title: Liver_Ciguatoxin (P-CTX-1)_24h_050+

city: Charleston

first: Frances

middle: M

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

description: 24 h exposure to 0.26 ng/g Pacific Ciguatoxin-1

hyb_protocol: One microgram each of Cy3 and Cy5 labeled targets were combined and hybridized to an Agilent catalog 44K whole genome mouse oligonucleotide array for 17 h at 60 °C in an Agilent DNA Microarray Hybridization Oven.  Arrays were then washed consecutively in solutions of 6X SSPE with 0.005% N-lauroylsarcosine and 0.06X SSPE with 0.005% N-Lauroylsarcosine for 1 m each at room temperature.  This was followed by a final 30 s wash in Agilent Stabilization and Drying solution.

scan_protocol: Microarrays were imaged on an Agilent microarray scanner at 10µm scan resolution.  Concurrent scans of the red and green PMT were performed.

data_processing: Agilent Feature Extraction software version A8.5.1 using Agilent Design File 012694_D_G220051010.

source_name: Liver from mice exposed to 1% Tween 60 in physiological saline (vehicle)

label_protocol: Four hundred fifty nanograms of total RNA from control and experimental animals was separately amplified and labeled with either Cy3 or Cy5 labeled CTP (Perkin Elmer) using Agilent’s Low Input Linear Amplification kit according to manufacturer’s protocol.  Following labeling and clean up, amplified RNA and dye incorporation were quantified using a NanoDrop ND-1000.

growth_protocol: Adult male C57-BL6 mice were maintained on a 12 h:12 h light:dark cycle and were given food and water ad libitum.  Radio frequency transmitters were implanted in the abdominal cavity of the mice to measure core temperature and motor activity.  The mice were allowed at least 10 days of recovery before testing while animal health was monitored.

extract_protocol: The livers of the 3 control mice for each time point were pooled prior to RNA extraction while RNA was extracted from livers of individual CTX exposed mice.  The livers were crushed using a BioPulverizer (BioSpec Products, Inc.) in liquid nitrogen, immediately placed in cooled Tri-Reagent (Molecular Research Center, Inc.) and homogenized using a Tissue-Tearor (United Lab Plastics).  All homogenates were processed according to the manufacturer’s protocol.  RNA was suspended in nuclease-free water and cleaned using an RNeasy midi-column (Qiagen).  RNA was quantified using a NanoDrop ND-1000 and qualified on an Agilent 2100 Bioanalyzer.

treatment_protocol: Three groups of control mice (n=3) were injected ip with a single dose of physiological saline with 1% Tween 60 (vehicle).  Three groups of experimental mice (n=3) were injected ip with a single dose of 0.26 ng/g Pacific Ciguatoxin-1 (P-CTX-1) in vehicle.  At 1, 4, and 24 h post-injection, 3 experimental mice and 3 time-matched controls were anesthetized with 50 mg/mL sodium pentobarbital ip.  Livers were immediately dissected, flash frozen in liquid nitrogen, and stored at -80 °C until RNA processing.

tag: Adult male C57-BL6 mice with frequency transmitters implanted in the abdominal cavity

source_name: Liver from mouse exposed to 0.26 ng/g Pacific Ciguatoxin-1


title: PN335_3

status: Public on May 08 2008

type: RNA

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

country: USA

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53851.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.92; Parameter Scan Time = 10:54:23; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 173416; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.92; Parameter Scan Time = 10:54:23; Parameter PMT Volts = 610; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 538219; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson

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

molecule: total RNA

organism: Homo sapiens

source_name: CRG

label_protocol: not provided

extract_protocol: not provided

tag: CRG

tag: Disease State

value: normal prostate

tag: Individual


title: Cells grown with p-coumarate #2

status: Public on May 07 2008

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

description: A high-density oligonucleotide microarray (Affymetrix GeneChip) was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions. cDNA synthesis, fragmentation, labeling, hybridization, and processing of custom designed Rhodopseudomonas palustris GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix Microarray Suite was used for initial data acquisition and processing.

label: Biotinylated GeneChip reagent

organism: Rhodopseudomonas palustris

source_name: Rhodopseudomonas palustris strain CGA010 with p-coumarate #2

extract_protocol: Rhodopseudomonas palustris cells were disrupted by treatment with by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.

tag: Rhodopseudomonas palustris cells grown with p-coumarate #2


title: Olineu_Y27631treat_rep5

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
- RNA quality control with Agilent Bioanalyzer 2100
- Dye incorporation with NanoDrop ND-1000
Keywords = oli neu, oligodendrocyte differentiation

hyb_protocol: - hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 micro gram labeled DNA per channel were mixed no fractionation probes were denatured for 3 min at 98 degree celsius hybridization at 63 degree celsius SSPE washes as recommended slides were dipped in acetonitril (10 s) then dried

scan_protocol: - scanned with a G2505B Microarray Scanner (Agilent Technologies) - quantification software: 'Automic Imageprocessing for Microarrays' (for details: http://www.techfak.uni-bielefeld.de/ags/ai/projects/microarray/)

data_processing:
- dye swap design
- Normalization of the log2(cy3/cy5)-ratios with pinwise non-linear loess regression
- variance homogenisation by division of each value with the standard deviation of the normalized log2-ratios
- as statistical software we use 'R'

organism: Mus musculus

source_name: olineu with Y27631 treatment

label_protocol:
- totalRNA was transcribed, amplified and labeled according to BD Atlas SMART fluorescent probe amplification kit with following modifications:
- RNA template was hydrolized after transcription (high pH, 30 min/70 degree celsius)
- PCR amplification progress was monitored and stopped before reaching saturation

extract_protocol:
- Trizol (Invitrogen) isolation according to the manufactures standard protocol
- Subsequent DNase I treatment

tag: Cell lysates from Olineu Y27631 treated

source_name: olineu untreated

tag: Cell lysates from Olineu untreated


title: Olineu_Y27631treat_rep6


title: Olineu_Y27631treat_rep3


title: Olineu_Neuron_treat_rep2

source_name: olineu neuron treatment

tag: olineu cell line in presence of neurons

source_name: olineu without neuron treatment

tag: olineu cell line in absense of neurons


title: Cells grown with succinate #2

scan_protocol: As recommended by the manufacturer (Affymetrix)

source_name: Rhodopseudomonas palustris strain CGA010 with succinate #2

tag: Rhodopseudomonas palustris cells grown with succinate #2


title: Olineu_Neuron_treat_rep4


title: Olineu_Y27631treat_rep1


title: Olineu_Y27631treat_rep4


title: Olineu_Neuron_treat_rep3


title: Olineu_Y27631treat_rep2


title: Chicken Liver fasted 48h_7

status: Public on May 06 2008

city: Rennes

first: Sandrine

last: Lagarrigue

address: 65 rue de St Brieuc

country: France

institute: Agrocampus Rennes/ INRA

description: Feeding- fasting transition study in chicken liver

hyb_protocol: The microarray was hybridized overnight at 42°C with Cy5-labeled Fed-2 cDNA and an aliquot of the Cy3-labeled reference cDNA using automatic hybridization chamber (Discovery from Ventana Medical System, Inc). Slides were washed in increasing stringency using salt sodium citrate.

scan_protocol: The microarray slides were scanned using a laser scanner (GenePix 4000A from Axon Instrument, CA) at 550 nM for Cy3 and 640 nM for Cy5 to generate two TIFF images for each slide.

data_processing: The two images from each slide were analyzed with GenepixPro 4.0 software (Axon instruments, Inc., Union City, CA). Pre-processing and normalization of data were accomplished using the R-project statistical and Bioconductor environment (http://www.r-project.org) (http://www.bioconductor.org). For the normalization step, data were filtered according to 3 criterions based on 1) the genepix flag automatically performed by GenepixPro 4.0; 2) the SNR 3) the asymmetry spot (see Desert et Al 2008). The ratio Cy5/Cy3 used was expressed as the Log(base 2) of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized using global LOWESS normalization.

organism: Gallus gallus

source_name: Fasted 48_7

label_protocol: Five µg of each mRNA sample were reverse-transcribed and Cy5 fluorescent-labelled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).

growth_protocol: Standard broiler chicken growth protocol. Livers were rapidly excised, frozen in liquid nitrogen and stored at –75 °C until RNA extraction

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA)

tag: Male broiler chicks fasted for 48h  Age

value: 4 weeks Tissue:Liver

source_name: Reference

label_protocol: Five µg of each mRNA sample were reverse-transcribed and Cy3 fluorescent-labelled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).

tag: Male broiler chicks fed ad libitum Age


title: Liver_Ciguatoxin (P-CTX-1)_24h_052+


title: Chicken Liver fasted 48h_6

source_name: Fasted 48_6

tag: Male broiler chicks fasted for 48h Age


title: Chicken Liver fasted 48h_10

source_name: Fasted 48_10


title: Olineu_Neuron_treat_rep1


title: Chicken Liver fasted 48h_ 4

source_name: Fasted 48_4

tag: Male broiler chicks fasted for 48h    Age


title: Chicken Liver fasted 48h_8

source_name: Fasted 48_8


title: Chicken Liver fasted 48h_ 5

source_name: Fasted 48_5


title: Olineu_Neuron_treat_rep6


title: Liver_Ciguatoxin (P-CTX-1)_24h_051-


title: Liver_Ciguatoxin (P-CTX-1)_4h_715-

description: 4 h exposure to 0.26 ng/g Pacific Ciguatoxin-1


title: Liver_Ciguatoxin (P-CTX-1)_4h_513-


title: Liver_Ciguatoxin (P-CTX-1)_4h_512+


title: Olineu_Neuron_treat_rep5


title: Chicken Liver fasted 48h_ 2

source_name: Fasted 48_2

tag: Male broiler chicks fasted for 48h   Age

value: 4 weeks   Tissue:Liver


title: Chicken Liver fasted 16h_ 6

source_name: Fasted 16 -6

tag: Male broiler chicks fasted for 16h  Age


title: Chicken Liver fasted 16h_5

source_name: Fasted 16 -5


title: Chicken Liver fasted 16h_10

source_name: Fasted 16 -10

tag: Male broiler chicks fasted for 16h   Age


title: Chicken Liver fed 5


title: Chicken Liver fed 8


title: Chicken Liver fasted 16h_ 8

source_name: Fasted 16 -8


title: Chicken Liver fed 7


title: Chicken Liver fed 2

hyb_protocol: The microarray was hybridized overnight at 42 C with Cy5-labeled Fed-2 cDNA and an aliquot of the Cy3-labeled reference cDNA using automatic hybridization chamber (Discovery from Ventana Medical System, Inc). Slides were washed in increasing stringency using salt sodium citrate.

