title: Csac grown on glucose vs xylose

status: Public on Apr 15 2008

city: Raleigh

first: Amy

last: VanFossen

address: 840 Main Campus Dr.  Rm3305

department: Chemical and Biomolecular Engineering

institute: NC State Unversity

description: Scatterplots were used to verify overall quality of the data making sure both channels are equal.

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer:  27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC

scan_protocol: Images were aquired with a scanarray 5000 (PE) with 2 lasers. Channels were balanced using the line scan feature and by balancing the overall signals without the use of external standards

data_processing: Signals for each channel were obtained using ScanArray express and were background substrated using the median local intensity around the spot.  Once all the slides were  quantitated, data from the loop was analyzed with JMP Genomics 3.0 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

label: Cy™3 dye (GE Healthcare)

organism: Caldicellulosiruptor saccharolyticus

label_protocol: Producing cDNA: In a sterile PCR tube add 20 ug RNA with 6 ug random primers. Then add nuclease free water so the volume is 10 uL. Incubate at 70 degree C for 10 min. Place tube on ice for 1 min. Add 8 uL of RT Master Mix (recipe below) to each tube and swirl to mix.  Quick spin before incubation. RT Master Mix: 4uL 5X strand buffer, 1uL 0.1M DTT, 1uL dNTP mix (see below), 2uL superscript III  Invitrogen. dNTP mix:  3uL dATP (100mM), 3uL dGTP (100mM), 3uL dCTP(100mM), 1.8uL dTTP (100mM), 2.4uL aa-dUTP(50mM) Ambion, 6.8uL nuclease free water. Incubate at 46 degree C for at least 3 hours. Hydrolyze RNA by adding 10uL 1N NaOH to each tube. To stop reaction add 10 uL 0.5M EDTA to each tube. Mix and incubate at 65 degree C for 15 min. Add 10uL 1N HCl to each tube neutralize reaction mix. Transfer samples into labeled tubes of appropriate sizes. Add five volumes PB Buffer (Qiagen) to each tube and mix well. Add 300 ul of RT product to a labeled Qiagen PCR cleanup column. Spin at 1,000 rpm for 15 sec., empty collection tube, and repeat until all of the solution has passed through the column. Complete wash One, add 750 ul of phosphate wash buffer (recipe below) to column and spin at 13,000 rpm for 1 min., empty tube. Complete wash Two, add 750 ul of phosphate wash buffer to column and spin at 13,000 rpm for 1 min., empty tube. Phosphate wash buffer: 0.1mL 1M KPO4( pH 8.5), 3.05mL autoclaved dH2O and 16.85mL 95% EtOH. Spin an additional 1 min. with the same collection tube and discard the flow through. Transfer to new 1.5 mL tube, add 60uL phosphate elution buffer to the membrane and incubate at room temp. for 1 min.  Spin at 13,000 rpm. Phosphate elution buffer: 4mM KPO4. Repeat phosphate elution into same tube using 60uL. Fluorescent Labeling: Dry all RT samples completely in speed vac. Resuspend each dried sample cDNA in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0.  Mix up and down with pipette for good mixing. Dissolve and mix thoroughlythe Cy™  dye to be used with 20uL of DMSO. Tpically Cye dyes contain four applications in each vial. Mix 4.5 uL of dye with prepared cDNA sample. Incubate in the dark for 2 hour @ R.T. Mix RT-PCR products with 35uL 100mM NaOAc PH 5.2 and mix by vortexing. Mix with 250uL Qiagen Buffer PB and filter through spin columns (13,000 rpm). Wash spin column  with 750 uL of Buffer PE (Qiagen). Spin an additional 1 min. with the same collection tube and discard the flow through. Elute labeled cDNA 2 times with 30 uL of EB Buffer (Qiagen). Combine different labeled probes Speed vacuum sample until dry (not too dry, i.e. don’t leave in speed vacuum for over 1 hour). Combine different labeled probes and speed vacuum sample until dry. Resuspend samples in 29uL sterilized dH2O

growth_protocol: C. saccharolyticus was subcultured (overnight) 3 times on the substrate of interest in modified DSMZ 640 medium before inoculating a pH-controlled (pH = 7) 1-liter fermentor containing 4 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (~OD660 = 0.3-0.4)

extract_protocol: RNA Isolation Protocol: Pump 50ml of cells into precooled Greiner tubes and cool down on ice. Spin down 20 min at 4600 rpm at 4 ºC. Store pellets at -80 ºC (at least overnight). Resuspend in 1 ml Trizol and incubate 5 min at room temperature. Tranfer to a new eppindoff tube and add 0.2 ml chloroform. Shake and incubate for 5 min at room temperature. Spin down for 15 min at 10.000 rpm at 4 ºC. Transfer aqueous phase to new tube. Add an equal amount of 70% EtOH. Transfer the sample  to an RNeasy spin column. Close lid and centrifuge for 15 sec at 10.000 RPM. After centrifugation, carefully remove the spin column form the collection tube so that the column does not contact the flow-through. Pipet the DNase I incubation mix (10 ml DNase I stock and 70 ml RDD buffer) directly onto the RNeasy membrane and incubate at room temperature for 15 min. Pipet 350 ml RW1 into the RNeasy column, incubate 5 min. and centrifuge 15s at 10.000 RPM. Wash with 700 ml RW1 and throw away the collection tube. Take a collection new tube and wash column twice with 500 ml RPE. Centrifuge the column 1 min at 10.000 RPM. Place the column onto a new tube and elute twice with 30 ml RNase free water, incubate for 5 min at room temperature. Store at -80°C.

tag: whole cells

label: Cy™5 dye (GE Healthcare)

label_protocol: same as channel 1

growth_protocol: same as channel 1

extract_protocol: same as channel 1


title: Csac grown on xylose vs mix

type: RNA

state: NC

country: USA

molecule: total RNA


title: Csac grown on mix vs rhamnose


title: Csac grown on rhamnose vs glucose


title: H3 acetylation in 6 hours IFNg-untreated human Hela cells-rep2 of 3

type: genomic

city: Toronto

first: Zhaodong

last: Xu

state: Ontario

address: Mc6-424, 399 Bathurst Street

department: Genetics & Development Division

country: Canada

institute: TWRI, UHN

description: Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucletide probes at 30bp intervals tiling over non-repetitive 122kb CIITA locus(HG17)

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html

data_processing: log_2(Signal for Cy5 / Signal for Cy3)

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells without IFNg treated for 6 hours

label_protocol:
For NimbleGen arrays, ChIP DNA prepared from LM-PCR was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers or Cy3 (ChIP DNA isolated from different antibody immunoprecipitated cells) per manufacturer's protocol.
(http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLa cells were human IFNg-induced for 6 hrs, cross-linked with 1% formaldehyde at room temperature for 10 min, washed twice with ice-cold PBS, collected in 1 ml of PBS (3 x 107 cells per tube) and centrifuged in a bench-top microfuge for 5 min at 5000 r.p.m. Cells were resuspended in 1ml lysis buffer (50mM Tris-Cl  pH 8.1, 10mM EDTA, 1% SDS) plus protease inhibitors, incubated on ice for 10 min and sonicated to an average size of 500 bp. Immunoprecipitation (IP) was performed overnight at 4°C with no antibody, anti-STAT1, anti-IRF1, anti-H3ac or anti-H4ac antibody. A aliquot of blocked Staph A cells (Calbiochem, 507862) were added per IP and incubated at RT for 15 min. Precipitates were washed sequentially with 1X dialysis buffer (2 mM EDTA, 50 mM Tris-Cl pH 8.0, 0.2% Sarkosyl) twice, IP wash buffer (100 mM Tris-Cl pH 9.0, 500 mM LiCl, 1% NP40, 1% deoxycholic acid) four times. Samples were extracted with IP elution buffer (50 mM NaHCO3 and 1% SDS), heated at 65°C overnight to reverse cross-links, and DNA fragments purified with QIAEX II gel extraction Kit. LM-PCR was performed using the annealed linker primers oJW102 (5'-GCGGTGACCCGGGAGATCTGAATTC-3') and oJW103 (5'-GAATTCAGATC-3'). Chromatin DNA was blunted using T4 DNA polymerase at 37oC for 45~60 min, and purified using Qiaquick PCR purification kit.  Blunted chromatin DNA was ligated to the linker at 16oC over night and purified. The sample was amplified with the following conditions: one cycle at 55oC for 2 min, 72oC for 5 min and 95oC for 2 min; followed by 20 cycles at 95oC for 30 seconds, 55oC for 30 seconds and 72oC for 1 min and one cycle at 72oC for 4 min.  DNA was finally purified using Qiaquick.

tag: HeLa cells

source_name: Input DNA from HeLa cells without IFNg treatment for 6 hours


title: Olfactory bulb; Large Wite; Female (OLFB_LW_F)

status: Public on Apr 16 2008

city: Bellaterra

first: Miguel

last: Perez-Enciso

address: Veterinary School

department: Animal Science

country: Spain

institute: Universitat Autonoma Barcelona

description: Olfactory bulb; Large Wite; Female

hyb_protocol: The hybridization was done according to Affymetrix standard protocols.

