title: rat liver treated with TBD, rep1

description: Gene expression data from livers of rats that were treated with TBD

source_name: rat liver treated with TBD

treatment_protocol: Rats were fed with Harlan Teklad diet treated with 100?l of 5-tert-butyl-3H-1,2-dithiole-3-thione  (TBD) once every other day for 5 days.


title: Oral2

status: Public on Dec 31 2008

type: genomic

city: Vancouver

first: Ivy

last: Tsui

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: Probes were combined, denatured and annealed in a solution containing 100 ug human Cot-1 DNA (Invitrogen) and 48 ul DIG Easy hybridization solution (Roche) containing sheared herring sperm DNA (Sigma-Aldrich) and yeast tRNA (Calbiochem). Probe was denautred at 85°C for 5 minutes, and repetitive sequences were blocked at 45°C for 1 hour prior to hybridization. The probe mixture was applied to the slide surface and hybridized for 36 hrs at 45°C. The arrays were washed 5 times in 0.1X SSC, 0.1% SDS at room temperature with agitation. Each array was then rinsed repeatedly in 0.1X SSC and dried by centrifugation.

scan_protocol: A charge-coupled device (CCD) scanner system (ARrayworx eAuto, API, Issaquah, WA) was used to determine the signal intensities of the Cyanine 5/Cyanine3 channels. Arrays were scanned at a 9.75um resolution; exposure times for each image wavelength were usually between 0.2 to 2 sec. Images were analyzed by SoftWoRx Tracker analysis software (Applied Precision, Issaquah, WA, USA).

data_processing: A three-step normalization procedure [Khojasteh et al. BMC Bioinformatics 6:274, 2005] was performed to each raw data.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Random prime probe labeling was performed to label sample and reference genomic DNA (250ng each). Each reaction was labeled with either  2 nmol of cyanine-3 or cyanine-5 dCTP.

extract_protocol: All lesoins were microdissected, and the dissected tissues were places in sodium dodecyl sulfate/proteinase K at 55°C and spiked twice a day for 72 hours with fresh proteinase K. Genomic DNA was extracted wth phenol/chloroform and precipictaed with ethanol.

tag: Formalin-fixed paraffin-embedded oral specimen

source_name: Normal female

tag: Novagen pooled normal female genomic DNA


title: rat liver treated with TBD, rep3

status: Public on Dec 30 2008

type: RNA

city: Memphis

first: Thomas

middle: R

last: Sutter

state: TN

address: 3774 Walker Ave.

department: Biology

country: USA

institute: University of Memphis

hyb_protocol: Following fragmentation, 20ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome U34 Array Set RG-U34A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner .

data_processing: The data were analyzed with Bioconductor using GC-RMA analysis.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Enzo labeling kit

extract_protocol: Stat-60 extraction

tag: Male Fischer F344 rats (80-100g)


title: rat liver treated with OLT, rep4

description: Gene expression data from livers of rats that were treated with OLT

source_name: rat liver treated with OLT

treatment_protocol: Rats were fed with Harlan Teklad diet treated with 100?l of 4-methyl-5-pyrazinyl-3H-1,2-dithiole-3-thione  (OLT) once every other day for 5 days.


title: rat liver treated with D3T, rep4

description: Gene expression data from livers of rats that were treated with D3T

source_name: rat liver treated with D3T

treatment_protocol: Rats were fed with Harlan Teklad diet treated with 100?l of 3H-1,2-dithiole-3-thione  (D3T) once every other day for 5 days.


title: rat liver treated with OLT, rep1


title: rat liver treated with TBD, rep2


title: rat liver without treatment, rep3

description: Gene expression data from livers of rats that were not treated with chemicals

source_name: rat liver without treatment

treatment_protocol: Rats were fed with Harlan Teklad diet treated with 100?l of saturated sucrose (control) once every other day for 5 days.


title: rat liver treated with TBD, rep4


title: rat liver without treatment, rep1


title: rat liver without treatment, rep4


title: rat liver treated with D3T, rep1


title: rat liver treated with D3T, rep2


title: rat liver without treatment, rep2


title: olt, rep3

hyb_protocol: Following fragmentation, 20ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Rat Liver treated with OLT

treatment_protocol: Rats were fed with Harlan Teklad Rodent diet, containing 4-methyl-5-pyrazinyl-3H-1,2-dithiole-3-thione (OLT 500mg/kg diet)

tag: Female Sprague Dawley rats


title: olt, rep5


title: olt, rep2


title: olt, rep1


title: olt, rep4


title: d3t, rep2

source_name: Rat Liver treated with D3T

treatment_protocol: Rats were fed with Harlan Teklad Rodent diet, containing 3H-1,2-dithiole-3-thione (D3T 600mg/kg diet)


title: control, rep5

source_name: Rat Liver without treatment

treatment_protocol: Rats were fed with Harlan Teklad Rodent diet, 4% mash diet (control)


title: bnf, rep4

description: Gene expression data from livers of rats that were treated with BNF

source_name: Rat Liver treated with BNF

treatment_protocol: Rats were fed with Harlan Teklad Rodent diet, containing 5,6-benzoflavone BNF (1650mg/kg diet)


title: d3t, rep3


title: control, rep1


title: Oral75

source_name: Normal male

tag: Novagen pooled normal male genomic DNA


title: Uninfected ovaries replicate 1, slide 3, Cy5-labeled

city: Berkeley

first: Sha

last: Sun

state: CA

address: 16 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Eight repeats/slides of dual channel arrays were performed using samples from five independent dissections of infected and uninfected ovaries. To avoid the bias from difference in the labeling efficiency with the two dyes, arrays were processed as though they are single channel with Cy3 and Cy5 signals treated independently.

hyb_protocol: Hybridization was done at 65°C for ~ 17 hrs using reagents, apparatus and a protocol from Agilent (Hughes et al, 2001, Nat Biotechnol).

scan_protocol: Arrays were scanned on an Axon 400B scanner and read with GenePix software.

data_processing: Values are processed in GenePix with background subtracted using "Morphological Closing Followed By Opening" and normalized using the ratio of medians for each corresponding hybridization slide.

organism: Drosophila melanogaster

source_name: Wolbachina uninfected wildtype adult previtellogenic ovaries

label_protocol: cDNA labeling procedures were as described in DGRC protocols (Conaty J, Bogart K, Andrews J, 2006, CGB Technical Report 2006-9 The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana. 26) using Amersham Biosciences CyScribe First Strand cDNA direct labeling kit. 20-25 ug total RNA was used in each cDNA sample preparation for Array hybridization.

growth_protocol: Flies were raised at 25°C in uncrowded conditions on a regular medium containing 6.5% cornmeal, 2.7% yeast, 1.6% sucrose, 8.2% Molasses, 0.7% agar, 0.75% Na Tartrate (4 hydrate), 0.06% CaCl2 (2 hydrate), 0.5% Propionic Acid, 0.09% Tegosept and 0.7% Ethanol.

extract_protocol: RNA preparation procedures were as described in DGRC protocols (Bogart K, Andrews J, 2006, CGB Technical Report 2006-10 The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana.) using Trizol RNA isolation and Qiagen RNeasy cleanup.

treatment_protocol: Female flies raised at 25°C were collected 0-2 hr after eclosion, and were aged for 1-3 hr at the room temperature before being dissected on ice. Ovaries from such females of 1-5 hr old females contain only pre-vitellogenic egg chambers of the oogenesis stages 1 to 6. The dissected ovaries were transferred directly to TRIzol and frozen at -80°C before RNA extraction.

tag: Strain

value: Canton-S wildtype;

tag: Gender

value: Female;

tag: Tissure

value: Ovary;

tag: Age

value: 1-5 hr after eclosion;

tag: Status

value: Uninfected.


title: Uninfected ovaries replicate 3, slide 4, Cy3-labeled


title: Uninfected ovaries replicate 5, slide 8, Cy5-labeled


title: Uninfected ovaries replicate 2, slide 2, Cy3-labeled


title: Infected ovaries replicate 5, slide 7, Cy5-labeled

source_name: Wolbachina infected wildtype adult previtellogenic ovaries

value: Infected.


title: Infected ovaries replicate 5, slide 8, Cy3-labeled


title: Uninfected ovaries replicate 1, slide 1, Cy5-labeled


title: control - rep4


title: Uninfected ovaries replicate 4, slide 6, Cy5-labeled


title: Uninfected ovaries replicate 5, slide 7, Cy3-labeled


title: d3t, rep5


title: bnf, rep1


title: Uninfected ovaries replicate 4, slide 5, Cy3-labeled


title: bnf, rep5


title: d3t, rep4


title: d3t, rep1


title: control, rep3


title: control, rep2


title: bnf, rep2


title: Infected ovaries replicate 4, slide 6, Cy3-labeled


title: Infected ovaries replicate 2, slide 2, Cy5-labeled


title: Infected ovaries replicate 1, slide 1, Cy3-labeled

description: Eight repeats/slides were performed using samples from five independent dissections of infected and uninfected ovaries.  To avoid the bias from difference in the labeling efficiency with the two dyes, arrays were processed as though they are single channel with Cy3 and Cy5 signals treated independently.

label_protocol: cDNA labeling procedures were as described in DGRC protocols (Conaty J, Bogart K, Andrews J, 2006, CGB Technical Report 2006-9 The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana. 26) using Amersham Biosciences CyScribe First Strand cDNA direct labeling kit.  20-25 ug total RNA was used in each cDNA sample preparation for Array hybridization.

treatment_protocol: Female flies raised at 25°C were collected 0-2 hr after eclosion, and were aged for 1-3 hr at the room temperature before being dissected on ice.  Ovaries from such females of 1-5 hr old females contain only pre-vitellogenic egg chambers of the oogenesis stages 1 to 6.  The dissected ovaries were transferred directly to TRIzol and frozen at -80°C before RNA extraction.


