title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy5_x_3G10R-Cy3_Exp1_Repl_1

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description: This hybridization is part of an experiment aimed at evaluating gene expression modulation during Xylella fastidiosa growth in two different media: PW (the standard complex medium normally used to cultivate X. fastidiosa under laboratory conditions) and 3G10R (a defined medium based on xylem chemical composition)

hyb_protocol: Labelled cDNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardts solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS´and 50% formamide. Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

data_processing: Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with less than 50% of the pixels with values lower than the median local background plus two SD have been flagged and excluded from further analyses. Raw data were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array

organism: Xylella fastidiosa 9a5c

source_name: Xylella fastidiosa cells grown in PW medium

label_protocol: Thirty micrograms (30 ug) of total P. brasiliensis RNA were mixed with 1 ul of a 4 ug/ul random primer solution (9-mers) in 20 ul of water and heated to 65oC for 10 min. The tube was briefly chilled on ice and mixed with 4 ul of 5mM dNTPs, 4 ul of 0.1 M DTT, 8 ul of 5X first-strand buffer (Invitrogen) and 1.5 ul of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42oC for 1.5 h and terminated by a 15-min incubation at 65oC. The RNA was degraded by adding 1 ul of 10 mg/ml RNAse A and incubation at 37oC for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 ul. One microliter (1 ul) of 4 ug/ul random primer solution (9-mers) and 4 ul of 10X Klenow buffer were then added to the system. The tube was then heated at 65oC for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 ul of 10X low dNTP solution (5mM dATP, 5mM dTTP, 5mM dGTP and 2mM dCTP), 1 ul of Cy5-labeled dCTP (1mM) (Amersham Biosciences) and 1 ul of the Klenow fragment (50 units/ul) (Invitrogen). The reaction was then incubated at 37oC for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

growth_protocol: Cells of Xf 9a5c have been routinely kept in our laboratory in 20 ml of liquid cultures, which were incubated in an orbital shaker at 28oC and 100 rpm. For the microarray hybridization experiments, 1 ml aliquots of exponentially-growing cultures were transferred to 19 ml of fresh PW medium and incubated as mentioned above for 3 days, until an OD600 = 0.25 (late phase of exponential growth) was reached. This culture was then transferred to 300 ml of fresh medium and incubated for another 3 days, untill an OD600 = 0.25 was reached again. Cells were then harvested for RNA extraction

extract_protocol: Total RNA from Xylella fastidiosa cells was extracted with the aid of the RNAeasy system (Qiagen), according to the manufacturer´s instructions

tag: Total RNA from Xylella fastidiosa (isolate 9a5c), grown in PW medium until late exponential growth phase

source_name: Xylella fastidiosa cells grown in 3G10R medium

label_protocol: Thirty micrograms (30 ug) of total P. brasiliensis RNA were mixed with 1 ul of a 4 ug/ul random primer solution (9-mers) in 20 ul of water and heated to 65oC for 10 min. The tube was briefly chilled on ice and mixed with 4 ul of 5mM dNTPs, 4 ul of 0.1 M DTT, 8 ul of 5X first-strand buffer (Invitrogen) and 1.5 ul of Superscript II (200 units/ml) (Invitrogen). The reaction was then incubated at 42oC for 1.5 h and terminated by a 15-min incubation at 65oC. The RNA was degraded by adding 1 ul of 10 mg/ml RNAse A and incubation at 37oC for 1 hour. The resulting first strand cDNA was purified and concentrated with the aid of a Microcon YM-30 cartridge and final volume was adjusted to 29 ul. One microliter (1 ul) of 4 ug/ul random primer solution (9-mers) and 4 ul of 10X Klenow buffer were then added to the system. The tube was then heated at 65oC for 5 min and allowed to cool to room temperature for ten min for primer annealing. Finally, fluorescence incorporation was performed by the addition of 4 ul of 10X low dNTP solution (5mM dATP, 5mM dTTP, 5mM dGTP and 2mM dCTP), 1 ul of Cy3-labeled dCTP (1mM) (Amersham Biosciences) and 1 ul of the Klenow fragment (50 units/ul) (Invitrogen). The reaction was then incubated at 37oC for 2 h and the final labeled cDNA was purified in a Microcon YM-30 cartridge (3 washes)

growth_protocol: Cells of Xf 9a5c have been routinely kept in our laboratory in 20 ml of liquid cultures, which were incubated in an orbital shaker at 28oC and 100 rpm. For the microarray hybridization experiments, 1 ml aliquots of exponentially-growing cultures were transferred to 19 ml of fresh 3G10R medium and incubated as mentioned above for 13 days, until an OD600 = 0.25 was reached. This culture was then transferred to 300 ml of fresh medium and incubated for another 13 days, untill an OD600 = 0.25 was reached again. Cells were then harvested for RNA extraction

tag: Total RNA from Xylella fastidiosa (isolate 9a5c), grown in 3G10R medium


title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy5_x_3G10R-Cy3_Exp1_Repl_2

status: Public on Dec 30 2006

type: RNA

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 90% PMT gain

molecule: total RNA


title: LARK_overexpression_adult_head_rep3

city: Boston

first: Yanmei

last: Huang

state: MA

address: 136 Harrison Ave, A305B

department: Neuroscience

country: USA

institute: Tufts University School of Medicine

description: The population contain a mixture of elav-gal4; uas-lark/+ male and elav-gal4/+; uas-lark/+ female.

hyb_protocol: Labeled RNAs were hybridized to the Drosophila genome array following standard protocol provided by Affymetrix. The array was washed and stained on a Affymetrix Fluidics Station 400 using standard protocols.

scan_protocol: An Agilent GeneArray Scanner was used to scan the array. Pixel size: 3 um, filter: 570nm, number of scan: 2

data_processing: Data generated by MAS5.0 with all default parameters and scaled to a target intensity of 100

label: biotin

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Drosophila adult head with overexpressing LARK, ZT6

label_protocol: Affymetrix one cycle cDNA synthesis kit and and IVT labeling kit were used to label the RNAs following the standard protocols provided by Affymetrix.

growth_protocol: Fly cultures were grown in 25oC on standard media made from receipt provided by the Bloomington stock center. The culture were entrained to a 12 hour:12 hour light:dark cycle.

extract_protocol: Total RNAs were extracted from the head collections using the TriZol reagent from Invitrogen.

treatment_protocol: Female elav-gal4 flies were mated to male uas-lark flies. Progenies from this cross were frozen at ZT6. Heads were collected from the frozen flies.

tag: Total RNA isolated from adult head of flies overexpressing LARK in their CNS neurons. Sample collected at ZT6.


title: A78:4-1 callus (cy5), G88:5-1 callus (cy3) 12770881

status: Public on Dec 27 2006

city: Uppsala

first: Johan

last: Wadenbäck

department: Plant Biology and Forest Genetics

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

description:
The microarray intensity data was normalized in the LCB Data Warehouse (LCB-DWH) v1.2.10 (Ameur et al., 2006), using the within slide print-tip loess normalization (Yang et al., 2002).
The significantly differentially expressed ESTs were determined using a mixed model system (ANOVA) (Brazma and Vilo 2000; Jin et al., 2001; Wolfinger et al., 2001; Stasolla et al., 2004) in SAS/STAT Software version 8 (SAS Institute Inc., Cary, NC, USA). This generalized linear model incorporates both fixed and random effects in signal intensities due to experimental variation and differences in gene expression.

hyb_protocol: Microarray hybridization and stringency washes have been described previously (Stasolla et al., 2004; Hegde et al., 2000). cDNA microarrays based on 2190 loblolly pine (Pinus taeda) ESTs from eight EST libraries of the NSF unigene set (Forest Biotechnology Group, NCSU, NC, USA) (Kirst et al., 2003) were hybridized with the labeled targets. 77% of the ESTs on the array came from a xylem library (21% NXCI, 1% NXLV, 21% NXNV, 1% NXPV, 1%NXRV, 28% NXSI), 26% from the shoot tip library (ST) and 1% from the pine cone library (PC).

scan_protocol: The slides were scanned using a ScanArray® 4000 Microarray Analysis System (GSI Lumonics, Ottawa, Canada). Raw intensity values were collected with QuantArray® software (GSI Lumonics) and spots were visually inspected for spot morphology and background. No background subtraction was applied.

data_processing: Print tip loess within arrays v4.0 (LCB-DWH)

organism: Picea abies

label_protocol: 2nd strand labelling with Klenow.

extract_protocol: Two biological replicates sampled from three individual Petri dishes were taken 14 days after subculture from each of the lines. The embryonic tissue was frozen in liquid nitrogen and ground with two 12 mm steel balls in plastic tubes on a MM2 ball mill (Retsch GmbH, Haan, Germany). The ground plant material was incubated in the extraction buffer of Chang et al. (1993) at 65°C for 30 min. The supernatant was subsequently purified with 24:1 chloroform:isoamylalcohol and centrifuged (30 min, 10,000 rpm) three consecutive times to separate the organic- and the water phase. The final supernatant was mixed with 0.5 volumes 99.5% RNase/DNase free ethanol, and immediately purified on RNeasy Columns (Qiagen, Valencia, CA, USA). The RNA was eluted with RNase-free water to which was added 0.25 volumes 10 M lithium chloride (Sigma, St Louis, MO, USA) for over-night precipitation at 4°C and centrifuged to retrieve the RNA pellet. The RNA pellet was dissolved in water and was again precipitated by adding 0.1 volumes 5 M ammonium acetate (Sigma) and 2.5 volumes of ethanol and centrifuged. The pellet after centrifugation was washed with 75% (v/w) ethanol, air-dried and dissolved in water. The purified RNA was examined on 1% agarose electrophoresis gels and by spectrofotometry. There was no visible degradation in the 18S and 28S rRNA and the ratios of absorbance at 260/280 nm and 260/230 nm were in general above 2.1 and 2.3 respectively, indicating high integrity and purity.

tag: A78:4-1, asCCR transgenic line.

tag: G88:5-1, transformed control.


title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy5_x_3G10R-Cy3_Exp2_Repl_1


title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy3_x_3G10R-Cy5_Exp2_Repl_2


title: A78:5-2 callus (cy5), G88:9-2 callus (cy3) 12770837

tag: A78:5-2, asCCR transgenic line.

tag: G88:9-2, transformed control.


title: 95:88:22-2 callus (cy5), A78:5-2 callus (cy3) 12770879

tag: 95:88:22-2, untransformed control.


title: LARK_overexpression_adult_head_rep2

data_processing: Data generated by MAS5.0 with all default parameters and scaled to a target intensity of 85


title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy3_x_3G10R-Cy5_Exp2_Repl_1


title: A78:4-2 callus (cy5), 95:88:22-2 callus (cy3) 12770880

tag: A78:4-2, asCCR transgenic line.

tag: 95:88:22-2, untransformed line.


title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy5_x_3G10R-Cy3_Exp2_Repl_2

growth_protocol: Cells of Xf 9a5c have been routinely kept in our laboratory in 20 ml of liquid cultures, which were incubated in an orbital shaker at 28oC and 100 rpm. For the microarray hybridization experiments, 1 ml aliquots of exponentially-growing cultures were transferred to 19 ml of fresh PW medium and incubated as mentioned above for 3 days, until an OD600 = 0.25 (late phase of exponential growth) was reached. This culture was then transferred to 300 ml of fresh medium and incubated for another 3 days, untill an OD600 = 0.25 was reached again. Cells were then harvested for RNA extract


title: CgtA-depleted

status: Public on Dec 28 2006

first: David

last: Raskin

address: 200 Longwood Avenue

department: Microbiology & Molecular Genetics

institute: Harvard Medical School

description: V. cholerae CgtA-depletion, 5 replicate experiments including dye-swaps

hyb_protocol: Mekalanos Hyb.