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray expression data were generated with GeneChip Operating Software (GCOS)

label: biotin

organism: Sus scrofa

source_name: Olfactory bulb; Large Wite; Female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Pigs with one month of age were housed simultaneously, fed the same diets during the fattening period, that lasted two months.

extract_protocol: Total RNA was extracted from 100 mg tissue using the RiboPure™ kit (Ambion, Austin, USA) according to the manufacturer’s protocol.

treatment_protocol: At necropsy, samples of 16 tissues were collected, snap frozen in liquid nitrogen and stored at -80 ºC, until de RNA extraction.

tag: weight

tag: Age

value: 87 days


title: STAT1 antibody in 6 hours IFNg-reated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using STAT1 antibody, HeLa cells with IFNg treatment for 6 hours

source_name: Input DNA from HeLa cells with IFNg treatment for 6 hours


title: ASK cells, ISAV isolate 2, day 1 post-infection

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: We have investigated intracellular responses during cytopathic ISAV infection in the macrophage-like Atlantic salmon kidney (ASK) cell line by microarray analysis (1.8K SFA2.0 immunochip) and a functional assay for glutathione.

scan_protocol: Scanning was performed with GSI Lumonics ScanArray 4000 (Packard Biosciences/PerkinElmer) and images were processed with GenePix 6.0 (Axon Instruments).

data_processing: Low-quality spots marked by GenePix were excluded from the analyses. After subtraction of background and normalization with Lowess, the differential expression was assessed by difference of the mean log-ER (Expression Ratio) from zero (six spot replicates of each gene, Student’s t-test).

label: Cy3 dUTP

organism: Salmo salar

source_name: Control cells

label_protocol: Control and test samples (10 µg RNA in each) were labeled with respectively Cy3-dUTP and Cy5-dUTP (Amersham Biosciences, UK) using the SuperScript™ Indirect cDNA Labeling System (Invitrogen). The cDNA synthesis was performed at 46 °C for 3 h in a 20 µl reaction volume, followed by RNA degradation with 0.2 M NaOH at 37 °C for 15 min and alkaline neutralization with 0.6 M hepes buffer. Labeled cDNA was purified with Microcon YM-30 (Millipore, MA, US). The slides were pretreated with 1 % BSA fraction V, 5 × SSC, 0.1 % SDS (30 min at 50 °C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight at 60 °C in a cocktail containing 1.3 × Denhardt’s, 3 × SSC, 0.3 % SDS, 0.67 µg/µl polyadenylate and 1.4 µg/µl yeast tRNA. After hybridization slides were washed at room temperature in 0.5 SSC and 0.1 % SDS (15 min), 0.5 SSC and 0.01 % SDS (15 min), and twice in 0.06 SSC (3 min each).

growth_protocol: Atlantic salmon kidney (ASK) cells were kindly provided by B. Krossøy (Department of Fisheries and Marine Biology, University of Bergen, Norway). Passages 40-70 were routinely split and cultured in L-15 medium (Cambrex Bio Sciences, Verviers, Belgium) supplemented with 50 μg ml-1 gentamicin, 4 mM L-glutamine, 40 μM β-mercaptoethanol and 10 % fetal calf serum. Cells were mock-infected and incubated at 15 °C in 75 cm2 culture flasks, and harvested at 1, 3, and 5 days post-infection for immediate RNA isolation.

extract_protocol: Total RNA was extracted and purified using combined Trizol/PureLink micro-midi kit (Invitrogen, CA, USA), quantified by Nanodrop (Thermo Fisher Scientific, USA) and checked by gel-electrophoresis. Samples for qPCR were DNAse-treated using Turbo DNA-freeTM (Ambion, TX, USA) according to manufacturer’s instructions. cDNA was synthesized from 1 μg total RNA using random hexamer primers and TaqMan® Reverse Transcription reagents (Applied Biosystems, CA, USA) according to manufacturer’s protocol.

tag: ASK cells, mock infected, day 1

label: Cy5 dUTP

source_name: Infected cells

treatment_protocol: Atlantic salmon kidney (ASK) cells were kindly provided by B. Krossøy (Department of Fisheries and Marine Biology, University of Bergen, Norway). Passages 40-70 were routinely split and cultured in L-15 medium (Cambrex Bio Sciences, Verviers, Belgium) supplemented with 50 μg ml-1 gentamicin, 4 mM L-glutamine, 40 μM β-mercaptoethanol and 10 % fetal calf serum. Cells were infected at MOI = 1 with ISAV isolates I2 (Mjaaland et al., 2005) and I4 (Glesvaer 2/90 strain). Infection was performed at 15 °C in 75 cm2 culture flasks as described (Jorgensen et al., 2006b), and cells were harvested at 1, 3, and 5 days post-infection for immediate RNA isolation

tag: ASK cells, ISAV isolate 2 infected, day 1


title: H4 acetylation in 6 hours IFNg-treated human Hela cells-rep1 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H4 antibody, HeLa cells with IFNg treated for 6 hours


title: H3 acetylation in 6 hours IFNg-untreated human Hela cells-rep1 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells with no IFNg treatment  for 6 hours


title: STAT1 antibody in 6 hours IFNg-treated human Hela cells-rep2 of 3


title: Olfactory bulb; Large Wite; Male (OLFB_LW_M)

description: Olfactory bulb; Large Wite; Male

source_name: Olfactory bulb; Large Wite; Male


title: IRF1 antibody in 6 hours IFNg-untreated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using IRF1 antibody, HeLa cells without IFNg treatment for 6 hours


title: normal 1050

city: Koto-ku

first: Yuichi

last: Ishikawa

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: Cancer Insitute

description: normal lung 1050

source_name: primary normal lung tissue 1050

source_name: lung reference


title: H3 acetylation in 6 hours IFNg-treated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using H3 acetylation antibody, HeLa cells with IFNg treatment for 6 hours


title: STAT1 antibody in 6 hours IFNg-treated human Hela cells-rep1 of 3


title: normal 1090

description: normal lung 1074

source_name: primary normal lung tissue 1090


title: adenocarcinoma 3806

description: Primary adenocarcinoma

source_name: adenocarcinoma 3806

source_name: lung reference mix


title: WUViro3P6-112; control

city: St. Louis

first: David

last: Wang

state: MO

address: 660 South Euclid Avenue

department: Molecular Microbiology

institute: Washington University School of Medicine

description: RNA extracted from whale liver

hyb_protocol: Samples were hybridized in a 40 ul volume containing 3X SSC (1X SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 25 mM HEPES, pH 7.0, 0.25% SDS, 10 ul of probe-70 labeled with Cy5 (spot marker) and 22 ul of sample labeled with Cy3.  Hybridization was carried out in a hybridzation chamber humidified with 20, 10 ul drops of 3X SSC.  The chamber was sealed and submerged in a 65 degree water bath for 12-16 hr.

scan_protocol: The Virochip was scanned with an Axon 4000B scanner (Axon Instruments) and GenePix software, version 3.0 (NCBI GEO, series GSE4191).

data_processing: Median feature intensity minus median background intensity

organism: Delphinapterus leucas

source_name: RNA extracted from whale liver

label_protocol: 200 ng of sample was reverse transcribed using primer A (GTTTCCCAGTCACGATA(N)8).  The sample was mixed with primer A and water and denatured at 65 C for 4 min and then allowed to cool to room temp for 4 min.  RT solution was added containing 1X RT Buffer, 500 uM dNTP mix, 10 mM DTT and 100 U RT (Stratascript) and incubated at 42 C for 30 min.  The samples were then denatured as above, 50 U of RT (Stratascript) was added and the samples were incubated at 42 C for an additional 30 min.  Samples were heated to 94 C 2 min and cooled to 10 C.  After the temperature reached 10 C, the samples were spun down and 10  L Sequenase mix (0.3X Sequenase Buffer and 3.9 U Sequenase) was added.  Samples were subjected to the following: ramped from 10 C to 37 C over 8 min, held at 37 C for 8 min, heated to 94 C for 2 min and cooled to 10 C. After the temperature reached 10 C, the samples were spun down and 1.2  L Sequenase mix (0.9 ul Dilute Sequenase Buffer and 3.9 U Sequenase) was added.  Samples were subjected to the following: ramped from 10 C to 37 C over 8 min, held at 37 C for 8 min, ramped to 94 C for 8 min and cooled to room temp) = Rd A sample.  6  l of Rd A sample was added to 94 ul containing: 1X PCR Buffer, 2 mM MgCl2, 250 uM dNTP mix, 100 pmol Primer B (GTTTCCCAGTCACGATA) and 2X Accuprime Taq (Invitrogen).  PCR was performed with the following conditions: an initial hold of 2 min at 94 C, followed by 40 cycles of 94 C for 30 sec, 40 C for 30 sec, 50 C for 30 sec and 72 C for 60 sec = Rd B sample.  10  l of Rd B sample was added to 90 ul containing: 1X PCR Buffer, 2 mM MgCl2, 250 uM aa-dNTP (contains 3:2 ratio of aa-dUTP; dTTP), 100 pmol Primer B (GTTTCCCAGTCACGATA) and 2.5U Taq (Invitrogen).  PCR was performed with the following conditions: 20 cycles of 94 C for 30 sec, 40 C for 30 sec, 50 C for 30 sec and 72 C for 60 sec = Rd C sample.  Rd C samples were cleaned via Zymo columns (Zymo research).