title: 358vsRef

status: Public on Dec 26 2008

city: Singapore

first: Sim

middle: Siew

last: Hoon

address: 27 Medical Drive

department: MCB

country: Singapore

institute: DSO National Laboratories

description: Series of 93 B. pseudomallei strains

hyb_protocol: J. David Gladstone Institutes Genomic Core Laboratory SOP

data_processing: GeneData Expressionist

organism: Burkholderia pseudomallei

source_name: Strain: 358

label_protocol: Test genomic DNA (2ug) was fluorescently labeled with Cy3-dCTP using nick-translation.

extract_protocol: genomic DNA extraction

organism: Burkholderia pseudomallei K96243

source_name: Reference: Strain K96243

label_protocol: Reference genomic DNA (2ug) was fluorescently labeled with Cy5-dCTP using nick-translation.


title: KASvsRef

description: Series of 93 B. pseudomallei strains

scan_protocol: J. David Gladstone Institutes Genomic Core Laboratory SOP

source_name: Strain: KAS

value: KAS


title: 4-D82316vsRef

description: Series of 93 B. pseudomallei strains


title: K1127 7244-293vsRef

description: Series of 93 B. pseudomallei strains


title: 3-D85239vsRef

description: Series of 93 B. pseudomallei strains


title: P6vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: P6


title: JAMvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: JAM

value: JAM


title: 65676vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 65676


title: Infected ovaries replicate 3, slide 4, Cy5-labeled


title: Infected ovaries replicate 4, slide 5, Cy5-labeled


title: G-ShepherdvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: G-Shepherd

value: G-Shepherd


title: I6 4043-3096vsRef

description: Series of 93 B. pseudomallei strains


title: 363679vsRef

description: Series of 93 B. pseudomallei strains


title: SW1T3vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: SW1T3


title: SW1T8vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: SW1T8


title: SW9T2vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: SW9T2


title: TRF661vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: TRF661


title: Infected ovaries replicate 1, slide 3, Cy3-labeled


title: SoilvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: Soil

value: Soil


title: EM1157vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: EM1157


title: 9-A57203vsRef

description: Series of 93 B. pseudomallei strains


title: 0-D10468vsRef

description: Series of 93 B. pseudomallei strains


title: 9-D38465vsRef

description: Series of 93 B. pseudomallei strains


title: 216408vsRef

description: Series of 93 B. pseudomallei strains


title: EM2107vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: EM2107


title: EB5661vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: EB5661


title: E371vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: E371


title: DR08726/01vsRef

description: Series of 93 B. pseudomallei strains


title: E359vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: E359


title: E38vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: E38


title: E358vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: E358

source_name: Reference: Strain K96243


title: EM10266/01vsRef

description: Series of 93 B. pseudomallei strains


title: AH3vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: AH3


title: DB61901/00vsRef

description: Series of 93 B. pseudomallei strains


title: DBvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: DB

value: DB


title: ATCC23343vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: ATCC23343


title: D7 3230-3018vsRef

description: Series of 93 B. pseudomallei strains


title: D10 7310-3154vsRef

description: Series of 93 B. pseudomallei strains


title: 6vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 6


title: 612vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 612


title: 79/96vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 79/96


title: DB30729/00vsRef

description: Series of 93 B. pseudomallei strains


title: DB19897/02vsRef

description: Series of 93 B. pseudomallei strains


title: 77/96vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 77/96


title: ATCC15682vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: ATCC15682


title: 59vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 59


title: 561vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 561


title: 54vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 54


title: 56vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 56


title: 504/96vsRef

description: Series of 93 B. pseudomallei strains


title: DCvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: DC

value: DC


title: 497/96vsRef

description: Series of 93 B. pseudomallei strains


title: 490vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 490


title: AH4vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: AH4


title: 8vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 8


title: 488vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 488

source_name: Reference: Strain K96243


title: 4094-225vsRef

description: Series of 93 B. pseudomallei strains


title: 48vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 48


title: 2663AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2663A


title: 2667AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2667A


title: 4vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 4


title: 2684AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2684A


title: 2689BvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2689B


title: 2664BvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2664B


title: 35/96vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 35/96


title: 4090-0390vsRef

description: Series of 93 B. pseudomallei strains


title: 4009-19vsRef

description: Series of 93 B. pseudomallei strains


title: 2644AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2644A


title: 4094-0081vsRef

description: Series of 93 B. pseudomallei strains


title: 2747AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2747A


title: 2694AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2694A


title: 35vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 35


title: 27/96vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 27/96


title: 33vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 33


title: 2635AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2635A


title: 2693AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2693A


title: 20vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 20

source_name: Reference: Strain K96243


title: 21/96vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 21/96


title: 15/96vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 15/96


title: 22vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 22


title: 17vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 17


title: 457/96vsRef

description: Series of 93 B. pseudomallei strains


title: 15-40vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 15-40


title: 2614AvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 2614A


title: 15-10bvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 15-10b


title: 15-10vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 15-10


title: 15-10avsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 15-10a


title: 12-40vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 12-40


title: 153vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 153


title: 115vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 115


title: 11vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 11


title: 109vsRef

description: Series of 93 B. pseudomallei strains


title: 15-10dvsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 15-10d


title: 10/96vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 10/96


title: 10vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 10


title: 107vsRef

description: Series of 93 B. pseudomallei strains

source_name: Strain: 107

source_name: Reference: Strain K96243


title: bnf, rep3

source_name: Rat Liver treated with BNF


title: Schizophrenia patient 3167

status: Public on Dec 25 2008

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Array CGH analysis of a patient with Schizophrenia

hyb_protocol: Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

scan_protocol: Slides were scanned using an Agilent scanner, PMT settings:100/100%.

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

source_name: DNA isolated from blood

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

extract_protocol: DNA was extracted from peripheral blood by a standard phenol-chloroform protocol.

tag: school performance

value: low school result

tag: severity of illness

value: severe

tag: family history

value: no

tag: age of onset

value: 32 yr

tag: tissue

value: blood

tag: disease state

value: Schizophrenia.

tag: gender

value: male

source_name: DNA isolated from blood (reference)

tag: sample

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 3101

value: no low school result

value: not severe

value: yes

value: 16 yr

value: female

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 1701

value: 11 yr


title: Schizophrenia patient 1314

value: 12 yr


title: Schizophrenia patient 3166

value: 23 yr


title: Schizophrenia patient 3373

value: 20 yr


title: Schizophrenia patient 3355

value: 19 yr


title: Schizophrenia patient 4055

value: low school result

value: severe

value: 15 yr


title: Schizophrenia patient 3378

value: no

value: blood

value: Schizophrenia.


title: Schizophrenia patient 2207

value: no low school result

value: 26 yr


title: Schizophrenia patient 1703

value: not severe


title: Schizophrenia patient 1622

value: yes


title: Schizophrenia patient 2129

value: 31 yr

value: female


title: Schizophrenia patient 4270

value: male

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 3269

value: 18 yr


title: Schizophrenia patient 3379

value: 20 yr


title: Schizophrenia patient 3255

value: 17 yr


title: Schizophrenia patient 4289

value: low school result

value: 29 yr


title: Schizophrenia patient 1607

hyb_protocol: Hybridization was done overnight at 42?C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

value: 24 yr

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 4119

value: severe

value: no

value: 23 yr

value: blood


title: Schizophrenia patient 4105

value: not severe

value: 27 yr

value: Schizophrenia.


title: Schizophrenia patient 4269

value: 25 yr


title: Schizophrenia patient 4079

value: 21 yr

value: male


title: Schizophrenia patient 4259

value: 28 yr

value: female


title: Schizophrenia patient 1700

value: no low school result

value: 12 yr

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 4109

value: 17 yr


title: Schizophrenia patient 3279

value: low school result


title: Schizophrenia patient 4287

value: severe

value: 19 yr

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 2226

value: no

value: 30 yr

value: blood


title: Schizophrenia patient 4111

value: yes

value: Schizophrenia.


title: Schizophrenia patient 2291

value: 15 yr


title: Schizophrenia patient 1184

value: not severe

value: 16 yr

value: male


title: Schizophrenia patient 4090


title: Schizophrenia patient 1351


title: Schizophrenia patient 4110

value: 42 yr

value: female


title: Schizophrenia patient 3331

value: 44 yr

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 3168

value: low school result

value: 20 yr


title: Schizophrenia patient 5522

value: severe

value: 24 yr


title: Schizophrenia patient 5040

value: no low school result

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 2185

value: no

value: 26 yr

value: blood


title: Schizophrenia patient 4096

value: yes

value: 17 yr

value: Schizophrenia.


title: Schizophrenia patient 4044

value: 22 yr


title: Schizophrenia patient 2271

value: not severe

value: 16 yr


title: Schizophrenia patient 1402

value: 21 yr

value: female


title: Schizophrenia patient 1704


title: Schizophrenia patient 4046

value: low school result

value: 30 yr


title: Schizophrenia patient 3256

value: 20 yr


title: Schizophrenia patient 4094

value: severe

value: 34 yr

value: male

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 2138

value: no low school result

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 1344

value: yes

value: 39 yr

value: blood


title: Schizophrenia patient 1183

value: no

value: Schizophrenia.


title: Schizophrenia patient 4053

value: 15 yr


title: Schizophrenia patient 4095

value: not severe

value: 33 yr


title: Schizophrenia patient 1356

value: 24 yr

value: female


title: Schizophrenia patient 4089

value: 20 yr


title: Schizophrenia patient 3268

value: severe

value: 29 yr


title: Schizophrenia patient 4263

value: low school result

value: 23 yr

value: male


title: Schizophrenia patient 4281

value: 31 yr

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 4203

value: 21 yr


title: Schizophrenia patient 3165

value: 25 yr

value: blood


title: Schizophrenia patient 3363

value: yes

value: Schizophrenia.