scan_protocol: Mekalanos Scan

data_processing: Mekalanos Rosetta Protocol

organism: Vibrio cholerae

source_name: V. cholerae WT

label_protocol: cDNA method

extract_protocol: Trizol method

tag: WT

source_name: V. cholerae CgtA-depletion

tag: CgtA-depleted


title: elavGal4_adult_head_rep2

description: The population contain a mixture of elav-gal4 male and elav-gal4/+ female.

source_name: Drosophila adult head with GAL4, ZT6

treatment_protocol: Female elav-gal4 flies were mated to male w1118 flies. Progenies from this cross were frozen at ZT6. Heads were collected from the frozen flies.

tag: Total RNA isolated from adult head of flies expressing GAL4 in their CNS neurons. Sample collected at ZT6.


title: A78:5-2 callus (cy5), 95:88:22-2 callus (cy3) 12770822


title: Stringent Response

description: V. cholerae Stringent Response, 2 replicate experiments

source_name: V. cholerae Stringent Response

tag: Serine Hydroxamate treated


title: 95:88:22-1 callus (cy5), A78:4-1 callus (cy3) 12770678

tag: 95:88:22-1, untransformed control.


title: A78:5-1 callus (cy5), 95:88:22-1 callus (cy3) 12770681

tag: A78:5-1, asCCR transgenic line.


title: LARK_overexpression_adult_head_rep1

data_processing: Data generated by MAS5.0 with all default parameters and scaled to a target intensity of 150


title: 95:88:22-2 callus (cy5), A78:4-2 callus (cy3) 12770816

tag: 95:88:22-2, untranformed control.


title: elavGal4_adult_head_rep1


title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy3_x_3G10R-Cy5_Exp1_Repl_1

tag: Total RNA from Xylella fastidiosa (isolate 9a5c), grown in PW medium until late exponential growth phase

tag: Total RNA from Xylella fastidiosa (isolate 9a5c), grown in 3G10R mediu


title: X. fastidiosa in 3G10-R and Periwinkle Wilt media PW-Cy3_x_3G10R-Cy5_Exp1_Repl_2

tag: Total RNA from Xylella fastidiosa (isolate 9a5c), grown in 3G10R medium


title: 95:88:22-1 callus (cy5), A78:5-1 callus (cy3) 12770686


title: A78:4-1 callus (cy5), 95:88:22-1 callus (cy3) 12770798

tag: A78:4-1, asCCR transgenic line.


title: G88:9-2 callus (cy5), A78:5-2 callus (cy3) 12770827


title: G88:5-1 callus (cy5), A78:4-1 callus (cy3) 12770814

tag: G88:5-1, transformed control.


title: G88:5-1 callus (cy5), A78:3-1 callus (cy3) 12754065

tag: A78:3-1, asCCR transgenic line.


title: A78:5-1 callus (cy5), G88:9-1 callus (cy3) 12326351

tag: G88:9-1, transformed control.


title: G88:9-2 callus (cy5), A78:3-2 callus (cy3) 12316980

tag: G88:9-2, transformed control.

tag: A78:3-2, asCCR transgenic line.


title: G88:9-1 callus (cy5), A78:5-1 callus (cy3) 12326349


title: G88:5-2 callus (cy5), A78:4-2 callus (cy3) 12316391

tag: G88:5-2, transformed control

tag: A78:4-2, asCCR transformed control


title: A78:3-2 callus (cy5), G88:5-2 callus (cy3) 12316333

tag: G88:5-2, transformed control.


title: A78:4-2 callus.l2 (cy5), G88:5-2 callus.l1 (cy3) 12316330

tag: A78:4-2, transgenic asCCR line.

tag: G88:5-2, transformed control line.


title: A78:3-2 callus.l2 (cy5), G88:9-2 callus.l1 (cy3) 12316310

tag: A78:3-2, transgenic asCCR line.

tag: G88:9-2, transformed control


title: A78:3-1 callus (cy5), G88:9-1 callus (cy3) 12316416


title: oral_squamous_cell_carcinoma_71_A

status: Public on Dec 26 2006

city: Zagreb

first: Maja

last: Herak Bosnar

address: Bijenicka 54

department: Div. Molecular Medicine

country: Croatia

institute: Rudjer Boskovic Institute

description:
Amount: 15µg fragmented cRNA
Amplification: cDNA (superscript II, Invitrogen), cRNA (ENZO, one cycle)

hyb_protocol: 1. Hybridization: 16 hours at 45°C and 60rpm, Affymetrix GeneChip Hybridization Oven 640, Affymetrix Fluidics Station 400 2. Washing and Staining: Post Hyb Wash #1: 10 cycles of of 2 mixes/cycle with Wash Buffer A at 25°C Post Hyb Wash #2:4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C Post Stain Wash:10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C 2nd Stain:Stain the probe array for 10 minutes in antibody solution at 25°C 3rd Stain:Stain the probe array for 10 minutes in SAPE solution at 25°C Final Wash:15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C 3. Buffers: Hybridization Buffer:100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20 Wash Buffer A: Nonstringent 6x SSPE, 0.01% Tween 20 Wash Buffer B: Stringent 100 mM MES, 0.1 M [Na+], 0.01% Tween 20 Stain Buffer:100 mM MES, 1 M [Na+], 0.05% Tween 20 SAPE Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin Antibody Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 0.1 mg/ml Normal Goat IgG, 3 μg/ml biotinylated Anti-Streptavidin

scan_protocol: Pixel Size: 3µm Filters: 570nm Number of Scans: 2 Agilent GeneArray Scanner Affymetrix Microarray Suite 5.0

label: Biotinylated Oligonucleotides

organism: Homo sapiens

source_name: oral squamous cell carcinoma

label_protocol: Biotinylated Oligonucleotides as provided in the IVT Labeling Kit (Affymetrix) following the instructions of the manufacturer.

growth_protocol: Cells were cultured in Dulbecco's modified Eagle medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, Life Technologies), 100ug/mL streptomycin, 2mM glutamine, 100 U/ml penicillin in humidified chamber with 5% CO2, at 37C

extract_protocol:
* TRIzol Reagent (Life Technologies)
* RNeasy mini spin columns followed by on-column DNase digestion (Qiagen) according to manufacturer’s instructions

treatment_protocol: CAL 27 cells stable transfected with pEGFPC1-nm23-H2 (overexpressing nm23-H2)

tag: Strain/Line

value: CAL 27 cells transfected with pEGFPC1-nm23-H2

tag: Cell line

value: oral squamous cell carcinoma

tag: Cell type

value: CAL 27 cells

tag: Disease state

value: poorly differentiated, G3 cells


title: G88:9-1 callus (cy5), A78:3-1 callus (cy3) 12326350

tag: A78:3-1, asCCR transformed line.


title: G88:5-2 callus (cy5), A78:3-2 callus (cy3) 12316332


title: A78:3-1 callus.l2 (cy5), G88:5-1 callus.l1 (cy3) 12316329

tag: A78:3-1, transgenic asCCR line.

tag: G88:5-1, transformed control.


title: Embryo vs. Callus BP2

status: Public on Dec 25 2006

city: New Haven

first: Kun

last: He

state: CT

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

institute: Yale University

description: Identification of genes differentially expressed during formation of somatic embryos.

hyb_protocol: 42C 50% formamide

scan_protocol: Axon GenePix 4000B

data_processing: To identify and remove systematic sources of variation, spot intensities from the GenePix Pro output files of all repeats of a given sample pair were normalized using the limma package in R. The print-tip lowess normalization method was used.

organism: Oryza sativa

source_name: Callus (reference)

label_protocol: amino-allyl and monofunctional dye

extract_protocol: Trizol/RNeasy

tag: indica rice cultivar 93-11

source_name: Embryo (experiment)


title: Root Vs. Embryo BP1

description: Identification of genes differentially expressed during formation of roots.

source_name: Embryo (reference)

source_name: Root (experiment)


title: Shoot Vs. Embryo BP1

description: Identification of genes differentially expressed during formation of shoots.

source_name: Shoot (experiment)


title: Embryo vs. Callus BP1


title: Stem_717_standard_growth_plant_4

city: Gainesville

first: Matias

last: Kirst

state: FL

address: 1376 Mowry Road

department: SFRC

institute: University of Florida

description: All information has already been provided.

hyb_protocol: Hybridization was performed by NimbleGen according to company standard procedures.

scan_protocol: Scanning was performed by NimbleGen according to company standard procedures.

data_processing: VALUEs represent data that was log2 transformed and then normalized using the proc standard proceedure in SAS

organism: Populus tremula x Populus alba

source_name: stems harvested from P. tremula X P. alba hybrid INRA 717-1B4

label_protocol: Labeling was performed by NimbleGen according to company standard procedures.

extract_protocol:
Total RNA was isolated using the following method:Chang S, Puryear, J., Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees.  Plant Molecular Biology Reporter 11: 113-116.
cDNA was synthesized by NimbleGen following company standard operating procedures (Invitrogen SuperscriptTM Double Stranded cDNA Synthesis Kit).

tag: Cuttings from P. tremula X P. alba hybrid INRA 717-1B4 were rooted under intermittent mist for 2 weeks.  Rooted plants were then planted in 2 gallon pots in Fafard #4 mix.  Plants were grown in a greenhouse with daily fertigation of Peters Professional 20-10-20 fertilizer diluted to 4mM nitrogen using an ebb and flow bench.  Plants were grown for 45 days until harvested.


title: Mature_Leaves_Standard_Growth_Plant27

organism: Populus trichocarpa

source_name: Mature Leaves harvested from Populus trichocarpa genotype Nisqually-1

tag: Cuttings from Nisqually-1 were rooted under intermittent mist for 2 weeks.  Rooted plants were then planted in 2 gallon pots in Fafard #4 mix.  Plants were grown in a greenhouse with daily fertigation of Peters Professional 20-10-20 fertilizer diluted to 4mM nitrogen using an ebb and flow bench.  Plants were grown for 45 days until harvested.


title: Embryo vs. Callus BP3


title: Young_Leaves_Standard_Growth_Plant44

source_name: Young leaves harvested from Populus trichocarpa genotype Nisqually-1


title: Shoot Vs. Embryo BP2


title: Roots_Standard_Growth_Plant44

source_name: Roots harvested from Populus trichocarpa genotype Nisqually-1


title: Young_Leaves_Standard_Gowth_Plant4


title: stem_717_standard_growth_plant7

source_name: stem harvested from P. tremula X P. alba hybrid INRA 717-1B4


title: Leaf_717_standard_growth_plant_7

source_name: Leaves harvested from P. tremula X P. alba hybrid INRA 717-1B4


title: Root Vs. Embryo BP3


title: Root Vs. Embryo BP2


title: Internodes_Standard_Growth_Plant1

source_name: Internodes harvested from Populus trichocarpa genotype Nisqually-1


title: Young_Leaves_Standard_Growth_Plant1


title: Nodes_Standard_Growth_Plant44

source_name: Nodes harvested from Populus trichocarpa genotype Nisqually-1


title: Young_Leaves_Standard_Growth_Plant27


title: Mature_Leaves_Standard_Growth_Plant1

source_name: Mature leaves harvested from Populus trichocarpa genotype Nisqually-1


title: Leaf_717_standar_growth_plant_4

source_name: leaves harvested from P. tremula X P. alba hybrid INRA 717-1B4


title: Nodes_Standard_Growth_Plant1


title: Roots_Standard_Growth_Plant4


title: Nodes_Standard_Growth_Plant4


title: Internodes_Standard_Growth_Plant4


title: Nodes_Standard_Growth_Plant 27


title: TIGR4 OD=0.2 rr09 mutant vs wt slide 159687b

status: Public on Dec 24 2006

city: Rotterdam

first: Wouter

last: Hendriksen

address: Dr. Molewaterplein 50

department: Pediatrics

country: Netherlands

institute: Erasmus MC

hyb_protocol: for experimental protocols see: Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent

data_processing: MicroPreP (PMID: 15907200)

organism: Streptococcus pneumoniae

source_name: TIGR4 rr09 mutant

tag: TIGR4 rr09 mutant

source_name: TIGR4 wild-type

tag: TIGR4 wild-type


title: Roots_Standard_Growth_Plant1

source_name: Roots  harvested from Populus trichocarpa genotype Nisqually-1


title: TIGR4 OD=0.2 rr09 mutant vs wt slide 159685b

scan_protocol: for experimental protocols see: Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent


title: Root Vs. Embryo AP1


title: Root Vs. Embryo AP3


title: D39 OD=0.2 rr09 mutant vs wt slide 159672b

source_name: D39 wild-type

label_protocol: for experimental protocols see: Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent

tag: D39 wild-type

source_name: D39 rr09 mutant

tag: D39 rr09 mutant


title: TIGR4 OD=0.1 rr09 mutant vs wt slide 164690b

extract_protocol: for experimental protocols see: Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent


title: Embryo vs. Callus AP3

source_name: Embryo (experiment)

source_name: Callus (reference)


title: TIGR4 OD=0.1 rr09 mutant vs wt slide 159669b

description: see: Hendriksen et al. 2006. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is Strain-Dependent


title: Internodes_Standard_Growth_Plant44


title: Shoot Vs. Embryo AP2

source_name: Embryo (reference)

source_name: Shoot (experiment)


title: D39 OD=0.2 rr09 mutant vs wt slide 159670b


title: Root Vs. Embryo AP2

source_name: Root (experiment)


title: Embryo vs. Callus AP2


title: TIGR4 OD=0.2 rr09 mutant vs wt slide 159668b


title: Embryo vs. Callus AP1


title: TIGR4 OD=0.1 rr09 mutant vs wt slide 159689b


title: Mature_Leaves_Standard_Growth_Plant44


title: Roots_Standard_Growth_Plant27

source_name: Roots harvested from Populus trichocarpa genotype Nisqually-1


title: D39 OD=0.2 rr09 mutant vs wt slide 159674b


title: D39 OD=0.1 rr09 mutant vs wt slide 159671b


title: Shoot Vs. Embryo AP1


title: Internodes_Standard_Growth_Plant27


title: D39 OD=0.1 rr09 mutant vs wt slide 159675b


title: D39 OD=0.1 rr09 mutant vs wt slide 159673b


title: Mature_Leaves_Standard_Growth_Plant4


title: 500microg/L_Zn_Exposed_rep3B

status: Public on Dec 22 2006

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

hyb_protocol: see the protocols at the website of Dr. Patrick O. Brown's laboratory at Stanford University

scan_protocol: Scanning was performed using an arrayWoRx Biochip Reader (Applied Precision, Issaquah, WA)

data_processing: Signal intensities determined by GenePix software version 3.01 (Axon Instruments, Union City, CA)

organism: Daphnia magna

source_name: whole organism, exposed 24-h to 500 microg/L Zn

growth_protocol: Genetically homogeneous Daphnia magna, purchased from Aquatic Research Organisms (Hampton, NH), were cultured in COMBO modified for water hardness (Kilham et al. 1998) and kept at 23.50 C in a Percival environmental chamber with a 16-hour light/ 8 hour dark cycle. The D. magna were maintained on a diet of YCT and Selenastrum capricornatum (Aquatic Research Organisms, Hampton, NH). Stock culture medium was renewed, cultures were fed, and neonates were separated from adults three times weekly.

extract_protocol: Trizol method (invitrogen)

treatment_protocol: 24-h waterbourne exposure to 500 microg/L Zinc Chloride

tag: Daphnia magna

value: Aquatic Research Organisms

tag: Age

source_name: whole organism, unexposed

extract_protocol: Trizol method (Invitrogen)

treatment_protocol: untreated 24 hours


title: 500microg/L_Zn_Exposed_rep4B

label_protocol: see the protocols at the website of Dr. Patrick O. Brown's laboratory at Stanford University


title: 500microg/L_Zn_Exposed_rep1A


title: 18microg/L_Cd_Exposed_rep2B

source_name: Chriswhole organism, exposed 24-h to 18 microg/L Cd

treatment_protocol: 24-h waterbourne exposure to 18 microg/L Cadmium Sulfate


title: 500microg/L_Zn_Exposed_rep3A


title: 500microg/L_Zn_Exposed_rep1B


title: Skin_Involved_GJ14

status: Public on Dec 23 2006

city: Nijmegen

first: Gys

middle: de

last: Jongh

state: Gelderland

address: Rene Descartesdreef 1

department: Dermatology

institute: Nijmegen Centre for Molecular Life Sciences

description: The study participants included patients with a clinical diagnosis of moderate to severe chronic plaque psoriasis and patients with moderate to severe chronic atopic dermatitis. None of the patients received systemic therapy or UVB-therapy at the time of biopsy taking, and patients were asked to discontinue the use of topical steroids at the biopsy site 2 wk before taking biopsy.Patients were allowed to use emollients. Punch biopsies were taken from chronic psoriasis plaques and from chronic atopic dermatitis lesions. Care was taken to exclude acute lesions or lesions with crusts or vesicles.In this experiment each patient was included only once.The medical ethical committee approved the study and all volunteers gave written informed consent. The study was conducted according to the Declaration of Helsinki principles.

hyb_protocol: Microarrays were blocked with 0.1% SDS, 0.1M Tris/HCl, 50 mM ethanolamine, pH 9.0 for 30 min at 50 degrees C. Washing was with 0.1% SDS , 4 x SSC (Invitrogen) for 30 min at 50 degrees C and with 0.1% SDS , 5 x SSC , 1% bovine serum albumin fraction V (Sigma-Aldrich Chemie B.V., Zwijndrecht The Netherlands) for 30 min at 42 degrees C. After the last wash with water the microarrays were spun to dryness. No agitation was applied during wash steps. Microarrays were not allowed to dry between wash steps. After each buffer the microarrays were washed extensively in water.The two coupling reactions were mixed. To prevent non-specific hybridisation 1.5 microliter poly-dA 10 mg/ml (Amersham) and 7.5 microliter Cot1 DNA 1 mg/ml (Invitrogen) was added. The volume was reduced to 50 microliter by vacuum centrifugation, heated for 3 min at 95 degrees C, cooled to 42 degrees C and supplemented with 50 microliter 2 x hybridisation mix: 50% formamide, 10 x SSC and 0.2% SDS. The 100 microliter hybridisation solution was and applied under a lifterslip (Erie Scientific, Portsmouth USA) to the microarry , pre-warmed to 42 degrees C. The microarray was mounted in a hybridisation chamber (Hybchamber Genemachines , San Carlos CA USA). The hybridisation chamber was incubated under water in a waterbath at 42 degrees C for 40 h. After hybridisation the microarrays was subjected to stringent sequential washings, and spun to dryness.

scan_protocol: Microarrays were scanned with a GenePix 4100A Laserscanner.The images were analysed with GenePix Pro 5.0 Microarray and analysis software.

data_processing:
1)All spots that are not real Genes were deleted because in our view this would greatly distort the regression procedure to follow.This included the non-printed spots , spots printed from an empty well , all control substances included by Antropogenetics that have a SPOT_ID.This yielded 18664 spots with real genes which were all measured once.

2)In channel 1 was a sample from a psoriatic patient labelled with Cy5 measured at 635 nm.In channel 2 was a sample from an Atopic patient labelled with Cy3 measured at 532 nm.For all measurements we used the median value of the measured pixels.

3)Let :
F635Median = Cy5 Signal, psoriatic patient, median of pixels
B635Median = Cy5 Background, psoriatic patient, median of pixels
F532Median = Cy3 Signal, Atopic patient, median of pixels
B532Median = Cy3 Background, Atopic patient, median of pixels

4)If F635Median =< B635Median than F0=0 otherwise F0 = 2Log(F635Median- B635Median).So negative values are replaced with 2^0 = 1

5)If F532Median =< B532Median than T0=0 otherwise T0 = 2Log(F532Median - B532Median).So negative values are replaced with 2^0 = 1

6)R0=(F0-T0)

7)A0=(F0+T0)/2

8)Select a spot for further analysis if at least one of the values F0 or T0 is > 4 . So a spot will be selected if it is "visible" in at least 1 channel or the net fluorescence is greater than 16 in at least 1 channel.The advantage of this procedure is that very high regulated genes (not visible in channel 1 but very high in channel 2) are not missed.The drawback is that very high regulated genes are measured with less precission.

9)The central paradigma for microarrays with spotted oligo's says that if a spot contains a bit more material by chance than there will be more of both substances in the spot and the Ratio of the channels will thus not change.So a plot of R0=Y against A0=X should be a straight line on the X-axis because most genes will not be regulated.In a less perfect world this plot shows a trend.The trend can ofcourse be removed by taking the trend line as the new X-Axis as follows :

10)For each pair (R0 , A0) R0 is predicted by a Lowess regression line (Y=R0 and X=A0)from A0.Let this be Rp.Let Rn be the distance from R0 to the Lowes regression line or Rn=R0-Rp

11)VALUE=Rn=R0-Rp is , in our view , the normalised 2log ( Psoriasis/Atopie) because a plot of Rn=Y against A0=X will now be a straight line on the X-axis because most genes are not regulated.Or :

VALUE=2Log( Psoriasis / Atopie ) , normalised over all samples by Lowess regression

source_name: Epidermis from severe chronic plaque psoriasis

label_protocol:
Amplification of total RNA
Two microgram of total RNA was dried by vacuum centrifugation at 35 degrees C. RNA was amplified with a protocol developed by Van Gelder (Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH:  Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. U. S. A 87:1663-1667, 1990) with the aid of  the Message Amp kit (Ambion, Huntingdon Cambridgeshire United Kingdom). Amplified antisense RNA (aRNA) was labelled according to ‘t Hoen ('t Hoen PA, de Kort F, van Ommen GJ, den Dunnen JT:  Fluorescent labelling of cRNA for microarray applications. Nucleic Acids Res. 31:e20, 2003). Briefly, during in vitro transcription the 7.5mM UTP in the Message Amp kit was replaced by 4.5mM UTP and 3.0 mM amino-allyl-UTP (Ambion, Huntingdon Cambridgeshire United Kingdom). The amount of labelled aRNA was determined spectrophotometrically and the molecular weight distribution was analyzed by denaturing formaldehyde gel electrophoresis (see above). We obtained 14 - 70 microgram labelled aRNA from 2 microgram total RNA, with the expected molecular weight distribution of 500-3000 nucleotides.
Coupling of dyes
One vial monoreactive dye Cy5, Amersham Biosciences Europe GmbH, Roosendaal The Netherlands) was dissolved in 20 microliter dry, pure DMSO divided in 2 microliter aliquots, dried to complete dryness by vacuum centrifugation and stored desiccated at 4 degrees C. Two microgram of amino-allyl modified aRNA was dissolved in 3.33 microliter water, 5.00 microliter DMSO , 1.67 microliter 0.3M carbonate buffer pH 9.0 and added to an aliquot of monoreactive dye. The mixture was incubated for 1h at room temperature in the dark and stopped by adding 4.5 microliter 4M hydroxylamine (Merck, Amsterdam, The Netherlands). The reaction product was purified on a microcon YM-30 membrane (Millipore, Amsterdam, The Netherlands) by 3 x 500 microliter washes and eluted from the membrane with 100 microliter water. This resulted in probe solutions with an absorbance of 0.15 - 0.20 at 650 nm using a 1 cm cuvet.

extract_protocol: Total RNA was purified from epidermal sheets by phenol/chloroform guanidine isothiocyanate extraction (Trizol, Invitrogen, Groningen, The Netherlands), followed by selective binding to a silica membrane (RNeasy, Qiagen, Venlo, The Netherlands) according to the manufacturer’s protocols with slight modifications. The aquous layer from the Trizol purification was mixed with one volume of 70% ethanol and applied to the RNeasy column. The column was eluted in 2 x 50 microliter water. Concentrations of RNA were determined spectrophotometrically (Shimadzu UV-160 A, 's-Hertogenbosch The Netherlands) in disposable, individually packed, RNase-free cuvettes (Uvette, Eppendorf AG , Hamburg Germany). The integrity of the RNA was assessed by electrophoresis of about 0.1 microgram RNA ,together with RNA markers, on a denaturing formaldehyde gel. (Millennium Markers, Northern Max 10x running buffer, Northern Max 10x denaturing gel buffer, all from Ambion, Huntingdon Cambridgeshire United Kingdom). After staining with SybrGold (Molecular Probes, Leiden, The Netherlands) clear ribosomal bands and absence of low molecular degradation products were seen in all samples. RNase inhibitor (Roche Diagnostics , Mannheim Germany) was added to a concentration of 50 Units/ml and RNA solutions were stored at -70 degrees C for further processing. About 3 - 6 microgram of total RNA was routinely obtained from a 4 mm diameter epidermal sheet.

treatment_protocol:
Preparation of pure epidermal tissue
In order to examine gene expression patterns exclusively in the epidermis we have previously developed a protocol that allows rapid separation of the epidermis from the underlying dermis under conditions that would minimize de novo expression or degradation of mRNA transcripts during the isolation procedure  (van Ruissen F, Jansen BJ, de Jongh GJ, Zeeuwen PL, Schalkwijk J:  A partial transcriptome of human epidermis. Genomics 79:671-678, 2002). Briefly, biopsies were taken with a 4 mm punch and immediately transferred in dispase solution at 4 degrees C. After 4-5 hours incubation at 4 degrees C, the epidermis could be removed in total and processed for mRNA isolation. We have previously shown by histology and mRNA analysis that normal and acanthotic epidermis could be reliably isolated, and none of the epidermal cell sub-populations was preferentially lost.

source_name: Epidermis from moderate to severe chronic atopic dermatitis

label_protocol:
Amplification of total RNA
Two microgram of total RNA was dried by vacuum centrifugation at 35 degrees C. RNA was amplified with a protocol developed by Van Gelder (Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH:  Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. U. S. A 87:1663-1667, 1990) with the aid of  the Message Amp kit (Ambion, Huntingdon Cambridgeshire United Kingdom). Amplified antisense RNA (aRNA) was labelled according to ‘t Hoen ('t Hoen PA, de Kort F, van Ommen GJ, den Dunnen JT:  Fluorescent labelling of cRNA for microarray applications. Nucleic Acids Res. 31:e20, 2003). Briefly, during in vitro transcription the 7.5mM UTP in the Message Amp kit was replaced by 4.5mM UTP and 3.0 mM amino-allyl-UTP (Ambion, Huntingdon Cambridgeshire United Kingdom). The amount of labelled aRNA was determined spectrophotometrically and the molecular weight distribution was analyzed by denaturing formaldehyde gel electrophoresis (see above). We obtained 14 - 70 microgram labelled aRNA from 2 microgram total RNA, with the expected molecular weight distribution of 500-3000 nucleotides.
Coupling of dyes
One vial monoreactive dye Cy3, Amersham Biosciences Europe GmbH, Roosendaal The Netherlands) was dissolved in 20 microliter dry, pure DMSO divided in 2 microliter aliquots, dried to complete dryness by vacuum centrifugation and stored desiccated at 4 degrees C. Two microgram of amino-allyl modified aRNA was dissolved in 3.33 microliter water, 5.00 microliter DMSO , 1.67 microliter 0.3M carbonate buffer pH 9.0 and added to an aliquot of monoreactive dye.The mixture was incubated for 1h at room temperature in the dark and stopped by adding 4.5 microliter 4M hydroxylamine (Merck, Amsterdam, The Netherlands). The reaction product was purified on a microcon YM-30 membrane (Millipore, Amsterdam, The Netherlands) by 3 x 500 microliter washes and eluted from the membrane with 100 microliter water. This resulted in probe solutions with an absorbance 0.20 - 0.30 at 550 nm using a 1 cm cuvet.


title: Skin_Involved_GJ12

tag: The study participants included patients with a clinical diagnosis of moderate to severe chronic plaque psoriasis and patients with moderate to severe chronic atopic dermatitis. None of the patients received systemic therapy or UVB-therapy at the time of biopsy taking, and patients were asked to discontinue the use of topical steroids at the biopsy site 2 wk before taking biopsy.Patients were allowed to use emollients. Punch biopsies were taken from chronic psoriasis plaques and from chronic atopic dermatitis lesions. Care was taken to exclude acute lesions or lesions with crusts or vesicles.In this experiment each patient was included only once.The medical ethical committee approved the study and all volunteers gave written informed consent. The study was conducted according to the Declaration of Helsinki principles.


title: Skin_Involved_GJ10


title: BxPC3 empty_vector

city: Tokyo

first: Wataru

last: Fujibuchi

state: Tokyo

address: 2-42 Aomi, Koto-ku

department: Computational Biology Research Center

country: Japan

institute: Advanced Industrial Science and Technology

description: Twist 1 expression was significantly associated with MSX2 expression in human pancreatic carcinomas and was down-regulated in MSX2 pancreatic cancer cells by transfected with a small interfering RNA expression vector to inactivated MSX2.

hyb_protocol: 10ug aliquots of total RNA was faragmented at 94C for 20 min in the presence of magnesium. The fragmented RNA was hybridized to Uniset Human Whole Genome Expression Bioarray slides in hybridization buffer at 37C for 24 hours in an INNOVATM 4080 Shaking Incubator (New Brunswick Scientific, Edison, NJ) at 300rpm. After hybridization the arrays were washed in 0.75x TNT buffer at 46C for 1 hour followed by incubation with Cy5-streptavidin at room temperature for 30 min in the dark. Arrays were then washed in 1x TNT four times for 5 min each followed by a rinse in 0.1x SSC/0.05% Tween 20 in water. The slides were then dried by centrifugation and kept in the dark until scanning.

scan_protocol: Array slides were scanned using an Array worx (GE Healthcare Bio-Sciences Corp., Piscatway, NJ), and expression values were measured and manipulated subsequently by CodeLinkTM Expression Analysis v.4.0 software (Amersham Biosciences).

data_processing: Processed by CodeLinkTM Expression Analysis v.4.0 software (Amersham Biosciences).

source_name: B3-EV, human pancreatic cancer cell line BxPC3 with empty vectors

label_protocol: Incubation with Cy5-streptavidin at room temperature for 30 min in the dark.

growth_protocol: Grown in modified Eagle’s medium (MEM, Invitrogen, Grand Island, NY) containing 10% fetal bovine serum (Miles, Kankakee, IL), maintained at 37C in 5% CO2 in a humidified environment.

extract_protocol: Procedures were performed according to the manufacturer (CodeLinkTM, whole Human Genome Expression Bioarray, Amersham Biosciences) ’s protocol.

treatment_protocol: Transfections of cells with expression vectors (MSX2 cDNA or vector alone) were performed using FuGENE 6 (Roche, Indianapolis, IN) as recommended by the supplier and cell lines were selected with 800ug/ml of G418 (Invitrogen).

tag: Tissue:pancreatic cancer cell line


title: D39 OD=0.1 rr09 mutant vs wt slide 164692b


title: 500microg/L_Zn_Exposed_rep2A


title: 18microg/L_Cd_Exposed_rep1B

source_name: whole organism, exposed 24-h to 18 microg/L Cd

source_name: untreated 24 hours


title: 18microg/L_Cd_Exposed_rep3B


title: 18microg/L_Cd_Exposed_rep2A


title: BxPC3 MSX2_vector

source_name: B7, MSX2-overexpressing BxPC3 with expression vectors


title: Skin_Involved_GJ16


title: 18microg/L_Cd_Exposed_rep3A


title: Skin_Involved_GJ11


title: 18microg/L_Cd_Exposed_rep1A


title: Candida glabrata transcription profile when grown in human urine (Exp 3-1)

city: Baltimore

first: Brendan

last: Cormack

state: MD

address: Hunterian Building 617, 725 N. Wolfe St.

department: Molecular Biology & Genetics

institute: Johns Hopkins Univ. School of Medicine

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM.

hyb_protocol: Both Cy5- and Cy3- cDNA probes were resuspened into hybridization buffer (35% formamide, 5*SSC, 0.1%SDS, 0.1 mg/ml denatured salmon sperm DNA) and combined to a total volume of 40 ul. The probe mix was denatured at 100 C for 10 s and quickly cooled on ice, then it was added on a microarray slides. The slides was covered with a cover glass and incubated in a chamber (Corning) at 42 C for 16-18 hrs. The washing protocol follows the manual for UltraGAPS coated slides (Corning).

scan_protocol: Hybridized slides was scaned by Axon 4000B microarray scanner with 100% power and PMT ranging 600-800. Data were acquired by Axon GenePix 5.0 software.

data_processing: The median signal captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate C. glabrata gene expression change when grown in human urine.

organism: Nakaseomyces glabratus

source_name: C. glabrata grown in urine sample #3 (Exp 3-1)

label_protocol: 20 ug of total RNA was used to synthesize Cy5-cDNA probes with an anchor primer [(dT)18(dA/dG/dC)] in the presence of Cy5-dCTP (PerkinElmer) using SuperscriptTM III reverse transcriptase (Invitrogen). The probe was purified using MinElute TM reaction Cleanup kit (Qiagen) and vaccum dried.

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 200 ml human urine sample #3 (supplemented with 2% glucose and filter sterilized) with an initial O.D.600 of 0.1. The cells were harvested after incubation at 30C in a floor shaker (150 rpm) for 5.5 hrs when O.D. reached 0.45.

extract_protocol: The cell pellet was disrupted using 0.5 mm glass beads in a fast bead-beater. Total RNA was extracted using acid phenol. The RNA was further purified by RNeasy Mini kit (Qiagen).

tag: Log phase C. glabrata cells grown in human urine supplemented with 2% glucose

source_name: C. glabrata grown in synthetic complete medium

label_protocol: same as above

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 200 ml SC medium with an initial O.D.600 of 0.1. The cells were harvested after an incubation at 30C in a floor shaker (150 rpm) for 4 hrs when O.D. reached 0.5.

extract_protocol: same as above

tag: Log phase C. glabrata cells grown in synthetic complete medium (SC medium, see Qbiogene catalog)


title: Skin_Involved_GJ13


title: 6microg/L_Cu_Exposed_rep3B

source_name: whole organism, exposed 24-h to 6 microg/L Cu

treatment_protocol: 24-h exposure to 6 microg/L Copper Sulfate


title: 6microg/L_Cu_Exposed_rep2A


title: Candida glabrata transcription profile when grown in human urine (Exp 2-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM152119.

source_name: C. glabrata grown in urine sample #2 (Exp 2-1)

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 200 ml human urine sample #2 (supplemented with 2% glucose and filter sterilized) with an initial O.D.600 of 0.1. The cells were harvested after incubation at 30C in a floor shaker (150 rpm) for 5.5 hrs when O.D. reached 0.6.


title: Candida glabrata transcription profile when grown in human urine (Exp 3-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM152130.

source_name: C. glabrata grown in urine sample #3 (Exp 3-2)


title: 6microg/L_Cu_Exposed_rep2B

tag: untreated 24 hours


title: Candida glabrata transcription profile when grown in human urine (Exp 1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM151934.

source_name: C. glabrata grown in urine sample #1 (Exp 1-2)

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 200 ml human urine sample #1 (supplemented with 2% glucose and filter sterilized) with an initial O.D.600 of 0.1. The cells were harvested after incubation at 30C in a floor shaker (150 rpm) for 5.5 hrs when O.D. reached 0.55.


title: 6microg/L_Cu_Exposed_rep3A


title: Candida glabrata transcription profile in response to Niacin limitation (Exp.2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM151880.

data_processing: The median signal captured from Cy5-channel (F635) and from Cy3-channel (F532) was used to calculate C. glabrata gene expression change in response to Niacin limitation

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 250 ml synthetic complete medium (containing 3.25 uM of nicotinic acid) with an initial O.D.600 of 0.07. The cells were harvested at hr 5 after an incubation at 30C in a floor shaker (150 rpm) when O.D. reached 0.6.

tag: Log phase C. glabrata cells grown in synthetic complete medium (containing 3.25 uM nicotinic acid)

source_name: C. glabrata grown under Niacin limitation

label_protocol: Same as above

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 250 ml synthetic medium containing 0.016 uM of nicotinic acid with an initial O.D.600 of 0.06. The cells were harvested at hr 5.5 after an incubation at 30C in a floor shaker (150 rpm) when O.D. reached 0.66.

extract_protocol: Same as above

tag: Log phase C. glabrata cells grown in synthetic medium containing 0.016 uM nicotinic acid


title: 6microg/L_Cu_Exposed_rep1B


title: Candida glabrata transcription profile when grown in human urine (Exp 1-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM152116.

source_name: C. glabrata grown in urine sample #1 (Exp 1-1)

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 200 ml SC medium  with an initial O.D.600 of 0.1. The cells were harvested after an incubation at 30C in a floor shaker (150 rpm) for 4 hrs when O.D. reached 0.5.


title: Candida glabrata transcription profile when grown in human urine (Exp 2-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 2 is deposited in GSM152118.

source_name: C. glabrata grown in urine sample #2 (Exp 2-2)


title: Candida glabrata transcription profile in response to Niacin limitation (Exp.1-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM151869.

growth_protocol: C. glabrata wild type Bg2 cells were inoculate into 250 ml synthetic medium containing 0.016 uM of nicotinic acid with an initial O.D.600 of 0.06. The cells were harvested at hr 5.5 after an incubation at 30C in a floor shaker (150 rpm) when O.D. reached 0.65.


title: Candida glabrata transcription profile in response to Niacin limitation (Exp.2-1)

description: This is experiment 1 of a dye-swap experiment. Experiment 2 is deposited in GSM151881.


title: 6microg/L_Cu_Exposed_rep1A

source_name: whole organism, unexposed

growth_protocol: Genetically homogeneous Daphnia magna, purchased from Aquatic Research Organisms (Hampton, NH), were cultured in COMBO modified for water hardness (Kilham et al. 1998) and kept at 23.50 C in a Percival environmental chamber with a 16-hour light/ 8 hour dark cycle.  The D. magna were maintained on a diet of YCT and Selenastrum capricornatum (Aquatic Research Organisms, Hampton, NH).  Stock culture medium was renewed, cultures were fed, and neonates were separated from adults three times weekly.


title: Candida glabrata transcription profile in response to Niacin limitation (Exp.1-2)

description: This is experiment 2 of a dye-swap experiment. Experiment 1 is deposited in GSM151863.


title: ZHTc6(Tc-), 0 hr, #3(16011321010148)

status: Public on Dec 21 2006

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: ZHTc6(Tc-), 72 hr

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

organism: Mus musculus

growth_protocol: The cells were derived from CGR8 ES cells and carry the transgenes for tetracycline-regulatable Oct-3/4 expression as described previously (Niwa et al., nature genetics 2000).  500000 cells were seeded on gelatinized 90 mm dish in ES medium with or without 1 uM tetracycline.

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

tag: embryonic stem cell 129/Ola male  gene knock in


title: ZHTc6(Tc-), 48 hr, #3(16011321010133)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 24 hr, #3(16011321010132)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 0 hr, #3(16011321010150)

description: ZHTc6(Tc-), 120 hr


title: ZHTc6(Tc-), 0 hr, #2(16011321010131)

description: ZHTc6(Tc-), 120 hr


title: ZHTc6(Tc-), 0 hr, #2(16011321010130)

description: ZHTc6(Tc-), 96 hr


title: ZHTc6(Tc-), 0 hr, #3(16011321010147)

description: ZHTc6(Tc-), 48 hr


title: ZHTc6(Tc-), 120 hr, #3(16011321010136)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 0 hr, #3(16011321010149)

description: ZHTc6(Tc-), 96 hr


title: ZHBTc4(Tc+), 0hr, #3(16011321010107)

description: ZHBTc4(Tc+), 120hr

source_name: ZHBTc4(Tc+), 0 hr, #3


title: ZHBTc4(Tc+), 0hr, #3(16011321010106)

description: ZHBTc4(Tc+), 96hr


title: ZHTc6(Tc-), 0 hr, #2(16011321010128)

description: ZHTc6(Tc-), 48 hr


title: ZHTc6(Tc-), 0 hr, #1(16011321010110)

description: ZHTc6(Tc-), 72 hr


title: ZHTc6(Tc-), 72 hr, #2(16011321010115)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 48 hr, #2(16011321010114)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 96 hr, #2(16011321010116)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 96 hr, #3(16011321010135)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 120 hr, #2(16011321010117)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 0 hr, #1(16011321010112)

description: ZHTc6(Tc-), 120 hr


title: ZHTc6(Tc-), 0 hr, #1(16011321010109)

description: ZHTc6(Tc-), 48 hr


title: ZHTc6(Tc-), 0 hr, #2(16011321010129)

description: ZHTc6(Tc-), 72 hr


title: ZHTc6(Tc-), 0 hr, #1(16011321010108)

description: ZHTc6(Tc-), 24 hr


title: ZHTc6(Tc-), 0 hr, #2(16011321010118)

description: ZHTc6(Tc-), 24 hr


title: ZHTc6(Tc-), 72 hr, #3(16011321010134)

description: ZHTc6(Tc-), 0 hr


title: ZHBTc4(Tc+), 0hr, #2(16011321010099)

description: ZHBTc4(Tc+), 72hr

source_name: ZHBTc4(Tc+), 0hr, #2


title: ZHBTc4(Tc+), 0hr, #3(16011321010105)

description: ZHBTc4(Tc+), 72hr


title: ZHBTc4(Tc+), 0hr, #3(16011321010103)

description: ZHBTc4(Tc+), 48hr


title: ZHTc6(Tc-), 0 hr, #3(16011321010146)

description: ZHTc6(Tc-), 24 hr


title: ZHBTc4(Tc+), 0hr, #3(16011321010104)

description: ZHBTc4(Tc+), 24hr


title: ZHTc6(Tc-), 24 hr, #2(16011321010113)

description: ZHTc6(Tc-), 0 hr


title: ZHBTc4(Tc+), 0hr, #2(16011321010100)

description: ZHBTc4(Tc+), 96hr


title: ZHBTc4(Tc+), 0hr, #2(16011321010102)

description: ZHBTc4(Tc+), 120hr


title: WTUT-136

city: Jacksonville

first: Yan

middle: W.

last: Asmann

address: 4500 San Pablo Road South

institute: Mayo Clinic

description: skeletal muscle, Transgenic mice, trained

data_processing: dChip PM-only normalized

source_name: skeletal muscle, Wild-type mice, NOT-trained

tag: Wild-type Mouse


title: WTUT-142


title: WTUT-138


title: WTUT-130


title: WTT-144

source_name: skeletal muscle, Wild-type mice, trained


title: WTUT-135


title: wtt-137


title: ZHTc6(Tc-), 0 hr, #1(16011321010111)

description: ZHTc6(Tc-), 96 hr


title: WTT-141


title: ZHBTc4(Tc+), 96hr, #3(16011321010058)

description: ZHBTc4(Tc+), 0hr


title: ZHTc6(Tc-), 24 hr, #1(16011321010066)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 120 hr, #2(16011321010070)

description: ZHTc6(Tc-), 0 hr


title: ZHTc6(Tc-), 72 hr, #1(16011321010068)

description: ZHTc6(Tc-), 0 hr


title: ZHBTc4(Tc+), 72hr, #3(16011321010057)

description: ZHBTc4(Tc+), 0hr


title: ZHBTc4(Tc+), 0hr, #2(16011321010098)

description: ZHBTc4(Tc+), 48hr


title: WTT-129


title: ZHBTc4(Tc+), 72hr, #2(16011321000113)

description: ZHBTc4(Tc+), 0hr


title: ZHBTc4(Tc+), 96hr, #2(16011321000114)

description: ZHBTc4(Tc+), 0hr


title: ZHBTc4(Tc+), 48hr, #3(16011321010056)

description: ZHBTc4(Tc+), 0hr


title: TGUT-147

source_name: skeletal muscle, Transgenic mice, NOT-trained

tag: mice over-expressing Myosine Heavy Chain -I (MHC-I)


title: wtt-134


title: ZHBTc4(Tc+), 120hr, #1(16011321000071)

description: ZHBTc4(Tc+), 0hr

treatment_protocol: Tet inducible system

source_name: ZHBTc4(Tc+), 0hr, #1


title: ZHBTc4(Tc+), 0hr, #1(16011321000068)

description: ZHBTc4(Tc+), 96hr


title: TGUT-146


title: ZHBTc4(Tc+), 0hr, #2(16011321010097)

description: ZHBTc4(Tc+), 24hr


title: ZHBTc4(Tc+), 24hr, #3(16011321010055)

description: ZHBTc4(Tc+), 0hr


title: ZHBTc4(Tc+), 48hr, #2(16011321000112)

description: ZHBTc4(Tc+), 0hr


title: TGUT-139


title: ZHBTc4(Tc+), 120hr, #2(16011321000115)

description: ZHBTc4(Tc+), 0hr


title: ZHBTc4(Tc+), 0hr, #1(16011321000059)

description: ZHBTc4(Tc+), 72hr


title: ZHBTc4(Tc+), 24hr, #2(16011321000111)

description: ZHBTc4(Tc+), 0hr


title: ZHBTc4(Tc+), 24hr, #1(16011321000056)

description: ZHBTc4(Tc+), 0hr


title: TGT-143

source_name: skeletal muscle, Transgenic mice, trained


title: ZHBTc4(Tc+), 0hr, #1(16011321000070)

description: ZHBTc4(Tc+), 120hr


title: ZHBTc4(Tc+), 0hr, #1(16011321000055)

description: ZHBTc4(Tc+), 24hr


title: TGUT-145


title: TGT-140

tag: mice over-expressing Myosine Heavy Chain -I (MH


title: ZHBTc4(Tc+), 0hr, #1(16011321000057)

description: ZHBTc4(Tc+), 48hr


title: ZHBTc4(Tc+), 48hr, #1(16011321000058)

description: ZHBTc4(Tc+), 0hr


title: ZHTc6(Tc-), 96 hr, #1(16011321010069)

description: ZHTc6(Tc-), 0 hr


title: ZHBTc4(Tc+), 72hr, #1(16011321000067)

description: ZHBTc4(Tc+), 0hr


title: ZHTc6(Tc-), 48 hr, #1(16011321010067)

description: ZHTc6(Tc-), 0 hr


title: daf19(WT)_daf12(sa204) replicate 2

city: Vancouver

first: BCGSC

last: BC Cancer Agency

state: BC

address: 675 West 10th Avenue

department: Gene Expression

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

description: Extracted RNA was subjected to rigorous quality assessment and quantitation using the RNA Nano LabChip Kit (Agilent Technologies) with the 2100 Bioanalyzer (Agilent Technologies). Numerical measures of RNA quality (rRNA ratio, RNA Integrity Number) were employed to ensure the high quality of extracted RNA.

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using fluidics script EukGE-WS2v4_450.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and scaling to all probe sets with a target signal value of 500 and normalization of 1.

organism: Caenorhabditis elegans

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: solid media

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) coupled with phase lock gel tubes (Eppendorf)

treatment_protocol: Eggs were prepared from gravid adults using a hypochlorite treatment (www.protocol-online.org), resuspended in 10 mM Tris-EDTA (pH 7.5) and stored at –80 oC. Thawed embryos were disrupted using syringes fit with a 26-gauge needle.

tag: whole worm preparation

tag: embryo


title: ZHBTc4(Tc+), 120hr, #3(16011321010059)

description: ZHBTc4(Tc+), 0hr


title: TGT-132


title: TGT-133


title: daf19(m86)_daf12(sa204) replicate 2


title: daf19(WT)_daf12(sa204) replicate 1


title: siTcl1(560uM)(251147218840)

description: Universal Mouse Reference RNA

growth_protocol: EB5 ES cells were transfected with siRNA. After transfection, cells were cultured for 24 hours, following by culturerin for more 24 hours in the presence of puromycin to ensure concentration of transfectants.

extract_protocol: standard method

tag: embryonic stem cell 129/Ola male  gene knock down

source_name: Universal Mouse Reference RNA

tag: Universale Mouse Reference


title: TGT-128


title: daf19(m86)_daf12(sa204) replicate 1


title: siTcl1(1120uM)(251147218943)

description: Universal Mouse Reference RNA


title: siGFP(251147218839)

description: Universal Mouse Reference RNA

source_name: siGFP


title: Panicle S3

status: Public on Dec 19 2006

first: Xiangfeng

last: Wang

address: 352 OML, 165 Prospect st

department: MCDB

description: Panicle S3

hyb_protocol: For hybridization to the rice array, we combined the labeled probe with 1 uL of 20 X SSPE (1 X SSPE is 0.115 M NaCl, 10 mM sodium phosphate, and 1 mM EDTA, pH 7.4), 1 uL of blocking solution, and 16 uL of hybridization solution to a final volume of 25 uL. This mixture was incubated at 90C for 2 min, cooled on ice, applied to the prehybridized microarray, covered with a cover slip, and incubated in a GeneMachines hybridization chamber at 42	C air for 16 to 20 hr. After 16 to 20 hr of incubation, the array was washed with 2 X SSC and 0.1% SDS, 0.2 X SSC and 0.1% SDS, 0.2 X SSC, and 0.02 X SSC for 10 min at room temperature. After washing, the slide was dried by spinning at 1100g for 5 minitues.

scan_protocol: Hybridized microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) with an Axon GenePix 4000B scanner (Foster City, CA) at 10-nm resolution, generating two separate TIFF images. Photomultiplier tube (PMT) voltages were adjusted manually to minimize background and to reduce the percentage of spots on the array with saturated signal values. The normalization of the two channels with respect to signal intensity also was achieved by adjusting the PMT voltage settings to result in a signal ratio of Cy3:Cy5 for the majority of control genes as close to 1.0 as possible.

data_processing: Microarray data were analyzed with Limma R Package program (Smyth et al., 2005), Print Tip Loess method was used to do normalization within a slides and Quantile method was performed to do normalization between replicates. Based on the distribution of negative controls within each slide, we determined an experimental cutoff for non-specific hybridization, and 90% of those negative controls have signals below this cutoff.

source_name: Panicle S3

label_protocol: For each sample, 100 ¦Ìg of total RNA was labeled with aminoallyl-dUTP (Sigma-Aldrich) by reverse transcription. After reverse transcription for 3 to 4 h, template RNA was degraded. The aminoallyl-dUTP¨Clabeled cDNAs were purified using a Microcon YM-30 filter (Millipore) and resuspended in 0.1 M NaHCO3. The cDNA probe was further fluorescently labeled by conjugating monofunctional Cy3 or Cy5 dye to the aminoallyl functional groups. After coupling at room temperature for 1 h, the labeling reaction was stopped by ethanolamine. The fluorescent dye¨Clabeled probe was separated from unincorporated dye using the QIAquick PCR purification kit (Qiagen) and concentrated for hybridization using a Microcon YM-30 filter.

growth_protocol: stage 1 (D1), the relative water content (RWC) in leaves was around 90-95%, and the leaf rolled slightly; stage 2 (D2), RWC was around 80-85%, and the leaf half rolled; stage 3 (D3), RWC in leaf was around 70-75%, the leaft rolled completely. For rehydration (D3R), at first the plants were subjected to drought treatment till the leaf rolled completely, then gave back enough water and samples were collected after 48-hour water recovery. For samples collection under high-salinity treatment (200mM NaCl), the plants of same growing stages as drought stress were used (also including three time-course points, S1, S2, and S3). Visible phenotype (leaf rolling) and RWC during the stress process were used as the criteria to collect samples.

extract_protocol: Total RNA was prepared from frozen samples using RNAwiz reagent (Ambion Co.)

tag: Panicle S3

source_name: Panicle without treatment as control sample


title: ZHBTc4(Tc+), 96hr, #1(16011321000069)

description: ZHBTc4(Tc+), 0hr


title: ZHTc6(Tc-), 0 hr, #1(16011472015649)

description: Universal Mouse Reference RNA


title: ZHTc6(Tc-), 0 hr, #2(16011472015650)

description: Universal Mouse Reference RNA


title: ZHBTc4(Tc+), 0hr, #3(16011472011833)

description: Universal Mouse Reference RNA


title: Panicle S1

description: Panicle S1

source_name: Panicle S1

tag: Panicle S1

tag: Panicle without treatment as control sample


title: ZHBTc4(Tc+), 0hr, #2(16011472010020)

description: Universal Mouse Reference RNA


title: Panicle D5

description: Panicle D5

source_name: Panicle D5

tag: Panicle D5


title: ZHBTc4(Tc+), 0hr, #1(16011472010019)

description: Universal Mouse Reference RNA


title: slim1-2-S1500, biological rep1

city: Yokohama

first: Akiko

last: Maruyama-Nakashita

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Plant Science Center

description: Gene expression data from root of slim1-2 plants vertically grown for 10 days on S1500 medium.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Agilent Technologies, Palo Alto, CA).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

source_name: Roots of slim1-2 plants

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

growth_protocol: Arabidopsis plants (Col-0) were grown at 22C under 16 h/8 h light and dark cycles for 10 days. Plants were grown on mineral nutrient media (Hirai et al. 1995 Plant Cell Physiology 36: 1331) containing 1% sucrose, 0.8% agar. For preparation of agar medium, agar was washed twice with 1 L of de-ionized water and vacuum filtrated. The agar medium with complete replacement of MgSO4 to MgCl2 contained approximately 10 µM of residual sulfate derived from agar. The S1500 agar media were prepared by adding 1500 µM of MgSO4.

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Root samples were transferred to liquid nitrogen before RNA extraction.

tag: slim1-2 was isolated as a response less mutant to sulfur limitation stress indicated as the GFP fluorescence of PSULTR1;2-GFP plants. The parental plant, PSULTR1;2-GFP plants, is the Arabidopsis thaliana cv. Columbia transformed with the T-DNA construct of pBI101 harbouring promoter region of SULTR1;2 fused to GFP (Maruyama-Nakashita et al. 2004 Plant Journal 38

tag: Tissue

value: roots


title: Panicle D3

description: Panicle D3

source_name: Panicle D3

tag: Panicle D3


title: Panicle D2

description: Panicle D2

source_name: Panicle D2

tag: Panicle D2


title: slim1-2-S1500, biological rep2


title: Shoot S2

description: Shoot S2

source_name: Shoot S2

tag: Shoot S2

source_name: Shoot without treatment as control sample


title: slim1-2-S15, biological rep2

description: Gene expression data from root of slim1-2 plants vertically grown for 10 days on S15 medium.

growth_protocol: Arabidopsis plants (Col-0) were grown at 22C under 16 h/8 h light and dark cycles for 10 days. Plants were grown on mineral nutrient media (Hirai et al. 1995 Plant Cell Physiology 36: 1331) containing 1% sucrose, 0.8% agar. For preparation of agar medium, agar was washed twice with 1 L of de-ionized water and vacuum filtrated. The agar medium with complete replacement of MgSO4 to MgCl2 contained approximately 10 µM of residual sulfate derived from agar. The S15 agar media were prepared by adding 15 µM of MgSO4 and 1485 µM of MgCl2.


title: Panicle D1

description: Panicle D1

source_name: Panicle D1

tag: Panicle D1


title: Shoot S3

description: Shoot S3

source_name: Shoot S3

tag: Shoot S3

tag: Shoot without treatment as control sample


title: Shoot D4

description: Shoot D4

source_name: Shoot D4

tag: Shoot D4


title: Panicle S2

description: Panicle S2

source_name: Panicle S2

tag: Panicle S2


title: TGUT-131

source_name: skeletal muscle, Transgenic mice, NOT-trained

tag: mice over-expressing Myosine Heavy Chain -I (MHC-I)


title: slim1-2-S15, biological rep1


title: slim1-1-S15, biological rep2

description: Gene expression data from root of slim1-1 plants vertically grown for 10 days on S15 medium.

source_name: Roots of slim1-1 plants

tag: slim1-1 was isolated as a response less mutant to sulfur limitation stress indicated as the GFP fluorescence of PSULTR1;2-GFP plants. The parental plant, PSULTR1;2-GFP plants, is the Arabidopsis thaliana cv. Columbia transformed with the T-DNA construct of pBI101 harbouring promoter region of SULTR1;2 fused to GFP (Maruyama-Nakashita et al. 2004 Plant Journal 38


title: Shoot S1

description: Shoot S1

source_name: Shoot S1

tag: Shoot S1


title: PAOSC11 from epithelia, replicate 1

city: Seattle

first: S

last: Chugani

state: WA

address: 1959 NE Pacific St, HSB I-420, Box 357242

institute: University of Washington

description: PAOSC11 washed from epithelial cells following a 5 h coincubation

data_processing: standard Affymetrix procedures

organism: Pseudomonas aeruginosa

source_name: PAOSC11 from epithelia

tag: PAO1 with mutations in exsA and rhlA


title: PAOSC11 from epithelia, replicate 2


title: Shoot D3

description: Shoot D3

source_name: Shoot D3

tag: Shoot D3


title: PAOSC11 in TSB, replicate 2

description: PAOSC11 grown in TS broth to OD600 of 0.85

source_name: PAOSC11 from broth


title: slim1-1-S15, biological rep1


title: Shoot D1

description: Shoot D1

source_name: Shoot D1

tag: Shoot D1


title: Shoot D2

description: Shoot D2

source_name: Shoot D2

tag: Shoot D2


title: slim1-1-S1500, biological rep2

description: Gene expression data from root of slim1-1 plants vertically grown for 10 days on S1500 medium.


title: Flag leaf S3

description: Flag leaf S3

source_name: Flag leaf S3

tag: Flag leaf S3

source_name: Flag leaf without treatment as control sample


title: PAOSC11 in TSB, replicate 1


title: PAO1 from epithelia, replicate 2

description: Wild type PAO1 washed from epithelial cells following a 5 h coincubation

source_name: PAO1 from epithelia

tag: Wild type PAO1


title: P-S15, biological rep2

description: Gene expression data from root of PSULTR1;2-GFP plants vertically grown for 10 days on S15 medium.

source_name: Roots of PSULTR1;2-GFP plants

tag: Arabidopsis thaliana cv. Columbia transformed with the T-DNA construct of pBI101 harbouring promoter region of SULTR1;2 fused to GFP (PSULTR1;2-GFP plants; Maruyama-Nakashita et al. 2004 Plant Journal 38

tag: Tissue


title: P-S15, biological rep1


title: slim1-1-S1500, biological rep1


title: ZHTc6(Tc-), 0 hr, #3(16011472015651)

description: Universal Mouse Reference RNA

tag: embryonic stem cell 129/Ola male  gene knock in

source_name: Universal Mouse Reference RNA

tag: Universale Mouse Reference


title: Flag leaf S1

description: Flag leaf S1

source_name: Flag leaf S1

tag: Flag leaf S1

tag: Flag leaf without treatment as control sample


title: Flag leaf S2

description: Flag leaf S2

source_name: Flag leaf S2

tag: Flag leaf S2


title: PAO1 in TSB, replicate 2

description: Wild type PAO1 grown in TS broth to OD600 of 0.85

source_name: PAO1 from broth


title: PAO1 from epithelia, replicate 1


title: Flag leaf D3

description: Flag leaf D3

source_name: Flag leaf D3

tag: Flag leaf D3


title: P-S1500, biological rep1

description: Gene expression data from root of PSULTR1;2-GFP plants vertically grown for 10 days on S1500 medium.


title: Flag leaf D4

description: Flag leaf D4

source_name: Flag leaf D4

tag: Flag leaf D4


title: PAO1 in TSB, replicate 1


title: Flag leaf D2

description: Flag leaf D2

source_name: Flag leaf D2

tag: Flag leaf D2


title: Flag leaf D1

description: Flag leaf D1

source_name: Flag leaf D1

tag: Flag leaf D1


title: LOU-aorta_3

status: Public on Dec 16 2006

city: Berlin

first: Oliver

last: Hummel

department: Experimental Genetics of Cardiovascular Diseases

country: Germany

institute: Max-Delbrück-Center

description:
Aortic Aneurysms
Aneurysms and dissections of the aorta usually result from degenerative changes in the aortic wall. In abdominal aortic aneurysms this degeneration is usually caused by a combination of factors including age, atherosclerosis, hypertension, and infectious, inflammatory, or autoimmune processes (Davies MJ, 1998). In contrast, thoracic aortic aneurysms and dissections are primarily associated with a characteristic histologic appearance known as 'medial necrosis' or 'Erdheim cystic medial necrosis' in which there is degeneration and fragmentation of elastic fibers, loss of smooth muscle cells, and an accumulation of basophilic ground substance.

hyb_protocol: The following reagents were mixed for a standard array : 20 µg fragmented cRNA 4 µl control oligonucleotide B2 (5 nM) 4 µl 100X control cRNA cocktail (BioB, BioC, BioD, cre) 4 µl herring sperm DNA (10 mg/ml) 10 µl acetylated BSA (20 mg/ml) 200 µl 2X MES Hybridization buffer The volume was made to 400 µl with DEPC-H2O and stored at 20°C until the hybridization procedure. The hybridization cocktail was heated to 95°C on a heat block for 5 minutes. Meanwhile, the array was filled with 200 µl 1X MES hybridization buffer and incubated for 10 minutes at 45°C with rotation. The denatured hybridization cocktail was equilibrated by incubation at 45°C for 5 minutes and centrifuged at maximum speed to pellet insoluble matter. Finally the 1xMES hybridization buffer in the array was replaced by the hybridization cocktail and put into a rotisserie box in an oven at 45°C for 16 hours.

scan_protocol: Scanning was done according to standard Affymetrix protocol: "EukGE-WS2" in a HP Gene Array Scanner

data_processing: data were RMA normalized

organism: Rattus norvegicus

source_name: abdominal aorta

label_protocol: Biotin-labelled cRNA for hybridization on Affymetrix gene chips was generated using the IVT kit from Enzo. The procedure was performed according to the manufacturers instructions. 0.5 µg of dsDNA, 2 µl 10X transcription buffer, 2 µl Biotin-Mix, 2µl RNAse Inhibitor Mix, 2µl T7 Polymerase Mix, were added to a final volume of 20 µl with DEPC-H20. The reaction mix was incubated for 4-5 hours and stopped by adding 1 µl of 500 mM EDTA. The resulting biotin-labeled cRNA was then purified by using the RNAeasy Kit from Qiagen. The volume of the elution buffer was 40 µl. 1 µl of the IVT product was kept for gel electrophoresis analysis.

growth_protocol: Rats were kept in standard conditions with chow and tap water ad libidum until maximum 18 wks of age.

extract_protocol: The total RNA from the thoracic aorta and abdominal aorta was isolated using Trizol and RNAeasy Kit. The extraction and cleaning of the RNA was performed in accordance to the manufacturers instructions. Briefly, the aortae were resuspended in 1 ml Trizol reagent and homogenized using a glass homogenizer. After adding 200 µl chloroform, the homogenate was vortexed and centrifuged to separate the phases. The upper aqeous phase contained the RNA and was collected in a new tube. Next, total RNA was precipitated and washed with ethanol and resuspended in DEPC-treated water. To ensure the purity of the total RNA, the RNAeasy kit (Qiagen) was used to clean the RNA once again. The recovery yield was always as good as 80-90 %.

treatment_protocol: No special treatment (measurement of strain effects).

tag: 'Strain

value: LOU',

tag: 'Age

value: 5 weeks',

value: abdominal aorta

tag: Global expression analysis was done in the abdominal aortae of 5 weeks old LOU rats


title: -DOX/+E2 48h_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Kröger et al., 2003. Oncogene 22:1045-1056

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

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

growth_protocol: DMEM, 10% FCS

extract_protocol: TRIZOL

treatment_protocol: 1 mM estradiol

tag: genetic modification

value: cells stably expressing the oncogenes c-myc and Ha-ras under the control of the Tet-off regulatable promoter, konstitutive expression of the estradiol activatabel IRF-1hER fusion protein

tag: tissue

value: fibroblast


title: LOU-aorta_2


title: BN-aorta_5

value: BN',

tag: Global expression analysis was done in the abdominal aortae of 5 weeks old BN rats


title: LOU-aorta_5


title: BN-aorta_4


title: BN-aorta_3


title: -DOX/-E2_2


title: LOU-aorta_4


title: +DOX/+E2_2

treatment_protocol: 2 µg/ml Doxicycline


title: 35/1-22 - Dox +48h E2_1

extract_protocol: Rneasy


title: 35/1-22 - Dox_1


title: BN-aorta_2


title: LOU-aorta_1


title: BN-aorta_1


title: Seedling_78h_rep3

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

description: starting DNA for labeling is ~300ng

hyb_protocol: standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Bioconductor Affy package

source_name: whole seedling, 78 hour

label_protocol: double-stranded cDNA labeled by Invitrogen BioPrime labeling system

extract_protocol:
total RNA extracted by Qiagen RNeasy Plant Mini Kit
mRNA enriched by Qiagen Oligotex Kit
double-stranded cDNA synthesis by Invitrogen cDNA synthesis system
double-stranded cDNA purified by Qiagen Quick PCR Cleanup Kit

tag: accession

value: Columbia

value: whole seedling

tag: stage

value: 78 hour on MS plate

tag: growth condition

value: Percival chamber, 12h light/12h dark, 20 degree


title: 35/1-22 + Dox_1


title: Seedling_78h_rep1

description: starting DNA for labeling is ~300ng

value: 78 hour

tag: growth medium

value: MS plate (0.5XMS, 0.7% agar)


title: rab3a-/- hippocampus hrm1 B

status: Public on Dec 15 2006

city: Philadelphia

first: Maja

last: Bucan

state: PA

address: 415 Curie Blvd

institute: UPENN

description: hippocampus from rab3a-/- mouse

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: hippocampus

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 50 mg of tissue was homogenized in 1 ml TriZol reagent and total RNA was extracted according to manufacture's protocol. Total RNA was cleaned up using an RNeasy kit (Qiagen).

tag: rab3a-/- hippocampus


title: rab3a-/- hippocampus hrm2 B

description: hippocampus from rab3a-/- mouse


title: rab3a-/- hippocampus hrm5 B

description: hippocampus from rab3a-/- mouse


title: rab3a+/+ hippocampus hrw3 B

description: hippocampus from rab3a+/+ mouse

tag: rab3a+/+ hippocampus


title: rab3a+/+ hippocampus hrw6 B

description: hippocampus from rab3a+/+ mouse


title: Seedling_78h_rep4

description: starting DNA for labeling is ~300ng


title: rab3a+/+ hippocampus hrw1 B

description: hippocampus from rab3a+/+ mouse


title: earlybird mutant hippocampus hem1 B

description: hippocampus from earlybird mutant mouse

tag: earlybird mutant hippocampus


title: rab3a-/- cortex crm6 B

description: cortex from rab3a-/- mouse

source_name: cortex

tag: rab3a-/- cortex


title: earlybird mutant hippocampus hem2 B

description: hippocampus from earlybird mutant mouse


title: rab3a-/- hippocampus hrm3 B

description: hippocampus from rab3a-/- mouse


title: rab3a-/- cortex crm5 B

description: cortex from rab3a-/- mouse


title: rab3a+/+ hippocampus hrw2 B

description: hippocampus from rab3a+/+ mouse


title: rab3a-/- cortex crm4 B

description: cortex from rab3a-/- mouse


title: rab3a+/+ hippocampus hrw5 B

description: hippocampus from rab3a+/+ mouse


title: rab3a-/- hippocampus hrm4 B

description: hippocampus from rab3a-/- mouse


title: earlybird mutant hippocampus hem3 B

description: hippocampus from earlybird mutant mouse


title: rab3a-/- cortex crm2 B

description: cortex from rab3a-/- mouse


title: rab3a-/- cortex crm1 B

description: cortex from rab3a-/- mouse


title: earlybird wildtype hippocampus hew1 B

description: hippocampus from wild type littermate of earlybird mutant mouse

tag: earlybird wildtype hippocampus


title: rab3a-/- cortex crm3 B

description: cortex from rab3a-/- mouse


title: Seedling_78h_rep2

description: starting DNA for labeling is ~300ng


title: rab3a+/+ cortex crw2 B

description: cortex from rab3a+/+ mouse

tag: rab3a+/+ cortex


title: rab3a+/+ cortex crw3 B

description: cortex from rab3a+/+ mouse


title: rab3a+/+ cortex crw6 B

description: cortex from rab3a+/+ mouse


title: earlybird mutant cortex cem1 B

description: cortex from earlybird mutant mouse

tag: earlybird mutant cortex


title: earlybird mutant cortex cem2 B

description: cortex from earlybird mutant mouse


title: rab3a+/+ cortex crw4 B

description: cortex from rab3a+/+ mouse


title: earlybird wildtype cortex cew2 B

description: cortex from wild type littermate of earlybird mutant mouse

tag: earlybird wildtype cortex


title: rab3a-/- hippocampus hrm5A

description: hippocampus from rab3a-/- mouse


title: rab3a-/- hippocampus hrm1A

description: hippocampus from rab3a-/- mouse


title: rab3a-/- hippocampus hrm2A

description: hippocampus from rab3a-/- mouse


title: rab3a+/+ cortex crw5 B

description: cortex from rab3a+/+ mouse


title: earlybird mutant cortex cem3 B

description: cortex from earlybird mutant mouse


title: earlybird wildtype cortex cew1 B


title: earlybird wildtype hippocampus hew3 B


title: earlybird wildtype cortex cew3 B


title: rab3a+/+ hippocampus hrw4A

description: hippocampus from rab3a+/+ mouse


title: rab3a+/+ hippocampus hrw4 B

description: hippocampus from rab3a+/+ mouse


title: rab3a+/+ hippocampus hrw3A

description: hippocampus from rab3a+/+ mouse


title: rab3a+/+ hippocampus hrw2A

description: hippocampus from rab3a+/+ mouse


title: rab3a+/+ cortex crw1 B

description: cortex from rab3a+/+ mouse


title: rab3a+/+ hippocampus hrw6A

description: hippocampus from rab3a+/+ mouse


title: rab3a-/- hippocampus hrm6A

description: hippocampus from rab3a-/- mouse


title: rab3a-/- hippocampus hrm3A

description: hippocampus from rab3a-/- mouse


title: earlybird wildtype hippocampus hew3A


title: earlybird mutant hippocampus hem3A

description: hippocampus from earlybird mutant mouse


title: rab3a-/- hippocampus hrm4A

description: hippocampus from rab3a-/- mouse


title: earlybird mutant hippocampus hem1A

description: hippocampus from earlybird mutant mouse


title: rab3a+/+ hippocampus hrw1A

description: hippocampus from rab3a+/+ mouse


title: rab3a+/+ cortex crw6A

description: cortex from rab3a+/+ mouse


title: rab3a-/- cortex crm1A

description: cortex from rab3a-/- mouse


title: earlybird wildtype hippocampus hew2A


title: rab3a+/+ cortex crw1A

description: cortex from rab3a+/+ mouse


title: rab3a-/- cortex crm5A

description: cortex from rab3a-/- mouse


title: earlybird mutant cortex cem3A

description: cortex from earlybird mutant mouse


title: rab3a+/+ cortex crw4A

description: cortex from rab3a+/+ mouse


title: rab3a+/+ cortex crw5A

description: cortex from rab3a+/+ mouse


title: rab3a-/- cortex crm2A

description: cortex from rab3a-/- mouse


title: rab3a-/- cortex crm6A

description: cortex from rab3a-/- mouse


title: earlybird wildtype cortex cew3A


title: earlybird mutant cortex cem2A

description: cortex from earlybird mutant mouse


title: rab3a+/+ cortex crw2A

description: cortex from rab3a+/+ mouse


title: rab3a-/- cortex crm4A

description: cortex from rab3a-/- mouse


title: earlybird wildtype hippocampus hew1A


title: rab3a-/- hippocampus hrm6 B

description: hippocampus from rab3a-/- mouse


title: rab3a+/+ cortex crw3A

description: cortex from rab3a+/+ mouse


title: earlybird wildtype cortex cew2A


title: earlybird mutant hippocampus hem2A

description: hippocampus from earlybird mutant mouse


title: Basal cell carcinoma_superficial_7

first: Kevin

last: McElwee

department: Dermatology and Skin Science

institute: University of British Columbia

description: All treated biologicaly replicated samples were hybridized with the same universal human reference RNA (reference).

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life And Analytical Sciences, Inc., Wellesley, MA).

data_processing: Arrays were scanned at excitation wave lengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes, respectively. Image analysis and quantification were conducted with commercial software, (ImaGene 7.0 software: BioDiscovery Inc., El Segundo, CA, USA). After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the Genespring 7.2 program (Silicon Genetics, Redwood City, CA, USA).

source_name: Basal cell carcinoma_superficial

label_protocol: 1 ug RNA were amplified using the SenseAmp plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. sense RNA from amplification was labeled with Cy5, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

growth_protocol: sample was stored in an RNA stabilization reagent

extract_protocol: Total RNA was isolated with an RNeasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's protocols.The quantity and quality of the RNAs was measured by electrophoresis using the Agilent 2100 bioanalyzer and RNA 6000 nano kit (Agilent Technologies, Palo Alto, CA).

treatment_protocol: sample was collected in the operating theater during Moh’s surgical excision

tag: Basal cell carcinoma_superficial

label_protocol: Total 10ug RNA universal human reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3 , with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

tag: The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.


title: earlybird wildtype cortex cew1A


title: Basal cell carcinoma_superficial_6

hyb_protocol: 3DNA array detection 350 kit (Genisphere)

source_name: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: Basal cell carcinoma_superficial_5

extract_protocol: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: Basal cell carcinoma_superficial_3

treatment_protocol: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: Basal cell carcinoma_superficial_4


title: rab3a+/+ hippocampus hrw5A

description: hippocampus from rab3a+/+ mouse


title: slit.robo, stage15, biological rep4

status: Public on Dec 14 2006

city: Coimbra

first: Tiago

middle: R

last: Magalhaes

address: Departamento Zoologia, Universidade Coimbra

department: Centro Neurociências

country: Portugal

institute: Universidade de Coimbra

description: This microarray belongs to an experiment that aims to understand the genetic pathways in axon guidance mechanisms. 17 mutants and transgenics of axon guidance genes were analyzed, with 4 to 5 technical replicates for each mutant or transgenic.

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

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

data_processing: The RMA algorithm was used as in Irizarry2003, NAR,31-e15, with the recommended quantile-quantile normalization procedure

source_name: Drosophila embryos stage 15

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

extract_protocol: RNA was extracted from the embryos using QIAGEN columns according to manufacturer recommendations.

tag: Homozygous for double mutant for slit and robo. The double mutant was obtained by recombination of slit(1) with robo(4) (Kidd1999, Cell,96-785).


title: slit.robo, stage15, biological rep3


title: slit.robo, stage15, biological rep1


title: Basal cell carcinoma_morphoeic form_4

source_name: Basal cell carcinoma_morphoeic form

tag: Basal cell carcinoma_morphoeic form


title: Basal cell carcinoma_morphoeic form_7


title: Basal cell carcinoma_morphoeic form_5


title: Basal cell carcinoma_morphoeic form_1

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately  using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life And Analytical Sciences, Inc., Wellesley, MA).

data_processing: Arrays were scanned at excitation wave lengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes, respectively. Image analysis and quantification were conducted with commercial software, (ImaGene 7.0  software: BioDiscovery Inc., El Segundo, CA, USA). After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the Genespring 7.2 program (Silicon Genetics, Redwood City, CA, USA).

label_protocol: Total 10ug RNA  universal human reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3 , with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.


title: Basal cell carcinoma_superficial_2


title: Basal cell carcinoma_morphoeic form_6


title: MCF7_inhibitor_HRG_AG1478_30min

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN RCAI

description: Early gene expression (up to 90min) induced by growth hormone stimulation with an EGFR kinase inhibitor.

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: The data were analyzed with GeneChip Operating System (GCOS) (ver.1.2) using Affymetrix default analysis settings and global scaling as normalization method. The Single-Array Expression Analysis function was used and the trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: breast epithelial cell, adherent, HRG, AG1478, 30min

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free DMEM medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment. The inhibitor, AG1478 (an EGFR kinase inhibitor) was added to 20 min prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: Cell line

value: MCF-7 (Obtained from ATCC (American Type Culture Collection)), Organ:mammary gland; breast, Cell type:epithelial, Disease:adenocarcinoma, Derived from metastatic site:pleural effusion, Age:69 years adult, Gender:female, Ethnicity:Caucasian


title: slit.robo, stage15, biological rep2


title: Basal cell carcinoma_morphoeic form_2


title: slit, stage15, biological rep3

tag: homozygous mutant for slit. the strain used is slit(2), comes from an EMS screen and is a point mutation (Rothberg1988 Cell55-1047).


title: slit, stage15, biological rep2


title: slit, stage15, biological rep4


title: slit/WT, stage15, biological rep4

tag: Heterozygous mutant for slit. It was obtained by crossing slit(2) with WT. The strain slit(2) comes from an EMS screen and is a point mutation (Rothberg1988, Cell,55-1047).


title: slit, stage15, biological rep1


title: slit/WT, stage15, biological rep2


title: slit/WT, stage15, biological rep1


title: robo2, stage15, biological rep4

tag: mutant homozygous for robo2. robo2{x123} is the strain and results from an excision of EP 2582 (Simpson2000, Neuron,28-753).


title: slit/WT, stage15, biological rep3


title: slit.robo, stage15, biological rep5


title: robo2, stage15, biological rep2


title: Basal cell carcinoma_superficial_8


title: robo2, stage15, biological rep3


title: Basal cell carcinoma_superficial_1


title: robo, stage15, biological rep1

tag: mutant homozygous for robo; the strain used is robo(4), a point mutation, as cited in Seeger1993, Neuron,10-409.


title: Basal cell carcinoma_morphoeic form_3


title: robo, stage15, biological rep2


title: robo, stage15, biological rep3


title: robo12, stage15, biological rep4

tag: Double mutant for robo and robo2. The double mutant results from the recombination of the robo mutant robo(4) with the robo2  robo2(x123) (robo(4) in Seeger1998, Neuron,10-409; robo(x123) in Simpson2000, Neuron,28-753).


title: robo12, stage15, biological rep3


title: robo2, stage15, biological rep1


title: robo12, stage15, biological rep1


title: robo, stage15, biological rep4


title: robo/WT, stage15, biological rep4

tag: mutant heterozygous for robo; the embryos result from crossing robo(4), with WT flies. robo(4) is a point mutation, as cited in Seeger1993, Neuron,10-409.


title: robo/WT, stage15, biological rep3


title: rab3a-/- cortex crm3A

description: cortex from rab3a-/- mouse


title: robo/WT, stage15, biological rep2


title: comm mutant, stage15, biological rep4

tag: The homozygous commissureless mutants result from a cross of comm.Deltae39 ( reference in Seeger,1993 Neuron,10-409) with comm.P (Tear1996, Neuron16,501). comm.Deltae39 is a null allele. comm.P is a 900 bp deletion of the 5' UTR and the transcription start site. Commissureless mutants have a CNS phenotype will all axons not crossing the midline.


title: robo12, stage15, biological rep2


title: comm mutant, stage15, biological rep3


title: comm mutant, stage15, biological rep2


title: earlybird mutant cortex cem1A

description: cortex from earlybird mutant mouse


title: comm mutant, stage15, biological rep1


title: comm/WT, stage15, biological rep1

tag: The heterozygous commissureless mutants result from a cross of comm.Deltae39 ( reference in Seeger,1993 Neuron,10-409) with with WT flies. The phenotype of these embryos is normal.


title: comm/WT, stage15, biological rep3


title: WT stage15, biological rep5

tag: robo Gain of Function, with specific muscle overexpression. Produced by crossing UAS-robo-yf flies with the mesodermal driver mef2Gal4 (Kramer2001 Science,292-737).


title: comm/WT, stage15, biological rep4


title: comm/WT, stage15, biological rep2


title: WT stage15, biological rep2


title: WT stage15, biological rep4


title: URyf, stage15, biological rep2

tag: UR.yf is a phenotypically stronger robo Gain of Function than UR, also presented in this study. URyf is obtained from the cross of UAS-robo-yf flies with the postmitotic driver elavGal4 (Bashaw2000, Cell101-703).


title: URyf.mef, stage15, biological rep1


title: UR2, stage15, biological rep3

tag: UR2 is a robo2 Gain of Function obtained by crossing the construct UAS-robo2 with the elavGal4 driver (Simpson2000 Neuron28-753).


title: URyf.mef, stage15, biological rep4


title: URyf, stage15, biological rep4


title: URyf.mef, stage15, biological rep5


title: URyf.mef, stage15, biological rep3


title: URyf, stage15, biological rep1


title: URyf, stage15, biological rep5


title: WT stage15, biological rep3


title: URyf, stage15, biological rep3


title: UR2, stage15, biological rep4


title: WT stage15, biological rep1


title: URyf.mef, stage15, biological rep2


title: UR2, stage15, biological rep2


title: UR2, stage15, biological rep1


title: UR, stage15, biological rep1

tag: UR is a robo Gain of Function that results from crossing UAS-robo flies with the postmitotic neural driver elavGal4 flies (Kidd1998, Kidd92-205).


title: UNC5, stage15, biological rep2

tag: UNC5 is the unc-5 Gain of Function, obtained by crossing, a GS-element insert located upstream of unc-5, with the elavGal4 driver (GSunc5 kindly provided by John Thomas).


title: UNC5, stage15, biological rep5


title: UNC5, stage15, biological rep4


title: robo/WT, stage15, biological rep1


title: UR, stage15, biological rep3


title: UNC5, stage15, biological rep3


title: UNC5, stage15, biological rep1


title: UR, stage15, biological rep4


title: UC2x, stage15, biological rep1

tag: UC2x is a stronger comm GOF than UC (also in this experiment) and was obtained using two copies of UAS-comm crossed with the driver elavGal4 (unpublished, more information with the depository).