extract_protocol: 30 mg of tissue was homogenized with a Magnalyser homogenizer (Roche) on dry ice. Total RNA was extracted from the whale liver specimens treated with RNA-Later-ICE (Ambion) using RNEasy (Qiagen).

tag: control whale liver


title: H3 acetylation in 6 hours IFNg-treated human Hela cells-rep1 of 3

description: nimbelgen

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells with IFNg treated for 6 hours

source_name: Input DNA from HeLa cells with IFNg treated for 6 hours


title: H4 acetylation in 6 hours IFNg-untreated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H4 antibody, HeLa cells without IFNg treatment for 6 hours

source_name: Input DNA from HeLa cells without IFNg treatment for 6 hours


title: normal 1037

description: normal lung 1037

source_name: primary normal lung tissue 1037


title: STAT1 antibody in 6 hours IFNg-untreated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using STAT1 antibody, HeLa cells without IFNg treatment for 6 hours


title: WUViro3P6-111; control

description: RNA extracted from whale liver


title: STAT1 antibody in 6 hours IFNg-untreated human Hela cells-rep2 of 3


title: WUViro3P6-113; SWCoV1

description: RNA extracted from whale liver

tag: SWCoV1 in whale liver


title: IRF1 antibody in 6 hours IFNg-treated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using IRF1 antibody, HeLa cells with IFNg treatment for 6 hours

source_name: Input DNA from HeLa cells with IFNg treatment for 6 hours


title: HCE-T cell line relative to normal duploid cell

city: Kyoto

first: Satoshi

last: Kawasaki

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Ophthalmology

institute: Kyoto Prefectural University of Medicine

description: The labeled genomic DNAs were pooled and masked against their repetitive sequences by Cot-1 DNA before hybridization.

hyb_protocol: The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.

data_processing: Data were extracted using Agilent's Feature Extraction software, version 9.1 (P/N G2565BA), Cy3 corresponding to the Processed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Normalized log2 ratio (Cy3/Cy5) was calculated using CGH-v4_95_Feb07 protocol of FE software.

source_name: Genomic DNA from homo sapiens corneal epithelial cell line labeled with Cy5 (red)

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating cy5 labeled dUTP.

growth_protocol: HCE-T cells were maintained at 37 degrees in DMEM/F12 medium supplemented with 10% FBS, 10 ng/ml EGF, 5 ƒÊmg/ml insulin, 0.1 ƒÊg/ml cholera toxin, and penicillin/streptomycin in an incubator supplied with 95% air and 5% CO2.

extract_protocol: DNA was extracted using the Qiagen DNAeasy blood and tissue kit according to the manufacturer's instructions

tag: Human corneal epithelial cell line immortalized by SV40 large T antigen

source_name: Normal human duploid genomic DNA

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating cy3 labeled dUTP.

growth_protocol: Purchased from Promega

extract_protocol: Purchased from Promega

tag: Normal human genomic DNA from female


title: STAT1 antibody in 6 hours IFNg-untreated human Hela cells-rep1 of 3


title: IRF1 antibody in 6 hours IFNg-treated human Hela cells-rep2 of 3


title: IRF1 antibody in 6 hours IFNg-treated human Hela cells-rep1 of 3


title: IRF1 antibody in 6 hours IFNg-untreated human Hela cells-rep1 of 3

source_name: Chromatin immunoprecipiated DNA using IRF1 antibody, HeLa cells without IFNg treatment for 6 hours


title: H4 acetylation in 6 hours IFNg-treated human Hela cells-rep2 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H4 antibody, HeLa cells with IFNg treatment for 6 hours


title: H4 acetylation in 6 hours IFNg-untreated human Hela cells-rep2 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H4 antibody, HeLa cells without IFNg treated for 6 hours


title: normal 1103

description: normal lung 1074

source_name: primary normal lung tissue 1103

source_name: lung reference


title: IRF1 antibody in 6 hours IFNg-untreated human Hela cells-rep2 of 3


title: H4 acetylation in 6 hours IFNg-treated human Hela cells-rep3 of 3


title: The gene expression profiles in response to fungal infection in hemocytes

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei Univ 134 Sinchon-dong Seodaemun-gu

country: South Korea

institute: Yonsei University

description: Hemocyte, white eye background wild type fly, B.bassiana infection.

hyb_protocol: 50ug of sample was hybridized to the twin array cDNA 6k chip (Digital-Genomics, Seoul, Korea) according to manufacturer.

scan_protocol: Microarray was scanned with a GenePix 4000B scanner (Axon Instruments, San Diego, CA, USA).

data_processing: The scanned image were analyzed using GenePix v3.0 software to obtain gene expression ratio. Raw data was normalized by locally weighted scatter-plot smoother (LOWESS) normalization method.

organism: Drosophila melanogaster

source_name: fungal infection

label_protocol:
To 50ug of total RNA, add necessary control RNA mixture, Mix and incubate at 70 Celcius degree for 10 min and add primer, RTase, aminoallyl-dNTP mixture to make cDNA. After clean-up cDNA, add NHS-ester Cy5 dye (prepared in DMSO). Keep them sequestered from light as much as possible. Incubate 1hr in the dark at the room temperature.
Clean up the coupling reaction and calculate the efficiency, and dry.

extract_protocol: Total RNA (1.0-1.3ug) was isolated with TRIzol (Invitrogen) from the dissected hemocytes (from 200-300 third instar larvae), and amplified with the RiboAmp RNA amplification kit (ARCTURUS KIT0201).

tag: Strain

value: W1118 (wild type control, GenExel, Daejon, Korea).

tag: Stage

value: Third instar larvae

tag: Tissue

value: Hemocyte

tag: Pathogen

source_name: Control (non-infected hemocytes)

label_protocol:
To 50ug of total RNA, add necessary control RNA mixture, Mix and incubate at 70 Celcius degree for 10 min and add primer, RTase, aminoallyl-dNTP mixture to make cDNA. After clean-up cDNA, add NHS-ester Cy3 dye (prepared in DMSO). Keep them sequestered from light as much as possible. Incubate 1hr in the dark at the room temperature.
Clean up the coupling reaction and calculate the efficiency, and dry.

value: Not infected.


title: H4 acetylation in 6 hours IFNg-untreated human Hela cells-rep1 of 3


title: H3 acetylation in 6 hours IFNg-treated human Hela cells-rep2 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells with IFNg treated for 6 hours

tag: HeLa Cells


title: E.coli/Hsp60-wt/wt(-/+)

status: Public on Apr 14 2008

city: Århus

first: Peter

last: Bross

address: Brendstrupgaardsvej 100

department: Institute for Clinical Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Isolated RNA from 2 parallel cultures originating from 2 individual transformants was pooled and used for cDNA synthesis and labelling.