tag: Male broiler chicks fed ad libitum	Age

value: 4 weeks	Tissue:Liver

tag: Male broiler chicks	Age


title: Liver_Ciguatoxin (P-CTX-1)_1h_717+

description: 1 h exposure to 0.26 ng/g Pacific Ciguatoxin-1

source_name: Liver from mice exposed to 1% Tween 60 in physiological saline (vehicle)

tag: Adult male C57-BL6 mice with frequency transmitters implanted in the abdominal cavity

source_name: Liver from mouse exposed to 0.26 ng/g Pacific Ciguatoxin-1


title: Chicken Liver fed 3


title: Cells grown with succinate #1

source_name: Rhodopseudomonas palustris strain CGA010 with succinate #1

label_protocol: As recommended by the manufacturer (Affymetrix)

tag: Rhodopseudomonas palustris cells grown with succinate #1


title: Chicken Liver fasted 16h_ 9

source_name: Fasted 16 -9


title: Embryo 16, derived from IVF, Cy5

status: Public on May 05 2008

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1392 Storrs Rd. Unit 4243

department: Center for Regenerative Biology

institute: University of Connecticut

description:
cDNA from Embryo RNA and the reference standard.
Keywords = Embryo
Keywords = cow
Keywords = IVF
Keywords = microarray

hyb_protocol: Each labeled sample was combined with a labeled reference,and suspended in a total of 40 µl containing ddH2O, 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 ug of T7dT24.  After denaturation for 2.5 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 02% SDS) is added and the mixture is hybridized to the microarray for 40 hrs at 42 degrees. Arrays were subsequently washed in a series of SSC/SDS washes to remove unbound cDNA.  After washing, arrays were spun dry and immediately scanned.

scan_protocol: microarray image was acquired using a GenePix 4000B scanner and analyzed using GenePix Pro 4.0. Fluoresecent images for both dye channels were obtained using a GenePix 4000B (Axon Instruments, Inc., CA) dual-laser confocal scanner and images were processed using GenePix Pro 4.0 (Axon Instruments, Inc., CA).

data_processing: Values are raw log2 tranformed ratios, no normalizations are performed.

organism: Bos taurus

source_name: Embryo 16, type: IVF,labeled with Cy5

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labeled cDNAs were purified separately with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, combined, and suspended in 40 µl containing ddH2O, 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 ug T7dT24.  After denaturation for 3 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 02% SDS) is added and mixture is hybridized to the microarray.

extract_protocol: RNA isolation was accomplished using Trizol. The RNA underwent three rounds of linear amplification (Baugh et. al. 2001), the aRNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.

tag: Single blastocyst total RNA isolated by Trizol

source_name: reference standard RNA, labeled with Cy3

label_protocol: The cDNA from sample and reference was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labeled cDNAs were purified separately with a QIAquick PCR purification column. Each labeled sample was analyzed using a spectrophotometer, after which sample and reference were speedvacced, combined and suspended in 40 µl containing ddH2O, 20 µg of bovine Cot1 DNA, 40 µg oligo dT and 20 ug T7dT24.  After denaturation for 3 min at 94°C, reannealing 10 min at 60°C, 2x Hybridization buffer (50% formamide,10x SSC, 02% SDS) is added and mixture is hybridized to the microarray.

extract_protocol: RNA isolation was accomplished using Trizol. The RNA underwent two rounds of linear amplification (Baugh et. al. 2001) , the aRNA was reverse-transcribed into cDNA with Superscript III reverse transcriptase for 15h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 1M NaOH, neutralization with 1M HCl,Tris was removed from the reaction with a Qiagen PCR-column.

tag: reference total RNA isolated by Trizol from EBTr, MDBK, and BL30 cell lines and brain tissue


title: Embryo 13, derived from IVF, Cy5

source_name: Embryo 13, type: IVF,labeled with Cy5


title: Embryo 16, derived from IVF, Cy3

source_name: Embryo 16, type: IVF,labeled with Cy3

source_name: reference standard RNA, labeled with Cy5


title: Embryo 18, derived from IVF, Cy5

source_name: Embryo 18, type: IVF,labeled with Cy5


title: Cells grown with p-coumarate #1

source_name: Rhodopseudomonas palustris strain CGA010 with p-coumarate #1

tag: Rhodopseudomonas palustris cells grown with p-coumarate #1


title: Embryo 12, derived from IVF, Cy5

source_name: Embryo 12, type: IVF,labeled with Cy5


title: Embryo 11, derived from IVF, Cy5

source_name: Embryo 11, type: IVF,labeled with Cy5


title: Embryo 19, derived from IVF, Cy3

source_name: Embryo 19, type: IVF,labeled with Cy3


title: Embryo 18, derived from IVF, Cy3

source_name: Embryo 18, type: IVF,labeled with Cy3


title: Embryo 12, derived from IVF, Cy3

source_name: Embryo 12, type: IVF,labeled with Cy3


title: Embryo 13, derived from IVF, Cy3

source_name: Embryo 13, type: IVF,labeled with Cy3


title: Embryo 10, derived from IVF, Cy5

source_name: Embryo 10, type: IVF,labeled with Cy5


title: Liver_Ciguatoxin (P-CTX-1)_1h_718+

source_name: Liver from mice exposed to 1% Tween 60 in physiological saline (vehicle)

source_name: Liver from mouse exposed to 0.26 ng/g Pacific Ciguatoxin-1


title: Embryo 5, derived from IVF, Cy5

source_name: Embryo 5, type: IVF,labeled with Cy5


title: Embryo 7, derived from IVF, Cy5

source_name: Embryo 7, type: IVF,labeled with Cy5


title: Embryo 7, derived from IVF, Cy3

source_name: Embryo 7, type: IVF,labeled with Cy3


title: Embryo 5, derived from IVF, Cy3

source_name: Embryo 5, type: IVF,labeled with Cy3


title: Embryo 9, derived from IVF, Cy5

source_name: Embryo 9, type: IVF,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 10, derived from IVF, Cy3

source_name: Embryo 10, type: IVF,labeled with Cy3

source_name: reference standard RNA, labeled with Cy5


title: Liver_Ciguatoxin (P-CTX-1)_1h_716-


title: Embryo 9, derived from IVF, Cy3

source_name: Embryo 9, type: IVF,labeled with Cy3


title: Embryo 6, derived from IVF, Cy5

source_name: Embryo 6, type: IVF,labeled with Cy5


title: Embryo 19, derived from IVF, Cy5

source_name: Embryo 19, type: IVF,labeled with Cy5


title: Embryo 3, derived from IVF, Cy5

source_name: Embryo 3, type: IVF,labeled with Cy5


title: Embryo 4, derived from IVF, Cy5

source_name: Embryo 4, type: IVF,labeled with Cy5


title: Embryo 1, derived from IVF, Cy3

source_name: Embryo 1, type: IVF,labeled with Cy3


title: Embryo 3, derived from IVF, Cy3

source_name: Embryo 3, type: IVF,labeled with Cy3


title: Embryo 4, derived from IVF, Cy3

source_name: Embryo 4, type: IVF,labeled with Cy3


title: Embryo 2, derived from IVF, Cy5

source_name: Embryo 2, type: IVF,labeled with Cy5


title: Embryo 1, derived from IVF, Cy5

source_name: Embryo 1, type: IVF,labeled with Cy5


title: Embryo 2, derived from IVF, Cy3

source_name: Embryo 2, type: IVF,labeled with Cy3


title: Embryo 12_4, derived from IVD, Cy3

description:
cDNA from Embryo RNA and the reference standard.
Keywords = Embryo
Keywords = cow
Keywords = IVD
Keywords = microarray

source_name: Embryo 12_4, type: IVD,labeled with Cy3


title: Embryo 11, derived from IVD, Cy3

source_name: Embryo 11, type: IVD,labeled with Cy3


title: Embryo 6, derived from IVF, Cy3

source_name: Embryo 6, type: IVF,labeled with Cy3


title: Chicken Liver fed 4

source_name: Reference

tag: Male broiler chicks Age


title: Embryo 12_2, derived from IVD, Cy3

source_name: Embryo 12_2, type: IVD,labeled with Cy3


title: Embryo 12_4, derived from IVD, Cy5

source_name: Embryo 12_4, type: IVD,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 12_3, derived from IVD, Cy3

