ltd.) with the following protocol – Step 1: 75°C, wash 10 s, soak 20 s, 1 cycle; probe injection: 85°C; denaturation: 95°C, 2 min; hybridization cycle 1: 65°C, time 35 min, agitation frequency medium; hybridization cycle 2: 55°C, time 35 min, agitation frequency medium; hybridization cycle 3: 50°C, time 2 h 30m, agitation frequency medium; wash cycle 1: 42°C, wash 10 s, soak 20 s, 2 cycles; wash cycle 2: 33°C, wash 15 s, soak 30 s, 2 cycles; wash cycle 3: 33°C, wash 20 s, soak 40 s, 2 cycles; slide drying: 30°C, 1 min 30 s.

scan_protocol: Microarrays were scanned immediately using a GenePix 4000B microarray scanner (Molecular Devices Ltd.). Data was captured using GenePix Pro version 5.0 software (Molecular Devices Ltd.).

data_processing: The working signal intensities were generated using the mean foreground intensity values minus the median background intensity values as outputted from the GenePix Pro 5.0 results file. Two methods of data pre-processing were used to flag unreliable data. If the signal intensity in one channel was less than 100 and if the signal intensity for the other channel is less than 200, the spot was flagged. If the signal intensity in one channel was less than 100 and the signal intensity was larger than 200 in the second channel, 100 was assigned to the intensity of the first channel. Median-based normalization corrects the data such that all arrays have the same median. The median value is less likely to be influenced by outlying values. A normalization factor was calculated by summing the intensities in both channels and adjusts both ratios to ensure a median of 1.0. Therefore, the median log expression ratio for all features on the array was adjusted to zero (corresponding to an expression ratio of 1.0).

organism: Bos taurus

source_name: Peripheral blood mononuclear cells (PBMC) sampled from 13 animals across a tuberculin stimulation time course

label_protocol: Each labelling reaction contained a total of 8 µg RNA per sample and 10 µg RNA from the CRR. Total RNA was used as the template in reverse transcription reactions (BD Atlas Powerscript fluorescent labelling system, BD Biosciences: www.bdbeurope.com) using oligo(dT) 15-18 as primer and incorporating amino-modified dUTPs. To provide a control for cDNA synthesis and labelling efficiency, hybridisation and slide orientation, 650 pg of synthetic lambda Q gene RNA containing an engineered poly A tail was spiked into each cDNA synthesis reaction. Test and CRR samples were differentially labelled using N-hydroxysuccinimide-(NHS) activated fluorescent Cy3 or Cy5 dyes (Amersham Biosciences/GE Healthcare: www.amershambiosciences.com). The dye couples to the cDNA by reacting with the amino functional groups on the incorporated amino-tagged dUTPs. Labelled cDNAs were purified to remove unincorporated dyes using a QIAquick purification kit and concentrated using Microcon® centrifugal filter devices according to the manufacturer’s instructions (Millipore Corp: www.millipore.com).

growth_protocol: A Trypan exclusion test was used to estimate cell numbers: 10 µl of the cell solution was added to 90 µl Trypan (100 ml trypan blue solution 0.4% - T8154, Sigma-Aldrich Ireland Ltd: www.sigmaaldrich.com) in a 96-well microtitre plate and left for 5 mins. Viable cells were counted by pipetting 10 µl of solution under the coverslip of a haemocytometer, using a light microscope. Cells from each animal were seeded at no less than 1E+07 for each of the two treatments and cultured in RPMI 1640 culture medium supplemented with 5% FBS, 0.1% mercaptoethanol and 0.1% gentamycin. PBMC were cultured in 75-ml culture flasks at 37 °C in a humidified atmosphere with 5% CO2. PBMC cultures from the eight animals were stimulated using 50 µg/ml bovine purified protein derivative (PPD-bovine) and unstimulated control cultures from the same animals were run in parallel. PBMC were harvested from all treatments at 0, 3 and 12 h post-stimulation and stored at -80°C in 1 ml of Trizol® reagent (Invitrogen Corp: www.invitrogen.com).

extract_protocol: Total RNA was extracted from PBMC using a combined TriReagent®, DNase treatment and Qiagen RNeasy® method (Qiagen Ltd: www.qiagen.com). Cells were removed from the -80°C freezer and thawed quickly on ice, 400 µl of chloroform was added and shaken for 10 s. After a 2 min room temperature incubation, tubes were centrifuged on maximum speed for one min to separate the phases. The upper aqueous phase was transferred to a new 1.5 ml tube and an equal volume of isopropanol was added. After shaking and incubating at room temperature for 20 mins, the samples were centrifuged on maximum speed at 4°C for 20 mins. The liquid was then removed and the RNA pellet washed with 1 ml 70% ethanol (stored at -20°C) by centrifugation at 4°C for 6 mins. The ethanol was removed by careful aspiration and the pellet was allowed to air dry for 10 mins after which it was resuspended in 100 µl of nuclease free water and incubated at 55°C to ensure complete resuspension. To remove any residual DNA, 5 µl DNase (1 U/µl) was added and incubated at 37°C for 15 mins. The extracted RNA was then ready for further purification using the Qiagen RNeasy® mini kit according to the manufacturer’s instructions and eluted twice, in 40 µl and 30 µl of nuclease free water, and stored at -80°C.

tag: Source

value: PBMC from eight M. bovis-infected cattle and five non-infected cattle. PBMC were stimulated with purified protein derivative (PPD) of Mycobacterium bovis (tuberculin) and sampled across a time course of T0 (no stimulation) T3 (3 hours post-stimulation) and T12 (12 hours post-stimulation). A total of 39 RNA samples were combined to form the common RNA reference (CRR) pool

growth_protocol: PBMC from each animal (control and infected) were seeded at 1E+07 per culture plate and cultured in RPMI 1640 culture medium supplemented with 5% FBS, 0.1% mercaptoethanol and 0.1% gentamycin. PBMC were cultured in 75-ml culture flasks at 37 °C in a humidified atmosphere with 5% CO2. Overnight culture was carried out to minimise noise in gene expression measurements potentially introduced by the mechanical disruption of cells associated with PBMC isolation.

treatment_protocol: PBMC cultures were stimulated using 50 µg/ml bovine purified protein derivative (PPD-bovine).

tag: PBMC were stimulated with purified protein derivative (PPD) of Mycobacterium bovis (tuberculin) and sampled 3 hours post-stimulation (time 'T3)


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T12_2

description: No additional information.

treatment_protocol: PBMC cultures from the eight animals were stimulated using 50 µg/ml bovine purified protein derivative (PPD-bovine) and unstimulated control cultures from the same animals were run in parallel.

tag: PBMC were stimulated with purified protein derivative (PPD) of Mycobacterium bovis (tuberculin) and sampled 12 hours post-stimulation (time 'T12)


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T3_6

description: No additional information.

tag: PBMC were stimulated with purified protein derivative (PPD) of Mycobacterium bovis (tuberculin) and sampled 3 hours post-stimulation (time 'T3')


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T12_4

description: No additional information.


title: GSE_Young_1

tag: Primary WI38 cells, Young, p53 inactivation by overexpression of GSE56


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T12_5

description: No additional information.