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

label: phycoerythrin

organism: Escherichia coli

source_name: E. coli B178 groESL(-) expressing human Hsp60 and Hsp10

label_protocol: Affymetrix standard

growth_protocol: Bacterial cells were grown in dYT medium (Miller, JH (1972) Experiments in Molecular Genetics (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY) supplemented with kanamycin (10 mg/L), ampicillin (100 mg/L) and IPTG (0.1mM) at 30°C in a shaking water bath. At a turbidity (measured at OD536) of approximately 0.1 bacteria were harvested by centrifugation at ambient temperature and resuspended in fresh dYT medium containing antibiotics and 0.2% arabinose. Growth was continued at 30°C and 10 hours after inducer shift 3ml sample were withdrawn, treated with RNAPROTECT (Qiagen, Ballerup), harvested by centrifugation and frozen.

extract_protocol: Total RNA was purified using the RNAeasy kit (Qiagen).

tag: E. coli strain B178 (Georgopoulos et al. (1973) J Mol Biol 76

value: 45-60) in which the endogenous groES and groEL genes have been deleted and that is maintained alive by the pOFX-tac1-derived plasmid carrying an IPTG-inducible operon with cDNA encoding human Hsp10 and the mature part of human wild type Hsp60 (Hansen et al., 2002). These cells were subsequently transformed by electroporation with a second plasmid, derivative of pBAD/hisA (Invitrogen), that contained an operon with Hsp10 and wild type Hsp60 under control of the arabinose-inducible BAD promoter. The pBAD/hisA-derived plasmids carry a pBR322 origin of replication and an ampicillin resistance gene and can be stably maintained in the same cell with the p15A-origin/kanamycin resistance gene containing pOFX-tac derivative.


title: placenta, matUPD12, U74A

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: Comparison of gene expression levels between matUPD12 and patUPD12 samples. Identification of highly differentially expressed transcripts. See UPD12 series record.

hyb_protocol: 15µg of labeled probe was hybridised to the array, washed and stained on the Affymetrix fluidics station 450. Standard protocol.

scan_protocol: The Affymetrix Scanner 3000 system was used. Standard protocol.

data_processing: MAS5/GCOS: TGT=500, otherwise default values.

label: Biotin

organism: Mus musculus

source_name: 15.5 dpc placenta, matUPD12

label_protocol: Total RNA was quantified on an Agilent Bioanalyser and 5 to 7µg were used to prepare biotin-labeled cRNA target, as prescribed in the Affymetrix expression manual (Affymetrix, 2004). The biotinylated cRNA target was purified using cRNA Cleanup spin columns (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified prior to hybridization on an Agilent Bioanalyser.

extract_protocol: Qiagen kit according to manufacturers protocol.

treatment_protocol: Tissues were snap frozen in liquid nitrogen, permanently stored at -80C, and put on dry ice during transport.

value: offspring of Rb(8.12)5Bnr/Rb(6.12)3Sic double heterozygote females on a BALB/c background crossed with Rb(8.12)5Bnr/Rb(4.12)9Bnr double heterozygote males on a C57BL/6J background (Development 127, 4719-4728 (2000)) with a maternally-derived uniparental disomy of whole Chr 12

value: placenta


title: E.coli/Hsp60-wt/VAL98Ile(-/+)

description: Isolated RNA from 3 parallel cultures originating from 3 individual transformants was pooled and used for cDNA synthesis and labelling.

source_name: E. coli B178 groESL(-) expressing human wt and Val98Ile Hsp60 and Hsp10

value: 45-60) in which the endogenous groES and groEL genes have been deleted and that is maintained alive by the pOFX-tac1-derived plasmid carrying an IPTG-inducible operon with cDNA encoding human Hsp10 and the mature part of human wild type Hsp60 (Hansen et al., 2002). These cells were subsequently transformed by electroporation with a second plasmid, derivative of pBAD/hisA (Invitrogen), that contained an operon with Hsp10 and the Val98Ile mutant variant of Hsp60 under control of the arabinose-inducible BAD promoter. The pBAD/hisA-derived plasmid carries a pBR322 origin of replication and an ampicillin resistance gene and can be stably maintained in the same cell with the p15A-origin/kanamycin resistance gene containing pOFX-tac derivative.


title: placenta, matUPD12, U74B


title: placenta, patUPD12, U74A

source_name: 15.5 dpc placenta, patUPD12

value: offspring of Rb(8.12)5Bnr/Rb(6.12)3Sic double heterozygote females on a BALB/c background crossed with Rb(8.12)5Bnr/Rb(4.12)9Bnr double heterozygote males on a C57BL/6J background (Development 127, 4719-4728 (2000)) with a paternally-derived uniparental disomy of whole Chr 12


title: placenta, patUPD12, U74B


title: normal 1074

description: normal lung 1074

source_name: primary normal lung tissue 1074


title: placenta, patUPD12, U74C


title: H3 acetylation in 6 hours IFNg-untreated human Hela cells-rep3 of 3

source_name: Chromatin immunoprecipiated DNA using acetylated histone H3 antibody, HeLa cells without IFNg treatment for 6 hours

source_name: Input DNA from HeLa cells without IFNg treatment for 6 hours


title: embryo, matUPD12, 430A

source_name: 15.5 dpc whole embryo, matUPD12

value: whole embryo


title: JASMONIC ACID_Shoot1

city: Tsukuba

first: Randeep

last: Rakwal

state: Ibaraki

address: AIST WEST, Onagawa 16-1

institute: AIST

description:
Keyword = rice
Keyword = JA

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of Gene Pix Scanner

data_processing: The GeneSpring Ver. 4 software was used for normalization.

organism: Oryza sativa

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown in MS medium in growth chamber for 7 days

extract_protocol: TRIZOL Reagent method

treatment_protocol: Healthy seedlings at 7 days, control

tag: Healthy plants, mock

treatment_protocol: Treated with JA for 7 days

tag: Treated plants


title: Hdh-HET-5 replicate1

status: Public on Apr 12 2008

city: dallas

first: hua

last: zhang

state: TX

address: 5323 harry hines

department: physiology

institute: utsw

hyb_protocol: performed according to the Illumina BeadStation 500× manual (revision C)

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner

data_processing: the data was analyzed using Illumina's BeadStudio software(Version 3).

source_name: MEF cells

label_protocol: Biotinylated cRNA was prepared using the Illumina RNA Amplification Kit (Ambion, Inc., Austin, TX) according to the manufacturer's directions starting with ~200 ng total RNA

growth_protocol: MEF cells were cultured in 10% FBS DMEM medium

extract_protocol: total RNA were extracted followed TRIZOL protocol, then transferred to RNAeasy mini spin columns for RNA purification

tag: Hdh-HET-5 replicate1


title: embryo, patUPD12, 430A

source_name: 15.5 dpc whole embryo, patUPD12


title: Hdh-KO-27 replicate1

tag: Hdh-KO-27 replicate1


title: JASMONIC ACID_Shoot2

description:
Keyword = rice
Keyword = JA


title: placenta, matUPD12, U74C

tag: Age


title: Hdh-KO-27 replicate2

tag: Hdh-KO-27 replicate2


title: Hdh-HET-3


title: U2OS-ER beta cells untreated, sample 3

city: San Francisco

first: Dale

last: Leitman

state: CA

address: 513 Parnassus Ave.

department: Ob/Gyn

institute: University of California, San Francisco

description: U2OS-ER beta cells, untreated

hyb_protocol: Standard protocol as recommended by Affymetrix.

growth_protocol: Human U2OS osteosarcoma cell lines stably expressing a tetracycline-regulated  ERß (U2OS-ERß) cDNA were grown in 5% stripped FBS with 50 µg/ml hygromycin B and 500 µg/ml zeocin.

treatment_protocol: Expression of ER in the U2OS-ERß cells was induced with doxycycline. The cells were treated in the absence or presence of 10 nM E2 for 18 h followed by incubation with TNF-{alpha} for 1 h.

tag: human osteosarcoma U2OS cells, stably transfected with ER-beta, untreated


title: U2OS-ER beta cells untreated, sample 1

description: U2OS-ER beta cells, untreated

scan_protocol: Standard protocol as recommended by Affymetrix.

source_name: human osteosarcoma U2OS cells, stably transfected with ER-beta


title: U2OS-ER beta cells treated with E2 and TNF, sample 4

label: Standard protocol as recommended by Affymetrix.

tag: human osteosarcoma U2OS cells, stably transfected with ER-beta, treated with E2 and TNF


title: U2OS-ER beta cells untreated, sample 2

description: U2OS-ER beta cells, untreated

label_protocol: Standard protocol as recommended by Affymetrix.


title: Hdh-KO-16 replicate2

tag: Hdh-KO-16 replicate2


title: Hdh-HET-5 replicate2

tag: Hdh-HET-5 replicate2


title: U2OS-ER beta cells treated with E2 and TNF, sample 2

extract_protocol: Standard protocol as recommended by Affymetrix.


title: Hdh-KO-16 replicate1

tag: Hdh-KO-16 replicate1


title: Hdh-KO-11


title: Hdh-HET-1


title: U2OS-ER beta cells treated with E2 and TNF, sample 1

tag: human osteosarcoma U2OS cells, stably transfected with ER-beta, treated with E2 and TNF, sample 1


title: U2OS-ER beta cells treated with TNF, sample 4

tag: human osteosarcoma U2OS cells, stably transfected with ER-beta, treated with TNF


title: Hdh-HET-2 replicate2

tag: Hdh-HET-2 replicate1


title: U2OS-ER beta cells treated with TNF, sample 3


title: Tg.AC vs FVB skin, Post Abrasion, Day 18

status: Public on Apr 11 2008

city: RTP

first: Hong

last: Dang

address: 111 TW. Alexander Dr

institute: NIEHS

description: Pooled total RNA from skins of 5 Tg.AC or FVB/N mice each, 18 days post epidermal abrasion.