source_name: Embryo 12_3, type: IVD,labeled with Cy3

source_name: reference standard RNA, labeled with Cy5


title: Embryo 12_2, derived from IVD, Cy5

source_name: Embryo 12_2, type: IVD,labeled with Cy5


title: Embryo 11, derived from IVD, Cy5

source_name: Embryo 11, type: IVD,labeled with Cy5


title: Embryo 12_1, derived from IVD, Cy3

source_name: Embryo 12_1, type: IVD,labeled with Cy3


title: Embryo 10, derived from IVD, Cy5

source_name: Embryo 10, type: IVD,labeled with Cy5


title: Embryo 10, derived from IVD, Cy3

source_name: Embryo 10, type: IVD,labeled with Cy3


title: Embryo 12_1, derived from IVD, Cy5

source_name: Embryo 12_1, type: IVD,labeled with Cy5


title: Embryo 9, derived from IVD, Cy5

source_name: Embryo 9, type: IVD,labeled with Cy5


title: Embryo 9, derived from IVD, Cy3

source_name: Embryo 9, type: IVD,labeled with Cy3


title: Embryo 8, derived from IVD, Cy5

source_name: Embryo 8, type: IVD,labeled with Cy5


title: Embryo 6, derived from IVD, Cy5

source_name: Embryo 6, type: IVD,labeled with Cy5


title: Embryo 8, derived from IVD, Cy3

source_name: Embryo 8, type: IVD,labeled with Cy3


title: Embryo 6, derived from IVD, Cy3

source_name: Embryo 6, type: IVD,labeled with Cy3


title: Embryo 12_3, derived from IVD, Cy5

source_name: Embryo 12_3, type: IVD,labeled with Cy5


title: Embryo 5, derived from IVD, Cy5

source_name: Embryo 5, type: IVD,labeled with Cy5


title: Embryo 5, derived from IVD, Cy3

source_name: Embryo 5, type: IVD,labeled with Cy3


title: Embryo 1, derived from IVD, Cy5

source_name: Embryo 1, type: IVD,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 4, derived from IVD, Cy3

source_name: Embryo 4, type: IVD,labeled with Cy3

source_name: reference standard RNA, labeled with Cy5


title: Embryo 11, derived from IVF, Cy3

source_name: Embryo 11, type: IVF,labeled with Cy3


title: Embryo 2, derived from IVD, Cy5

source_name: Embryo 2, type: IVD,labeled with Cy5


title: Embryo 3, derived from IVD, Cy5

source_name: Embryo 3, type: IVD,labeled with Cy5


title: Embryo 1, derived from IVD, Cy3

source_name: Embryo 1, type: IVD,labeled with Cy3


title: Embryo 3, derived from IVD, Cy3

source_name: Embryo 3, type: IVD,labeled with Cy3


title: Embryo 17, derived from AI, Cy3

description:
cDNA from Embryo RNA and the reference standard.
Keywords = Embryo
Keywords = cow
Keywords = AI
Keywords = microarray

source_name: Embryo 17, type: AI,labeled with Cy3


title: Embryo 4, derived from IVD, Cy5

source_name: Embryo 4, type: IVD,labeled with Cy5


title: Embryo H3, derived from AI, Cy5

source_name: Embryo H3, type: AI,labeled with Cy5


title: Embryo H5, derived from AI, Cy5

source_name: Embryo H5, type: AI,labeled with Cy5


title: Embryo 2, derived from IVD, Cy3

source_name: Embryo 2, type: IVD,labeled with Cy3


title: Embryo H1, derived from AI, Cy3

source_name: Embryo H1, type: AI,labeled with Cy3


title: Embryo 17, derived from AI, Cy5

source_name: Embryo 17, type: AI,labeled with Cy5


title: mast cells rep 2

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: mast cells

hyb_protocol: standard Affymetrix procedures except for use of custom GNF chip washer

scan_protocol: standard Affymetrix procedures using GCS3000 scanner

label: biotin

source_name: mast cells

label_protocol: 5 ug total RNA was used in a standard Affymetrix single amplification protocol.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol:
Bone marrow cells from tibias, femurs and hip bones from 8-10 week old C57BL/6 mice were harvested, lysed with 1x ammonium chloride lysing reagent (PharMlyse BD cat# 555899) for 5 minutes and resuspended  with RPMI medium  (Mediatech, Inc.) supplemented with 10% FBS (Hyclone), 100 U/ml penicillin G, 100 U/ml streptomycin, and 292 ?g/ml of l-glutamine, 10 mM Hepes (pH 7.4),
0.1 mM nonessential amino acid, 1 mM sodium pyruvate, and 50 uM 2-mercaptoethanol with SCF (50 ng/ml) and IL-3–conditioned medium (final concentration of IL3 was 25 ng/ml).  During the first 2-3 weeks of culture the medium was changed every 3 days, and the cells were transferred to new dishes to separate them from adherent cells. Cells were cultured for another 6-8 weeks with media change once a week until BMMC reach full differentiation.
Mature mast cells are determined by FACS confirmation of c-Kit and FceR1 expression in >95% of the cell population containing double positives for both receptors.  WEHI-3 cells were obtained from ATCC and were used as a source of IL3 to supplement the BMMC growth medium .  WEHI-3 cells were cultured in IMDM containing 1.5g/L sodium bicarbonate, 100U/ml pen/strep, 1% L-glutamine,  0.05 mM 2-mercaptoethanol, and 10% FBS.

tag: mast cells


title: Embryo 14, derived from AI, Cy5

source_name: Embryo 14, type: AI,labeled with Cy5


title: Embryo H1, derived from AI, Cy5

source_name: Embryo H1, type: AI,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 15, derived from AI, Cy5

source_name: Embryo 15, type: AI,labeled with Cy5


title: mast cells

description: mast cells


title: Embryo 14, derived from AI, Cy3

source_name: Embryo 14, type: AI,labeled with Cy3

source_name: reference standard RNA, labeled with Cy5


title: Embryo H5, derived from AI, Cy3

source_name: Embryo H5, type: AI,labeled with Cy3


title: Embryo 16, derived from AI, Cy3

source_name: Embryo 16, type: AI,labeled with Cy3


title: Embryo H3, derived from AI, Cy3

source_name: Embryo H3, type: AI,labeled with Cy3


title: Embryo 15, derived from AI, Cy3

source_name: Embryo 15, type: AI,labeled with Cy3


title: Embryo 16, derived from AI, Cy5

source_name: Embryo 16, type: AI,labeled with Cy5


title: macrophage_7hrLPS rep 2

treatment_protocol:
Specific, homogenous bone marrow-derived macrophages (BMM) were obtained by ex vivo differentiation from mouse bone marrow progenitors in the presence of recombinant CSF1 as described previously ( Tushinski, R. J., I. T. Oliver, L. J. Guilbert, P. W. Tynan, J. R. Warner, and E. R. Stanley. 1982.
Survival of mononuclear phagocytes depends on a lineage-specific growth factor that the differentiated cells selectively destroy. Cell 28:71-81; Hume, D. A., and S. Gordon. 1983. Optimal conditions for proliferation of bone marrow-derived mouse macrophages in culture: the roles of CSF-1, serum, Ca2+, and adherence. J Cell Physiol 117:189-194).
All mice were specific pathogen free (SPF), male and 6 to 8 weeks old at the time of bone marrow collection. The femoral and/or tibial bone was extracted, remaining muscle removed and the bone sterilised in 70% ethanol.  The bone cavity was flushed with a 27-gauge needle using complete media (RPMI 1640 supplemented with 5 to 10% fetal bovine serum, 20 U/ml penicillin and 20 ug/ml streptomycin, 2 mM L-glutamine.
The pooled bone marrow progenitors were cultured on bacteriological plastic at two to six plates per bone.  Media was replaced on day five and cells re-seeded at day six onto tissue culture plastic. Cells were stimulated with lipopolysaccharide (LPS, Sigma) early on day seven and harvested over a time course (0, 1, 7h). Cells were harvested and RNA extracted using an  RNeasy kit (Qiagen), according to manufacturer’s instructions.


title: macrophage_7hrLPS


title: macrophage_unstimulated rep 2


title: macrophage_1hrLPS


title: Embryo 13, derived from AI, Cy5

source_name: Embryo 13, type: AI,labeled with Cy5


title: osteoclasts

description: osteoclasts

source_name: osteoclasts

treatment_protocol:
Bone marrow cells were harvested and washed in the same manner as used for BMM preparation, except that DMEM was substituted for RPMI-1640.
The cells were resuspended for differentiation in DMEM+Pen/Strep+Glutamax+10% heat inactivated FCS with 50 µg/mL ascorbic acid + 20 ng/mL human soluble RANKL (Peprotech) + 1 x 104 U/mL human soluble CSF-1 (Cetus). Medium was changed on day 3 and day 6, and cells were harvested for RNA on day 7.
Medium was changed on day 3 and day 6, and cells were harvested for RNA on day 7.

tag: osteoclasts


title: osteoclasts rep 2

description: osteoclasts


title: macrophage_1hrLPS rep 2


title: Embryo 7, derived from AI, Cy3

source_name: Embryo 7, type: AI,labeled with Cy3


title: macrophage_unstimulated


title: osteoblasts_day21

treatment_protocol:
Primary osteoblast cells were isolated by 10-minute sequential digestion of 2 day-old (specific pathogen free) neonatal C57BL/6 calvaria with 0.25 U/ml collagenase D (Roche Diagnostics, Indianapolis, IN, USA) and 2.2 U/ml dispase (Invitrogen, Carlsbad, CA, USA).  Digest fractions 2 to 6 were pooled as primary calvarial osteoblasts.
Osteoblasts were cultured in complete MEM media supplemented with 10% heat-inactivated FBS, 20 U/mL penicillin, 20 ug/mL streptomycin and 2 mM L-glutamine (Invitrogen).  Osteoblasts were differentiated in complete BGJb media supplemented with 10% heat-inactivated FBS, 20 U/mL penicillin, 20 ?g/mL streptomycin and 2 mM L-glutamine (Invitrogen) with 50 ?g/ml of ascorbate acid (Sigma-Aldrich, St Louis, MO, USA) and 10 mM ?-glycerophosphate (Sigma-Aldrich) from day 7 of culture.
Cells were harvested on day 5 (proliferation phase), day 14 (differentiation phase) and day 21 (mineralization phase) representing different stages of osteoblast differentiation and RNA was extracted using an RNeasy kit (Qiagen), according to manufacturer’s instructions.