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T3_4

description: No additional information.


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T3_5

description: No additional information.


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T12_6

description: No additional information.


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T3_2

description: No additional information.


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T3_3

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T3_2

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T3_1

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T3_3

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T3_5

description: No additional information.


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T12_3

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T3_6

description: No additional information.


title: PBMC_CRR-vs-BTB-infected-tuberculin-stimulated_T12_1

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T3_4

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T12_6

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T12_2

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T12_3

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T12_1

description: No additional information.


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T12_4

description: No additional information.


title: uterosacral ligament_control_postmenopause_subject9

city: Honolulu

first: Shawna

middle: S

last: Brizzolara

state: HI

address: 1319 Punahou St #824

department: Obstetrics and Gynecology

institute: Shawna Brizzolara, MD

hyb_protocol: Ten micrograms of cRNA were  hybridized to the arrays at 55°C for 18 hours. Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence detection kit, 1700 Chemiluminescent Microarray Analyzer and 1700 Chemiluminescent Microarray Analyzer software v1.1 following the manufacturer's protocol. In brief, after hybridization the arrays were washed and scanned. The resulting images were auto-gridded, the signal was quantified, corrected for background noise and spot- and spatially-normalized. The data was exported and the control probes were removed.

scan_protocol: Microarrays were scanned with Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following the manufacturer's protocol.

data_processing: Images were auto-gridded and the chemiluminescent signals were quantified, background subtracted, and finally, spot- and spatially-normalized (quantile normalization) using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391).

label: Digoxigenin

label_protocol: Applied Biosystems (Foster City, CA) Human Genome Survey Micoarrays V2.0 were used to analyze differential gene expression profiles. Each of these arrays contains 32,878 probes interrogating 29,098 genes. Probe labelling:Digoxigenin-UTP-labeled cRNA was generated and linearly amplified from 5ug of RNA using Applied Biosystems Chemiluminescence RT-IVT v 1.0 protocol. The labeled cRNA was washed and the quality and quantity was assessed using the NanoDrop (NanoDrop, Wilmington, DE).

extract_protocol: Total RNA was extracted using Tri Reagent (Molecular Research Center, Inc., Cincinnati, OH), according to the manufacturer's protocol and consecutively purified using Qiagen's RNeasy Mini Kit with -on-column DNAse treatment (Valencia, CA). RNA yield was quantified by spectrophotometry (NanoDrop, Wilmington, DE) and the integrity was assessed by capillary-electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies, CA).

tag: sex

value: female, age:52, hysterectomy indication:fibroid uterus, menopausal status:postmenopause, mixed race:Hawaiian and Chinese


title: PBMC_CRR-vs-BTB-control-tuberculin-stimulated_T12_5

description: No additional information.


title: uterosacral ligament_control_postmenopause_subject16

value: female, age:64, hysterectomy indication:uterine bleeding, menopausal status:postmenopause, mixed race:Hawaiian and Chinese


title: round ligament_control_postmenopause_subject21

value: female, age:65, hysterectomy indication:ovarian mass, menopausal status:postmenopause, race:Caucasian


title: round ligament_control_premenopause_subject14

value: female, age:42, hysterectomy indication:cervical intraepithelial neoplasia, menopausal status:premenopause race:Caucasian


title: uterosacral ligament_control_postmenopause_subject21


title: uterosacral ligament_control_premenopause_subject22

value: female, age:24, hysterectomy indication:uterine bleeding menopausal status:premenopause mixed race:Hawaiian and others


title: round ligament_control_postmenopause_subject16


title: uterosacral ligament_control_premenopause_subject14


title: uterosacral ligament_control_premenopause_subject17

value: female, age:42, hysterectomy indication:bleeding and uterine fibroids, menopausal status:premenopause race:Chinese


title: round ligament_control_premenopause_subject22


title: uterosacral ligament_control_premenopause_subject2

value: female, age:48, hysterectomy indication:bleeding and fibroid uterus, menopausal status:premenopause, race:Korean


title: uterosacral ligament_control_premenopause_subject8

value: female, age:42, hysterectomy indication:uterine fibroids, menopausal status:premenopause, race:Chinese


title: uterosacral ligament_control_premenopause_subject6

value: female, age:49, hysterectomy indication:bleeding and uterine fibroids, menopausal status:premenopausal race:Filipino


title: round ligament_control_postmenopause_subject9


title: uterosacral ligament_POP_postmenopause_subject25

value: female, age:70, hysterectomy indication:uterine prolapse stage 3, menopausal status:postmenopause, race:Japanese


title: round ligament_control_premenopause_subject8


title: round ligament_control_premenopause_subject17


title: uterosacral ligament_POP_premenopausal_subject24

value: female, age:44, hysterectomy indication:uterine prolapse stage 3, menopausal status:premenopause race:Filipino


title: uterosacral ligament_POP_premenopausal_subject10

value: female, age:46, hysterectomy indication:uterine prolapse stage 3, menopausal status:premenopause, mixed race:Hawaiian and African American


title: round ligament_control_premenopause_subject2


title: round ligament_control_premenopause_subject6


title: uterosacral ligament_POP_premenopausal_subject12

value: female, age:45, hysterectomy indication:uterine prolapse stage 3, menopausal status:premenopause, mixed race:Hawaiian, Japanese and caucasian


title: uterosacral ligament_POP_premenopausal_subject1

value: female, age:45, uterine prolapse stage 4, premenopause, mixed race:Japanese, Hawaiian


title: round ligament_POP_postmenopause_subject25


title: uterosacral ligament_POP_premenopausal_subject7

value: female, age:28, hysterectomy indication:prolapse uterine stage 2, menopausal status:premenopause, mixed race:hispanic and caucasian