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 2294

value: no low school result

value: not severe


title: Schizophrenia patient 3381

value: no

value: 27 yr


title: Schizophrenia patient 2225

value: severe

value: 22 yr


title: Schizophrenia patient 4114

value: 32 yr

value: female


title: Schizophrenia patient 3110

value: 17 yr

value: male


title: Schizophrenia patient 5023

tag: DNA isolated from blood of a patient with Schizophrenia.  Gender

tag: DNA pool of 50 healthy males.


title: Schizophrenia patient 4092

value: 30 yr

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 1355

value: 13 yr


title: Schizophrenia patient 3108

value: 21 yr

value: blood


title: Schizophrenia patient 5010

value: yes

value: 18 yr

value: Schizophrenia.


title: Schizophrenia patient 4118

value: no low school result

value: not severe

value: 16 yr


title: Schizophrenia patient 4285

value: low school result

value: no

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 1317

value: severe

value: 32 yr

value: female


title: Schizophrenia patient 2286

value: 20 yr

value: male


title: Schizophrenia patient 4208

value: 25 yr

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 1329

value: 13 yr

value: blood


title: Schizophrenia patient 3120

value: yes

value: 18 yr


title: Schizophrenia patient 4003

value: no low school result

value: 23 yr

value: Schizophrenia.


title: Schizophrenia patient 3356

value: not severe


title: Schizophrenia patient 4278

value: no

value: 16 yr


title: Schizophrenia patient V0204

tag: DNA pool of 50 healthy females.


title: Schizophrenia patient 4284

value: low school result

value: severe

value: 24 yr


title: Schizophrenia patient 4275

value: 22 yr

value: female

value: DNA pool of 50 healthy females.


title: Schizophrenia patient 3386

value: 12 yr

value: male

value: DNA pool of 50 healthy males.


title: Schizophrenia patient 4260

value: 19 yr

value: blood


title: Schizophrenia patient 2400

value: no low school result

value: yes

value: 15 yr


title: Schizophrenia patient 3383

value: not severe

value: 32 yr

value: Schizophrenia.


title: Schizophrenia patient 1427

value: no

value: 25 yr


title: Schizophrenia patient 3265

value: 28 yr


title: Experiment 2, 3 uM THC -treated, 24h CY5

status: Public on Dec 21 2008

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: cDNA CNIO Oncochip Array

hyb_protocol: Hybridization was performed in 4x standard saline citrate, 1x bovine serum albumin, 2 µg/ml DNAs, and 0.1% sodium dodecyl sulphate at 42°C for 15 hours.

scan_protocol: Slides were washed, dried and then scanned in a Scanarray 5000 XL scanner (GSI Lumonics Kanata, Ontario, Canada) at wavelengths of 635 and 532 nm for Cy5 and Cy3 dyes, respectively.

data_processing: GenePix 6.0 - log2 ratio

extract_protocol: TRIZOL

tag: LABELING CY5

source_name: Experiment 2, 0h CY3

label_protocol: DIRECT

tag: LABELING CY3


title: V915_Patient with Amyotrophic Lateral Sclerosis

description: Array CGH analysis of a patient with ALS

hyb_protocol: Hybridisation was done overnight at 42?C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

scan_protocol: Slides were scanned using an Agilent scanner. PMT settings: 100/100

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalised by subgrid LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Mar. 2007)

source_name: DNA isolated from EBV-transformed lymphoblastoid cell line

extract_protocol: DNA was extracted from patient cell line using the QIAamp Blood DNA Midi Kit

tag: male ALS patient

source_name: DNA isolated from EBV-transformed cell line (reference)

extract_protocol: DNA was extracted from EBV-transformed lymphoblastoid cell line using standard phenol-chloroform extraction procedures

tag: healthy male donor


title: V1295_Patient with Amyotrophic Lateral Sclerosis

tag: female ALS patient

tag: healthy female donor


title: Experiment 2, vehicle-treated, 24h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, vehicle-treated, 24h CY5


title: V1291_Patient with Amyotrophic Lateral Sclerosis


title: Experiment 2, 3 uM THC -treated, 24h CY3

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, 0h CY5


title: Experiment 1, 3 uM THC-treated, 24h CY3

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, 3 uM THC-treated, 24h CY3

source_name: Experiment 1, 0h CY5


title: Experiment 2, 5 uM THC -treated, 24h CY5

description: cDNA CNIO Oncochip Array


title: Experiment 2, 5 uM THC -treated, 8h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, 5M THC -treated, 8h CY5


title: V894_Patient with Amyotrophic Lateral Sclerosis


title: Experiment 2, 5 uM THC -treated, 24h CY3

description: cDNA CNIO Oncochip Array


title: Experiment 1, 5 uM THC-treated, 24h CY3

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, 5 uM THC-treated, 24h CY3


title: V1290_Patient with Amyotrophic Lateral Sclerosis


title: Experiment 1, vehicle-treated, 24h

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, vehicle-treated, 24h CY3


title: Experiment 1, 3 uM THC -treated, 24h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, 0h CY3


title: Experiment 1, 5 uM THC -treated, 24h CY5

description: cDNA CNIO Oncochip Array


title: Experiment 1, vehicle-treated, 24h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, vehicle-treated, 24h CY5


title: Experiment 2, vehicle-treated, 24h CY3

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, vehicle-treated, 24h CY3


title: Schizophrenia patient 3267

tag: school performance

value: 23 yr


title: Experiment 2, 5 uM THC -treated, 8h CY3

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, 5M THC -treated, 8h CY3


title: Experiment 1, 5uM THC -treated, 8h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, 5M THC -treated, 8h CY5


title: V1289_Patient with Amyotrophic Lateral Sclerosis


title: K008

status: Public on Dec 24 2008

city: Boston

first: Stephen

last: Hodi

state: MA

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Copy-number analysis of mucosal and cutaneous melanoma cell-line samples.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner GCS3000.

data_processing: CEL, txt files were generated by Affymetrix GCOS.

source_name: Cutaneous melanoma cell-line genomic DNA

label_protocol: Standard Affymetrix protocol

extract_protocol: Qiagen DNAeasy

tag: Cutaneous melanoma cell-line derived from metastasis


title: Rat17 LUSH 3D rep2

status: Public on Dec 18 2008

city: Pittsburgh

first: Wei

last: Wu

state: PA

address: MUH 628 NW, 3459 Fifth Ave

department: Medicine/PACCM

institute: University of Pittsburgh

hyb_protocol: According to standard CodeLink protocols; see details at http://www1.gelifesciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28281090525-B500%29?OpenDocument&hometitle=WebDocs

scan_protocol: Microarray slides were scanned using a GenePix Array Scanner. For details, see the protocol at http://www1.gelifesciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28281090525-B500%29?OpenDocument&hometitle=WebDocs

data_processing: The raw intensity values were normalized by the CyclicLoess normalization method as described in Wu W, et. al, BMC Bioinformatics. 2005 Dec 28;6:309. The data was also preprocessed and postprocessed using the protocol described in the same paper and the submitted paper.

source_name: lung tissue

label_protocol: Briefly, the RNAs extracted from whole lung tissue of each rat (mixed with spiked-in bacterial RNAs served as positive controls) were reverse transcribed into double stranded cDNAs; then the cDNAs were amplified into cRNAs by in vitro transcription. The cRNAs were labeled with a red (Cy5) fluorescent dye and hybridized to a CodeLink Bioarray which is presynthesized with probes.

growth_protocol: Adult inbred Sprague-Dawley male rats (weights: 250-275g) were placed in chambers in which oxygen and carbon dioxide concentrations were carefully monitored and controlled.

extract_protocol: To prepare RNAs for microarray experiments and quantitative RT-PCRs, 1 ml per 50 mg of frozen lung tissues were homogenized in ice cold Trizol, and phase separated with Chlorophorm (0.2ml per 1ml Trisol reagent). The RNAs were precipitated from the aqueous phase using Isopropanol (0.5ml per 1ml Trisol). The RNA pallet then was washed with 75%Ethanol. Next the extracted RNAs were purified further using the RNeasy Mini Cleanup protocol (Qiagen 74104) according to the manufacturer’s recommendations. The quantities of RNAs were determined by OD measurements at 260nm, and their qualities were assessed by Agilent Bioanalyzer and by running the RNAs on formamide formaldehyde denaturing gels

treatment_protocol: Rats subject to the intermittent hypoxia (IH) treatment were exposed to 90 second cycles of 10% inspired oxygen followed by 90 seconds of 21% inspired oxygen for 12 hours of simulated daylight when rats sleep; for the remaining 12 hours during the night, the rats were exposed to 21% inspired oxygen.  Rats subject to the sustained hypoxia (SH) treatment were exposed to 10% inspired oxygen at all times. Time sacrifices of these rats exposed to IH and SH respectively were performed on days 1, 3, 7, 14, and 30.