title: Embryo 7, derived from AI, Cy5

source_name: Embryo 7, type: AI,labeled with Cy5


title: Embryo 8, derived from AI, Cy3

source_name: Embryo 8, type: AI,labeled with Cy3


title: Embryo 8, derived from AI, Cy5

source_name: Embryo 8, type: AI,labeled with Cy5


title: osteoblasts_day21 rep 2


title: osteoblasts_day5


title: Embryo 6, derived from AI, Cy3

source_name: Embryo 6, type: AI,labeled with Cy3


title: Embryo 5, derived from AI, Cy3

source_name: Embryo 5, type: AI,labeled with Cy3


title: Embryo 5, derived from AI, Cy5

source_name: Embryo 5, type: AI,labeled with Cy5

source_name: reference standard RNA, labeled with Cy3


title: Embryo 6, derived from AI, Cy5

source_name: Embryo 6, type: AI,labeled with Cy5


title: Embryo 1, derived from AI, Cy3

source_name: Embryo 1, type: AI,labeled with Cy3

source_name: reference standard RNA, labeled with Cy5


title: osteoblasts_day14 rep 2


title: osteoblasts_day14


title: osteoblasts_day5 rep 2


title: Embryo 1, derived from AI, Cy5

source_name: Embryo 1, type: AI,labeled with Cy5


title: Embryo 3, derived from AI, Cy5

source_name: Embryo 3, type: AI,labeled with Cy5


title: Mycobacterium bovis NO -rep 2

status: Public on May 03 2008

city: Aurora

first: Ryan

middle: William

last: Honaker

state: CO

department: Microbiology

institute: University of Colorado Denver

description: 12 different BCG strains were examined as well as M. tuberculosis H37Rv and M. bovis. Two arrays per strain were analyzed, one with the addition of nitric oxide and the other utilizing hypoxia treatment, both conditions shown to induce expression of the dormancy regulon.

hyb_protocol: Arrays were prehybridized in water, SSC, BSA, and SDS. Labeling reaction was concentrated to 5ul in a microcon 10 filter tube, added to tRNA, SSC, formamide, and SDS, and heated to 98 C for two minutes. Samples were hybridzed overnight at 50 C.

scan_protocol: Scanned on Molecular Device's Genepix 4000B

data_processing: see Voskuil, et al., J Exp Med. 2003 Sep 1;198(5):705-13

organism: Mycobacterium tuberculosis H37Rv

source_name: total RNA from untreated log phase bacterial culture

label_protocol: 1.5 ug of RNA was primed with N6 primers, heated for two minutes at 98 C, then incubated 10 minutes at 25 C followed by 90 minutes at 42 C. 5mM A,G,C and 0.2mM T dNTP mix was used.

growth_protocol: Log phase shaking bacterial culture was used for reference samples and for nitric oxide or hypoxia treatment.

extract_protocol: Cell pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 40 seconds. Resulting cell lysate was added to chloroform and nucleic acids were then precipitated in isopropanol, rehydrated in 75% ethanol, then DNAse treated. Fur further purification, Quiagen RNeasy kit was used according to the manufacturer's instructions.

treatment_protocol: Log phase broth culture treated with 10mM nitric oxide for 1 hour or grown anaerobically in a gaspak for four hours

tag: log phase broth culture

organism: Mycobacterium tuberculosis variant bovis

source_name: total RNA from treated log phase bacterial culture

tag: AN5 strain

tag: log phase broth culture treated with 10mM nitric oxide for 1 hour


title: Mycobacterium bovis hypoxa -rep 2

tag: log phase broth culture grown anaerobically in a gaspak for four hours


title: Mycobacterium tuberculosis H37Rv -hypoxia

tag: M. tuberculosis wild-type strain H37Rv


title: Embryo 3, derived from AI, Cy3

source_name: Embryo 3, type: AI,labeled with Cy3


title: Embryo 13, derived from AI, Cy3

source_name: Embryo 13, type: AI,labeled with Cy3


title: Mycobacterium bovis NO -rep 1


title: Mycobacterium tuberculosis H37Rv NO


title: Mycobacterium bovis hypoxia -rep 1


title: BCG Pasteur 133a hypoxia

organism: Mycobacterium tuberculosis variant bovis BCG

tag: bacille Calmette-Guerin (BCG) Pasteur 133a strain


title: BCG Pasteur 133a NO


title: loop2 L3_Ha (Cy5) vs. L3_Ch (Cy3) (12770820)

city: Raleigh

first: Chris

last: Smith

state: NC

address: 840 Main Campus Dr

department: Bioinformatics Research Center

institute: NCSU

description: L3_Ha (Cy5) vs. L3_Ch (Cy3) (12770820)

hyb_protocol: Hybridization and stringency washes were done according to the protocol from North Carolina State University (van Zyl, U.S. Provisional Patent Application Nos. 60/372,872 and 60/390,142).

scan_protocol: Slides were scanned with a ScanArray 4000 (GSI Lumonics, Oxnard, CA, USA) and raw non-normalized intensity values were registered using Quantarray software (GSI Lumonics).

data_processing: Raw intensity generated with QuantArray and statistically analysed using 2-interconnected mixed linear model approach.

organism: Picea abies

source_name: Picea abies cambium L3_Ha (Cy5)

label_protocol: The cDNA generated from the tissue was labelled using a Klenow method following the protocol from North Carolina State University (van Zyl, U.S. Provisional Patent Application Nos. 60/372,872 and 60/390,142).

extract_protocol: Total RNA was isolated from infected and control tissue samples as described by Chang (1993). The cDNA was synthesised from 1 microgram of RNA using SMART PCR cDNA synthesis kit (Clontech, USA).

treatment_protocol: Picea abies clones were infected with Heterobasidion parviporum and harvested at 20 days. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

tag: Picea abies of low resistance to Heterobasidion parviporum, challenged for 20 days with

value: Heterobasidion parviporum

source_name: Picea abies cambium L3_Ch (Cy3)

treatment_protocol: Healthy Picea abies clones (no treatment). Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

value: Healthy control


title: loop2 M_Cw (Cy5) vs. M2_Ha (Cy3) (12770626)

description: M_Cw (Cy5) vs. M2_Ha (Cy3) (12770626)

source_name: Picea abies cambium M_Cw (Cy5)

treatment_protocol: Picea abies clones were wounded and harvested at 20 days. Total RNA was extracted and used for cDNA synthesis with SMART PCR cDNA synthesis kit (Clontech, USA).

tag: Picea abies of medium resistance to Heterobasidion parviporum, wounded control

source_name: Picea abies cambium M2_Ha (Cy3)

tag: Picea abies of medium resistance to Heterobasidion parviporum, challenged for 20 days with


title: BCG Moscow hypoxia

tag: bacille Calmette-Guerin (BCG) Moscow strain


title: BCG Moscow NO


title: loop2 M_Cw (Cy5) vs. H3_Ha (Cy3) (12770624)

description: M_Cw (Cy5) vs. H3_Ha (Cy3) (12770624)

source_name: Picea abies cambium H3_Ha (Cy3)

tag: Picea abies of high resistance to Heterobasidion parviporum, challenged for 20 days with


title: BCG Tice NO

tag: bacille Calmette-Guerin (BCG) Tice strain


title: BCG Tice hypoxia


title: loop2 M1_Ha (Cy5) vs. M1_Ch (Cy3) (12770502)

description: M1_Ha (Cy5) vs. M1_Ch (Cy3) (12770502)

source_name: Picea abies cambium M1_Ha (Cy5)

source_name: Picea abies cambium M1_Ch (Cy3)


title: loop2 L_Cw (Cy5) vs. L3_Ha (Cy3) (12770634)

description: L_Cw (Cy5) vs. L3_Ha (Cy3) (12770634)

source_name: Picea abies cambium L_Cw (Cy5)

tag: Picea abies of low resistance to Heterobasidion parviporum, wounded control

source_name: Picea abies cambium L3_Ha (Cy3)


title: BCG Brazil NO

tag: bacille Calmette-Guerin (BCG) Brazil strain


title: BCG Brazil hypoxia


title: BCG Russia hypoxia

tag: bacille Calmette-Guerin (BCG) Russia strain


title: loop2 H3_Ha (Cy5) vs. H3_Ch (Cy3) (12770818)

description: H3_Ha (Cy5) vs. H3_Ch (Cy3) (12770818)

source_name: Picea abies cambium H3_Ha (Cy5)

source_name: Picea abies cambium H3_Ch (Cy3)


title: loop2 H1_Ha (Cy5) vs. H1_Ch (Cy3) (12770501)

description: H1_Ha (Cy5) vs. H1_Ch (Cy3) (12770501)

source_name: Picea abies cambium H1_Ha (Cy5)

source_name: Picea abies cambium H1_Ch (Cy3)


title: BCG Denmark NO

source_name: total RNA from untreated log phase bacterial culture

tag: bacille Calmette-Guerin (BCG) Denmark strain


title: loop2 M2_Ha (Cy5) vs. M2_Ch (Cy3) (12770492)

description: M2_Ha (Cy5) vs. M2_Ch (Cy3) (12770492)

source_name: Picea abies cambium M2_Ha (Cy5)

source_name: Picea abies cambium M2_Ch (Cy3)


title: BCG Denmark hypoxia

source_name: total RNA from treated log phase bacterial culture


title: loop2 L1_Ha (Cy5) vs. L1_Ch (Cy3) (12770493)

description: L1_Ha (Cy5) vs. L1_Ch (Cy3) (12770493)

source_name: Picea abies cambium L1_Ha (Cy5)

source_name: Picea abies cambium L1_Ch (Cy3)


title: loop2 L2_Ch (Cy5) vs. L1_Ha (Cy3) (12770477)

description: L2_Ch (Cy5) vs. L1_Ha (Cy3) (12770477)

source_name: Picea abies cambium L2_Ch (Cy5)

source_name: Picea abies cambium L1_Ha (Cy3)


title: loop2 H3_Ch (Cy5) vs. H2_Ha (Cy3) (12770490)

description: H3_Ch (Cy5) vs. H2_Ha (Cy3) (12770490)

source_name: Picea abies cambium H3_Ch (Cy5)

source_name: Picea abies cambium H2_Ha (Cy3)