title: uterosacral ligament_POP_postmenopause_subject3

value: female, age:60, hysterectomy indication:uterine prolapse stage 2 menopausal status:postmenopause race:Filipino


title: uterosacral ligament_POP_postmenopause_subject5

value: female, age:67, hysterectomy indication:uterine prolapse stage 3, menopausal status:postmenopause, race:Caucasian


title: round ligament_POP_postmenopause_subject3


title: round ligament_POP_premenopause_subject24


title: round ligament_POP_premenopause_subject10


title: round ligament_POP_postmenopause_subject5


title: Chondrocytes stimulated with methotrexate treated RASF rep 2

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

country: Germany

institute: Charité

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with methotrexate

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 11, stimulated with supernatant from methotrexate treated RASF

label_protocol: 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

growth_protocol: Human chondrocytes obtained from lateral condyle of femur bones of 6 donors post mortem were amplified by cultivation in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, subsequently 3D cultured in alginate beads for 14 days in presence of 170µM L-ascorbic acid 2-phosphate and finally stimulated with conditioned medium of RASF, NDSF, or treated RASF

extract_protocol: Prior to RNA extraction, alginate beads were solubilized on ice in 55mM sodium citrate, 30mM EDTA and 150mM NaCl and cells were centrifuged at 800g for 5min (4°C). Total RNA isolation was proceeded according to the manufacturer’s protocol. Additionally, a proteinase K and DNase I digestion were performed.   Isolation of total RNA was done for the different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes  were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF

treatment_protocol: Human chondrocytes were isolated by enzymatic digestion (1 U collagenase P, 333 U collagenase II and 33 U hyaluronidase), passage 2 chondrocytes were encapsulated in alginate beads (20 Mio cells/ml in 1,5% (w/v) alginate) and stimulated with conditioned medium of NDSF, RASF or treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with methotrexate for 48h


title: round ligament_POP_premenopause_subject12


title: Embryo_sptntlMO_rep2

city: Berkeley

first: Aaron

last: Garnett

address: 555 LSA

institute: UC Berkeley

hyb_protocol: The microarrays were hybridized in 6X SSPE with 50% formamide at 37 degree C for 20h, washed in 0.75X TNT at 46 degree C for 1 h, followed by blocking in TNB at RT for 30 min. and then processed by using direct detection method of the biotin-containing transcripts by Streptavidinin-Alexa 647 conjugated in TNB buffer (1:500) at RT for 30 min. Stained chips were washed in 1X TNT wash buffer at room temperature for 60 min with changing fresh buffer every 15 min.

scan_protocol: Processed chips were scanned by using a Perkin-Elmer ScanArray XL5000, software version 3.1, at a scan resolution of 10 microns. Images were quantified by Perkin-Elmer QuantArray Software 3.0. The fixed circle quantification method was used and output was given as total intensities.

data_processing: The raw intensity for each probe was normalized to the median intensity for the probes on the array.

label: Biotin + Streptavidin-Alexa 647

organism: Danio rerio

source_name: 75% epiboly embryo, spt+ntl MO-injected

label_protocol:
The biotin-labeled cRNA target is prepared by a linear amplification method. Poly (A) RNA from 5 μg of total RNA is primed for reverse transcription by a DNA oligonucleotide containing a T7 RNA polymerase promoter 5′ to a d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template in an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT is performed in the presence of biotinylated nucleotides to label the target cRNA: Total RNA (5 μg) was incubated with T7 primer at 70 °C for 10 min before addition of Superscript reverse transcriptase reaction mix and further incubation at 37 °C for 1 h. The first-strand cDNA was added to polymerase mix and incubated in a TropiCooler incubator at 16 °C for 2 h.
Double-strand cDNA was precipitated in isopropanol at −80 °C for 20 min, centrifuged at 14k rpm for 20 min, and pellet resuspended in ddH2O after air-drying for 30 min. In vitro transcription was performed using the Ambion MEGAscript T7 kit. Biotinylated UTP, NTPs and enzyme reaction mix were added to dried cDNA and incubated at 37 °C overnight. Synthesized cRNA was purified using the Qiagen RNeasy kit. Concentration and quality of cRNA was measured by an Eppendorf Biophotometer. The target labeling by the KCC/TJU standard procedure results in a 50- to 200-fold linear amplification of the input poly(A) RNA.

extract_protocol: For each sample 20 embryos were dechorionated, vortexed in Trizol and phenol-chloroform extracted.  They were treated with Dnase and cleaned up using a Qiagen RNeasy kit

tag: Fish strain:ABC


title: Chondrocytes stimulated with azathioprine (imurek) treated RASF rep 1

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with azathioprine (imurek)

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from azathioprine (imurek) treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with azathioprine (imurek) for 48h


title: Chondrocytes stimulated with azathioprine (imurek) treated RASF rep 2

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from azathioprine (imurek) treated RASF


title: Chondrocytes stimulated with methylprednisolone (urbason) treated RASF rep 1

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with methylprednisolone (urbason)

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 6, stimulated with supernatant from methylprednisolone (urbason) treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with methylprednisolone (urbason) for 48h


title: Chondrocytes stimulated with sodium aurothiomalate (tauredon) treated RASF rep 1

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with sodium aurothiomalate (tauredon)

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from sodium aurothiomalate (tauredon) treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with sodium aurothiomalate (tauredon) for 48h


title: Embryo_sptMO_rep2

source_name: 75% epiboly embryo, spt MO-injected


title: Chondrocytes stimulated with methylprednisolone (urbason) treated RASF rep 2

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 7, stimulated with supernatant from methylprednisolone (urbason) treated RASF


title: Chondrocytes stimulated with prednisolone (solu-decortin) treated RASF rep 2

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with prednisolone (solu-decortin)

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 9, stimulated with supernatant from prednisolone (solu-decortin) treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with prednisolone (solu-decortin) for 48h


title: Embryo_sptntlMO_rep1


title: Embryo_sptMO_rep3


title: round ligament_POP_premenopause_subject1


title: Embryo_ntlMO_rep3

source_name: 75% epiboly embryo, ntl MO-injected


title: Chondrocytes stimulated with chloroquine phosphate (resochin) treated RASF rep 2

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with chloroquine phosphate (resochin)