hyb_protocol: The labeled RNAs were mixed, and co-hybridized to Agilent mouse oligo DNA microarrays at the NIEHS Microarray Center according to manufactuer’s instructions.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Spot features were extracted using the Agilent Feature Extraction software version A6.1.1 with default settings. Background was adjusted globally across the whole chip and local background values were used for signal subtraction.  Dye bias between Cy3 and Cy5 was corrected using rank consistency filters and locally weighted linear regression (LOWESS).  Differential expression was calculated on the log10 ratio between red/green channels and the p value was derived using the conservative error model between propagating and universal error models.

source_name: Tg.AC skin, post abrasion day 18

label_protocol: 60 micro-gram of pooled RNAs were labeled using the direct labeling protocol (Agilent).

growth_protocol: Female mice at 20 weeks of age.

extract_protocol: Tissues collected on days 3, 5, 9, 18, and 30 post treatment; pulverized to a homogeneous powder in liquid nitrogen using a mortar and pestle on dry ice for total RNA isolation. Total RNA was extracted using Trizol, purified using the Qiagen RNeasy kit, following the manufacturer’s protocol. The quantity and quality of the RNA from each animal were further analyzed using agarose gel electrophoresis, and the Agilent Bioanalyzer.

treatment_protocol: One day prior to abrasion, the dorsal skin surface was shaved with battery-operated clippers.  The next day, the shaved skin of Nembutal-anesthetized animals was depilated with Nair (2 minutes), rinsed with warm water, wiped with 70% ethanol, then lightly abraded with a hand-held Dremel (Robert Bosch Tool Corporation, Mount Prospect, IL) tool fitted with a felt wheel.  Sham treated animals were treated identically but were not subjected to felt wheel abrasion.

tag: Tissue

value: skin

tag: Strain

value: Tg.AC mice x 5

tag: Treatment

value: abrasion

tag: Time post treatment

value: day 18

source_name: FVB skin, post abrasion day 18

value: FVB\N mice x 5


title: U2OS-ER beta cells treated with TNF, sample 2

description: U2OS-ER beta cells treated with TNF, sample 1.

data_processing: MAS5 was used to generate the CHP files.

growth_protocol: Human U2OS osteosarcoma cell lines stably expressing a tetracycline-regulated  ERβ (U2OS-ERβ) cDNA were grown in 5% stripped FBS with 50 µg/ml hygromycin B and 500 µg/ml zeocin.

treatment_protocol: Expression of ER in the U2OS-ERβ cells was induced with doxycycline. The cells were treated in the absence or presence of 10 nM E2 for 18 h followed by incubation with TNF-{alpha} for 1 h.


title: Tg.AC vs FVB skin, Post Abrasion, Day 3, Dye-swap

description: Pooled total RNA from skins of 5 Tg.AC or FVB/N mice each, 3 days post epidermal abrasion.

source_name: FVB skin, post abrasion day 3

value: day 3

source_name: Tg.AC skin, post abrasion day 3


title: Hdh-HET-2 replicate1


title: U2OS-ER beta cells treated with E2 and TNF, sample 3


title: Tg.AC vs FVB skin, Post Abrasion, Day 9

description: Pooled total RNA from skins of 5 Tg.AC or FVB/N mice each, 9 days post epidermal abrasion.

source_name: Tg.AC skin, post abrasion day 9

value: day 9

source_name: FVB skin, post abrasion day 9


title: U2OS-ER beta cells treated with TNF, sample 1

source_name: human U2OS cells

tag: human osteosarcoma U2OS cells, stably transfected with ER-beta


title: Tg.AC vs FVB skin, Post Abrasion, Day 5

description: Pooled total RNA from skins of 5 Tg.AC or FVB/N mice each, 5 days post epidermal abrasion.

source_name: Tg.AC skin, post abrasion day 5

value: day 5

source_name: FVB skin, post abrasion day 5


title: Tg.AC vs FVB skin, Post Abrasion, Day 9, Dye-swap


title: FVB skin, Abraded vs sham, Day 30

description: Pooled total RNA from skins of 5 FVB/N mice each, 30 days post epidermal abrasion or sham treatment.

source_name: FVB skin, post abrasion day 30

value: day 30

source_name: FVB skin, post sham treatment day 30

value: sham


title: Hdh-KO-12


title: FVB skin, Abraded vs sham, Day 18, Dye-swap

description: Pooled total RNA from skins of 5 FVB/N mice each, 18 days post epidermal abrasion or sham treatment.

source_name: FVB skin, post sham treatment day 18


title: Tg.AC vs FVB skin, Post Abrasion, Day 30

description: Pooled total RNA from skins of 5 Tg.AC or FVB/N mice each, 30 days post epidermal abrasion.

source_name: Tg.AC skin, post abrasion day 30


title: Tg.AC vs FVB skin, Post Abrasion, Day 30, Dye-swap


title: FVB skin, Abraded vs sham, Day 30, Dye-swap


title: Tg.AC vs FVB skin, Post Abrasion, Day 5, Dye-swap


title: Pvivax Sal1 vs Pvivax patient1 251485710006

city: Barcelona

first: Hernando

middle: A

last: del Portillo

state: Barcelona

address: rosello, 132 (4a)

institute: Barcelona Centre for International Health Research

description: Agilent's recommended procedures

hyb_protocol: Agilent's recommended procedures

scan_protocol: Agilent's recommended procedures

data_processing: The VALUE field is the normalized log-ratio: log2(Cy5/Cy3). Cy5 is the "F635 Mean - B635" column and Cy3 is the "F532 Mean - B532" column. Normalization is achieved by usual standardization (mean centering and standard deviation re-scaling). Therefore, mean(VALUE) = 0 and sd(VALUE) = 1.

organism: Plasmodium vivax

source_name: Plasmodium vivax Sal-1

label_protocol: Agilent's recommended procedures

growth_protocol: monkey-adapted strain`passaged into monkeys

treatment_protocol: monkey leukocytes were removed by CF11 columns

tag: monkey-adapted strain

source_name: Plasmodium vivax patient 1

treatment_protocol: Stored in Tryzol reagent at -80oC prior to extraction with Tryzol reagent

tag: P. vivax isolate from Rondonia (775)


title: Pvivax Sal1 vs Pvivax patient2 251485710007

description: Agilent's recommended procedures

source_name: P. vivax isolate patient 2

tag: Pv isolate from patient Rondonia (393)


title: Tg.AC vs FVB skin, Post Abrasion, Day 3


title: Pvivax vs Pfalciparum control specificity 251485710001

description: Agilent's recommended procedures

source_name: Plasmodium vivax Sal1 strain

tag: P. vivax asexual blood stage parasites obtained from infected monkeys

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

growth_protocol: Parasites were grown in vitro according to Trager and Jansen

tag: P. falciparum 3D7 strain maintained in the laboratory at USP


title: Tg.AC vs FVB skin, Post Abrasion, Day 18, Dye-swap

source_name: FVB skin, post abrasion day 18

source_name: Tg.AC skin, post abrasion day 18


title: FVB skin, Abraded vs sham, Day 18


title: FVB skin, Abraded vs sham, Day 5

description: Pooled total RNA from skins of 5 FVB/N mice each, 5 days post epidermal abrasion or sham treatment.

source_name: FVB skin, post sham treatment day 5


title: FVB skin, Abraded vs sham, Day 9

description: Pooled total RNA from skins of 5 FVB/N mice each, 9 days post epidermal abrasion or sham treatment.

source_name: FVB skin, post sham treatment day 9


title: FVB skin, Abraded vs sham, Day 3

description: Pooled total RNA from skins of 5 FVB/N mice each, 3 days post epidermal abrasion or sham treatment.

source_name: FVB skin, post abrasion day 3

source_name: FVB skin, post sham treatment day 3


title: FVB skin, Abraded vs sham, Day 5, Dye-swap


title: Ovary cultured GDNF rep2

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: mRNA from 4-day old rat ovaries cultured two days  with GDNF treatment.