tag: exposed to sustained hypoxia


title: Rat21 LUSH 30D rep2


title: Rat20 LUSH 14D rep1


title: Rat18 LUSH 7D rep2


title: Rat18 LUSH 7D rep1


title: Rat19 LUSH 14D rep1


title: Rat22 LUSH 30D rep1


title: Rat22 LUSH 30D rep2


title: Experiment 1, 5 uM THC-treated, 8h

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, 5 uM THC-treated, 8h CY3


title: Rat16 LUSH 1D rep1


title: Rat16 LUSH 1D rep2


title: Rat21 LUSH 30D rep1


title: Experiment 1, vehicle-treated, 8h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, vehicle-treated, 8h

tag: Experiment 1, vehicle-treated, 8h	LABELING Cy5

source_name: Experiment 1, 0h

tag: Experiment 1, 0h	LABELING Cy3


title: Experiment 2, vehicle-treated, 8h CY3

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, vehicle-treated, 8h

tag: Experiment 2, vehicle-treated, 8h LABELING CY3

tag: Experiment 2, 0h LABELING CY5


title: Experiment 1, vehicle-treated, 8h

description: cDNA CNIO Oncochip Array

tag: Experiment 1, vehicle-treated, 8h	LABELING Cy3

tag: Experiment 1, 0h LABELING CY5


title: Rat15 LUIH 30D rep1

tag: exposed to intermittent hypoxia


title: Experiment 1, 3 uM THC -treated, 8h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 1, 3M THC -treated, 8h CY5


title: Experiment 2, vehicle-treated, 8h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, vehicle-treated, 8h CY5

source_name: Experiment 2, 0h CY3


title: Rat15 LUIH 30D rep2


title: MEL40

source_name: Mucosal melanoma cell-line genomic DNA

tag: Mucosal melanoma cell-line derived from metastasis


title: Experiment 2, 3uM THC -treated, 8h CY5

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, 3 uM THC -treated, 8h CY5

tag: LABELING CY5


title: Experiment 2, 3 uM THC -treated, 8h CY3

description: cDNA CNIO Oncochip Array

source_name: Experiment 2, 3M THC -treated, 8h CY3

tag: LABELING CY3

source_name: Experiment 2, 0h CY5


title: MEL1


title: M34


title: GIST

source_name: Gastrointestinal stromal tumor cell-line genomic DNA

tag: Gastrointestinal stromal tumor cell-line derived from metastasis


title: Rat14 LUIH 14D rep3


title: Rat17 LUSH 3D rep1


title: M6


title: K029


title: Rat13 LUIH 14D rep1


title: Rat7 LUIH 3D rep1


title: Rat12 LUIH 14D rep1


title: Rat8 LUIH 3D rep1


title: Rat5 LUIH 1D rep1


title: Rat3 LURA rep4

tag: exposed to room air


title: Rat6 LUIH 1D rep1


title: Rat4 LUIH 1D rep1


title: Rat3 LURA rep5


title: Rat11 LUIH 7D rep1


title: Rat11 LUIH 7D rep2


title: Rat10 LUIH 7D rep1


title: Rat2 LURA rep3


title: Rat14 LUIH 14D rep1


title: Rat2 LURA rep1


title: Rat3 LURA rep1


title: Rat3 LURA rep3


title: Rat1 LURA rep5


title: Rat1 LURA rep3


title: Rat1 LURA rep4


title: Rat2 LURA rep2


title: Rat2 LURA rep4


title: Rat1 LURA rep2


title: Rat9 LUIH 7D rep1


title: Rat1 LURA rep1


title: PC19_rep1

status: Public on Dec 17 2008

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Cancer Research UK

description: Hybridised on Sanger CGH arrays with 1 Mb resolution

hyb_protocol: Hybridisation was carried out at 37°C for 36h in a hybridisation chamber (GeneMachines, San Carlos, CA, USA).

scan_protocol: Fluorescence intensities were measured on an Axon 4000B scanner (Axon Instruments Inc., Burlingame, CA, USA).

data_processing:
The raw images were analysed using the GenePix Pro 4.0 software (Axon). Grid placement, spot quality, data normalisation and fluorescence quantification of the array image were performed using the UCSF "SPOT" software. The software automatically calculates a log2 ratio using duplicate spots from the identical clones on each array. Duplicate hybridisations were performed in 22 out of 29 samples to verify the reproducibility of the data (the average correlation coefficient was 0.93±0.18) and the median of a normalised log2 ratio in each clone was used for the further analysis.
The genomic positions of BAC/PAC clones on the array were mapped according to the Ensembl genome browser (Ver39, June 2006) (http://www.ensembl.org/index.html). Chromosome Y was not analysed and the data from 22 clones were excluded from the analysis due to either printing problems of the spots or unambiguous genomic positions. Finally, the log2-transformed data from a total of 3,036 clones were used as a final dataset of each case.

source_name: Genomic DNA from microdissected PC19 tissues labelled with Cyanine-5 (Cy5)

label_protocol: Tumour and reference DNAs (300 ng) were labelled with Cy5-dCTP and Cy3-dCTP using the BioPrime DNA Labeling Kit (Invitrogen Ltd, Paisley, UK), respectively.

extract_protocol: Genomic DNA extracted using SePaGene (Sankoujunyaku, Tokyo, Japan) following manufacturer's instructions

tag: Microdissected PC19 tissues

source_name: Genomic DNA from lymphocytes of healthy volunteers labelled with Cyanine-3 (Cy3)

tag: Lymphocytes of healthy volunteers


title: SUIT2_rep2

source_name: Genomic DNA from SUIT2 cell line labelled with Cyanine-5 (Cy5)

tag: SUIT2 cell line


title: Cfpac1_rep1

source_name: Genomic DNA from Cfpac1 cell line labelled with Cyanine-5 (Cy5)

tag: Cfpac1 cell line


title: RWP1_rep1

source_name: Genomic DNA from RWP1 cell line labelled with Cyanine-5 (Cy5)

tag: RWP1 cell line


title: PC19_rep2


title: PC34_rep1

source_name: Genomic DNA from microdissected PC34 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC34 tissues


title: PC20_rep2

source_name: Genomic DNA from microdissected PC20 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC20 tissues


title: SUIT2_rep1


title: PC34_rep2


title: MiaPaCa2_rep1

source_name: Genomic DNA from MiaPaCa2 cell line labelled with Cyanine-5 (Cy5)

tag: MiaPaCa2 cell line


title: PC36_rep1

source_name: Genomic DNA from microdissected PC36 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC36 tissues


title: PC35_rep2

source_name: Genomic DNA from microdissected PC35 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC35 tissues


title: PC20_rep1


title: PaTu1_rep1

source_name: Genomic DNA from PaTu1 cell line labelled with Cyanine-5 (Cy5)

tag: PaTu1 cell line


title: PC36_rep2


title: PC35_rep1


title: Panc1_rep1

source_name: Genomic DNA from Panc1 cell line labelled with Cyanine-5 (Cy5)

tag: Panc1 cell line


title: HMEC Lactosis 6

city: Durham

first: Julia

middle: Ling-Yu

state: NC

address: CIEMAS Rm.2141, 101 Science Dr.

institute: Duke university

description: gene expression data from HMEC cells

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data was normalized with RMA and MAS5 and further analyzed with hierarchical clustering as well as binary regression.

source_name: Human Mammary Epithelial Cell

label_protocol: Affymetrix standard protocol

growth_protocol: Human mammary epithelial cells were induced into replicative arrest by growth factor/serum withdrawl for 24 hrs and then exposed to different cultural environments.

extract_protocol: RNAs were extracted with miRVana kit from Ambion

treatment_protocol: The first set of experiments were done in triplicate by exposing cells to control, 25mM lactic acidosis of pH6.7, 2%hypoxia, and the combination of lactic acidosis and hypoxia. The second set of experiments were done in replica of six replicates and cells were exposed to control, acidosis with the addition of HCl to reach pH 6.7 and 25mM sodium lactate.

tag: HMEC in media with 25mM sodium lactate under normoxia


title: PC18_rep2

source_name: Genomic DNA from microdissected PC18 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC18 tissues


title: PC15_rep1

source_name: Genomic DNA from microdissected PC15 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC15 tissues


title: PC18_rep1


title: PC17_rep2

source_name: Genomic DNA from microdissected PC17 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC17 tissues


title: PC14_rep2

source_name: Genomic DNA from microdissected PC14 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC14 tissues


title: PC15_rep2


title: PC17_rep1


title: PC14_rep1


title: PC16_rep2

source_name: Genomic DNA from microdissected PC16 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC16 tissues


title: PC16_rep1

source_name: Genomic DNA from lymphocytes of healthy volunteers labelled with Cyanine-3 (Cy3)

tag: Lymphocytes of healthy volunteers


title: PC13_rep2

source_name: Genomic DNA from microdissected PC13 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC13 tissues


title: PC11_rep2

source_name: Genomic DNA from microdissected PC11 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC11 tissues


title: PC11_rep1


title: PC13_rep1


title: Rat14 LUIH 14D rep2

source_name: lung tissue

tag: exposed to intermittent hypoxia


title: PC12_rep1

source_name: Genomic DNA from microdissected PC12 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC12 tissues


title: PC7_rep1

source_name: Genomic DNA from microdissected PC7 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC7 tissues


title: PC6_rep2

source_name: Genomic DNA from microdissected PC6 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC6 tissues


title: PC6_rep1


title: PC7_rep2


title: PC10_rep2

source_name: Genomic DNA from microdissected PC10 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC10 tissues


title: PC10_rep1


title: PC8_rep1

source_name: Genomic DNA from microdissected PC8 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC8 tissues


title: PC9_rep1

source_name: Genomic DNA from microdissected PC9 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC9 tissues


title: PC12_rep2


title: PC8_rep2


title: PC4_rep2

source_name: Genomic DNA from microdissected PC4 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC4 tissues


title: PC2_rep1

source_name: Genomic DNA from microdissected PC2 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC2 tissues


title: PC2_rep2


title: PC9_rep2


title: PC4_rep1


title: PC5_rep1

source_name: Genomic DNA from microdissected PC5 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC5 tissues


title: PC1_rep1

source_name: Genomic DNA from microdissected PC1 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC1 tissues


title: PC3_rep1

source_name: Genomic DNA from microdissected PC3 tissues labelled with Cyanine-5 (Cy5)

tag: Microdissected PC3 tissues


title: PC3_rep2


title: PC1_rep2


title: AQZ048

status: Public on Dec 15 2008

city: Evry

first: Olivier

last: ALIBERT

address: 2 rue Gaston Crémieux

department: IRCM

institute: CEA

description: Not relevant.