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from chloroquine phosphate (resochin) treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with chloroquine phosphate (resochin) for 48h


title: Chondrocytes stimulated with prioxicam treated RASF rep 2

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with piroxicam

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from prioxicam treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with piroxicam for 48h


title: Chondrocytes stimulated with chloroquine phosphate (resochin) treated RASF rep 1

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from chloroquine phosphate (resochin) treated RASF


title: Chondrocytes stimulated with diclofenac treated RASF rep 2

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with diclofenac

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from diclofenac treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with diclofenac for 48h


title: Chondrocytes stimulated with methotrexate treated RASF rep 1

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 10, stimulated with supernatant from methotrexate treated RASF


title: Embryo_ntlMO_rep2


title: Chondrocytes stimulated with prednisolone (solu-decortin) treated RASF rep 1

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 8, stimulated with supernatant from prednisolone (solu-decortin) treated RASF


title: round ligament_POP_premenopause_subject7


title: Embryo_sptntlMO_rep3

hyb_protocol: The microarrays were hybridized in 6X SSPE with 50% formamide at 37 degree C for 20h, washed in 0.75X TNT at 46 degree C for 1 h, followed by blocking in TNB at RT for 30 min. and then processed by using direct detection method of the biotin-containing transcripts by Streptavidin-Alexa 647 conjugated in TNB buffer (1:500) at RT for 30 min. Stained chips were washed in 1X TNT wash buffer at room temperature for 60 min with changing fresh buffer every 15 min.


title: Embryo_sptMO_rep1


title: Chondrocytes stimulated with diclofenac treated RASF rep 1

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from diclofenac treated RASF


title: Chondrocytes stimulated with prioxicam treated RASF rep 1

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from prioxicam treated RASF


title: NDSF stimulated chondrocytes rep 2 GSM253286

description: Gene expression data of human chondrocytes stimulated with supernatant of NDSF

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, NDSF stimulated

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of NDSF cultured in the same medium


title: Embryo_uninj_rep3

source_name: 75% epiboly embryo, mock injected


title: Embryo_ntlMO_rep1


title: Patient 4

status: Public on Sep 19 2008

city: Stockholm

first: Alberto

last: Cagigi

address: Nobelsvag 16

country: Sweden

institute: Karolinska Institutet

description: Patient 4

hyb_protocol: GEArray Q Series membranes were pre-hybridized at 60oC overnight and thereafter hybridized with the cDNA probes

scan_protocol: Membranes were then washed, blocked and incubated with alkaline phosphatase-conjugated streptavidin and the labelled biotin was detected by chemoluminescence using GEArray Chemoluminescence Detection Kit (D-01) (SuperArray, Frederick, MD, USA)

data_processing: The luminescence intensities of hybridised cDNA probes were analyzed by GEArray Expression Analysis Suite software (SuperArray, Frederick, MD, USA). Local background was subtracted for each point and obtained values were adjusted to a common mean of 100.0 and minimal positive value was set to 10.0 percent of mean

label: biotin on cDNA

source_name: Peripheral B-cells

label_protocol: 0,5 mg of total RNA was reverse-transcribed using Ampolabelling (LPR) Kit (SuperArray, Frederick, MD, USA) with biotin-16-dUTP (Enzo Life Science, Famingdale, New York) and amplification of cDNA was performed during 30 cycles. The biotinylated cDNA probes were denatured and added to the hybridisation solution

extract_protocol: Purified B-cells from patients (n=4) and controls (n=4) were collected in RLT lysis buffer for total RNA extraction using RNeasy Mini Kit (Qiagen, Stockhom, Sweden). Approximately 10-20 mg of RNA was purified from each individual sample, and cDNA expression microarray analysis was performed using the GEArray Q series Human Chemokines and Receptors Gene Array (SuperArray, Frederick, MD, USA)

tag: HIV-1 infected


title: Patient 3

description: Patient 3


title: liver-LE-TCDD-19h rep 4

city: Toronto

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: liver, LE, TCDD, 19 hours

hyb_protocol: Manufacturer's protocol

scan_protocol: Manufacturer's protocol

data_processing: Array data were loaded into the R statistical environment (v2.3.1) using the affy package (v1.10.0) of the BioConductor open-source library (Gentleman et al., 2004).  The array data were pre-processed with the GCRMA algorithm (v2.4.1, (Irizarry et al., 2003)).

source_name: liver, LE, TCDD, 19 hours

label_protocol: Manufacturer's protocol

growth_protocol: Two dioxin-sensitive rat strains/lines, L-E and LnC (which express wildtype AHR), and two dioxin-resistant rat strains/lines, H/W and LnA, (that have a deletion in the AHR transactivation domain, (Pohjanvirta et al., 1998)) were from breeding colonies of the National Public Health Institute, Division of Environmental Health, Kuopio, Finland.  All animals were males 10-12 weeks old.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer's instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver was harvested between 8:30 and 11:00 from rats treated by gavage with a single 100 µg/kg dose of TCDD or with corn oil vehicle for 3 or 19 h.


title: Embryo_uninj_rep2


title: Control 4

description: Control 4

tag: Healthy control


title: Patient 1

description: Patient 1


title: Patient 2

description: Patient 2


title: NDSF stimulated chondrocytes rep 1 GSM253285

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 1, NDSF stimulated


title: liver-LE-TCDD-19h rep 2

description: liver, LE, TCDD, 19 hours


title: liver-LE-TCDD-19h rep 1

description: liver, LE, TCDD, 19 hours


title: Control 3

description: Control 3


title: Embryo_uninj_rep1


title: RASF stimulated chondrocytes rep 1 GSM253283

description: Gene expression data of human chondrocytes stimulated with supernatant of RASF