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: Auto-scale ON (1-1000).  Scaling = all probe sets.  The microarray image data were converted to numerical data with GeneChip Operating Software using MAS5 preprocessing and a scaling factor of 125.

organism: Rattus norvegicus

source_name: 4-day rat ovary cultured 2 days

label_protocol: standard Affymetrix procedures

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

treatment_protocol: Ovaries dissected from four-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 um Millicell-CM; Millipore Corp., Billerica, MA) in 0.5 ml DMEM-Ham’s F-12 medium (1:1, vol/vol; Life Technologies, Inc., Rockville, Maryland) containing 0.1% BSA (Sigma, St. Louis, MO), 0.1% albumax (Life Technologies, Inc., Rockville, Maryland), 200 ng/ml insulin (rh Insulin; Sigma, St. Louis, 10 MO), 0.05 mg/ml L-ascorbic acid (Sigma, St. Louis, MO) and 27.5 ug/ml transferrin (Sigma, St. Louis, MO) in a four-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA). Medium was supplemented with final concentration 5 ug/ml gentamicin, 3.25 ug/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control).  Each sample contained 6-10 pooled ovaries, and no two ovaries from the same animal were placed into the same group.

tag: ovaries dissected from 4-day old Sprague-Dawley rats and cleaned of ovarian bursa.


title: FVB skin, Abraded vs sham, Day 9, Dye-swap

source_name: FVB skin, post abrasion day 9


title: Ovary cultured GDNF rep1


title: Chimp 190 week 32 biopsy

status: Public on Apr 10 2008

city: rockville

first: Mike

last: havert

address: 1401 Rockville Pike

institute: CBER/FDA

description: acute infection

hyb_protocol: Cy 5 and Cy3 labeled probes were mixed 1:1 with hybridization buffer overnight at 42 degrees and washed.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Pan troglodytes

source_name: chimp biopsy

label_protocol: 10 µg of total RNA were primed and reversed transcribed with perkin elmer labeling kit

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and amplified with arcturus mRNA amplification kit

tag: baseline

tag: week 32


title: Ovary cultured control rep2

description: mRNA from 4-day old rat ovaries cultured two days as controls with no treatment.


title: FVB skin, Abraded vs sham, Day 3, Dye-swap


title: Chimp 190 week 21 biopsy

description: acute infection

tag: week 21


title: X236

city: Basel

first: Wolfgang

middle: Ernst Gustav

last: Budach

address: Klybeckstrasse

department: BMD/NV&D

country: Switzerland

institute: Novartis Pharma AG

description: Tissue samples from a series of 41 chemotherapy-naïve non-small cell lung cancer patients and 15 control patients with inflammatory lung diseases.

hyb_protocol: A Tecan HS 4800 Hybridization station from Tecan, Inc. is used for prewash/hybridization/postwash of the microarrays. Prewash consists of 3 cycles with wash buffer at RT/75°C/50°C (each 20 s) followed by an additional 10 s wash with hybridization buffer at 50°C. One hundred L sample (100 ng labeled RNA) in hybridization buffer is then injected into the flow chambers at 50°C and agitated for 1 min. Subsequently, after 10 min at 75°C, the temperature is adjusted to 42°C for 16 h (agitation). The postwash consists in 4 cycles wash buffer at 42°C followed by an additional wash at 23°C (each 20 s). Finally, the slides are washed 3 times with diluted wash buffer at RT, dried in N2 stream, and scanned immediately with an Agilent LS fluorescence scanner (gain 80%).

scan_protocol: Agilent laser scanner at 100% gain, 10micron resolution, Cy5 channel. Files stored as 16bit TIF.

data_processing: The fluorescence images is analyzed by means of Array Pro (Mediacybernetics, Inc. US). Net signals is calculated by subtracting the 75 percentile of local corner background from trimmed mean of each spot (20% trimming on both sides of the intensity histogram). Individual samples are processed on separate slides in single color mode (Cy5). The 75 percentile of intensity histogram is adjusted to 200 counts (a.u.) for normalization of the microarrays. The image analysis is configured in a way that allowed an automated assessment of the quality of individual fluorescence spots (criteria: local fluorescence background, spots symmetry, presence in salt image/Print QC). Only microarrays with >98% qualified spots are used for further analysis.

source_name: Lung Biopsy

label_protocol: Commercial human reference RNA (Stratagene) was labeled per protocol and materials of the Ambion labelling kit (#1753). Labeling of RNA samples will be based on Ambion Amino Allyl MessageAmp II aRNA Amplification Kit (#q1753). 50 ng of total RNA was used for each labeling. The first step is a reverse transcription to synthesize first-strand cDNA with an oligo(dT) primer with a T7 promoter. Subsequently, the second-strand cDNA is synthesized. The cDNA was used for processing with the Ambion kit according to the protocol as template for in vitro transcription (IVT) with T7 RNA polymerase. During this amplification step, 5-(3- aminoallyl)-UTP (aaUTP) is incorporated into the cRNA. The resulting amplified RNA (aRNA) is then chemically coupled to N-hydroxysuccinimidyl ester-derivatized Cy5-dyes (NHS ester Cy5-dyes). Once purified, concentration and yield/dye incorporation are determined. The labeled products are aliquoted and stored at -80°C for further use

extract_protocol: Lysis and homogeneization is performed with 1 mL pre-warmed (60°C) TRIzol Reagent (Invitrogen Cat. No. 15596-026) and 5 mm stainless steel beads (Qiagen Cat. No. 69989, 2 times 2 min at 25 Hz in tissue lyser Mixer Mill 300 for 2-3 mm Ø biopsies). The extraction is completed by adding Phase Lock Gel (Eppendorf Cat. No. 0032007.970) during the phase extraction. Molecular biology grade glycogen (Roche Diagnostics GmbH, Cat. N. 901393) is added to the aqueous phase during the precipitation step. After purification step on RNeasy Microkit columns (Qiagen, Cat. No. 74004), the final cleaned total RNA is eluted in 14 µL of RNase free water and stored at -80°C. RNA levels, quality and purity are assessed with the use of RNA 6000 Nano and Pico assay on the Agilent 2100 Bioanalyzer.

tag: Phenotype

value: NSCLC-Adeno

tag: gender

tag: age

tag: status

tag: Surv

tag: stage

value: IV

tag: T

tag: N

tag: M

tag: mat

value: bx

tag: Tumor Prop


title: X261


title: Chimp 190 week 20 biopsy

description: acute infection

tag: week 20


title: X381


title: Ovary cultured control rep1


title: X110

value: NSCLC-squa.

value: x


title: X308

value: IIb


title: X290


title: X370


title: X105


title: X377


title: X378


title: X280

value: NSCLC-NOS


title: X204


title: Chimp 190 week 19 biopsy

description: acute infection

tag: week 19


title: X374


title: X302


title: X299


title: X309


title: X220

value: IIIb


title: X284


title: L_305

value: IIa


title: X371


title: L_315T

value: Ib

value: tu


title: X344


title: X326


title: L_205


title: L_337T

value: IIIa


title: L_188


title: L_342T


title: X369


title: L_321


title: L_170b


title: L_258


title: L_216


title: L_341T


title: L_206


title: L_229


title: L_286


title: L_340T


title: L_306


title: L_169a


title: L_7NSCLC


title: L_335T


title: X194


title: L_265


title: L_230

value: Ia


title: L.202


title: L_311T


title: L_331T


title: L.285


title: L.217


title: L_338T


title: L307


title: L.297


title: Sprague Dawley I/R rep3

first: Jose Luis

last: Viñas

address: rosellon 161 7ª

department: Experimental Pathology

institute: IIBB-CSIC

description: Tissue from Sprague Dawley rat strain

hyb_protocol: Digoxigenin-labelled cRNA targets were hybridized to Applied Biosystems Rat Whole Genome Survey Microarrays using the Applied Biosystems Chemiluminescent Detection Kit. Briefly, 15 μg of labelled cRNA targets were fragmented via incubation for 30 min at 60 ◦C with fragmentation buffer provided in the kit. Fragmented targets were hybridized to microarrays during 16 h of incubation at 55 ◦C with buffers and reagents from the Chemiluminescent Detection Kit. Post-hybridization washes and anti-digoxigenin-alkaline phosphatase binding were performed according to the kit protoco

scan_protocol: Chemiluminescence detection, image acquisition and analysis were performed using the Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following the manufacturer’s protocols. Images were autogridded and the chemiluminescent signals were quantified, corrected for background and, finally, spot- and spatially normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software version 1.1 (for more information see Applied Biosystems 1700 Chemiluminescent Microarray Analyzer user bulletin in ABI's website)

data_processing: The data obtained after the process described in the scan protocol section were normalized by LOWESS (Locally weighted least mean squares scatter Plot smoother), this was the statistical algorithm for performing a non linear normalization and corrects deviations of the backbone of the data cloud from the expected main diagonal. Data were LOWESS normalized excluding the controls on the microarray and using only the transcripts with a S/N ratio to > 2.

label: Digoxigenin-labelled cRNA

source_name: Sprague Dawley I/R

label_protocol: All RNA targets were labelled using the Applied Biosystems RT-IVT Labelling Kit Version 2.0. Briefly, 1.5 μg of the total RNA sample was reverse transcribed via 2 h incubation at 42 ◦C with ArrayScript RT enzyme (Ambion, Austin, TX, USA) and oligo dT-T7 primer. Double-stranded cDNA was produced following 2 h incubation with E. coli DNA polymerase and RNase H at 16 ◦C. Double-stranded cDNA was purified according to the RT-IVT kit protocol. In vitro transcription was performed by incubation of the cDNA product with T7 RNA polymerase, 0.75 mM digoxigenin-11-UTP (Roche Applied Science, Indianapolis, IN, USA) and all other NTPs for 9 h. Labelled cRNA was purified according to the RT-IVT kit protocol and analyzed for quality and quantity using standard UV spectrometry and the Bioanalyzer.