hyb_protocol: The microarray slides were pre-hybridized in 3,5x SSC, 0,1% SDS and 1% BSA for 30 mn at 50°C. Prior to hybridization, the purified Cy3 and Cy5 labeled cDNAs were mixed. 10 ug of poly(dA), 10 ug of yeats tRNA and 10 ug of human Cot1 DNA were added and subsequently precipitated. Labeled samples were resuspended in 60 ul hybridization buffer containing 50% formamide, 2,5x Denhardts, 0,5% SDS and 6x SSPE. Hybridization mix was denatured by boiling for 2 mn. After cooling, hybridization mix was applied to a pre-hybridized microarray slide and covered with a plastic coverslip (Sigma Hybrislip). The slide was placed in a Corning hybridization chamber and hybridised for 14-16 hours at 42°C in the dark. Following hybridization, slides were washed for 15 mn at room temperature in 0,1x SSC and 0,1% SDS with agitation. Slides were then washed two times for 15 mn at room temperature in 0,1x SSC. Finally, slides were dried by centrifugation.

scan_protocol: Arrays were scanned with Genepix 4000B scanner. Feature extraction was performed with Genepix Pro 4.0 software(Axon Instruments).

data_processing: The data in the VALUE column correspond to lowess normalized log ratio of "treatment vs reference".

organism: Mus musculus

source_name: Mature ctrl, 8h

label_protocol: Amplified RNA was labeled by coupling with aminoallyl-modified dUTP (Sigma), followed by a subsequent incorporation of monofunctionnal Cy3 or Cy5-N-succinimide esters (Amersham Biosciences). For each labeling experiment, amplified RNA (2,7 µg) was reverse-trancribed using random hexamers in the presence of 200 µM aminoallyl-dUTP, 500 µM each dATP, dCTP, dGTP, 300 µM dTTP, 400 U of Superscript II polymerase (Invitrogen) in a final volume of 30 µl. After incubation at 42°C for 2 hours, RNA was hydrolyzed by adding 2 units of DNAse-free RNAse H (Invitrogen) and incubating at 37°C for 15 minutes. The volume was adjusted to 400 µl with H20, aminoallyl-cDNA was purified by centrifugation in a microcon (YM-30 Millipore Amicon), eluted with 20 µl of water and then dried in a vacuum to 10µl. One µl sodium bicarbonate 0.5 M was added to aminoallyl-cDNA and subsequently mixed with vacuum-dried monofunctional dye. Coupling reaction was performed during 1 hour at room temperature in the dark and the excess dyes were thereafter quenched by hydroxylamine. Sample and reference cDNAs were then mixed and purified with a nucleospin column (Macherey Nagel), eluted with 100 µl of TE, mixed with 10 µg of human Cot-1 DNA, 10µg poly(A) and 10µg of yeast tRNA, then concentrated using YM-30 Microcon and dried by speed-vac.

extract_protocol: Total RNA was extracted from sorted T1 immature and mature B cells using Trizol Reagent (Invitrogen) following manufacturer’s protocol.

tag: Stain

tag: Gender

value: Male

tag: Age

value: 6 weeks

tag: Tissue

value: Spleen

source_name: Reference

extract_protocol: Not relevant

tag: Stratagen's Universal Mouse Reference RNA. Catalog #740100


title: AQZ045

description: Not relevant.

source_name: Mature BCR, 8h


title: AQZ050

description: Not relevant.

source_name: Immature BCR, 2h


title: AQZ036

description: Not relevant.

source_name: Mature ctrl, 2h


title: AQZ031

description: Not relevant.

source_name: Immature ctrl, 8h


title: AQZ049

description: Not relevant.


title: AQZ033

description: Not relevant.

source_name: Mature BCR, 24h


title: AQZ032

description: Not relevant.


title: AQZ037

description: Not relevant.


title: AQZ042

description: Not relevant.

source_name: Mature, 0h


title: AQZ044

description: Not relevant.


title: AQZ040

description: Not relevant.

source_name: Immature ctrl, 24h


title: AQZ041

description: Not relevant.


title: AQZ046

description: Not relevant.

source_name: Immature, 0h


title: AQZ038

description: Not relevant.

source_name: Immature BCR, 24h


title: AQZ051

description: Not relevant.


title: AQZ034

description: Not relevant.


title: AQZ030

description: Not relevant.


title: AQZ043

description: Not relevant.


title: AQZ035

description: Not relevant.


title: AQZ025

description: Not relevant.


title: AQZ029

description: Not relevant.

source_name: Mature BCR, 2h


title: AQZ027

description: Not relevant.


title: AQZ024

description: Not relevant.


title: AQZ022

description: Not relevant.


title: AQZ039

description: Not relevant.


title: AQZ023

description: Not relevant.


title: AQZ021

description: Not relevant.


title: AQZ028

description: Not relevant.


title: AQZ026

description: Not relevant.


title: AQZ020

description: Not relevant.


title: AQZ018

description: Not relevant.


title: AQZ017

description: Not relevant.

source_name: Immature ctrl, 2h


title: AQZ012

description: Not relevant.


title: AQZ019

description: Not relevant.


title: AQZ007

description: Not relevant.


title: AQZ015

description: Not relevant.

source_name: Immature BCR, 8h


title: AQZ016

description: Not relevant.


title: AQZ014

description: Not relevant.


title: AQZ010

description: Not relevant.


title: AQZ005

description: Not relevant.

source_name: Mature ctrl, 24h


title: AQZ009

description: Not relevant.


title: AQZ004

description: Not relevant.


title: AQZ013

description: Not relevant.


title: AQZ003

description: Not relevant.


title: AQZ008

description: Not relevant.


title: AQP050

description: Not relevant.


title: AQZ002

description: Not relevant.


title: AQZ011

description: Not relevant.


title: AQP048

description: Not relevant.


title: AQP049

description: Not relevant.


title: AQP045

description: Not relevant.


title: AQZ006

description: Not relevant.


title: AQP043

description: Not relevant.


title: AQP046

description: Not relevant.


title: AQP041

description: Not relevant.


title: AQP044

description: Not relevant.


title: AQP040

description: Not relevant.


title: AQP047

description: Not relevant.


title: AQP035

description: Not relevant.


title: AQP030

description: Not relevant.


title: AQP038

description: Not relevant.


title: AQP042

description: Not relevant.


title: AQP033

description: Not relevant.


title: AQP036

description: Not relevant.


title: AQP031

description: Not relevant.


title: AQP032

description: Not relevant.


title: AQP037

description: Not relevant.


title: AQP039

description: Not relevant.


title: AQP034

description: Not relevant.


title: AQP026

description: Not relevant.


title: AQP025

description: Not relevant.


title: AQP029

description: Not relevant.


title: AQP024

description: Not relevant.


title: AQP022

description: Not relevant.


title: AQP027

description: Not relevant.


title: AQP023

description: Not relevant.


title: AQP021

description: Not relevant.


title: AQP017

description: Not relevant.


title: AQP028

description: Not relevant.


title: AQP016

description: Not relevant.


title: AQP020

description: Not relevant.


title: AQP013

description: Not relevant.


title: AQP012

description: Not relevant.


title: AQP018

description: Not relevant.


title: AQP014

description: Not relevant.


title: AQP015

description: Not relevant.


title: AQP019

description: Not relevant.


title: AQP010

description: Not relevant.


title: AQP009

description: Not relevant.


title: AMK023

description: Not relevant.

treatment_protocol:
Mature splenic B lymphocytes isolated by negative depletion as CD43[-] fraction with MACS, and then sorted as CD93[-] & CD23[+] sub-population by FACS.
Cells were stimulated for 8 hours with F(ab')2 fragments of anti-IgM antibodies.


title: AMK025

description: Not relevant.


title: AXF045

description: Not relevant.

hyb_protocol: Direct hybridization sample (Cy5 vs Cy3)

scan_protocol: Arrays were scanned with Agilent G2505B Scanner . Feature extraction was performed with Genepix Pro 6.0 software(Axon Instruments).

data_processing: The data in the VALUE column correspond to lowess normalized log ratio of  F635_MEDIAN vs F532_MEDIAN.

source_name: Ptger4-/-  BCR+PGE 24h

label_protocol: Labeling were performed using 2.5 ug of aRNA per reaction and were carried out according to the manufacturer's rpotocol (Ambion) using the MessageAmp kit with 1/2 quantity.

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's protocol and the integrity of the RNAs was verified using the Agilent Bioanalyzer.
Message RNA amplification with T7 RNA Polymerase was carried out according to the manufacturer's protocol (Ambion) using the MessageAmp kit with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies) .

treatment_protocol:
Splenic B cells were isolated from Ptger4-/- mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 24 hours with F(ab')2 antibodies and PGE2 in IMDM medium.

value: Female

value: 2 months

source_name: Ptger4+/+  BCR+PGE 24h

treatment_protocol:
Splenic B cells were isolated from Ptger4+/+ mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 24 hours with F(ab')2 antibodies and PGE2 in IMDM medium.


title: AXF044

description: Not relevant.

source_name: Ptger4-/-  BCR 24h

treatment_protocol:
Splenic B cells were isolated from Ptger4-/- mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 24 hours with F(ab')2 antibodies in IMDM medium.


title: AMK024

description: Not relevant.

source_name: Reference

treatment_protocol: Not relevant


title: AXF032

description: Not relevant.

source_name: Ptger4+/+ BCR 24h

treatment_protocol:
Splenic B cells were isolated from Ptger4+/+ mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 24 hours with F(ab')2 antibodies in IMDM medium.

treatment_protocol:
Splenic B cells were isolated from Ptger4+/+ mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 24 hours with F(ab')2 antibodies and PGE2  in IMDM medium.


title: AXF039

description: Not relevant.

source_name: Ptger4+/+  BCR 2h

treatment_protocol:
Splenic B cells were isolated from Ptger4+/+ mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 2 hours with F(ab')2 antibodies in IMDM medium.

source_name: Ptger4+/+  ctrl 2h

treatment_protocol:
Splenic B cells were isolated from Ptger4+/+mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 2 hours in IMDM medium.


title: AXF035

description: Not relevant.


title: AXF034

description: Not relevant.