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 1, RASF stimulated

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium


title: Control 2

description: Control 2


title: liver-LE-cornoil-19h rep 4

description: liver, LE, COil, 19 hours

source_name: liver, LE, COil, 19 hours


title: liver-LE-cornoil-19h rep 1

description: liver, LE, COil, 19 hours


title: RASF stimulated chondrocytes rep 2 GSM253284

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, RASF stimulated


title: Passage 1 mesenchymal stem cells 15 days in culture

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

description: Bone marrow aspirate of about 2 ml from a healthy donor 19-49 years old was used to separate plastic adherent nucleated cells. After 14 days in culture, adherent cells were recovered from the monolayer by incubation with trypsin/EDTA and replated at 100 cells/cm2. The cells were then cultured for 15 days with changes of medium every 2–3 days. The culturing of cells was done in hMSC complete medium (alpha-minimal essential medium, 20% fetal calf serum (FCS), 100 units/ml penicillin, 100 ug/ml streptomycin, 2 mM glutamine). Total RNA was extracted from 1 million cells using High Pure Kit (Roche Diagnostics). 8 ug of total RNA was used to synthesize double-stranded DNA (Superscript Choice System; Invitrogen). The DNA was purified by phenol/chloroform extraction and concentrated by ethanol precipitation. In vitro transcription was performed to produce biotin-labeled cRNA using a BioArray HighYield RNA transcription labeling kit (Enzo Diagnostics). Biotinylated cRNA was cleaned with the RNeasy minikit (Qiagen) and quantified. 25 ug of biotinylated cRNA was fragmented to 50–200 nucleotides and hybridized for 16 h at 45 °C into HG-U133A array. After washing, the array was stained with streptavidin/phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories Inc.) followed by secondary staining with streptavidin/phycoerythrin. The array was scanned on a Hewlett-Packard GeneArray Scanner. The data was analyzed using Microarray Suite 5.0 (Affymetrix) and dChip 1.3+ programs. The arrays in the set were normalized against the baseline array with a median probe intensity level (Day5, [235]). Model based expression values were calculated in dChip using the signals form perfect-match and mis-match oligonucelotides. Negative values were assigned a value of 1.

label: Biotin

source_name: Passage 1 mesenchymal stem cells from bone marrow stroma cultured for 15 days

label_protocol: 8 ug of total RNA was used to synthesize double-stranded DNA(Superscript Choice System; Invitrogen). The DNA was purified by phenol/chloroform extraction and concentrated by ethanol precipitation. In vitro transcription was performed to produce biotin-labeled cRNA using a BioArray HighYield RNA transcription labeling kit (Enzo Diagnostics). Biotinylated cRNA was cleaned with the RNeasy minikit(Qiagen) and quantified.


title: liver-LE-cornoil-19h rep 3

description: liver, LE, COil, 19 hours


title: Carotid endarterectomy #165-06

city: Göteborg

first: Daniel

last: Hägg

address: Vita Stråket 15

department: Department of Molecular and Clinical Medicine

institute: Göteborg University

description: Gene expression profile

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: Carotid endarterectemy

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: Carotid endarterectemy


title: Carotid endarterectomy #150-05

description: Gene expression profile


title: B2KO; Isoproterenol-treated #4

city: stanford

first: Rani

last: Agrawal

address: 300 Pasteur Drive, Dept of Anesthesia

department: Anesthesia

institute: Stanford University

description: Gene expression data from mice heart

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430-2 Mouse Gene array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000.

data_processing: GC-RMA

source_name: Heart

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

extract_protocol: Twenty WT FVB, WT C57, and B2KO mice were given intraperitoneal injections of avertin (100μl/10g body weight) and sacrificed by cervical dislocation.  Half of the mice in each group had undergone fourteen day isoproterenol infusions.  RNA was extracted from the mouse hearts using Quiagen RNeasy® Midi kit.  Samples were homogenized in buffer containing guanidine isothiocyanate and beta mercaptoethanol.  Ethanol was then added to the lysate.  The sample was then applied to the RNeasy column.  RNA was eluted from the column using 80 ul of RNase-free water.

treatment_protocol: Mice of each genotype were randomly assigned to fourteen day infusions of isoproterenol (120 µg/g/day) or no treatment

tag: 10 weeks old


title: liver-LE-cornoil-19h rep 2

description: liver, LE, COil, 19 hours


title: liver-LE-TCDD-19h rep 3

description: liver, LE, TCDD, 19 hours


title: Carotid endarterectomy #149-05

description: Gene expression profile


title: Control 1

description: Control 1


title: Legionella_rnr_37_rep6

status: Public on Sep 18 2008

city: New York

first: Xavier

last: Charpentier

state: NY

address: 701 West 168th Street Rm 1216

department: Microbiology

institute: Columbia University

description: LELA559 is a rnr::Tn903dIIlacZ (lpg0092) mutant. These samples were grown at 37°C.

hyb_protocol: UV cross-linked slides were pre-hybridized in 5x SSC, 0.1% SDS, and 0.1mg/mL BSA for 45 min at 37°C. Slides were then rinsed in 0.1 x SSC and dried. Labeled cDNA was added to hybridization solution (40% formamide, 5x SSC, 0.1% SDS, 10mM Tris HCl pH 7.5, 1mg/mL human placental DNA) and hybridized to microarrays in hybridization chambers (GraceBio Inc, Bend, OR) at 37°C overnight with rotation. Slides were washed twice with 5x SSC 0.1% SDS, 0.1x SSC 0.1% SDS, rinsed shortly with 0.01x SSC and dried with high-pressure air using dust remover.

scan_protocol: Slides were scanned with 5-µm resolution using ScanArray Express Microarray Scanner (Perkin Elmer Inc, Wellesley, MA) and spot analysis was performed using Pro Scan Array Express software (Perkin Elmer Inc, Wellesley, MA).

data_processing: Raw signal intensities were corrected for dye labeling effects within and between all slides using normalize.lowess() R-function implemented in Bioconductor affy microarray analysis package.

label: Alexa 546

organism: Legionella pneumophila

source_name: Strain JR32

label_protocol: RNA samples (20μg) were reverse-transcribed with Superscript II Plus RNase H- reverse transcriptase (Invitrogen, Carlsbad, CA), random primers and mixture of dNTPs containing aminoallyl-modified dUTP (Sigma-Aldrich, St Louis, MO). RNA templates were removed by alkaline hydrolysis and aminoallyl-cDNA were purified using the QiaQuick PCR purification kit (QIAGEN Inc, Valencia, CA) and coupled with Alexa Fluor 546 or 647 dyes (Invitrogen, Carlsbad, CA).

growth_protocol: L. pneumophila strains (wild-type or rnr mutant) were grown on solid media ACES-buffered charcoal yeast extract (CYE) plates. One colony of the strain was patched on CYE plate and grown at 30 degrees celsius or 37 degrees celsius for 24 hours and then sujected to RNA extraction.