title: BCG Russia NO


title: BCG Vietnam NO

tag: bacille Calmette-Guerin (BCG) Vietnam


title: loop2 M2_Ha (Cy5) vs. M_Cw (Cy3) (12769252)

description: M2_Ha (Cy5) vs. M_Cw (Cy3) (12769252)

source_name: Picea abies cambium M_Cw (Cy3)


title: BCG Vietnam hypoxia

tag: log phase broth culture


title: loop2 H2_Ch (Cy5) vs. H1_Ha (Cy3) (12770500)

description: H2_Ch (Cy5) vs. H1_Ha (Cy3) (12770500)

source_name: Picea abies cambium H2_Ch (Cy5)

source_name: Picea abies cambium H1_Ha (Cy3)


title: BCG Japan hypoxia

tag: bacille Calmette-Guerin (BCG) Japan strain


title: loop2 M3_Ch (Cy5) vs. M1_Ha (Cy3) (12764027)

description: M3_Ch (Cy5) vs. M1_Ha (Cy3) (12764027)

source_name: Picea abies cambium M3_Ch (Cy5)

source_name: Picea abies cambium M1_Ha (Cy3)


title: BCG Connaught NO

tag: bacille Calmette-Guerin (BCG) Connaught strain

tag: log phase broth culture treated with 10mM nitric oxide for 1 hour


title: BCG Connaught hypoxia

tag: log phase broth culture grown anaerobically in a gaspak for four hours


title: loop2 M3_Ha (Cy5) vs. M3_Ch (Cy3) (12763997)

description: M3_Ha (Cy5) vs. M3_Ch (Cy3) (12763997)

source_name: Picea abies cambium M3_Ha (Cy5)

source_name: Picea abies cambium M3_Ch (Cy3)


title: loop2 M2_Ch (Cy5) vs. M3_Ha (Cy3) (12763975)

description: M2_Ch (Cy5) vs. M3_Ha (Cy3) (12763975)

source_name: Picea abies cambium M2_Ch (Cy5)

source_name: Picea abies cambium M3_Ha (Cy3)


title: loop2 M1_Ch (Cy5) vs. L_Cw (Cy3) (12763998)

description: M1_Ch (Cy5) vs. L_Cw (Cy3) (12763998)

source_name: Picea abies cambium M1_Ch (Cy5)

source_name: Picea abies cambium L_Cw (Cy3)


title: BCG Japan NO

source_name: total RNA from untreated log phase bacterial culture

source_name: total RNA from treated log phase bacterial culture


title: loop2 H1_Ch (Cy5) vs. L_Cw (Cy3) (12763955)

description: H1_Ch (Cy5) vs. L_Cw (Cy3) (12763955)

source_name: Picea abies cambium H1_Ch (Cy5)


title: loop2 L_Cw (Cy5) vs. H1_Ch (Cy3) (12764000)

description: L_Cw (Cy5) vs. H1_Ch (Cy3) (12764000)

source_name: Picea abies cambium L_Cw (Cy5)

source_name: Picea abies cambium H1_Ch (Cy3)


title: loop2 H2_Ha (Cy5) vs. H2_Ch (Cy3) (12763956)

description: H2_Ha (Cy5) vs. H2_Ch (Cy3) (12763956)

source_name: Picea abies cambium H2_Ha (Cy5)

source_name: Picea abies cambium H2_Ch (Cy3)


title: BCG Sweden hypoxia

tag: bacille Calmette-Guerin (BCG) Sweden strain


title: BCG Pasteur hypoxia

tag: bacille Calmette-Guerin (BCG) BCG Pasteur 140 strain


title: loop2 L1_Ch (Cy5) vs. M_Cw (Cy3) (12763877)

description: L1_Ch (Cy5) vs. M_Cw (Cy3) (12763877)

source_name: Picea abies cambium L1_Ch (Cy5)

tag: Picea abies of low resistance to Heterobasidion parviporum, challenged for 20 days with

source_name: Picea abies cambium M_Cw (Cy3)

tag: Picea abies of medium resistance to Heterobasidion parviporum, wounded control


title: loop2 L3_Ch (Cy5) vs. L2_Ha (Cy3) (12763879)

description: L3_Ch (Cy5) vs. L2_Ha (Cy3) (12763879)

source_name: Picea abies cambium L3_Ch (Cy5)

source_name: Picea abies cambium L2_Ha (Cy3)


title: loop2 L2_Ha (Cy5) vs. L2_Ch (Cy3) (12763880)

description: L2_Ha (Cy5) vs. L2_Ch (Cy3) (12763880)

source_name: Picea abies cambium L2_Ha (Cy5)

source_name: Picea abies cambium L2_Ch (Cy3)


title: BCG Connaught JPG hypoxia

tag: bacille Calmette-Guerin (BCG) Connaught JPG strain


title: loop2 L_Cw (Cy5) vs. M1_Ch (Cy3) (12763954)

description: L_Cw (Cy5) vs. M1_Ch (Cy3) (12763954)

source_name: Picea abies cambium M1_Ch (Cy3)

tag: Picea abies of medium resistance to Heterobasidion parviporum, challenged for 20 days with


title: BCG Connaught JPG NO


title: BCG Pasteur NO


title: BCG Sweden NO


title: loop2 H3_Ha (Cy5) vs. M_Cw (Cy3) (12763873)

description: H3_Ha (Cy5) vs. M_Cw (Cy3) (12763873)

source_name: Picea abies cambium H3_Ha (Cy5)

tag: Picea abies of high resistance to Heterobasidion parviporum, challenged for 20 days with


title: loop1 H1_Ha (Cy5) vs. L_Cw (Cy3) (12770821)

description: H1_Ha (Cy5) vs. L_Cw (Cy3) (12770821)

source_name: Picea abies cambium H1_Ha (Cy5)

treatment_protocol: Picea abies clones were infected with Heterobasidion parviporum and harvested at 20 days. Total RNA was extracted and used for cDNA synthesis with SMART(tm) PCR cDNA synthesis kit (Clontech, USA).

tag: Picea abies of high resistance to Heterobasidion parviporum, challenged for 20 days with Heterobasidion parviporum

treatment_protocol: Picea abies clones were wounded and harvested at 20 days. Total RNA was extracted and used for cDNA synthesis with SMART(tm) PCR cDNA synthesis kit (Clontech, USA).

tag: Picea abies of low resistance to Heterobasidion parviporum, wounded control


title: loop1 M3_Ha (Cy5) vs. M_Cw (Cy3) (12770633)

description: M3_Ha (Cy5) vs. M_Cw (Cy3) (12770633)

source_name: Picea abies cambium M3_Ha (Cy5)

tag: Picea abies of medium resistance to Heterobasidion parviporum, challenged for 20 days with Heterobasidion parviporum


title: loop1 H2_Ha (Cy5) vs. M_Cw (Cy3) (12770817)

description: H2_Ha (Cy5) vs. M_Cw (Cy3) (12770817)


title: 22 h post LH surge, biological rep 1

city: Bangalore

first: jyotsna

middle: U

last: rao

state: Karnataka

address: C.V. Raman Road

department: MRDG

country: India

institute: Indian Institute of Science

description: Probe level measurements produced by robust multichip average (RMA) algorithm

scan_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001) using scanner 3000 series

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).

label: Biotin

organism: Bubalus bubalis

source_name: Granulosa cells collected 22 h post LH surge from buffalo cows

extract_protocol: Total RNA was isolated using Trizol reagent (Sigma Aldrich Co., St.Louis, MO) according to manufacturer’s instructions.

treatment_protocol: For the purpose of microarray analysis, GnRH (100 µg, i.m.) was administered 36 h post PGF2alpha, Ovaries were collected at 24 h post GnRH, from which granulosa cells were isolated (n=3).


title: loop1 L1_Ha (Cy5) vs. H1_Ha (Cy3) (12770632)

description: L1_Ha (Cy5) vs. H1_Ha (Cy3) (12770632)

source_name: Picea abies cambium L1_Ha (Cy5)

tag: Picea abies of low resistance to Heterobasidion parviporum, challenged for 20 days with Heterobasidion parviporum

source_name: Picea abies cambium H1_Ha (Cy3)


title: 22 h post LH surge, biological rep 3

hyb_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001)

tag: Granulosa cells collected 22 h post LH surge


title: wt-rgd-sam3-high-rep6

city: Ithaca

first: Michael

middle: J

last: Scanlon

state: NY

address: 140 Emerson Hall

department: Department of Plant Biology

institute: Cornell University

description: Biological replicate 6 of 6.

hyb_protocol: Fluorescent targets were hybridized as described in the “cDNA microarray protocol” file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Scanned on an ScanArray Lite (Packard Bioscience) scanner. Image quantification was performed with ScanArray Express

data_processing: Raw signals were first corrected by background intensity within each slide, followed by LOWESS normalization to remove intensity-dependent dye bias (Dudoit et al., 2002). Median centering was used to normalize data across slides from each channel (Yang et al., 2002).  A mixed linear model was applied to the normalized data to identify the differentially expressed genes among rgd2-R mutant and non-mutant samples as described (Dudoit et al., 2002; Zhang et al., 2007).

organism: Zea mays

source_name: RNA from nonmutant

label_protocol: 2.5µg of amplified RNA were indirectly labeled by amino allyl incorporation as described (Nakazono et al, 2003).  To remove dye bias, Cy dyes were swapped between the RNA samples

growth_protocol: Maize seedlings of Non-mutant and rgd2-R mutant (introgressed into Mo17 for 5 generations) were grown under the same controlled condition and harvested for laser microdissection at 14 days after germination.

extract_protocol: Total RNA were extracted using the PicoPure™ RNA extraction kit, and two rounds of RNA amplification were performed using RiboAmp™ HS RNA amplification kit

tag: scan with high laser power and PMT gain settings

source_name: RNA from rgd2-R


title: 1 h post LH surge, biological rep 2

description: Probe level measurements were produced by robust multichip average (RMA) algorithm

source_name: Granulosa cells collected 1 h post LH surge from buffalo cows

label_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001)

treatment_protocol: For the purpose of microarray analysis, GnRH (100 µg, i.m.) was administered 36 h post PGF2alpha, Ovaries were collected at 3 h post GnRH, from which granulosa cells were isolated (n=3).