extract_protocol:
Total RNA from cells was isolated using an RNeasy system (Qiagen, Valencia, CA, USA) and were further purified by passage through RNeasy mini-columns (QIAGEN, Valencia, CA) according to manufacturer’s protocols for RNA clean-up. Final RNA preparations were resuspended in RNase-free water and stored at -80°C.
The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm. The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Only high-quality RNA with RNA integrity numbers (RINs) greater than 7.5 were used for microarray experiments

tag: Tissue from Sprague Dawley rat strain


title: L.301


title: MDA-MB435-3B2

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Cells expressing SEMA 3B

hyb_protocol: 1.5 microgram of biotin-labeled cRNA was hybridized to Illumina Human WG-6 BeadChips at 55 °C for 18hrs. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

data_processing: Data were normalized with the Illumina Beadstudio software, using rank-invariant normalization

label_protocol: Five hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

growth_protocol: Cells were grown in standard medium supplemented with with L-glutamine and 10% FBS

extract_protocol: Total RNA from tumor cell lines was isolated by using RNeasy Protect Mini Kit (Qiagen) according to the manufacturer instruction

treatment_protocol: Cells were transduced with lentiviral vectors either encoding SEMA3B (“3B”) or a non-coding empty vector (“EV”).

tag: MDA-MB435 transduced with lentiviral vector encoding SEMA 3B, Melanoma-derived Cell Line


title: RIG328L

city: Stanford

last: Wong

address: 269 Campus Drive

institute: Stanford University

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68839.gif
LZRS retroviral transduction: inserted gene name: GFP+Ras+IkB
Extracted molecule: RNA

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 10:33:55; Parameter PMT Volts = 460; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 77910; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 10:33:55; Parameter PMT Volts = 530; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 247846; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Universal Reference

label_protocol: not provided

extract_protocol: not provided

tag: Universal Reference


title: MDA-MB435-EV1

description: Control cells

tag: MDA-MB435 transduced with a non-coding empty vector, Melanoma-derived Cell Line


title: MDA-MB435-EV2

description: Control cells

source_name: MDA-MB435 transduced with a non-coding empty vector


title: L295

tag: Phenotype


title: Brown Norway I/R rep 3

description: Tissue from Brown Norway rat strain

source_name: Brown norway rat tissue

tag: Tissue from Brown Norway rat strain


title: L.116

tag: gender

tag: age


title: Brown Norway control replicate 3

description: Tissue from Brown Norway rat strain

source_name: Brown Norway I/R


title: MDA-MB435-3B1

description: Cells expressing SEMA 3B

source_name: MDA-MB435 transduced with lentiviral vector encoding SEMA 3B


title: Sprague Dawley control rep3

description: Tissue from Brown Norway rat strain


title: RIM334R

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68842.gif
LZRS retroviral transduction: inserted gene name: Myc+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 4120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.28; Parameter Scan Time = 13:35:48; Parameter PMT Volts = 480; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 78056; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.28; Parameter Scan Time = 13:35:48; Parameter PMT Volts = 530; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 247991; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: RIG328R

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68838.gif
LZRS retroviral transduction: inserted gene name: GFP+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 640, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.06; Parameter Scan Time = 10:49:59; Parameter PMT Volts = 460; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 77927; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.06; Parameter Scan Time = 10:49:59; Parameter PMT Volts = 530; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 247863; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: RIG693R CGH

description:
Simple annotation: Solid tumor, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72328.gif
LZRS retroviral transduction: inserted gene name: GFP+Ras+IkB
Extracted molecule: DNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 4520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.21; Parameter Scan Time = 12:44:39; Parameter PMT Volts = 550; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 18244; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.21; Parameter Scan Time = 12:44:39; Parameter PMT Volts = 660; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 261030; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: normal male genomic DNA

tag: normal male genomic DNA

source_name: RIG693R CGH

tag: RIG693R CGH


title: Rik1_2_WT

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, Rik1-Myc ChIP(chromatin immunoprecipitation)-on-chip replicate 2

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 12.5 ul Agilent 10X control targets and 12.5 ul of Human Cot-1(1.0mg/ml)

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformadehyde at 18C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde/dimethyl adipimidate

tag: Chromatin DNA not enriched for Rik1-Myc

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

tag: Chromatin DNA enriched for Rik1-Myc


title: RIM334L

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68837.gif
LZRS retroviral transduction: inserted gene name: Myc+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 4000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 13:17:36; Parameter PMT Volts = 480; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 78040; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 13:17:36; Parameter PMT Volts = 530; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 247975; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: RIM336L

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68841.gif
LZRS retroviral transduction: inserted gene name: Myc+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.46; Parameter Scan Time = 13:57:01; Parameter PMT Volts = 460; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 78079; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.46; Parameter Scan Time = 13:57:01; Parameter PMT Volts = 540; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 248015; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.42; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: RIE711L CGH

description:
Simple annotation: Solid tumor, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72327.gif
LZRS retroviral transduction: inserted gene name: E2F3+Ras+IkB
Extracted molecule: DNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 4640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 12:55:11; Parameter PMT Volts = 570; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 18254; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 12:55:11; Parameter PMT Volts = 650; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 261040; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: RIE711L CGH

tag: RIE711L CGH


title: RIM695L CGH

description:
Simple annotation: Solid tumor, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72326.gif
LZRS retroviral transduction: inserted gene name: Myc+Ras+IkB
Extracted molecule: DNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 4440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 12:16:21; Parameter PMT Volts = 570; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 18216; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 12:16:21; Parameter PMT Volts = 650; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 261002; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: RIM695L CGH

tag: RIM695L CGH


title: Danio_Liver_Starved_5 (2LS5)

status: Public on Apr 09 2008

city: Moscow

first: Robert

middle: Edward

last: Drew

state: ID

address: Life Sciences South Rm 252

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Microarrays were hybridized with fragmented biotinylated cRNA for 16 h at 45°C with constant rotation (45 r.p.m.), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.  This was followed by another round of SAPE prior to scanning using a GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: All analyses of microarray data were conducted using Bioconductor for R (www.R-project.org).  Data for brain and liver were normalized and analyzed separately because variances of expression differed considerably between the tissues.  The microarray data were filtered as described by Robison et al. (2008).  Filtered probesets were then normalized using Robust Multiarray Average (RMA).

organism: Danio rerio

source_name: Liver

label_protocol: For each array, up to 10 ug of total RNA were converted to cDNA.  Biotinylated cRNA was then produced in vitro using the GeneChip Expression 3' amplification one-cycle target labeling kit (Affymetrix).

extract_protocol: Total RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA) following the manufacturer's protocol.  After extraction, RNA from three fish was pooled for each tank for analysis.

treatment_protocol: Groups of eight females of the same age were randomly assigned to each of twelve 3-L tanks (10 cm wide x 15 cm tall x 25 cm deep) arranged on the same shelf of a flow-through rearing system.  Test tanks were assigned to starved or control treatments in an alternating manner so that treatments were uniformly distributed across fish ages and tank location.  Fish in the starved treatment received no food for 21 days, while fish in the control treatment continued to be fed to apparent satiety three times daily.

tag: Strain

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:9152005, Start date:432006, Mean Mass:337.9, Mean Length:25.9, Mean SGR:-0.511, Mean GSI:0.113


title: Danio_Liver_Starved_4 (2LS4)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:9232005, Start date:432006, Mean Mass:415.5, Mean Length:27.9, Mean SGR:-0.608, Mean GSI:0.077


title: RIG695R CGH

first: David

description:
Simple annotation: Solid tumor, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72329.gif
LZRS retroviral transduction: inserted gene name: GFP+Ras+IkB
Extracted molecule: DNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 4240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 12:28:13; Parameter PMT Volts = 570; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 18228; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 12:28:13; Parameter PMT Volts = 660; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 261015; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: RIG695R CGH

tag: RIG695R CGH


title: kernel_development_10DAP_to_5DAP_rep2_A

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

country: China

institute: Chinese Academy of Agricultural Sciences

description: Gene expression data from maize kernel

hyb_protocol: Hybridization and post hybridization wash were performed according to the protocal of the Maize Oligo Array Project (http://www.maizearray.org/).

scan_protocol: Hybridized slides were scanned by a Genepix 4000B (Axon, USA).

data_processing: Raw data from microarray hybridization, exported from GenePix suites 6.0 (Axon, USA), was imported into LIMMA with annotation and spot types. Spots with a negative flag value were assigned a weight of 0.1 in the subsequent analysis. Background-subtracted signal intensities were normalized using a two-step normalization: print-tip group loss (within-array normalization) and then between-array scale normalization.