extract_protocol: Bacteria from the 24H patch on CYE plates were scrapped off the plate and total RNA were extracted with using the RNeasy kit (QIAGEN Inc, Valencia, CA)

treatment_protocol: No treatment applied before RNA extraction

tag: reference strain JR32 grown at 37 degrees celsius

label: Alexa 647

source_name: Strain LELA559 (rnr mutant)

tag: rnr mutant grown at 37 degrees celsius


title: Legionella_rnr_30_rep6

description: LELA559 is a rnr::Tn903dIIlacZ (lpg0092) mutant. These samples were grown at 30°C.

tag: reference strain JR32 grown at 30 degrees celsius

tag: rnr mutant grown at 30 degrees celsius


title: Legionella_rnr_37_rep5


title: Carotid endarterectomy #164-06

description: Gene expression profile


title: Carotid endarterectomy #148-05

description: Gene expression profile


title: Legionella_rnr_37_rep1


title: Legionella_rnr_37_rep4


title: Legionella_rnr_37_rep2


title: Legionella_rnr_37_rep3


title: Carotid endarterectomy #151-05

description: Gene expression profile


title: Legionella_rnr_30_rep5


title: Male brain repl 3 at stage 29

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description:
1. The male and female brain samples by genetic sexing were pooled and homogenized. Pooled samples ranged from 5 to 8 embryos. Specifically, 4g of total RNA from the pooled samples was used for labeling. Probe synthesis from total RNA samples, hybridization, detection, and scanning were performed according to standard protocols from Affymetrix
2. The quality of the array image was assessed as described in the Affymetrix GeneChip® expression analysis manual

hyb_protocol: the biotin-labeled IVT-RNA was fragmented. The fragmented cRNA was hybridized to the GeneChip® Chicken Genome Array at 45°C for 16 h according to the manufacturer’s instructions.

scan_protocol: After hybridization, the arrays were washed in a GeneChip® Fluidics Station 450 with a non-stringent wash buffer at 25°C, followed by a stringent wash buffer at 50°C. After washing, the arrays were stained with a streptavidin-phycoerythrin complex, and the intensities were determined with a GeneChip® scanner, which was controlled by the GeneChip® Operating Software (GCOS; Affymetrix).

data_processing: All arrays were processed using a robust multi-array average (Irizarry RA et al., 2003) using the R package Affy (Gautier L et al., 2004). Expression values were computed in detail from raw CEL files by applying the RMA model of the probe-specific correction of perfect-match probes. These corrected probe values were then subject to quantile normalization, and a median polish was applied to compute one expression measure from all probe values. The resulting RMA expression values were log2-transformed. The individual gene expression levels of male and female brains at stage 29 were compared using the unpaired Student’s t-test, and Benjamini-Hochberg correction for the false discovery rate (FDR) was used for all probe-level normalized data. For identification of differentially expressed genes, we selected genes with an FDR-adjusted p-value < 0.01 using an unpaired Student’s t-test and a fold-change of greater than 2 (absolute log fold change > 1).

organism: Gallus gallus

source_name: male brain repl #3

label_protocol: cDNA was synthesized using the One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA, USA). Single-stranded cDNA was synthesized using Superscript II reverse transcriptase and T7-oligo(dT) primers at 42°C for 1 h. Double-stranded (ds) cDNA was obtained using DNA ligase, DNA polymerase I, and RNase H at 16°C for 2 h, followed by T4 DNA polymerase at 16°C for 5 min. After cleanup with a Sample Cleanup Module (Affymetrix), ds-cDNA was used for in vitro transcription (IVT). cDNA was transcribed using the Affymetrix GeneChip® IVT Labeling Kit in the presence of biotin-labeled CTP and UTP

extract_protocol: samples of brains at stage 29 were homogenized and total RNA from both genetic male and female brains was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA quality was checked on an agarose gel and RNA quantity was determined by spectrophotometry at 260/280-m absorption ratios and then purified with an RNeasy kit (QIAGEN, Valencia, CA, USA).

tag: white Leghorn

tag: Gender

value: male

tag: Age

value: stage 29 (6-6.5 day incubation)

tag: Tissue

value: brain


title: Legionella_rnr_30_rep4


title: B2KO; Isoproterenol-treated #9

description: Gene expression data from mice heart


title: Passage 1 Mesenchymal stem cells 5 days in culture

description: Bone marrow aspirate of about 2 ml from a healthy donor 19-49 years old was used to separate plastic adherent nucleated cells. After 14 days in culture, adherent cells were recovered from the monolayer by incubation with trypsin/EDTA and replated at 100 cells/cm2. The cells were then cultured for 5 days with changes of medium every 2–3 days. The culturing of cells was done in hMSC complete medium (alpha-minimal essential medium, 20% fetal calf serum (FCS), 100 units/ml penicillin, 100 ug/ml streptomycin, 2 mM glutamine). Total RNA was extracted from 1 million cells using High Pure Kit (Roche Diagnostics). 8 ug of total RNA was used to synthesize double-stranded DNA (Superscript Choice System; Invitrogen). The DNA was purified by phenol/chloroform extraction and concentrated by ethanol precipitation. In vitro transcription was performed to produce biotin-labeled cRNA using a BioArray HighYield RNA transcription labeling kit (Enzo Diagnostics). Biotinylated cRNA was cleaned with the RNeasy minikit (Qiagen) and quantified. 25 ug of biotinylated cRNA was fragmented to 50–200 nucleotides and hybridized for 16 h at 45 °C into HG-U133A array. After washing, the array was stained with streptavidin/phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories Inc.) followed by secondary staining with streptavidin/phycoerythrin. The array was scanned on a Hewlett-Packard GeneArray Scanner. The data was analyzed using Microarray Suite 5.0 (Affymetrix) and dChip 1.3+ programs. The arrays in the set were normalized against the baseline array with a median probe intensity level (Day5, [235]). Model based expression values were calculated in dChip using the signals form perfect-match and mis-match oligonucelotides. Negative values were assigned a value of 1.

source_name: Passage 1 Mesenchymal stem cells from bone marrow stroma cultured for 5 days


title: Legionella_rnr_30_rep3


title: Passage 1 mesenchymal stem cells 10 days in culture

description: Bone marrow aspirate of about 2 ml from a healthy donor 19-49 years old was used to separate plastic adherent nucleated cells. After 14 days in culture, adherent cells were recovered from the monolayer by incubation with trypsin/EDTA and replated at 100 cells/cm2. The cells were then cultured for 10 days with changes of medium every 2–3 days. The culturing of cells was done in hMSC complete medium (alpha-minimal essential medium, 20% fetal calf serum (FCS), 100 units/ml penicillin, 100 ug/ml streptomycin, 2 mM glutamine). Total RNA was extracted from 1 million cells using High Pure Kit (Roche Diagnostics). 8 ug of total RNA was used to synthesize double-stranded DNA (Superscript Choice System; Invitrogen). The DNA was purified by phenol/chloroform extraction and concentrated by ethanol precipitation. In vitro transcription was performed to produce biotin-labeled cRNA using a BioArray HighYield RNA transcription labeling kit (Enzo Diagnostics). Biotinylated cRNA was cleaned with the RNeasy minikit (Qiagen) and quantified. 25 ug of biotinylated cRNA was fragmented to 50–200 nucleotides and hybridized for 16 h at 45 °C into HG-U133A array. After washing, the array was stained with streptavidin/phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories Inc.) followed by secondary staining with streptavidin/phycoerythrin. The array was scanned on a Hewlett-Packard GeneArray Scanner. The data was analyzed using Microarray Suite 5.0 (Affymetrix) and dChip 1.3+ programs. The arrays in the set were normalized against the baseline array with a median probe intensity level (Day5, [235]). Model based expression values were calculated in dChip using the signals form perfect-match and mis-match oligonucelotides. Negative values were assigned a value of 1.

source_name: Passage 1 mesenchymal stem cells from bone marrow stroma cultured for 10 days


title: Legionella_rnr_30_rep2


title: Male brain repl 1 at stage 29

source_name: male brain repl #1


title: Male brain repl 2 at stage 29

source_name: male brain repl #2


title: Legionella_proQ_rep3

description: LELA3825 is a proQ (lpg0133) mutant (proQ::Tn903dIIlacZ).

growth_protocol: L. pneumophila strains were grown on solid media ACES-buffered charcoal yeast extract (CYE) plates. One colony of the strain was patched on CYE plate and grown at 37 degrees celsius for 24 hours and then sujected to RNA extraction.

tag: reference strain JR32

source_name: Strain LELA3825 (proQ mutant)

tag: proQ mutant of the reference strain JR32


title: Legionella_rnr_30_rep1


title: Legionella_proQ_rep1


title: Legionella_proQ_rep2


title: Legionella_comR_rep3

description: KS79 is a markerless comR (lpg2717) mutant (de Felipe et al, PloS Pathogen, 2008).

source_name: Strain KS79 (comR mutant)

tag: comR mutant of the reference strain JR32


title: Legionella_comR_rep2


title: Female brain repl 2 at stage 29

source_name: female brain repl #2

value: female


title: Female brain repl 1 at stage 29

source_name: female brain repl #1


title: Yeast_myo1_replicate#6

city: San Juan

first: José

middle: R

last: Rodríguez-Medina

state: PR

department: Biochemistry

institute: University of Puerto Rico Medical Sciences Campus

description: The microarrays raw data generated with Imagene 3.0 were analyzed using Limma software (Bioconductor Package 1.7). The data was prepared for analysis by correcting for background intensity.  The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array.  After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated.  The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change (VALUE) after background correction and normalization.  An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed by Limma. Genes with a p-value ≤ 0.01 were established as a cutoff for differential expression. In addition, a false discovery rate (FDR) test was performed by Limma.

hyb_protocol: To each fluorescent cRNA sample, 4  microliters of  25X fragmentation buffer was added, then incubated at 60°C for 30 minutes.  After the incubation, 100 microliters of 2X hybridization buffer were added to the sample. Samples were placed into the array slides. The array slides were placed in the hybridization chambers and incubated at 60°C for 17 hours. Array slides were washed in Wash solution 1(6X SSPE, 0.005%N-Lauroylsarcosine), Wash solution 2 (0.06X SSPE, 0.005%N-Lauroylsarcosine) and finally acetonitrile as stabilization and drying solution.

scan_protocol: Arrays were scanned in versarray scanner (from Biorad) with a detector sensitiity of 800 and laser power of 85% with a resolution of 5 micrometers. The images were saved and pre-processed with the Imagene 3.0 software (Biodiscovery) to locate spots, adjust the appropriate grid, and obtain the Cy3 and Cy5 text files (microarray raw data).

organism: Saccharomyces cerevisiae

source_name: Cy3: MGD353(wild type)

label_protocol: Fluorescent cRNA synthesis was produced following the low input fluorescent linear amplification kit from Agilent technologies. As a summary, 1.0 microgram of total was mixed with 2.4 microliters of T7 promoter primer and nuclease free water. The reaction mix was incubated at the 65°C for 10 minutes and then placed the reactions on ice for 5 minutes. 8.5 microliters of cDNA master mix was added to each reaction and incubated at 40°C for two hours.  Then the reaction was incubated at 65°C for 15 minutes, to inactivate the reverse transcriptase reaction. Cyanine 3-CTP (10mM) was added to the reaction.   57.6 microliters of transcription master mix was added to the reaction and then incubated at 40°C, to produce the cRNA.  The cRNA produced was purified RNeasy mini spin column from Qiagen.

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the MGD353 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Hilden, Germany) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA) following manufacturer’s instructions.

tag: The sample of channel 1 was extracted from total-RNA of Saccharomyces cerevisiae cells. The strain used for this study is MGD353 (wild type striain). This strain was provided by Dr. Brian Rymond's laboratory from the University of Kentucky. Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base).

source_name: Cy5_YJR6(myo1 delta mutant)

label_protocol: Fluorescent cRNA synthesis was produced following the low input fluorescent linear amplification kit from Agilent technologies. As a summary, 1.0 microgram of total was mixed with 2.4 microliters of T7 promoter primer and nuclease free water. The reaction mix was incubated at the 65°C for 10 minutes and then placed the reactions on ice for 5 minutes. 8.5 microliters of cDNA master mix was added to each reaction and incubated at 40°C for two hours.  Then the reaction was incubated at 65°C for 15 minutes, to inactivate the reverse transcriptase reaction. Cyanine 5-CTP (10mM) was added to the reaction.   57.6 microliters of transcription master mix was added to the reaction and then incubated at 40°C, to produce the cRNA.  The cRNA produced was purified RNeasy mini spin column from Qiagen.