source_name: Ptger4-/- BCR 2h

treatment_protocol:
Splenic B cells were isolated from Ptger4-/- mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 2 hours with F(ab')2 antibodies in IMDM medium.

source_name: Ptger4-/- ctrl 2h

tag: Cells were incubated for 2 hours in IMDM medium.


title: Ferret lung with H5N1 at Day 4, biological rep2

status: Public on Dec 09 2008

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

institute: Toronto General Research Institute

description: Gene expression data from ferret on Day 4 after infection

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with PLIER using ArrayAssist (Stratagene) default analysis settings.

organism: Mustela putorius furo

source_name: Ferret

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

treatment_protocol: Ferrets were inoculated intranasally with 10(6) EID50 of either A/Vietnam/1203/04 (H5N1) or A/Panama/2007/99 (H3N2).  At 2, 4 and 6 days post-infection (DPI), ferrets were euthanized and lung tissue was excised and placed on ice in the TRIzol solution (Invitrogen) and homogenized immediately.

value: lung

tag: Virus Strain


title: Ferret lung with H5N1 at Day 6, biological rep1

description: Gene expression data from ferret on Day 6 after infection


title: Ferret lung with H5N1 at Day 6, biological rep2


title: AMK026

description: Not relevant.


title: Ferret lung with H5N1 at Day 6, biological rep3


title: Ferret lung with H5N1 at Day 4, biological rep3


title: AXF025

description: Not relevant.

source_name: Ptger4-/- BCR 24h

source_name: Ptger4-/- BCR+PGE 24h


title: AXF028

description: Not relevant.

source_name: Ptger4+/+ BCR+PGE 24h


title: Ferret lung with H5N1 at Day 4, biological rep1


title: AXF012

description: Not relevant.

source_name: Ptger4+/+ ctrl 2h

treatment_protocol:
Splenic B cells were isolated from Ptger4+/+ mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 2 hours in IMDM medium.

source_name: Ptger4+/+ BCR 2h

extract_protocol:
Agilent Bioanalyzer.
Message RNA amplification with T7 RNA Polymerase was carried out according to the manufacturer's protocol (Ambion) using the MessageAmp kit with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies) .

treatment_protocol:
Splenic B cells were isolated from Ptger4+/+ mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 2 hours with F(ab')2 fragments of anti-IgM antibodies in IMDM medium.


title: Ferret lung with H3N2 at Day 0, biological rep2

description: Gene expression data from ferret before infection


title: Ferret lung with H5N1 at Day 0, biological rep3


title: Ferret lung with H3N2 at Day 0, biological rep1


title: AXF004

description: Not relevant.

treatment_protocol:
Splenic B cells were isolated from Ptger4-/- mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 2 hours in IMDM medium.

treatment_protocol:
Splenic B cells were isolated from Ptger4-/- mice using B Cell Isolation Kit (Miltenyi Biotech).
Cells were incubated for 2 hours with F(ab')2 fragments of anti-IgM antibodies in IMDM medium.


title: Ferret lung with H5N1 at Day 2, biological rep3

description: Gene expression data from ferret on Day 2 after infection


title: Ferret lung with H5N1 at Day 2, biological rep1


title: GGS27_BR2_3F_12896190annot_MDS_MDS.tav.refIsIB.out

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: Information covered in other sections

hyb_protocol: Prehybridization: 1. Prepare prehybridization buffer containing 5x SSC, 0.1% SDS and 1% bovine serum albumin. Place slides to be analyzed into a Coplin jar  fill with prehybridization buffer, and incubate at 42 degree Celsius for 45 minutes. 2. Wash slides in distilled water 4-8 times to remove excess prehybridization buffer. 3. Dip the slides in room temperature isoproponol 10 times and dry in slide spinner. 4. Slides should be used immediately following prehybridization. We have found that hybridization efficiency decreases rapidly if the slides are allowed to dry for more than one hour. Hybridization: 1. Resuspend the probe in 70ul hybridization buffer (50% formamide, 5x SSC, 1mg/ml salmon sperm DNA, syringe filtered). 2. Incubate at 98 degree Celsius for 15 minutes to resuspend as much probe as possible and spin for 5 minutes at maximum angular velocity to collect any remaining solid at the bottom of the tube. 3. Place a polyethylene hydrophobic lifterslip on each prehybridized slide so that it covers the array. 4. Apply the probe to one end of the coverslip and allow capillary action to draw the liquid through to cover the whole array.  Place the slide in a sealed hybridization chamber, add 20 ul of 20x SSC to the chamber at each end of the slide. 5. Place the sealed chamber in a 42 degree Celsius water bath and incubate for a minimum 18-20 hours. 6. Remove the array from the hybridization chamber, taking care not to disturb the coverslip. 7. Place the slide in a staining dish with low-stringency wash buffer containing 1x SSC and 0.2% SDS at 42 degree Celsius. 8. Gently remove the coverslip while the slide is in solution and agitate for 2-4 minutes. Wash again in 1xSSC and 0.2% SDS for 2-4 minutes. 9. Wash the slide twice at high-stringency in a staining dish containing 0.1x SSC and 0.2% SDS at room temperature, agitating for 2-4 minutes. 10. Wash the slide twice in 0.1x SSC, agitating for 2-4 minutes. 11. Provide one final wash by dipping each slide 6-7 times in a 0.05x SSC solution immediately prior to drying. 12. Dry the slide in a slide spinner.

scan_protocol: Slides were promptly scanned post-hybridization at a 10 um resolution using an Axon 4000B scanner with GenePix 4.0 software. PMT values were optimized during scanning to balance channel intensities.

data_processing:
Processing of 16-bit TIFF images from hybridized arrays were produced using the TIGR TM4 package (www.tm4.org). Intensity values for Cy3 and Cy5 channels were obtained using TIGR-Spotfinder software.
Normalization was performed using the LOWESS algorithm available in TIGR-MIDAS using block mode and a smooth parameter of 0.33. All intensity values less than two times greater than background were removed from subsequent analysis and replicate reporter intensities on one slide (one technical replicate) were reduced to a single value by computing the geometric mean.

organism: Geobacter sulfurreducens

source_name: Geobacter sulfurreducens strain DL1 cell cultures in chemostats under conditions of acetate was supplied in excess with fumarate supplied as the sole electron acceptor and limiting factor

label_protocol: cDNA was labeled from total RNA with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5) via an indirect coupling method. First cDNA was synthesized from total RNA with aminoallyl-dUTP incorporated into the first strand cDNA to which Cy-3 and Cy-5 fluorescent dye molecules are subsequently coupled.

growth_protocol:
General growth conditions of the G. sulfurreducens DL1 cells were that they were cultured anaerobically in chemostats.  Two growth conditions were tested. In the first, the electron donor (acetate 5mM) was limiting
and fumarate was the electron acceptor. In the second condition, acetate as sole electron donor was provided in excess and fumarate was the limiting substrate. A dilution rate of 0.05 per hour was used for all chemostats. Additional details concerning the growth of G. sulfurreducens are given in the following reference: Esteve-Nunez, A., M. Rothermich, M. Sharma, and L. D. 2005. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7(5):641-648.

extract_protocol:
Total RNA was extracted as previously described by first mechanically disrupting cells using a FastPrep instrument (Qbiogene, Carlsbad, CA) with Lysing Matrix B (Qbiogene, Carlsbad, CA), followed by nucleic acid
extraction with TRIzol reagent (Invitrogen, Carlsbad, CA) (a monophasic solution of phenol and guanidine isothiocyanate) (Methe et al. 2005). Any residual DNA was removed using RNase-free DNase according to the
manufacturer’s instructions  (Ambion, Austin, TX), and treated RNA was subsequently cleaned and concentrated with RNeasy minicolumns (QIAGEN Inc., Valencia, CA). The quality of total RNA was assessed by agarose-formaldehyde gel electrophoresis and the oncentration determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: G. sulfurreducens was anaerobically cultured in chemostats under two conditions: 1) in which acetate was the sole electron donor and the limiting growth substrate, and fumarate was the sole electron acceptor and 2) acetate was the sole electron donor and supplied in excess while fumarate was the sole electron acceptor and the substrate that limited growth.

tag: Strain DL1, grown under steady state conditions in chemostats

tag: Query

source_name: Geobacter sulfurreducens strain DL1 cell cultures in chemostats under conditions of acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor

tag: Reference


title: GGS27_BR3_2F_12896165annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR3_1F_12896166annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR1_2F_12896679annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR1_1F_12896682annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR2_2F_12896187annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR3_3F_12896189annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR2_4F_12896595annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR1_4F_12896565annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR2_5F_12896594annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR3_1S_12896169annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: GGS27_BR1_3F_12896188annot_MDS_MDS.tav.refIsIB.out

description: Information covered in other sections


title: GGS27_BR3_3S_12896168annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: GGS27_BR3_2S_12896170annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: GGS27_BR2_5S_12896646annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: Ferret lung with H5N1 at Day 0, biological rep1


title: Ferret lung with H5N1 at Day 0, biological rep2


title: GGS27_BR2_2S_12896223annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: GGS27_BR2_1S_12896224annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: Ferret lung with H3N2 at Day 6, biological rep3


title: Ferret lung with H3N2 at Day 4, biological rep1


title: Ferret lung with H3N2 at Day 6, biological rep2


title: GGS27_BR1_6S_12896619annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: Ferret lung with H3N2 at Day 4, biological rep2


title: GGS27_BR2_4S_12896615annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: GGS27_BR1_5S_12896616annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections

data_processing: Processing of 16-bit TIFF images from hybridized arrays were produced using the TIGR TM4 package (www.tm4.org). Intensity values for Cy3 and Cy5 channels were obtained using TIGR-Spotfinder software. Normalization was performed using the LOWESS algorithm available in TIGR-MIDAS using block mode and a smooth parameter of 0.33. All intensity values less than two times greater than background were removed from subsequent analysis and replicate reporter intensities on one slide (one technical replicate) were reduced to a single value by computing the geometric mean.