organism: Zea mays

label_protocol: Cy5-cDNA were prepared according to the recommendations of the Maize Oligo Array Project (http://www.maizearray.org/).

growth_protocol: Natural conditions, growing season begins from May to September, on the China Agricultural University research farm in Beijing, China.

extract_protocol: Total RNA was extracted using a modified hot phenol method.

tag: Zea mays, Kernel, Development

label_protocol: Cy3-cDNA were prepared according to the recommendations of the Maize Oligo Array Project (http://www.maizearray.org/).


title: kernel_development_35DAP_to_25DAP_rep1_A

description: Gene expression data from maize kernel


title: kernel_development_15DAP_to_10DAP_rep2_A

description: Gene expression data from maize kernel


title: kernel_development_10DAP_to_5DAP_rep1_A

description: Gene expression data from maize kernel


title: kernel_development_25DAP_to_15DAP_rep2_A

description: Gene expression data from maize kernel


title: kernel_development_35DAP_to_25DAP_rep2_A

description: Gene expression data from maize kernel


title: kernel_development_1DAP_to_35DAP_rep1_A

description: Gene expression data from maize kernel


title: kernel_development_5DAP_to_1DAP_rep1_A

description: Gene expression data from maize kernel


title: kernel_development_15DAP_to_10DAP_rep1_A

description: Gene expression data from maize kernel


title: kernel_development_1DAP_to_35DAP_rep2_A

description: Gene expression data from maize kernel


title: RIE708L

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74326.gif
LZRS retroviral transduction: inserted gene name: E2F3+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 4440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.11; Parameter Scan Time = 11:03:54; Parameter PMT Volts = 480; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 26175; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.11; Parameter Scan Time = 11:03:54; Parameter PMT Volts = 710; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 269772; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: RIM334R-2

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74327.gif
LZRS retroviral transduction: inserted gene name: Myc+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 4440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 11:19:27; Parameter PMT Volts = 480; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 26191; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 11:19:27; Parameter PMT Volts = 650; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 269787; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: Danio_Liver_Starved_3 (2LS3)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:8172005, Start date:432006, Mean Mass:298.9, Mean Length:24.3, Mean SGR:-0.649, Mean GSI:0.065


title: Danio_Liver_Starved_1 (2LS1)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:10252005, Start date:432006, Mean Mass:265.3, Mean Length:25.7, Mean SGR:-0.907, Mean GSI:0.055


title: Danio_Liver_Starved_2 (2LS2)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:10182005, Start date:432006, Mean Mass:189.0, Mean Length:22.9, Mean SGR:-0.715, Mean GSI:0.041


title: Danio_Liver_Control_5 (2LC5)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:9152005, Start date:432006, Mean Mass:537.5, Mean Length:27.9, Mean SGR:0.210, Mean GSI:0.189


title: RIM693L CGH

description:
Simple annotation: Solid tumor, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72324.gif
LZRS retroviral transduction: inserted gene name: Myc+Ras+IkB
Extracted molecule: DNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 13:07:07; Parameter PMT Volts = 570; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 18266; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 13:07:07; Parameter PMT Volts = 650; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 261053; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: RIM693L CGH

tag: RIM693L CGH


title: RIE713L

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74325.gif
LZRS retroviral transduction: inserted gene name: E2F3+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 4440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.78; Parameter Scan Time = 10:49:57; Parameter PMT Volts = 480; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 26160; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.78; Parameter Scan Time = 10:49:57; Parameter PMT Volts = 690; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 269756; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: RIG329L

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68840.gif
LZRS retroviral transduction: inserted gene name: GFP+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 11:11:25; Parameter PMT Volts = 460; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 77945; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 11:11:25; Parameter PMT Volts = 530; Parameter Scan Date = 2006-06-02; Parameter Pixel Size = 10; Parameter Laser on time = 247881; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: RIE711L

description:
Simple annotation: Solid tumor, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74324.gif
LZRS retroviral transduction: inserted gene name: E2F3+Ras+IkB
Extracted molecule: RNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 3800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.53; Parameter Scan Time = 10:36:08; Parameter PMT Volts = 480; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 26147; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.53; Parameter Scan Time = 10:36:08; Parameter PMT Volts = 710; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 269744; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong


title: Danio_Liver_Control_4 (2LC4)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:9152005, Start date:432006, Mean Mass:438.5, Mean Length:26.1, Mean SGR:0.210, Mean GSI:0.115


title: RIE713L CGH

description:
Simple annotation: Solid tumor, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2007-02/72325.gif
LZRS retroviral transduction: inserted gene name: E2F3+Ras+IkB
Extracted molecule: DNA

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Wong Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 13:17:28; Parameter PMT Volts = 590; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 18277; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: David,,Wong Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 13:17:28; Parameter PMT Volts = 640; Parameter Scan Date = 2007-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 261064; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Wong

source_name: RIE713L CGH

tag: RIE713L CGH


title: Double knockout, biol rep 1 (430A)

first: Holger

last: Willenbring

address: 35 Medical Center Way

institute: UCSF

description: Global gene expression in adult mouse liver sample.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hours at 45 degree Celsius on MG 430A 2.0 or MG 430 2.0 GeneChip arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed in the Affymetrix GCOS version 1.4.0.036 software using the Microarray Suite version 5.0 (MAS 5.0) algorithm, and global scaling was used as the normalization method. The mean target intensity of each array was set to 350 and alpha1 and alpha2 were set to 0.05 and 0.065, respectively.

source_name: liver, Fah, p21 knockout mouse off NTBC

label_protocol: Standard one cycle cDNA synthesis followed by in vitro transcription (Affymetrix) to produce biotinylated cRNA.

growth_protocol: Adult mice 10 weeks of age were used for this study.

extract_protocol: RNA isolation with RNeasy (Qiagen) from 10 mg of liver tissue stabilized with RNAlater.

treatment_protocol: Mice were either kept on NTBC or treated with water 14 days before liver analysis.

tag: Fah, p21 knockout, male, 10 weeks old, 129 strain


title: Single knockout, biol rep 2 (430A)

source_name: liver, Fah knockout mouse off NTBC

tag: Fah knockout, male, 10 weeks old, 129 strain


title: kernel_development_1DAP_to_35DAP_rep2_B

description: Gene expression data from maize kernel


title: SCG from P0 NGF-Bax double null mouse sample 1 moe430B

city: Baltimore

middle: D

last: Ginty

address: 725 N. Wolfe St.

department: Neuroscience

institute: Johns Hopkins University School of Medicine

description: standard protocol was applied by JHMI microarray core facility

hyb_protocol: 16 hour at 45C with rotation(60RPM) as described by affymetrix in their  gene chip expression analysis technical manual, 2004.

scan_protocol: Using affymetrix gene chip scanner 3000 7G and default parameters described by the manufacturer in their gene chip expression analysis technical manual 2004

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer's specifications. Global scaling of images to target intensity of 150.

label_protocol: One round amplification protocol for total RNA following Affymetrix specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT Kit. (www.affymetrix.com, genchip expression analysis, technical manual, 2003)

extract_protocol: RNA was isolated using the RNeasy kit (Qiagen)

tag: superior cervical ganglia


title: Single knockout, biol rep 3 (430A)


title: SCG from P0 Bax null mouse sample 1 moe430B


title: Danio_Brain_Starved_3 (X2BS3)

source_name: Brain


title: Danio_Liver_Control_1 (2LC1)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:10182005, Start date:432006, Mean Mass:410.2, Mean Length:25.7, Mean SGR:0.214, Mean GSI:0.119


title: Danio_Liver_Control_3 (2LC3)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:9232005, Start date:432006, Mean Mass:631.5, Mean Length:28.8, Mean SGR:0.232, Mean GSI:0.152


title: Single knockout, biol rep 1 (430A)


title: Danio_Brain_Starved_4 (X2BS4)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:9232005, Start date:432006, Mean Mass:415.5, Mean Length:27.9, Mean SGR:-0.608, Mean GSI:0.0767


title: Danio_Liver_Control_2 (2LC2)

value: Scientific Hatcheries, Sex:Female, N:3 fish, Birthdate:8172005, Start date:432006, Mean Mass:452.8, Mean Length:26.4, Mean SGR:0.148, Mean GSI:0.123


title: Normal, biol rep 4 (430A)

source_name: liver, Fah, p21 knockout mouse on NTBC


title: SCG from P0 NGF-Bax double null mouse sample 2 moe430B


title: kernel_development_35DAP_to_25DAP_rep2_B

description: Gene expression data from maize kernel


title: kernel_development_25DAP_to_15DAP_rep1_A

description: Gene expression data from maize kernel


title: kernel_development_35DAP_to_25DAP_rep1_B

description: Gene expression data from maize kernel