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the YJR6 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.

tag: For channel 2

value: YJR6 is a myo1 delta::HIS5 strain generated by homologous recombination in the parental haploid wild type strain, MGD-353-46D using a PCR based method. Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in histidine dropout media (CSM-HIS-) with continuous shaking at 200 rpm.


title: Female brain repl 3 at stage 29

source_name: female brain repl #3


title: Legionella_comR_rep1


title: Yeast_myo1_replicate#4

data_processing: The microarrays raw data generated with Imagene 3.0 were analyzed using Limma software (Bioconductor Package 1.7). The data was prepared for analysis by correcting for background intensity.  The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array.  After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated.  The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change (VALUE) after background correction and normalization.  An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed by Limma. Genes with a p-value ≤ 0.01 were established as a cutoff for differential expression. In addition, a false discovery rate (FDR) test was performed by Limma.

source_name: Cy3_MGD353(wild type)

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the MGD353-46D strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.


title: Yeast_myo1_replicate#5

source_name: Cy3_YJR6(myo1 delta mutant)

tag: For channel 1

source_name: Cy5_MGD353(wild type)

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the MGD353 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.

tag: The sample of channel 2 was extracted from total-RNA of Saccharomyces cerevisiae cells. The strain used for this study is MGD353 (wild type striain). This strain was provided by Dr. Brian Rymond's laboratory from the University of Kentucky. Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base).


title: Yeast_myo1_replicate#2

source_name: Cy3_YJR13 (myo1 delta mutant)

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the YJR13 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Hilden) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions

tag: The sample of channel 1 was extracted from total-RNA of Saccharomyces cerevisiae cells. YJR13 (myo1∆) strain was obtained as haploid segregant from a cross between YJR6 (myo1∆) and BY4741 (wild type,obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in histidine dropout media (CSM-HIS-,2% glucose, 1X Nitrogen base)) with continuous shaking at 200 rpm.

source_name: Cy5_YJR12(wild type)

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the YJR12 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Hilden) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.

tag: The sample of channel 2 was extracted from total-RNA of Saccharomyces cerevisiae cells. YJR12 (wild type)  strain was obtained as haploid segregants from a cross between YJR6(myo1) and BY4741 (wild type, obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) or histidine dropout media (CSM-HIS-) with continuous shaking at 200 rpm.


title: Yeast_myo1_replicate#1

scan_protocol: Arrays were scanned in VersArray scanner (from Biorad) with a detector sensitiity of 800 and laser power of 85% with a resolution of 5 micrometers. The images were saved and pre-processed with the Imagene 3.0 software (Biodiscovery) to locate spots, adjust the appropriate grid, and obtain the Cy3 and Cy5 text files (microarray raw data).

source_name: Cy3_YJR12 (wild type)

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the YJR12 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Hilden, Germany) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions

tag: The sample of channel 1 was extracted from total-RNA of Saccharomyces cerevisiae cells. YJR12 (wild type)  strain was obtained as haploid segregant from a cross between YJR6(myo1) and BY4741 (wild type, obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) with continuous shaking at 200 rpm.

source_name: Cy5_YJR13(myo1 delta mutant)

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the YJR13 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions

tag: The sample of channel 2 was extracted from total-RNA of Saccharomyces cerevisiae cells. YJR13 (myo1∆) strain was obtained as haploid segregant from a cross between YJR6 (myo1∆) and BY4741 (wild type,obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in histidine dropout media (CSM-HIS-,2% glucose, 1X Nitrogen base)) with continuous shaking at 200 rpm.


title: Chondrocytes stimulated with sodium aurothiomalate (tauredon) treated RASF rep 2

source_name: Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from sodium aurothiomalate (tauredon) treated RASF

tag: Human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium and treated with sodium aurothiomalate (tauredon) for 48h


title: Yeast_myo1_replicate#3

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the YJR12 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Hilden, Germany) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.

tag: The sample of channel 1 was extracted from total-RNA of Saccharomyces cerevisiae cells. YJR12 (wild type)  strain was obtained as haploid segregants from a cross between YJR6(myo1) and BY4741 (wild type, obtained from ATTC). Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) with continuous shaking at 200 rpm.

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from triplicate biological replicate cultures of the YJR13 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen) following manufacturer’s instructions.  RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies).  The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.


title: Zebrafish_mutant_sk8_24hpf, biological rep2

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Gene expression data from mutant embryos at 24 hours post fertilization

hyb_protocol: According to manufacturer's (Affymetrix) recommendations

data_processing: Gene intensity values for the Affymetrix Zebrafish Genome Array CEL files were obtained using the GC-RMA package from Bioconductor.

source_name: Zebrafish embryo harvested at 24hpf

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

treatment_protocol: Equal number of embryos (WT siblings vs. fogsk8 mutants) at 24 hpf was dechorionated manually or by Pronase K treatment and Trizol (Invitrogen) used to extract total RNA.

tag: Zebrafish mutant whole-embryo RNA


title: Zebrafish_mutant_sk8_24hpf, biological rep3

scan_protocol: According to manufacturer's (Affymetrix) recommendations


title: Zebrafish_mutant_sk8_24hpf, biological rep1

label_protocol: According to manufacturer's (Affymetrix) recommendations


title: TORRES_EHEC_WT_8624_OD0.5_DMEM

city: Baltimore

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description:
All protocols were done according to manufacturers specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data included in file has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli

source_name: Escherichia coli 8624 (wt), growth in DMEM to OD600=0.5

growth_protocol: Cells were grown from an overnight culture of the 8624 strain and diluted 1:100 into fresh DMEM media (Gibco) and allowed to grow to OD600=0.5

tag: EHEC 8624 is an O157:H7 strain


title: Zebrafish_wt_24hpf, biological rep2

description: Gene expression data from wild-type embryos at 24 hours post fertilization

tag: Zebrafish wild-type whole-embryo RNA


title: Zebrafish_wt_24hpf, biological rep3


title: TORRES_EHEC_RCV02_OD0.5_DMEM

hyb_protocol: All protocols were done according to manufacturers specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: Escherichia coli RCV02 mutant, groth in DMEM to OD600=0.5

growth_protocol: Cells were grown from an overnight culture of the RCV02 strain and diluted 1:100 into fresh DMEM media (Gibco) and allowed to grow to OD600=0.5

tag: RCV02 mutant is cadA deficient and contains Chloramphenicol and Streptomycin resistance markers


title: Zebrafish_wt_24hpf, biological rep1