title: 1 h post LH surge, biological rep 1

tag: Granulosa cells collected 1 h post LH surge


title: Before LH surge, biological rep 3

source_name: Granulosa cells collected before LH surge from buffalo cows

extract_protocol: Total RNA was isolated using Trizol reagent according to manufacturer’s instructions.

treatment_protocol: For the purpose of microarray analysis, Ovaries were collected at 36 h post PGF2alpha, from which granulosa cells were isolated (n=3).

tag: Granulosa cells collected before gonadotropin surge


title: 22 h post LH surge, biological rep 2


title: Before LH surge, biological rep 2


title: wt-rgd-sam3-high-rep5

description: Biological replicate 5 of 6.


title: loop1 M_Cw (Cy5) vs. M1_Ha (Cy3) (12770598)

description: M_Cw (Cy5) vs. M1_Ha (Cy3) (12770598)

source_name: Picea abies cambium M_Cw (Cy5)

source_name: Picea abies cambium M1_Ha (Cy3)


title: wt-rgd-sam3-high-rep3

description: Biological replicate 3 of 6.


title: wt-rgd-sam3-high-rep1

description: Biological replicate 1 of 6.


title: wt-rgd-sam3-high-rep2

description: Biological replicate 2 of 6.


title: wt-rgd-sam1-high-rep3

description: Biological replicate 3 of 6.


title: wt-rgd-sam3-high-rep4

description: Biological replicate 4 of 6.


title: 1 h post LH surge, biological rep 3


title: wt-rgd-sam1-high-rep5

description: Biological replicate 5 of 6.


title: loop1 L3_Ha (Cy5) vs. H3_Ha (Cy3) (12770596)

description: L3_Ha (Cy5) vs. H3_Ha (Cy3) (12770596)

source_name: Picea abies cambium L3_Ha (Cy5)

source_name: Picea abies cambium H3_Ha (Cy3)


title: loop1 M3_Ha (Cy5) vs. L3_Ha (Cy3) (12770507)

description: M3_Ha (Cy5) vs. L3_Ha (Cy3) (12770507)

source_name: Picea abies cambium L3_Ha (Cy3)


title: wt-rgd-sam1-high-rep4

description: Biological replicate 4 of 6.


title: loop1 L2_Ha (Cy5) vs. H1_Ha (Cy3) (12770506)

description: L2_Ha (Cy5) vs. H1_Ha (Cy3) (12770506)

source_name: Picea abies cambium L2_Ha (Cy5)


title: loop1 M2_Ha (Cy5) vs. H2_Ha (Cy3) (12770514)

description: M2_Ha (Cy5) vs. H2_Ha (Cy3) (12770514)

source_name: Picea abies cambium M2_Ha (Cy5)

source_name: Picea abies cambium H2_Ha (Cy3)


title: wt-rgd-sam1-mid-rep6

description: Biological replicate 6 of 6.

tag: scan with median laser power and PMT gain settings


title: loop1 H3_Ha (Cy5) vs. L2_Ha (Cy3) (12770505)

description: H3_Ha (Cy5) vs. L2_Ha (Cy3) (12770505)

source_name: Picea abies cambium H3_Ha (Cy5)

source_name: Picea abies cambium L2_Ha (Cy3)


title: loop1 M2_Ha (Cy5) vs. L1_Ha (Cy3) (12770504)

description: M2_Ha (Cy5) vs. L1_Ha (Cy3) (12770504)

source_name: Picea abies cambium L1_Ha (Cy3)


title: wt-rgd-sam3-mid-rep5

description: Biological replicate 5 of 6.


title: wt-rgd-sam3-mid-rep4

description: Biological replicate 4 of 6.


title: wt-rgd-sam3-mid-rep6

description: Biological replicate 6 of 6.


title: wt-rgd-sam1-high-rep1

description: Biological replicate 1 of 6.


title: wt-rgd-sam3-mid-rep3

description: Biological replicate 3 of 6.


title: loop1 H2_Ha (Cy5) vs. M1_Ha (Cy3) (12770503)

description: H2_Ha (Cy5) vs. M1_Ha (Cy3) (12770503)

source_name: Picea abies cambium H2_Ha (Cy5)


title: wt-rgd-sam3-mid-rep1

description: Biological replicate 1 of 6.


title: IAP-flanking region vs whole genome (C57BL-Exp2)

type: genomic

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

description: See above.

hyb_protocol: Hybridization and post hybridization wash were carried out essentially according to the manufacturers’ protocol (version 2) for oligonucleotide array-based CGH for genomic DNA analysis (Agilent).

scan_protocol: Hybridized arrays were scanned using the Axon 4000B scanner (Axon Instruments, Burlingame, CA) and processed using GenePix Pro 5.1 software (Axon Instruments).

data_processing: Fluorescence ratios were normalized so that the mean of the ratio of medians of all of the features is equal to 1.

molecule: genomic DNA

source_name: IAP-flanking C57BL/6J genomic DNA fragments

label_protocol: Affinity-purified DNA fragments containing the LTR sequence were digested by Rsa I and AluI, and then labeled fluorescently by Cy3. Clean-up of digested or fluorescently-labeled DNA was carried out with QIAprep Spin Miniprep Kit (Qiagen) or Microcon YM-30 filters (Millipore, Billerica, MA), respectively.

extract_protocol: Genomic DNA was isolated according to standard procedures using proteinase K and phenol-chloroform extraction. Two methods were employed in the generation of genomic DNA fragments containing a common sequence at both ends; the degenerate oligonucleotide-primed PCR (DOP-PCR) method and the digestion by restriction enzymes followed by linker ligation. The digestion by restriction enzymes was carried out with the following three enzymes; Bam HI, Bgl II and Fba I.  One g of genomic DNA was digested by these enzymes independently, or in combination with another enzyme (double digestions).  Subsequently, all restricted fragments were mixed, purified by using a QIAquick PCR Purification Kit and ligated to a linker. DNA fragments containing the contiguous sequences covering the LTR region of IAP element and its flanking region were purified using the affinity with the biotin labeled oligonucleotides which had highly conserved sequences within LTR.

tag: C57BL/6J tale

source_name: C57BL/6J genomic DNA fragments

label_protocol: Genomic DNA was digested by Rsa I and AluI, and labeled fluorescently by Cy5. Clean-up of digested or fluorescently-labeled DNA was carried out with QIAprep Spin Miniprep Kit (Qiagen) or Microcon YM-30 filters (Millipore, Billerica, MA), respectively.

tag: C57BL/6J female tale


title: wt-rgd-sam1-mid-rep5

description: Biological replicate 5 of 6.

source_name: RNA from nonmutant

source_name: RNA from rgd2-R


title: wt-rgd-sam1-mid-rep4

description: Biological replicate 4 of 6.


title: IAP-flanking region vs whole genome (C57BL-Exp1)

description: See above.

extract_protocol: Genomic DNA was isolated according to standard procedures using proteinase K and phenol-chloroform extraction.


title: loop1 M_Cw (Cy5) vs. M3_Ha (Cy3) (12770473)

description: M_Cw (Cy5) vs. M3_Ha (Cy3) (12770473)

source_name: Picea abies cambium M3_Ha (Cy3)


title: wt-rgd-sam1-mid-rep3

description: Biological replicate 3 of 6.


title: loop1 L_Cw (Cy5) vs. H3_Ha (Cy3) (12770475)

description: L_Cw (Cy5) vs. H3_Ha (Cy3) (12770475)

source_name: Picea abies cambium L_Cw (Cy5)


title: wt-rgd-sam3-low-rep5

description: Biological replicate 5 of 6.

tag: scan with low laser power and PMT gain settings


title: loop1 M1_Ha (Cy5) vs. L1_Ha (Cy3) (12770491)

description: M1_Ha (Cy5) vs. L1_Ha (Cy3) (12770491)

source_name: Picea abies cambium M1_Ha (Cy5)


title: wt-rgd-sam1-mid-rep2

description: Biological replicate 2 of 6.


title: loop1 M1_Ha (Cy5) vs. M_Cw (Cy3) (12763999)

description: M1_Ha (Cy5) vs. M_Cw (Cy3) (12763999)

source_name: Picea abies cambium M_Cw (Cy3)


title: wt-rgd-sam3-low-rep6

description: Biological replicate 6 of 6.


title: wt-rgd-sam3-mid-rep2

description: Biological replicate 2 of 6.


title: wt-rgd-sam1-mid-rep1

description: Biological replicate 1 of 6.


title: wt-rgd-sam3-low-rep4

description: Biological replicate 4 of 6.


title: wt-rgd-sam3-low-rep3

description: Biological replicate 3 of 6.


title: wt-rgd-sam1-low-rep6

description: Biological replicate 6 of 6.


title: loop1 L_Cw (Cy5) vs. L2_Ha (Cy3) (12763977)

description: L_Cw (Cy5) vs. L2_Ha (Cy3) (12763977)


title: loop1 L3_Ha (Cy5) vs. M2_Ha (Cy3) (12763957)

description: L3_Ha (Cy5) vs. M2_Ha (Cy3) (12763957)

source_name: Picea abies cambium L3_Ha (Cy5)

source_name: Picea abies cambium M2_Ha (Cy3)


title: wt-rgd-sam3-low-rep2

description: Biological replicate 2 of 6.


title: wt-rgd-sam3-low-rep1

description: Biological replicate 1 of 6.


title: wt-rgd-sam1-low-rep5

description: Biological replicate 5 of 6.


title: wt-rgd-sam1-low-rep4

description: Biological replicate 4 of 6.


title: wt-rgd-sam1-low-rep3

description: Biological replicate 3 of 6.


title: wt-rgd-sam1-high-rep6

description: Biological replicate 6 of 6.


title: wt-rgd-sam1-low-rep1

description: Biological replicate 1 of 6.


title: loop1 M3_Ha (Cy5) vs. H2_Ha (Cy3) (12763882)

description: M3_Ha (Cy5) vs. H2_Ha (Cy3) (12763882)

source_name: Picea abies cambium M3_Ha (Cy5)


title: wt-rgd-sam1-low-rep2

description: Biological replicate 2 of 6.


title: loop1 H3_Ha (Cy5) vs. L_Cw (Cy3) (12763948)

description: H3_Ha (Cy5) vs. L_Cw (Cy3) (12763948)

source_name: Picea abies cambium L_Cw (Cy3)


title: loop1 L2_Ha (Cy5) vs. M2_Ha (Cy3) (12679249)

description: L2_Ha (Cy5) vs. M2_Ha (Cy3) (12679249)

source_name: Picea abies cambium L2_Ha (Cy5)


title: Before LH surge, biological rep 1

source_name: Granulosa cells collected before LH surge from buffalo cows


title: M. sedula grown on yeast extract (YE) vs. yeast extract+ferrous sulfate (YEF)

status: Public on May 02 2008

first: Kathryne

middle: Sherlock

last: Auernik

address: Partners II, rm 3309, 849 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

description: Scatterplots of signal intensities are reviewed to check for balance between channels.