growth_protocol: General growth conditions of the G. sulfurreducens DL1 cells were that they were cultured anaerobically in chemostats.  Two growth conditions were tested. In the first, the electron donor (acetate 5mM) was limiting and fumarate was the electron acceptor. In the second condition, acetate as sole electron donor was provided in excess and fumarate was the limiting substrate. A dilution rate of 0.05 per hour was used for all chemostats. Additional details concerning the growth of G. sulfurreducens are given in the following reference: Esteve-Nunez, A., M. Rothermich, M. Sharma, and L. D. 2005. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7(5):641-648.

extract_protocol: Total RNA was extracted as previously described by first mechanically disrupting cells using a FastPrep instrument (Qbiogene, Carlsbad, CA) with Lysing Matrix B (Qbiogene, Carlsbad, CA), followed by nucleic acid extraction with TRIzol reagent (Invitrogen, Carlsbad, CA) (a monophasic solution of phenol and guanidine isothiocyanate) (Methe et al. 2005). Any residual DNA was removed using RNase-free DNase according to the manufacturer’s instructions  (Ambion, Austin, TX), and treated RNA was subsequently cleaned and concentrated with RNeasy minicolumns (QIAGEN Inc., Valencia, CA). The quality of total RNA was assessed by agarose-formaldehyde gel electrophoresis and the oncentration determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).


title: Ferret lung with H3N2 at Day 2, biological rep2


title: Ferret lung with H3N2 at Day 6, biological rep1


title: Ferret lung with H3N2 at Day 0, biological rep3


title: Ferret lung with H3N2 at Day 2, biological rep1


title: iHMC_serum_6h_rep2

status: Public on Dec 04 2008

city: Sao Paulo

first: Rodrigo

last: Tambellini

address: Rua Boticatu, 740

country: Brazil

institute: Federal university of Sao Paulo

description: RNA extracted from 3 culture dishes was pooled, producing one sample. A total of three samples (9 culture dishes) were hybridized for each group (1 samples/array).

hyb_protocol: Ten micrograms of fragmented target cRNA was used for hybridization of each UniSet Human I Expression Bioarray chip as described in manufacturer's protocol (CodeLink Expression Analysis Tutorial Version 4.0).

scan_protocol: Processed slides were scanned using an Axon GenePix Scanner with the laser set to 635 nm, 600V, 100% power laser and the scan resolution to 10 µm.

data_processing: Slides were scanned using CodeLinkTM Expression Scanning Software and images for each slide analyzed using the CodeLinkTM Expression Analysis Software and Microsoft Excel.

source_name: human mesangial cell, serum, 6h

label_protocol: Two micrograms of total RNA was labeled according to manufacturer's protocol (CodeLink Expression Analysis Tutorial Version 4.0).

growth_protocol: Cells were grown in low-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (serum), containing 2 g/L sodium bicarbonate and antibiotics at pH 7.4

extract_protocol: QIAGEN RNeasy Mini Kit

treatment_protocol: cells were cultured in serum-containg media until confluence, when cells were kept for 24 hours in DMEM 0.5% FBS. Cells were stimulated with 10% FBS or serum free-medium for 6 hours.

tag: human mesangial cell from a 16-weeks-old female fetus with 36 h after spontaneous abortion; primary cell obtained from Clonetics Corp. (San Diego, CA) and later immortalized with a SV40 large T antigen expression plasmid.


title: BEAS-2B treated with MTX Array 3

status: Public on Dec 06 2008

city: seoul

first: mee

last: song

address: P.O. Box 131, cheongryang

country: South Korea

institute: KIST

description: MTX vs Control

hyb_protocol: Stratagene FairPlay III microarray labeling kit

scan_protocol: PixelSize=5 DateTime=2006/10/02 10:15:03 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software

data_processing: The fluorescence intensity of each spot was calculated by local median background subtraction. We used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000 ). A significance analysis of microarray (SAM) was performed for genes with significant changes in expression.

source_name: BEAS-2B treated MTX labeled with Cy5

extract_protocol: Trizol extraction

tag: Cell line

tag: (human normal bronchial cells)

source_name: BEAS-2B treated DMSO labeled with Cy3


title: iHMC_control_6h_rep2

source_name: mesangial cell, control, 6h


title: GGS27_BR1_3S_12896681annot_MDS_MDS.tav.refIsIA.out

description: Information covered in other sections


title: iHMC_serum_6h_rep3


title: BEAS-2B treated with MTX Array 2

description: MTX vs Control

scan_protocol: PixelSize=5 DateTime=2006/10/02 10:03:38 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software

data_processing: The fluorescence intensity of each spot was calculated by local median background subtraction. We used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000 ). A significance analysis of microarray (SAM) was performed for genes with significant changes in expression

label_protocol: Stratagene FairPlay III microarray labeling kit


title: BEAS-2B treated with MTX Array 1

description: MTX vs Control

scan_protocol: PixelSize=5 DateTime=2006/10/02 09:52:48 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software


title: iHMC_serum_6h_rep1


title: iHMC_control_6h_rep1

source_name: human mesangial cell, control, 6h

tag: human mesangial cell from a 16-weeks-old female fetus with 36 h after spontaneous abortion; primary cell obtained from Clonetics Corp. (San Diego, CA), and later immortalized with a SV40 large T antigen expression plasmid.


title: Contralateral LGN layer 3 (non-deprived layer) of Monocular Deprived for 4 months

status: Public on Dec 01 2008

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

description: Ten micron section of OCT-embedded Lateral Geniculate Nucleus was placed on Leica membrane slides.

hyb_protocol: Standard Affymetrix hybridization protocol was used in an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Hewlett-Packard Gene Array Scanner was used for microarray scanning.

data_processing: Affymetrix GeneChip Operating Software (GCOS) version 1.4 was used for the data processing.

label: biotinylated cRNA

organism: Macaca mulatta

source_name: Lateral Geniculate Nucleus underwent Monocular Deprived for 4 months

label_protocol: Two rounds of linear T7-based RNA amplification was used utilizing T7 RNA polymerase.

extract_protocol: Laser Capture Microdissection was used to cut each individual layer from each Lateral Geniculate Nucleus. Total RNA from each layer was isolated using the PicoPure RNA kit from Arcturus.

tag: Lateral Geniculate Nucleus were used from female Macaque monkeys using tarsoraphoplasty underwent Monocular Deprived for 4 months.


title: Contralateral LGN layer 6 (deprived layer) of Monocular Deprived for 4 months


title: Ipsilateral LGN layer 6 (non-deprived layer) of Monocular Deprived for 4 months


title: Contralateral LGN layer 5 (non-deprived layer) of Monocular Deprived for 4 months


title: Contralateral LGN layer 2 (non-deprived layer) of Monocular Deprived for 4 months


title: Ipsilateral LGN layer 4 (non-deprived layer) of Monocular Deprived for 4 months


title: Ipsilateral LGN layer 5 (deprived layer) of Monocular Deprived for 4 months


title: Contralateral LGN layer 1 (deprived layer) of Monocular Deprived for 4 months


title: Ipsilateral LGN layer 3 (deprived layer) of Monocular Deprived for 4 months


title: Contralateral LGN layer 5 (non-deprived layer) of Monocular Deprived for 2 months

source_name: Lateral Geniculate Nucleus underwent Monocular Deprived for 2 months

tag: Lateral Geniculate Nucleus were used from male Macaque monkeys using opaque dark contact lens underwent Monocular Deprived for 2 months.


title: Contralateral LGN layer 1 (deprived layer) of Monocular Deprived for 2 months


title: Ipsilateral LGN layer 2 (deprived layer) of Monocular Deprived for 4 months


title: Contralateral LGN layer 4 (deprived layer) of Monocular Deprived for 4 months


title: Contralateral LGN layer 3 (non-deprived layer) of Monocular Deprived for 2 months


title: Contralateral LGN layer 6 (deprived layer) of Monocular Deprived for 2 months


title: iHMC_control_6h_rep3


title: Ferret lung with H3N2 at Day 2, biological rep3


title: Contralateral LGN layer 2 (non-deprived layer) of Monocular Deprived for 2 months


title: Ferret lung with H5N1 at Day 2, biological rep2


title: Ipsilateral LGN layer 1 (non-deprived layer) of Monocular Deprived for 4 months


title: Ipsilateral LGN layer 6 (non-deprived layer) of Monocular Deprived for 2 months


title: Ipsilateral LGN layer 1 (non-deprived layer) of Monocular Deprived for 2 months

tag: Lateral Geniculate Nucleus were used from male Macaque monkeys using opaque dark contact lens underwent Monocular Deprived for 2 months


title: YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 5 ENC843_hela_yy1_122204_670_600.gpr

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: Nimblegen

scan_protocol: Nimblegen

data_processing: raw data

source_name: Chromatin immunoprecipitated DNA from HeLa Chromatin cells using YY1 antibody

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: Nimblegen

source_name: Input DNA from HeLa Chromatin cells

tag: Input DNA from HeLa Chromatin cells


title: YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 1 ENC832_hela_yy1_121704_680_600.gpr

tag: Chromatin immunoprecipitated DNA from HeLa Chromatin cells using YY1 antibody


title: Ipsilateral LGN layer 2 (deprived layer) of Monocular Deprived for 2 months


title: CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 3 2007-08-08_LK_ENC13577886_CTCF_IMR90_Cy3-750_Cy5-800.gpr

source_name: Chromatin immunoprecipitated DNA from IMR90 Chromatin cells using CTCF antibody

source_name: Input DNA from IMR90 Chromatin cells

tag: Input DNA from IMR90 Chromatin cells


title: Contralateral LGN layer 4 (deprived layer) of Monocular Deprived for 2 months


title: CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 4 2007-08-08_LK_ENC13577909_CTCF_IMR90_Cy3-750_Cy5-800.gpr

tag: Chromatin immunoprecipitated DNA from IMR90 Chromatin cells using CTCF antibody


title: CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 2 2007-08-08_LK_ENC13577673_CTCF_IMR90_Cy3-700_Cy5-800.gpr


title: YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 2 ENC839_hela_yy1_121904_660_600.gpr


title: H4Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 2 ENC2062_H4Ac_K562_B.gpr

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H4Ac antibody

source_name: Input DNA from K562 Chromatin cells

tag: Input DNA from K562 Chromatin cells


title: YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 4 ENC842_hela_yy1_122204_660_600.gpr


title: Ipsilateral LGN layer 3 (deprived layer) of Monocular Deprived for 2 months


title: H4Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 1 ENC2031_H4Ac_K562_C.gpr

tag: Chromatin immunoprecipitated DNA from K562 Chromatin cells using H4Ac antibody


title: Glucose-limited chemostat in absence of PAA strain Wisconsin 14-1255 -3

city: Delft

first: Marco

middle: Alexander

last: van den Berg

address: PO Box 425

country: Netherlands

institute: DSM Anti Infectives

hyb_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

data_processing: Data analysis Acquisition and quantification of array images were performed using Affymetrix GeneChip® Operating Software (GCOS version 1.2). CHP file targeted at 100.

label: Biotin

organism: Penicillium chrysogenum

source_name: Chemostat culture  steady state

growth_protocol:
Chemostat cultivation Aerobic glucose-limited chemostat cultivation was performed at 25 °C in 3 - L turbine stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermenter was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 hours of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device, which has been described previously (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006)). The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH) was discontinuously added at timed intervals.
Media The mineral medium was set at pH 5.5 with KOH pellets and contained per liter of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O and was set at pH 6.0 by adding NaOH pellets. Glucose was heat-sterilized separately (110 °C) and added to the medium in a concentration of 7.5 g•L-1. After filter sterilization and during the chemostat experiments the medium vessel was mixed continuously by a magnetic stirrer.

extract_protocol: Sampling and RNA extraction procedures 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminum foil, quenched in liquid nitrogen and subsequently stored at -80 °C until further use. For total RNA extraction half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was precipitated for 30 minutes at -20°C in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 minutes and dissolved in RNAse free H2O.

treatment_protocol: Liquid nitrogen quenching

tag: Penicillium chrysogenum Wisconsin 14-1255 Penicillin G low producing prototrophic strain (Elander, R. Strain improvement and preservation of beta-lactam producing microorganisms.. In A.L.Demain and N. Solomon (eds.). Antibiotics containing the beta-lactam structure I. Springer-Verlag, New York, N.Y., 97-146 (1983))


title: Glucose-limited chemostat in presence of PAA strain Wisconsin 14-1255 -1

scan_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: H4Ac K562 Chromatin RenLab ENCODE PCR tiling array replicate 3 ENC2085_H4Ac_K562_A.gpr


title: Glucose-limited chemostat in presence of PAA strain Wisconsin 14-1255 -3

label_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum  MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: Ipsilateral LGN layer 4 (non-deprived layer) of Monocular Deprived for 2 months


title: YY1 HeLa Chromatin RenLab ENCODE PCR tiling array replicate 3 ENC840_hela_yy1_121904_660_600.gpr


title: Ipsilateral LGN layer 5 (deprived layer) of Monocular Deprived for 2 months


title: Glucose-limited chemostat in absence of PAA strain Wisconsin 14-1255 -2


title: p300(C-20) HeLa Chromatin RenLab ENCODE PCR tiling array replicate 3 ENC2044_p300_HeLa_1_repeat2.gpr

source_name: Chromatin immunoprecipitated DNA from HeLa Chromatin cells using p300(C-20) antibody


title: Glucose-limited chemostat in presence of PAA strain DS17690 -4

growth_protocol:
Chemostat cultivation Aerobic glucose-limited chemostat cultivation was performed at 25 °C in 3 - L turbine stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermenter was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 hours of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device, which has been described previously (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006)). The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH) was discontinuously added at timed intervals.
Media The mineral medium was set at pH 5.5 with KOH pellets and contained per liter of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O and was set at pH 6.0 by adding NaOH pellets. Production of penicillinG was induced by adding 0.58 g•L-1 phenylacetic acid (PAA) to the medium. The appropriate amount of PAA was dissolved in demineralised water. After the pH was set to 5.5 with KOH pellets, the PAA solution was autoclaved for 40 min at 121 °C. All other components were dissolved in demineralised water and added to the PAA solution in the medium vessel via filter sterilization with a sterile 0.2 µm capsule filter (Supor®DCF™; Pall Corporation, East Hills, USA). Glucose was heat-sterilized separately (110 °C) and added to the medium in a concentration of 7.5 g•L-1. After filter sterilization and during the chemostat experiments the medium vessel was mixed continuously by a magnetic stirrer.

tag: Penicillium chrysogenum DS17690 Penicillin G high producing prototrophic strain (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum

value: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006). DS17690 is derived from the strain improvement program of DSM after several classical mutagenesis rounds and is an offspring of the sequenced Wisconsin 54-1255 strain.


title: Glucose-limited chemostat in absence of PAA strain DS17690 -3


title: Glucose-limited chemostat in presence of PAA strain DS17690 -3


title: p300(C-20) HeLa Chromatin RenLab ENCODE PCR tiling array replicate 1 ENC1708_p300_HeLa_1.gpr

tag: Chromatin immunoprecipitated DNA from HeLa Chromatin cells using p300(C-20) antibody


title: Glucose-limited chemostat in absence of PAA strain DS17690 -1


title: CTCF IMR90 Chromatin RenLab ENCODE PCR tiling array replicate 1 2007-07-20_LK_ENC1357751_CTCF_IMR90_Cy3-710_Cy5-750.gpr


title: Glucose-limited chemostat in presence of PAA strain DS17690 -1


title: Glucose-limited chemostat in absence of PAA strain Wisconsin 14-1255 -1


title: Glucose-limited chemostat in presence of PAA strain DS17690 -2


title: p300(C-20) HeLa Chromatin RenLab ENCODE PCR tiling array replicate 2 ENC1725_p300_HeLa_7_repeat2.gpr


title: Soleus_Control_24hr_rep3

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent Mouse Oligo Arrays (catalogue number G4122F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol The hybridisation was performed for 17 h at 65 ºC at 10 rpm. Slides were them washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min at 22 ºC in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326). Slides were incubated for 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505B US45102871 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). The VALUE column came from the gProcessedSignal column of the result table.

source_name: Soleus muscle, freely ambulating control, 24hr, animal #3

label_protocol: 600 ng RNA and 3 µl Agilent One-Color RNA Spike-In RNA were labelled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacture’s instructions as follows:  1.2 µl T7 Promoter Primer was added to 600 ng RNA and 3 µl spike in control and denatured at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut was added. The cDNA was synthesised during the following incubation step (2h at 40 ºC). After 10 min denaturation at 65 ºC and the addition of Cy-labelled CTP, Transcription Buffer, DTT, NTP, PEG, RNaseOUT, Inorganic Phosphatase, and T7 RNA Polymerase the synthesis of the fluorescent labelled cRNA was performed during the second incubation step (2 h at 40 ºC).  The labelled cRNA was purified with the Qiagen RNeasy Mini Kit according to Manufacturer’s protocol.

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum. At 1 wk after arrival, the animals were separated into individual cages for a 3-day acclimation period then were randomly assigned to either of two experimental groups: freely ambulating controls and hindlimb-unloaded animals.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit Qiagen.  The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol: Hindlimb muscles were unloaded using methods described previously (Matuszczak, Arbogast, Reid 2004). Briefly, Elastoplast tape (Beiersdorf-Jobst, Rutherford College, NC) was used to wrap the tail of each animal. A metal clip on the tape was attached to a nylon monofilament line via a stainless steel swivel. The distal end of the nylon line was attached to an overhead support and shortened to suspend the animal in a 45° head-down tilt position. The swivel enabled the animal to explore the cage (360° range of motion) and obtain food and water freely. Animals were observed daily for changes in appearance and activity. Each animal was weighed and the angle of hindlimb suspension was adjusted if necessary. After 24hr, each animal was deeply anesthetized in the hindlimb-unloaded condition. The animal was removed from the unloading device, the soleus and gastrocnemius muscles were excised with the animal under surgical anesthesia, and the animal was euthanized.  Muscle was immediately placed in RNAlater (Ambion) and stored until RNA extraction.

tag: Strain

value: ICR

tag: Gender

tag: Age

value: 6 months

tag: Body weight 31.3g

tag: Tissue

value: soleus muscle


title: Soleus_HLS_24hr_rep3

source_name: Soleus muscle, muscle unloaded by hind-limb suspension, 24hr, animal #3

tag: Body weight 25.53g


title: Soleus_Control_24hr_rep4

source_name: Soleus muscle, freely ambulating control, 24hr, animal #4

tag: Body weight 28.89g


title: Gastrocnemius_HLS_24hr_rep4

source_name: Gastrocnemius muscle, muscle unloaded by hind-limb suspension, 24hr, animal #4

tag: Body weight 29.34g

value: gastrocnemius muscle


title: Soleus_HLS_24hr_rep2

source_name: Soleus muscle, muscle unloaded by hind-limb suspension, 24hr, animal #2

tag: Body weight 28.67g


title: Soleus_HLS_24hr_rep1

source_name: Soleus muscle, muscle unloaded by hind-limb suspension, 24hr, animal #1

tag: Body weight 27.15g


title: Soleus_Control_24hr_rep2

source_name: Soleus muscle, freely ambulating control, 24hr, animal #2

tag: Body weight 28.78g


title: Soleus_HLS_24hr_rep5

source_name: Soleus muscle, muscle unloaded by hind-limb suspension, 24hr, animal #5

tag: Body weight 25.67g