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

scan_protocol: Images were aquired with a Perkin Elmer ScanArray Lite scanner containing 2 lasers. Channels were balanced using the line scan feature and by balancing the overall signals without the use of external standards

data_processing: Signals for each channel were obtained using ScanArray® Express 2.1 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once both slides were quantitated, data from the dye-flip was analyzed with JMP Genomics 3.0 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

label: Cy™3 or Cy™5dye (GE Healthcare)

organism: Metallosphaera sedula

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy5 or Cy3 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning). (Auernik et al, 2008)

growth_protocol:
(Auernik et al, 2008): Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% yeast extract (YE). An initial density of mid 10^6 cells/mL was used in [two] 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in 0.1%YE-supplemented DSMZ 88 media.

extract_protocol: At harvest, cells were quickly chilled and then centrifuged at 9510 x g for 15 minutes at 4C. RNA was extracted and purified using an RNAqueous kit (Ambion). (Auernik et al, 2008)

tag: whole cells

label: Cy™5 dye or Cy™3 (GE Healthcare)

treatment_protocol: Prior to inoculation of final passage, approximately 7.5 g/L of FeSO4∙7H2O was added to 0.1% YE-supplemented DSMZ 88. Harvest of final passage occurred at mid-10^7 cells/mL (~24hrs post-inoculation).


title: Met_LymphNode_EWD_10 LN

first: Wendy

last: Dye

institute: UCDHSC

description: Human Breast Cancer Cells grown in Mouse

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human X3P Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent Bioanalyzer 2100

data_processing: Data analyzed with Partek, imported and RMA normalized

source_name: Laser Captured Metastastic Lymph Node from EWD treated mouse #10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Laser Capture was performed on frozen sections. After laser capture of cells, RNA PCR amplified.

treatment_protocol: Estrogen pellets implanted in mice, removed for 1 week for Estrogen withdrawal

tag: Strain

value: nu/nu Gender:female Age:20 weeks

tag: Tissue:breast cancer metastatic lymph node


title: Primary_MGTumor_E_11 MGT

source_name: Laser Captured Primary Xenograft Tumor from E treated mouse #11

tag: Tissue:breast cancer xenograft in mammary gland


title: Triple-7

status: Public on May 01 2008

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

description: three standards were applied. First, if the intensity of the gene was at least 2 SD above the background value, it was considered to be a genuine signal. Second, only relative changes equal to, or greater than, two-fold levels of gene expression were considered to represent up or down-regulation. In addition, if the signal intensity of a given gene was changed from negative (below the signal threshold) to positive or from positive to negative, the gene was considered being up or down regulated respectively. Finally the absolute difference in signal intensity between two samples was at least more than 2 SD of the background value

hyb_protocol: The array membranes were prehybridized at 65°C for 2 hours in hybridization solution (5X SSPE, 2% (w/v) SDS, 5X Denhardt’s reagent and 100 µg/ml sonicated, salmon DNA). Labeled probes were added to 3 ml fresh hybridization solution and allowed to hybridize to the array membranes at 65°C overnight. After hybridization, membranes were washed two times with solution 1 (0.5 x SSC and 1% SDS), twice with solution 2 (0.1 x SSC and 1% SDS) for 20 minutes at 65°C and finally exposed to a phosphorus screen for 7 days

scan_protocol: The cDNA microarrays were scanned and exported as img. and inf. files using a Fuji Bio-image Analyzer BAS2000 (Fuji Photo Film Co Ltd., Japan). The images and quantitative data of gene expression levels were analyzed using the Fuji Image Reader FLA-3000/3000G software

data_processing: Raw Data: raw signal output from the image analysis algorithm;Raw - Background: raw data mius the average backgroud value;VALUE: raw-backgroud, normalized by 9 housekeeping genes

source_name: total RNA from gastric mucosa

label_protocol: cDNA probe preparation and membrane hybridization were performed according to the respective kit manuals (R&D Systems). Briefly, 4µg of total RNA was reverse transcribed into cDNA by AMV reverse transcriptase using a human cytokine-specific primer mix in the presence of [a33P]-dCTP (2000 Ci/mmol; Amersham Pharmacia, Uppsala, Sweden) and 0.3 mM of a dATP/dGTP/dTTP mixture at 42°C for 2 hours. Labeled cDNA was subsequently separated from unincorporated nucleotides using Sephadex G-25 spin columns (R&D Systems).

extract_protocol: Total RNA was isolated from 20~30 mg frozen gastric biopsy samples (2 biopsies) using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA samples from antrum and corpus biopsies were prepared separately. In addition to the standard procedure, Dnase I (Qiagen) was used to remove trace amount of genomic DNA

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 39 years old , female


title: Triple-6

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 58years old , female


title: TRIPLE-4

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 42years old , female


title: Pulvinar Replicate 2

city: Davis

first: Karl

middle: Daniel

last: Murray

address: 1544 Newton Court

institute: UC Davis

hyb_protocol: Affymetrix recomended hybridization protocol was used.

scan_protocol: U133A GeneChips were scanned using a Affymetrix GeneChip Scanner 7G according to the manufactureres instructions.

data_processing: Raw values obtained from Affymetrix Cel files were preprocessed for RMA in GeneSpring GX (version 7.3.1) followed by per-gene and per-chip median polishing.

organism: Macaca mulatta

source_name: Adult brain

label_protocol: Affymetrix recomended labelling protocol was used.

extract_protocol: Triazol (Invitrogen, Carlsbad, CA) regent followed by RNeasy (Qiagen, Valencia, CA) lipid mini kit cleanup

tag: Material from adult monkey dorsal thalamus


title: Triple-2

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 33years old , female


title: Centre Median Replicate 1


title: Centre Median Replicate 2


title: Primary_MGTumor_E_14 MGT

source_name: Laser Captured Primary Xenograft Tumor from E treated mouse #14


title: Medial Thalamus Replicate 1


title: Ventral Thalamus Replicate 2


title: Primary_MGTumor_EWD_10 MGT

source_name: Laser Captured Primary Xenograft Tumor from EWD treated mouse #10


title: Met_LymphNode_EWD_9 LN

source_name: Laser Captured Metastastic Lymph Node from EWD treated mouse #9


title: Ventral Thalamus Replicate 1

tag: material from adult monkey dorsal thalamus


title: Met_LymphNode_E_11 LN

source_name: Laser Captured Metastastic Lymph Node from E treated mouse #11


title: Pulvinar Replicate 1


title: Anterior Thalamus Replicate 2


title: Anterior Thalamus Replicate 1

source_name: Adult Brain

tag: Material From adult monkey dorsal thalamus


title: Medial Thalamus Replicate 2


title: Triple-3

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 25years old , female


title: Met_LymphNode_E_6 LN

source_name: Laser Captured Metastastic Lymph Node from E treated mouse #6


title: Met_LymphNode_EWD_19 LN

source_name: Laser Captured Metastastic Lymph Node from EWD treated mouse #19


title: Met_LymphNode_E_14 LN

source_name: Laser Captured Metastastic Lymph Node from E treated mouse #14


title: Primary_MGTumor_EWD_19 MGT

source_name: Laser Captured Primary Xenograft Tumor from EWD treated mouse #19


title: Triple+5

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 40years old , female


title: Triple-1

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 26years old , female


title: Hp negative 8

tag: total RNA from human gastric mucos, antrum, Non-Helicobacter pylori infected, 33 years old , female.


title: Triple+1

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 30years old , female


title: Triple+3

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 32years old , female


title: Hp negative 2

tag: total RNA from human gastric mucos, antrum, Non-Helicobacter pylori infected, 54 years old , female.


title: Hp negative 7

tag: total RNA from human gastric mucos, antrum, Non-Helicobacter pylori infected, 79years old , female


title: Hp negative 4

tag: total RNA from human gastric mucos, antrum, Non-Helicobacter pylori infected, 48years old , male.


title: Hp negative 3

tag: total RNA from human gastric mucos, antrum, Non-Helicobacter pylori infected, 58years old , female.


title: Hp negative 1

extract_protocol: Total RNA was isolated from 20~30 mg frozen gastric biopsy samples (2 biopsies) using the RNeasy mini kit (Qiagen, Hilden, Germany).  RNA samples from antrum and corpus biopsies were prepared separately. In addition to the standard procedure, Dnase I (Qiagen) was used to remove trace amount of genomic DNA


title: Triple+4

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 46years old , female


title: Hp negative 5

tag: total RNA from human gastric mucos, antrum, Non-Helicobacter pylori infected, 35years old , male


title: Triple+10

tag: total RNA from human gastric mucos, antrum, Helicobacter infected, 40 years old , female.


title: Hp negative 6

tag: total RNA from human gastric mucos, antrum, Non-Helicobacter pylori infected, 87 years old , male.


title: Triple+6

source_name: total RNA from gastric mucos

tag: total RNA from human gastric mucos, antrum, Helicobacter infected, 50 years old , female.


title: triple+7

tag: total RNA from human gastric mucos, antrum, Helicobacter infected, 55 years old , male.


title: Triple+8

tag: total RNA from human gastric mucos, antrum, Helicobacter infected, 53 years old , female.


title: Triple+9

tag: total RNA from human gastric mucos, antrum, Helicobacter infected, 35 years old , male.


title: Triple+2

tag: total RNA from human gastric mucos, antrum, Helicobacter pylori infected, 33years old , female


title: E_071022_02_DS7784_W E

status: Public on Apr 30 2008

city: SEATTLE

middle: A

last: Stamatoyannopoulos

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: DnaseI enriched

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays.  Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software; linearly scaled to intesity of 500, 2-sided upper quantile normalization.

label_protocol: Fragments were cleaned using Qiagen PCR columns.  Samples were amplified using the Sigma WGA amplification kit.  Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase.  (See Affymetrix Chip Chip protocol)

growth_protocol: (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

extract_protocol: Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI

tag: GM69; Coriell


title: E_071022_01_DS7748_W E

description: DnaseI enriched


title: E_071015_01_DS7775_W E

description: DnaseI enriched


title: E_070920_02_DS7784_W E

description: DnaseI enriched


title: E_080213_06_DS8626_W E

description: DnaseI enriched

tag: GM12878; Coriell


title: E_080213_05_DS8623_W E

description: DnaseI enriched


title: C_080204_02_DS8582_W E

description: Control genomic dna (untreated)

source_name: GM12878;Coriell:GM12878;B-Lymphocyte;normal;blood;adult/female;RPMI;;Control genomic dna (untreated)

extract_protocol: Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40.  Nuclei were lysed using SDS and treated overnight with Proteinase K


title: C_080204_01_DS8582_W E

description: Control genomic dna (untreated)


title: C_080204_03_DS8582_W E

description: Control genomic dna (untreated)


title: E_070920_01_DS7748_W E

description: DnaseI enriched


title: GM12273_GroupedSamplesNormProbeProfile

status: Public on Apr 10 2008

city: Rockville

first: Andrew

middle: W

last: Bergen

state: MD

address: 6120 Executive Blvd

department: Cancer Epidemiology & Genetics

institute: NCI/NIH

description: Data extraction and processing was performed as described in Kuhn et al., A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 2004, 14: 2347-2356.

hyb_protocol: Array hybridization, washing and staining was performed as described in Kuhn et al., A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 2004, 14: 2347-2356.

scan_protocol: Scanning and image acquisition was performed as described in Kuhn et al., A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 2004, 14: 2347-2356.

data_processing: VALUE was generated using a global background subtraction and rank-invariant normalization algorithm, averaging three replicate arrays.

source_name: lymphoblastoid cell culture

label_protocol:
Labeling was performed as described in Kuhn et al., A novel, high-performance random array platform for quantitative gene expression
profiling. Genome Res 2004, 14: 2347-2356.

growth_protocol:
We cultured N=30 Coriell Cell Repository lymphoblastoid cell lines, in
triplicate under standardized conditions; when cells per milliliter exceeded 2X107, the cells were harvested, the pellets were washed once with PBS and frozen at -80ºC. Same lot cell culture reagents were used, with three technicians each dedicated to culturing N=10 of these cell lines, with replicate cell cultures cultured in series.

extract_protocol:
Total RNA was prepared from frozen cell pellets using the Qiagen RNeasy Midi-kit (Valencia, CA). Ten cell culture pellets were extracted at a time by a single technician with a single assistant; cell pellets were removed one-at-a-time from the -80ºC freezer, quick thawed by rubbing between gloved hands, and Qiagen denaturant immediately added. Ethanol was added to each sample, vortexed, and the samples applied to Qiagen Midi columns, washed as specified, treated with RNase-free DNase “on-column”, followed by additional washes before elution of the RNA with the provided buffer. After elution, sample volume was
determined by weight, sodium acetate was added to 0.3 M, the sample was split and ethanol added at 3X volume to each aliquot and stored at -20ºC.

tag: See Coriell catalog # GM12273


title: wt-rgd-sam1-high-rep2

description: Biological replicate 2 of 6.

source_name: RNA from rgd2-R

tag: scan with high laser power and PMT gain settings

source_name: RNA from nonmutant


title: GM13618_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM13618


title: GM13619_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM13619


title: GM11993_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM11993


title: GM12749_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM12749


title: GM12863_GroupedSamplesNormProbeProfile

source_name: lymphoblastoid

tag: See Coriell # GM12863


title: GM12813_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM12813


title: GM12841_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM12841


title: GM13617_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM13617


title: GM12912_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM12912


title: GM11524_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM11524


title: GM11525_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM11525


title: GM11522_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM11522


title: GM10860_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10860


title: GM12911_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM12911


title: GM10861_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10861


title: GM12909_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM12909


title: GM10859_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10859


title: GM11523_GroupedSamplesNormProbeProfile

data_processing: VALUE was generated using a global background subtraction and rank-invariant normalization algorithm, averaging three replicate arrays. Note that in the analysis that will be submitted after receiving the submission number from GEO, we dropped on of the GM11523 arrays beacuse of a within cell individual cell line linear r2 correlation for all genes of <95%, while all remaining within individual cell line correlations were ~99%. To recreate the data file that we used, one would need to drop the ungrouped (unique) normal probe file data from GM11523_56_2_C_H07, and use the remaining two GM11523 arrays, GM11523_36_2_S_D05 and GM11523_46_2_L_F06 and average the probe values from these two files.

tag: See Coriell catalog # GM11523


title: GM10832_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10832


title: GM10831_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10831


title: GM10858_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10858


title: GM06990D_GroupedSamplesNormProbeProfile

data_processing: VALUE was generated using a global background subtraction and rank-invariant normalization algorithm, averaging the three replicate arrays.

source_name: lymphoblastoid cell line

extract_protocol:
Total RNA was prepared from frozen cell pellets using the Qiagen RNeasy Midi-kit (Valencia, CA). Ten cell culture pellets were extracted at a time by a single technician with a single assistant; cell pellets were removed one-at-a-time from the -80ºC freezer, quick thawed by rubbing
between gloved hands, and Qiagen denaturant immediately added. Ethanol was added to each sample, vortexed, and the samples applied to Qiagen Midi columns, washed as specified, treated with RNase-free DNase “on-column”, followed by additional washes before elution of the RNA with the provided buffer.  After elution, sample volume was
determined by weight, sodium acetate was added to 0.3 M, the sample was split and ethanol added at 3X volume to each aliquot and stored at -20ºC.

tag: See Coriell catalog #GM06990


title: GM07349D_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM07349


title: GM07038D_GroupedSamplesNormProbeProfile

tag: See Coriell catelog # GM07038


title: GM10833_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10833


title: GM07348D_GroupedSamplesNormProbeProfile

tag: See Coriell catalog #GM07348


title: GM10849_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM10849


title: GM07057D_GroupedSamplesNormProbeProfile

tag: See Coriell catalog # GM07057


title: GM06987D_GroupedSamplesNormProbeProfile

extract_protocol:
Total RNA was prepared from frozen cell pellets using the Qiagen RNeasy Midi-kit (Valencia, CA). Ten cell culture pellets were extracted at a time by a single technician with a single assistant; cell pellets were removed one-at-a-time from the -80ºC freezer, quick thawed by rubbing between gloved hands, and Qiagen denaturant immediately added. Ethanol was added to each sample, vortexed, and the samples applied to Qiagen Midi columns, washed as specified, treated with RNase-free DNase “on-column”, followed by additional washes before elution of the RNA with the provided buffer.  After elution, sample volume was
determined by weight, sodium acetate was added to 0.3 M, the sample was split and ethanol added at 3X volume to each aliquot and stored at -20ºC.

tag: See Coriell catalog # GM06987


title: NF-PTZ 14th day Female Replicate 1

status: Public on Mar 25 2008

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: The data in the file is ratio normalized. The ratio in the value column was derived from normalized data.

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65 ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37 ºC for 16 hrs.

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.6) and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations

organism: Drosophila melanogaster

source_name: Drosophila melanogaster, virgin, treated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 7 days and then flies were shifted to vials containing normal media for another 7 days. Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

tag: Strain

value: Oregon-R

tag: Age

value: 3-4 days old

tag: Sex

value: Female

tag: Tissue

value: Head

source_name: Drosophila melanogaster, virgin, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 + 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 7 days then again flies were shifted to vials containing normal media. Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

value: Oregon R


title: NF-PTZ 14th day Female Replicate 2

description: The data in the file is ratio normalized. The ratio in the value column was derived from normalized data as discussed in the manuscript.

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 7 days and then shifted to normal (NF) food for another 7 days. Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereo microscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 7 days and then again shifted to normal food for another 7 days.Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NF-PTZ 7th Day Female Replicate 2

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65 ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

source_name: Drosophila melanogaster,virgin, treated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy5 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 7 days   .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 7 days.Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NF-PTZ 14th day Female Replicate 3 (Dye Swap)

description: The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data.

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 7 days then again flies were shifted to vials containing normal media  .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 7 days and then flies were shifted to vials containing normal media  .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NF-PTZ 7th day Female Replicate 4 (Dye Swap)

description: The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37 ºC for 16 hrs.

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 7 days and then flies were shifted to vials containing normal media for seven days .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NF-PTZ 7th day Female Replicate 3 (Dye Swap)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 7 days. Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

value: oragon R


title: NF-PTZ 7th day  Female Replicate 1


title: NF-PTZ 12 hrs Female Replicate 2

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) 12 hours .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 12 hours .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC