title: Sigma1278b_ureaVSarg_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on arginine

source_name: Sigma1278b ; minimum medium ; NS = arginine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = arginine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSorn_rep2

status: Public on Sep 01 2006

type: RNA

city: gosselies

first: Patrice

last: Godard

address: rue des professeurs Jeener et Brachet, 12

department: IBMM

country: Belgium

institute: Université Libre de Bruxelles

description: comparison of Sigma1278b transcriptome during growth on urea and on ornithine

scan_protocol: The hybridized microarray was scanned with a GMS418 fluorescence reader (Genetic MicroSystems, Woburn, MA) having a resolution of 10 µm; the laser power was set at 100%. The slide was scanned twice to get the Cy5 and Cy3 signals, once with the PMT (Photo Multiplier Tube) gain set at 80% and once with it set at 20%. Signal quantification for each probe on the microarray was performed with GenePix 4.01.17 image acquisition software (Axon Instruments, Union City, CA). Spots with a diameter greater than 210 µm or smaller than 80 were considered low-quality spots as were spots having (median pixel intensity - mean pixel intensity)> 40% of the median pixel intensity for each channel and spots having less than 95% of their spot pixels more than two standard deviations above background in either the green or the red channel. Low-quality spots were excluded from further analysis.

data_processing: Intensity values from high-PMT-gain pictures were used, except in the case of saturated spots. In the latter case, intensity values from low-PMT-gain pictures were used after scale correction. Intensity-dependent within-tip-group and scale normalization were applied as described by Yang et al. 2002 (PMID = 11842121) using Bioconductor tools (Gentleman et al. 2004 : PMID = 15461798).  Fluorescence ratios were computed on the basis of hybridization signals normalized with background corrections.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Sigma1278b ; minimum medium ; NS = urea

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = urea (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

source_name: Sigma1278b ; minimum medium ; NS = ornithine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = ornithine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVScit_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on citrulline

source_name: Sigma1278b ; minimum medium ; NS = citrulline

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = citrulline (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSala_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on alanine

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = urea (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

source_name: Sigma1278b ; minimum medium ; NS = alanine

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = alanine (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSasn_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on asparagine

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%;
 Nitrogen source = urea (10 mM);
 Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

source_name: Sigma1278b ; minimum medium ; NS = asparagine

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%;
 Nitrogen source = asparagine (10 mM);
 Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSgln_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on glutamine

source_name: Sigma1278b ; minimum medium ; NS = glutamine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = glutamine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_alaVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on alanine and on urea.

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = alanine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = urea (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSile_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on isoleucine

source_name: Sigma1278b ; minimum medium ; NS = isoleucine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = isoleucine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVStrp_rep1

description: comparison of Sigma1278b transcriptome during growth on urea and on tryptophan

source_name: Sigma1278b ; minimum medium ; NS = tryptophan

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = tryptophan (5 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_thrVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on threonine and on urea.

source_name: Sigma1278b ; minimum medium ; NS = threonine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = threonine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVStyr_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on tyrosine

source_name: Sigma1278b ; minimum medium ; NS = tyrosine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = tyrosine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ornVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on ornithine and on urea.

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = ornithine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSser_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on serine

source_name: Sigma1278b ; minimum medium ; NS = serine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = serine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVSgaba_rep2

description: comparison of Sigma1278b transcriptome during growth on urea and on GABA

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = urea (10 mM);
 Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

source_name: Sigma1278b ; minimum medium ; NS = GABA

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229); Carbon source = glucose 3%; Nitrogen source = gamma-amino butyric acid (10 mM);
 Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVStyr_rep1


title: Sigma1278b_pheVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on phenylalanine and on urea.

source_name: Sigma1278b ; minimum medium ; NS = phenylalanine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = phenylalanine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_proVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on proline and on urea.

source_name: Sigma1278b ; minimum medium ; NS = proline

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = proline (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_metVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on methionine and on urea.

source_name: Sigma1278b ; minimum medium ; NS = methionine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = methionine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ureaVStrp_rep2


title: Sigma1278b_valVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on valine and on urea.

source_name: Sigma1278b ; minimum medium ; NS = valine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = valine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_serVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on serine and on urea.

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = serine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_ileVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on isoleucine and on urea.

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = isoleucine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_citVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on citrulline and on urea.

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = citrulline (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = urea (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per m


title: Sigma1278b_gabaVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on GABA and on urea.

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%;
Nitrogen source = gamma-amino butyric acid (GABA)  (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%;
Nitrogen source = urea (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_asnVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on asparagine and on urea.

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = asparagine (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = urea (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_aspVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on aspartate and on urea.

source_name: Sigma1278b ; minimum medium ; NS = aspartate

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = aspartate (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_amVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on ammonium and on urea.

source_name: Sigma1278b ; minimum medium ; NS = ammonium

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = ammonium sulfate (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

source_name: Sigma1278b ; minimum medium ; NS = urea


title: Sigma1278b_leuVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on leucine and on urea.

source_name: Sigma1278b ; minimum medium ; NS = leucine

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = leucine (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = urea (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_gltVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on glutamate and on urea.

source_name: Sigma1278b ; minimum medium ; NS = glutamate

growth_protocol: Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = glutamate (10 mM); Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: Sigma1278b_glnVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on glutamine and on urea.

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = glutamine (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);Carbon source = glucose 3%; Nitrogen source = urea (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: 60 d vs 7 wk oligo 4

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

country: USA

institute: Michigan State University

description: Skeletal muscle tissue samples were obtained from the hind limbs of pig fetuses at 60 days of gestation and postnatal pigs at 7 weeks of age.  For fetal samples, tissues from several pigs within each litter were pooled, whereas postnatal samples were obtained from individual animals.

data_processing: Log ratio of Loess normalized data

molecule: total RNA

organism: Sus scrofa

source_name: skeletal muscle 60 d A

tag: Age

value: 60 days of gestation

source_name: skeletal muscle 7 wk D

value: 7 weeks postnatal


title: 60 d vs 7 wk oligo 7

source_name: skeletal muscle 60 d C

source_name: skeletal muscle 7 wk F


title: 60 d vs 7 wk oligo 3


title: GnRH_10nM_2

status: Public on Aug 31 2006

city: San Diego

first: Richard

middle: B

last: Roth

state: CA

address: 12790 El Camino Real

department: Molecular Medicine

institute: Neurocrine Biosciences, Inc.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA

label: biotin

organism: Rattus norvegicus

source_name: rat pituitary organ culture

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

extract_protocol: Total RNA extracted using standard Trizol protocol, followed by Qiagen RNeasy column clean-up

tag: treated


title: Sigma1278b_argVSurea_rep1

description: comparison of Sigma1278b transcriptome during growth on arginine and on urea.

source_name: Sigma1278b ; minimum medium ; NS = arginine

growth_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = arginine (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)

treatment_protocol:
Medium = minimum medium: Jacobs et al. 1980 (PMID = 6251229);
Carbon source = glucose 3%;
Nitrogen source = urea (10 mM);
Cells were harvested during exponential growth after at least 10 generations and at low density (~1.E06 cells per ml)


title: 60 d vs 7 wk oligo 6

source_name: skeletal muscle 60 d B

source_name: skeletal muscle 7 wk E


title: C6 PBMC_20µg hgh/mL_180min_rep 2

city: Seibersdorf

first: René

last: Stempfer

address: Reaktorstr.

department: Life Sciences

country: Austria

institute: ARC Seibersdorf research GmbH

description: mRNA

data_processing: Data were fed into the BASE database, filtered for valid spots and Lowess normalised

organism: Homo sapiens

source_name: mRNA

treatment_protocol: hgh treated

tag: Peripheral blood mononuclear cells isolated from donated blood by Ficoll gradient centrifugation

treatment_protocol: control


title: E5 PBMC_2µg hgh/mL_180min_rep 2

description: mRNA


title: GnRH_10nM_1


title: E3 PBMC_20µg hgh/mL_180min_rep 1

description: mRNA


title: GnRH_10nM_3


title: C5 PBMC_2µg hgh/mL_180min_rep 2

description: mRNA


title: D6 PBMC_20µg hgh/mL_180min_rep 2

description: mRNA


title: D5 PBMC_2µg hgh/mL_180min_rep 2

description: mRNA


title: B3 PBMC_20µg hgh/mL_180min_rep 1

description: mRNA


title: D3 PBMC_20µg hgh/mL_180min_rep 1

description: mRNA


title: D2 PBMC_2µg hgh/mL_180min_rep 1

description: mRNA


title: A6 PBMC_20µg hgh/mL_180min_rep 2

description: mRNA


title: B5 PBMC_2µg hgh/mL_180min_rep 2

description: mRNA


title: B2 PBMC_2µg hgh/mL_180min_rep 1

description: mRNA


title: A5 PBMC_2µg hgh/mL_180min_rep 2

description: mRNA


title: E2 PBMC_2µg hgh/mL_180min_rep 1

description: mRNA


title: B6 PBMC_20µg hgh/mL_180min_rep 2

description: mRNA


title: C3 PBMC_20µg hgh/mL_180min_rep 1

description: mRNA


title: control_3

tag: control


title: C2 PBMC_2µg hgh/mL_180min_rep 1

description: mRNA


title: control_2


title: 60d vs 7wk oligo 2

description:
Skeletal muscle tissue samples were obtained from the hind limbs of pig fetuses at 60 days of gestation and postnatal pigs at 7 weeks of age.  For fetal samples, tissues from several pigs within each litter were pooled, whereas postnatal samples were obtained from individual animals.
Keywords = pig, skeletal muscle, microarray


title: control_1


title: A2 PBMC_2µg hgh/mL_180min_rep 1

description: mRNA


title: R12 RA-1_20µg hgh/mL_180min_rep 1

description: Reference RNA

tag: RA-1 B lymphocytes

source_name: Stratagene Universal human reference RNA

tag: control RNA, Human Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of human genes


title: R13 RA-1_20µg hgh/mL_180min_rep 2

description: Reference RNA


title: R9 RA-1_2µg hgh/mL_180min_rep 2

description: Reference RNA


title: A3 PBMC_20µg hgh/mL_180min_rep 1

description: mRNA


title: R5 RA-1_0µg hgh/mL_0min_rep 1

description: Reference RNA


title: R6 RA-1_0µg hgh/mL_0min_rep 2

description: Reference RNA


title: R8 RA-1_2µg hgh/mL_180min_rep 1

description: Reference RNA


title: H4 H9_2µg hgh/mL_180min_rep 2

description: Reference RNA

tag: H9 T lymphocytes


title: H6 H9_20µg hgh/mL_180min_rep 2

description: Reference RNA


title: TU 26.5. THP-1_0µg hgh/mL_0min_rep 2

description: Reference RNA

tag: THP-1 monocytes


title: T8 THP-1_20µg hgh/mL_180min_rep 1

description: Reference RNA


title: H5 H9_20µg hgh/mL_180min_rep 1

description: Reference RNA


title: H2 H9_0µg hgh/mL_0min_rep 2

description: Reference RNA


title: H1 H9_0µg hgh/mL_0min_rep 1

description: Reference RNA


title: T11 THP-1_0.2µg hgh/mL_180min_rep 1

description: Reference RNA


title: T12 THP-1_0.2µg hgh/mL_180min_rep 2

description: Reference RNA


title: T5 THP-1_2µg hgh/mL_30min_rep 2

description: Reference RNA


title: E14 molar TCDD 1

status: Public on Aug 19 2006

city: Helsinki

first: Carin

last: Sahlberg

address: PL 63, Haartmaninkatu 8

department: Institute of Dentistry

country: Finland

institute: University of Helsinki

description: Gene expression data from pooled samples of E14 mouse embryo tooth germs

hyb_protocol: Following fragmentation, 16 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome U74 Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Genechip System confocal scanner (Aligent)

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

organism: Mus musculus

source_name: E14 molar teeth, TCDD exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 11 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The basal culture medium was Dulbecco’s modified Eagle’s medium (DMEM) containing Glutamax-1 (Gibco BRL, Paisley, Scotland) supplemented with 10% fetal calf serum (FCS; Gibco BRL)

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen). Extraction was performed according to the manufacturer's instructions.

treatment_protocol:
Tissue culture for 24 hours,
with TCDD added to the medium at 1 µM

tag: Strain

value: NMRI mouse

value: 14 day embryo

tag: Tissue

value: molar tooth germ


title: T7 THP-1_2µg hgh/mL_180min_rep 2

description: Reference RNA


title: E14 molar TCDD 2

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome U74 Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol:
Tissue culture for 24 hours,
with TCDD added to the culture at 1 µM


title: T6 THP-1_0.2µg hgh/mL_30min_rep 2

description: Reference RNA


title: T4 THP-1_2µg hgh/mL_180min_rep 1

description: Reference RNA


title: T3 THP-1_0.2µg hgh/mL_30min_rep 1

description: Reference RNA


title: T2.1 THP-1_20µg hgh/mL_30min_rep 1

description: Reference RNA


title: T10 THP-1_0µg hgh/mL_0min_rep 1

description: Reference RNA


title: T1 THP-1_2µg hgh/mL_30min_rep 1

description: Reference RNA


title: T2.2 THP-1_20µg hgh/mL_30min_rep 2

description: Reference RNA


title: E14 molar DMSO 1

source_name: E14 molar teeth, DMSO control

growth_protocol: The basal culture medium was Dulbecco’s modified Eagle’s medium (DMEM) containing Glutamax-1 (Gibco BRL, Paisley, Scotland) supplemented with 10% fetal calf serum (FCS; Gibco BRL).

treatment_protocol:
Tissue culture for 24 hours,
with DMSO added to the medium at 0,65%


title: E14 molar DMSO 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The basal culture medium was Dulbecco’s modified Eagle’s medium (DMEM) containing Glutamax-1 (Gibco BRL, Paisley, Scotland) supplemented with 10% fetal calf serum (FCS; Gibco BRL) and ascorbic acid (100 Ag/ml; Sigma, St. Louis, MO).

value: 14 d embryo

value: molar tooth germs


title: hrpL-MM-38404

status: Public on Aug 01 2006

city: manhattan

first: Xiaoyan

last: Tang

email: xtang@ksu.edu, llan@ksu.edu

state: KS

address: 4702 Throckmorton

department: Plant Pathology

institute: Kansas State University

description: Gene expression data from hrpL mutant (from DC3000) when grown in MM at 6hr(King et al., 1954).

hyb_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.

data_processing: For each probe on the array, the median signal intensity was calculated using the NimbleGen extraction software. The data were normalized by using quantile normalization (Bolstad et al., 2003)available through the Bioconductor projec(http://www.bioconductor.org), and gene calls were generated by using the RMA algorithm (Robust Multichip Average) (Irizarry et al., 2003). The relative fluorescent intensities of each ORF were scaled by assuming a constant mean signal intensity of 1,000 signal units for each array.

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Pseudomonas syringae pv. tomato DC3000.

extract_protocol: Total RNA was extracted using a modified hot phenol procedure (Aiba et al. 1981), then purified by using RNeasy Midi kit following the manufacture instruction (Qiagen, Valencia, CA).

tag: hrpL mutant derived from DC3000 were grown in KB (King et al., 1954) to ~0.7x109 cfu/mL,The bacteria were centrifuged, washed twice with MM (Huynh et al., 1989), and resuspended in MM to 3x108 cfu/mL. The bacteria were cultured in MM for 6 h before being harvested for RNA extraction.


title: H3 H9_2µg hgh/mL_180min_rep 1

description: Reference RNA


title: 7d dark root 1h dark light, biological rep3

status: Public on Aug 15 2006

city: Gainesville

first: Melanie

last: Correll

state: FL

address: 142 Frazier Rogers Hall

department: Agricultural and Biological Engineering

institute: University of Florida

description: Gene expression data from 1cm root tips of  7day old dark grown seedlings+ 1h dark rep 3 of 3

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on ATH1 Arabidopsis GeneChip Array. GeneChips were washed (Molecular Probes, OR).

scan_protocol: GeneChips were scanned using a GeneCHip Scanner 3000 (Affymetrix).

organism: Arabidopsis thaliana

source_name: Arabidopsis 1cm root tips 7d dark

label_protocol: Biotinylated cRNA were prepared using GeneChip One-Cycle Target Labeling Kit (Affymetrix) from 5ug of total RNA.  First strand synthesis was primed with T7dT24 oligonuclided primer containing a T7 RNA polymerase promoter seqyance on the 5'end. Second strand products were cleaned and used for IVT with biotin-labeled nucelotides.

growth_protocol: Roots were grown in 23°C dark for 7 days and then transferred to dark for 1 hour

extract_protocol: Seeds collected in RNAlater (Ambion) and roots excised for further analysis , Qiagen RNAEASY kit

treatment_protocol: Seeds were sterilized with 70% ethanol 5min, two rinses  90% ethanol 10s, 4 rinses sterile water. Seeds were plated on 1/2 MS media + 1% (w/v) sucrose, 1.2% agar, pH5.6, incubated at 23 °C in the dark for 7 days. Seedlings illuminated with 1 h of 12-14 umol m-2 s-1 red light 630 nm max wavelength.

tag: Landsberg erecta, 7-day-old roots from dark grown seedlings 1cm root tips

value: 7 day old


title: 7d dark root 1h red light, biological rep2

description: Gene expression data from 1cm root tips of  7day old dark grown seedlings+ 1h red light rep2 of 3

source_name: Arabidopsis 1cm root tips 7d dark 1hour red light

growth_protocol: Roots were grown in 23°C dark for 7 days and then transferred to 1 hour red light

extract_protocol: Seeds collected in RNAlater (Ambion) and roots excised for further analysis

tag: Landsberg erecta, 7-day-old roots from dark grown seedlings 1cm root tips illuminated with 1 hour red light (12 umol m-2 s-1)


title: hrpL-MM1-42485

scan_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.


title: hrpL-MM1-43982

label_protocol: According to the standard protocol provided by NimbleGen Systems Inc., Madison, WS.


title: 7d dark root 1h red light, biological rep3

description: Gene expression data from 1cm root tips of  7day old dark grown seedlings+ 1h red light rep 3 of 3


title: hrpR-MM-36132

description: Gene expression data from hrpRS mutant (from DC3000) when grown in MM at 6hr(King et al., 1954).

tag: hrpRS mutant derived from DC3000 were grown in KB (King et al., 1954) to ~0.7x109 cfu/mL,The bacteria were centrifuged, washed twice with MM (Huynh et al., 1989), and resuspended in MM to 3x108 cfu/mL. The bacteria were cultured in MM for 6 h before being harvested for RNA extraction.


title: 7d dark root 1h dark light, biological rep2

description: Gene expression data from 1cm root tips of  7day old dark grown seedlings+ 1h dark rep2 of 3


title: DC-MM11-43981

description: Gene expression data from DC3000 when grown in MM at 6hr(King et al., 1954).

tag: DC3000 were grown in KB (King et al., 1954) to ~0.7x109 cfu/mL,The bacteria were centrifuged, washed twice with MM (Huynh et al., 1989), and resuspended in MM to 3x108 cfu/mL. The bacteria were cultured in MM for 6 h before being harvested for RNA extraction.


title: 7d dark root 1h red light, biological rep1

description: Gene expression data from 1cm root tips of  7day old dark grown seedlings+ 1h red light replicate 1 of 3


title: DC-KB2-68692

description: Gene expression data from DC3000 when grown in KB (King et al., 1954) to ~0.7x109 cfu/mL.

tag: DC3000 were grown in KB (King et al., 1954) to ~0.7x109 cfu/mL and then are harvested for RNA extraction.


title: DC-KB1-47382


title: hrpR-MM1-41886


title: DC-MM-39324


title: Mili-/- mouse D10 testes mRNA

city: Suita

first: Satomi

middle: Kuramochi

last: Miyagawa

state: Osaka

address: Yamada-oka 2-2

country: Japan

institute: Osaka university

description: Spermatogenesis in Mili-KO mice was blocked completely at sarly prophase of the first meiosis during the zygotene or early pachytene stage.  Apoptotic cells in KO testis were first observed at day11 after birth.

data_processing: all

label: mili-/- D10 testes

source_name: Mili-/- mouse D10 testes

tag: mRNA from D10 whole testes


title: DC-KB-36131

data_processing: For each probe on the array, the median signal intensity was calculated using the NimbleGen extraction software. The data were normalized by using quantile normalization (Bolstad et al., 2003)available through the Bioconductor projec(http://www.bioconductor.org), and gene calls were generated by using the RMA algorithm (Robust MultichipnAverage) (Irizarry et al., 2003). The relative fluorescent intensities of each ORF were scaled by assuming a constant mean signal intensity of 1,000 signal units for each array.


title: DC-MM1-43588


title: Mili+/- mouse D10 testes mRNA

label: mili+/- D10 testes

source_name: Mili+/- mouse D10 testes


title: T9 THP-1_20µg hgh/mL_180min_rep 2

description: Reference RNA


title: 7d dark root 1h dark light, biological rep1

description: Gene expression data from 1cm root tips of  7day old dark grown seedlings+ 1h dark  replicate 1 of 3

extract_protocol: Seeds collected in RNAlater (Ambion) and roots excised for further analysis , Qiagen RNeasy kit

tag: Age


title: Daudi_IL4_6h_rep3

status: Public on Jul 31 2006

city: Bunkyo-ku, Tokyo

first: Hiroshi

last: Fukasawa

address: Kadokawa Hongo Bldg. 4F, 5-24-5 Hongo

institute: Institute of Medicinal Molecular Design, Inc.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 18 hr at 37C on CodeLink Human Whole Genome Bioarrays. Bioarrayss were washed and stained with Cy-5 Streptavidin

scan_protocol: Bioarrays were scanned using arrayWoRx scanner.

data_processing: CodeLink Expression Analysis software was used for primary data (raw data) extraction from bioarray images. Multiple bioarray data were normalized by mean using Spotfire.

source_name: Daudi cells

label_protocol: Biotinylated cRNA were prepared with CodeLink Expression Assay Kit according to the standard manufacture's protocol from 2 microg total RNA

growth_protocol: Daudi cells were cutured in RPMI1640 with 10% FBS. Cells were stimulated with IL-4 for 6 hr.

extract_protocol: RNeasy kit

treatment_protocol: Daudi cells were stimulated with 10 ng/mL IL-4 for 6 hr. After wash with cold PBS twice, cells were lysed in RLT buffer. Total RNA was extracted using an RNeasy

tag: Burkitt's lymphoma

tag: 16-year-old Black male


title: Daudi_antiCD40+IL-4_6h rep1

growth_protocol: Daudi cells were cutured in RPMI1640 with 10% FBS. Cells were stimulated with agonistic anti-CD40 and IL-4 for 6 hr.

treatment_protocol: Daudi cells were stimulated with 1 ug/mL agonistic anti-CD40 and 10 ng/mL IL-4 for 6 hr. After wash with cold PBS twice, cells were lysed in RLT buffer. Total RNA was extracted using an RNeasy


title: Daudi_antiCD40_6h_rep3

growth_protocol: Daudi cells were cutured in RPMI1640 with 10% FBS. Cells were stimulated with agonistic anti-CD40 for 6 hr.

treatment_protocol: Daudi cells were stimulated with 1 ug/mLagonistic anti-CD40 for 6 hr. After wash with cold PBS twice, cells were lysed in RLT buffer. Total RNA was extracted using an RNeasy


title: Daudi_IL4_6h_rep2


title: Daudi_antiCD40+IL4_6h rep3


title: Daudi_antiCD40_6h_rep1


title: Daudi_control rep3

growth_protocol: Daudi cells were cutured in RPMI1640 with 10% FBS.

treatment_protocol: Daudi cells were cultured in RPMI1640 with 10% FBS. After wash with cold PBS twice, cells were lysed in RLT buffer. Total RNA was extracted using an Rneasy


title: Daudi_antiCD40_6h_rep2


title: Daudi_control rep2


title: Daudi_IL4_6h_rep1


title: Daudi_control rep1


title: Daudi_control_rep2


title: human_leftventricle_maleVSfemale_<40years_rep2

status: Public on Jul 09 2006

city: Berlin

first: Joerg

last: Isensee

address: Hessische Str. 3-4

department: Center for Cardiovascular Research

country: Germany

institute: Charite Berlin

description: Image analysis with Feature Extraction software 7.1.1 (Agilent)

hyb_protocol: Samples were vacuum-centrifuged and resuspended in 7.5 µl nuclease-free water, 2.5 µl deposition control targets (Agilent) and 15 µl DIG hybridisation buffer (Roche). Denatured samples (98°C, 2 min) were hybridised on cDNA microarrays (Agilent) in a humidified chamber at 42°C for 15 h.

scan_protocol: Agilent Microarray scanner (G2565BA)

data_processing: Linear and LOWESS dye normalization

source_name: human left ventricle, <40 years old, male pool

label_protocol: For reverse transcription (Superscript III, Invitrogen) in the presence of cyanine dye (Cy3 or Cy5) coupled dCTP (Amersham) 50 µg total RNA was used in a 30 µl reaction. Labelled cDNAs were combined with 380 µl TE (10 mM Tris, 1 mM EDTA), 20 µg human Cot1 DNA and 20 µg Oligo(dA) and purified with a Microcon YM-30 column (Millipore).

extract_protocol: TRIzol® (Invitrogen) method

tag: 'Gender

value: male',

tag: 'Age

value: <40 years',

tag: 'Tissue

value: left ventricle sample of expl. heart',

tag: 'Pool

value: n=4 individuals'

source_name: human left ventricle, <40 years old, female pool

value: female',

value: n=3 individuals'


title: Daudi_antiCD40+IL4_6h rep2


title: human_leftventricle_femaleVSmale_<40years_rep3


title: Daudi_AICAR1h_antiCD40+IL4_6h_rep3

growth_protocol: Daudi cells were cutured in RPMI1640 with 10% FBS. Cells were treated with 2.5 mM AICAR for 1 hr, then stimulated with agonistic anti-CD40 and IL-4 for 6 hr.

treatment_protocol: Daudi cells were treated with 2.5 mM AICAR hor 1 hr, then stimulated with 1 ug/mL anti-CD40 and 10 ng/mL IL-4 for 6 hr. After wash with cold PBS twice, cells were lysed in RLT buffer. Total RNA was extracted using an RNeasy


title: Daudi_AICAR_7h_rep1

growth_protocol: Daudi cells were cutured in RPMI1640 with 10% FBS. Cells were trated with 2.5 mM AICAR for 7 hr.

treatment_protocol: Daudi cells were cultured in the presence of 2.5 mM AICAR for 7 hr. After wash with cold PBS twice, cells were lysed in RLT buffer. Total RNA was extracted using an RNeasy


title: Daudi_control_rep3


title: Daudi_antiCD40+IL4_6h_rep2

treatment_protocol: Daudi cells were stimulated with 1 ug/mL anti-CD40 and 10 ng/mL IL-4 for 6 hr. After wash with cold PBS twice, cells were lysed in RLT buffer. Total RNA was extracted using an RNeasy


title: Daudi_AICAR_7h_rep3


title: human_leftventricle_maleVSfemale_>50years_rep4

source_name: human left ventricle, 50-65 years old, male pool

value: n=5 individuals'

source_name: human left ventricle, 50-65 years old, female pool


title: Daudi_antiCD40+IL4_6h_rep1


title: Daudi_antiCD40+IL4_6h_rep3


title: human_leftventricle_femaleVSmale_<40years_rep1


title: Daudi_AICAR_7h_rep2


title: human_leftventricle_maleVSfemale_<40years_rep4


title: Daudi_control_rep1


title: Daudi_AICAR1h_antiCD40+IL4_6h_rep2


title: RPTEC CAA 080405

status: Public on Jun 30 2006

city: Munich

first: Andreas

last: Benesic

state: Bavaria

address: Marchioninistr. 15

department: Dept. of medicine 2

institute: University Hospital Grosshadern, Munich

description: Chronic renal damage is observed especially in children treated with the chemotherapeutic agent ifosfamide. Renal injury presents frequently as Fanconi´s syndrome with partial or complete loss of proximal tubule cell function. Since the ifosfamide metabolite chloroacetaldehyde is suspected to be the nephrotoxic agent, changes in signalling pathways after chloroacetaldehyde exposure in human RPTEC in primary cuilture were screened using cDNA Microarrays

hyb_protocol: according to user manual for Q-Series cDNA microarrays www.superarray.com

scan_protocol: After data acqusition on X-Ray Film using the CDP Star reagent, Films were scanned and TIF-Images analysed using spotfinder 3.1.0 (TIGR)

data_processing: Values were normalized for GAPDH

source_name: human proximal tubule epithelial cells

label_protocol: according to user manual for Q-Series cDNA microarrays, using the AMPO-Labelling Kit www.superarray.com

growth_protocol: Cells were grown in DMEM/HAM F-12 medium supllemented with 0.5% fetal calf serum, supplemented with 1.1 g/l NaHCO3, 3.57 g/l, 4-(2-hydroxyethyl)-1-piperazineethanesulphonic acid (HEPES), 5 mg/l human apo-transferrin, 5 mg/l (bovine)insulin, 500 µg/l hydrocortisone, 10 µg/l mouse EGF, 5 µg/l Na-selenite, 0.5% fetal calf serum (Biochrom, Berlin, Germany), 6.5 µg/l thyroxin and 500 µg/l epinephrine under standard cell culture conditions (37 °C, 5% CO2)

extract_protocol: Array Grade mRNA Extraction Kit available at www.superarray.com procedures according to user manual

treatment_protocol: After 24 h serum starvation in DMEM/HAM F-12 medium without additives, cells were incubated for 24 h in presence an absence of 15 micromolar chloroacetaldehyde under standard cell culture conditions (37 °C, 5% CO2)

tag: human proximal tubule epithelial cells in primary culture


title: Daudi_AICAR1h_antiCD40+IL-4_6h_rep1


title: RPTEC control 080405


title: 300505 RPTEC control


title: RPTEC CAA 220305

label_protocol:
according to user manual for Q-Series cDNA microarrays, using the AMPO-Labelling Kit
www.superarray.com

extract_protocol:
Array Grade mRNA Extraction Kit available at www.superarray.com
procedures according to user manual


title: 110505 RPTEC CAA


title: 300505 RPTEC CAA


title: 110505 RPTEC control


title: human_leftventricle_maleVSfemale_>50years_rep2

description: Image analysis with Feature Extraction software 7.1.1 (Agilent

label_protocol:
For reverse transcription (Superscript III, Invitrogen) in the presence of cyanine dye (Cy3 or Cy5) coupled dCTP (Amersham) 50 µg total RNA was used in a 30 µl reaction. Labelled cDNAs were combined with 380 µl TE (10 mM Tris, 1 mM EDTA), 20 µg human Cot1 DNA
and 20 µg Oligo(dA) and purified with a Microcon YM-30 column (Millipore).


title: human_leftventricle_femaleVSmale_>50years_rep1

label_protocol: For reverse transcription (Superscript III, Invitrogen) in the presence of cyanine dye (Cy3 or Cy5) coupled dCTP (Amersham) 50 µg total RNA was used in a 30 µl reaction. Labelled cDNAs were combined with 380 µl TE (10 mM Tris, 1 mM EDTA), 20 µg human Cot1 DNA and 20 µg Oligo(dA) and purified with a Microcon YM-30 column (Millipore)


title: wild-type intestine Chip 4

status: Public on Jul 01 2006

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

institute: University of Lübeck

data_processing: GCOS™ 1.1 files were read analyzed with Dchip 1.4 and normailzed using a PM/MM algorithm

source_name: adult male small intestine

extract_protocol: QIAGEN RNeasy Micro Kit

tag: strain

tag: gender

value: male

tag: age

tag: tissue

value: small intestine (medial section)


title: PKCa -/- intestine Chip 8

data_processing: GCOS™ 1.1 files were read with Dchip 1.4 and normailzed using a PM/MM algorithm

value: 129SV gender:male age:50-60 d tissue:small intestine (medial section)


title: PKCa -/- intestine Chip 10


title: wild-type intestine Chip 5


title: su(Hw)-GFP_IP-LarvalWingDisc5b

status: Public on Jun 20 2006

type: genomic

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description: Identification of in vivo Su(Hw) binding sites in the Drosophila 3rd instar larval wing discs.

hyb_protocol: As described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/

data_processing: VSN normalisation- VALUE is the VSN normalised ratio of Su(hw) enriched to control. All other data are raw un-normalised values.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: anti-GFP

label_protocol: Enriched chromatin labelling as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/

growth_protocol: Egg laying at 25oC

extract_protocol: Chromatin purified as described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip/

tag: Chromatin from Drosophila melanogaster 3rd instar larval wing discs carrying GFP-tagged Su(Hw). Genotype- y[2]; P{su(Hw).GFP}; Df(3R)su(Hw)V, P{casX/K-RpII15} (Gerasimova, TI, Byrd, K and VG Corces (2000) Mol. Cell. 6:p1025) Immunopurified with anti-GFP.

source_name: Control sera IP

tag: Chromatin from Drosophila melanogaster 3rd instar larval wing discs carrying GFP-tagged Su(Hw).  Genotype-   y[2]; P{su(Hw).GFP}; Df(3R)su(Hw)V, P{casX/K-RpII15} (Gerasimova, TI, Byrd, K and VG Corces (2000) Mol. Cell. 6:p1025) Immunopurified with normal rabbit serum.


title: su(Hw)-GFP_IP-LarvalWingDisc1b

scan_protocol: As described in Birch-Machin et al (2005) Genome Biology 6:R63, detailed protocol from http://www.flychip.org.uk/protocols/chip


title: su(Hw)-GFP_IP-LarvalWingDisc2b


title: su(Hw)-GFP_IP-LarvalWingDisc4a

source_name: Control Sera IP


title: su(Hw)-GFP_IP-LarvalWingDisc1a


title: su(Hw)-GFP_IP-LarvalWingDisc4b


title: su(Hw)-GFP_IP-LarvalWingDisc5a


title: su(Hw)-GFP_IP-LarvalWingDisc3a


title: human_leftventricle_femaleVSmale_>50years_rep3


title: su(Hw)-GFP_IP-LarvalWingDisc3b


title: su(Hw)-GFP_IP-LarvalBrain1a

description: Identification of in vivo Su(Hw) binding sites in the Drosophila 3rd instar larval brain.

tag: Chromatin from Drosophila melanogaster 3rd instar larval brains carrying GFP-tagged Su(Hw).  Genotype-   y[2]; P{su(Hw).GFP}; Df(3R)su(Hw)V, P{casX/K-RpII15} (Gerasimova, TI, Byrd, K and VG Corces (2000) Mol. Cell. 6:p1025) Immunopurified with normal rabbit serum.

tag: Chromatin from Drosophila melanogaster 3rd instar larval brains carrying GFP-tagged Su(Hw). Genotype- y[2]; P{su(Hw).GFP}; Df(3R)su(Hw)V, P{casX/K-RpII15} (Gerasimova, TI, Byrd, K and VG Corces (2000) Mol. Cell. 6:p1025) Immunopurified with anti-GFP.


title: su(Hw)-GFP_IP-LarvalBrain3a


title: su(Hw)-GFP_IP-LarvalBrain4a


title: su(Hw)-GFP_IP-LarvalBrain2b


title: su(Hw)-GFP_IP-LarvalBrain5a


title: TGF-beta stimulated human mast cells, sample5

status: Public on Jun 23 2006

city: Budapest

first: Zoltan

last: Wiener

address: Nagyvarad ter 4.

department: Dept of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: cord blood-derived mast cells, unst or TGF-beta stimulation 4 days, 2ng/ml

data_processing: Agilent FE 7.5

source_name: human mast cell, control (Cy3)

source_name: human mast cell, TGF (Cy5)


title: su(Hw)-GFP_IP-LarvalBrain1b


title: su(Hw)-GFP_IP-LarvalBrain4b


title: su(Hw)-GFP_IP-LarvalBrain2a


title: su(Hw)-GFP_IP-EmbryoChromatin6b

description: Identification of in vivo Su(Hw) binding sites in Drosophila embryos.

tag: Chromatin from 0-20 hr Drosophila melanogaster embryos carrying GFP-tagged Su(Hw).  Genotype-   y[2]; P{su(Hw).GFP}; Df(3R)su(Hw)V, P{casX/K-RpII15} (Gerasimova, TI, Byrd, K and VG Corces (2000) Mol. Cell. 6:p1025) Immunopurified with normal rabbit serum.

tag: Chromatin from 0-20 hr Drosophila melanogaster embryos carrying GFP-tagged Su(Hw). Genotype- y[2]; P{su(Hw).GFP}; Df(3R)su(Hw)V, P{casX/K-RpII15} (Gerasimova, TI, Byrd, K and VG Corces (2000) Mol. Cell. 6:p1025) Immunopurified with anti-GFP.


title: TGF-beta stimulated human mast cells, sample4


title: su(Hw)-GFP_IP-LarvalBrain5b


title: su(Hw)-GFP_IP-LarvalBrain3b


title: su(Hw)-GFP_IP-EmbryoChromatin6a


title: TGF-beta stimulated human mast cells, sample2

source_name: human mast cell, TGF-beta (Cy5)


title: su(Hw)-GFP_IP-EmbryoChromatin5b


title: Su(Hw)-GFP_IP-EmbryoChromatin1b


title: su(Hw)-GFP_IP-EmbryoChromatin3a


title: su(Hw)-GFP_IP-EmbryoChromatin5a


title: Su(Hw)-GFP_IP-EmbryoChromatin2b


title: TGF-beta stimulated human mast cells, sample3


title: Su(Hw)-GFP_IP-EmbryoChromatin2a


title: su(Hw)-GFP_IP-EmbryoChromatin3b


title: Su(Hw)-GFP_IP-EmbryoChromatin1a

tag: Chromatin from 0-20 hr Drosophila melanogaster embryos carrying GFP-tagged Su(Hw).  Genotype-   y[2]; P{su(Hw).GFP}; Df(3R)su(Hw)V, P{casX/K-RpII15} (Gerasimova, TI, Byrd, K and VG Corces (2000) Mol. Cell. 6:p1025) Immunopurified with anti-GFP.


title: su(Hw)-GFP_IP-EmbryoChromatin4a


title: The effect of TGF-beta on human mast cells, sample1

source_name: human mast cell unst (Cy3)

source_name: human mast cell TGF-treated (Cy5)


title: su(Hw)-GFP_IP-EmbryoChromatin4b


title: TGF-beta stimulated human mast cells, sample3 (Dye-swap)

source_name: human mast cell, TGF (Cy3)

source_name: human mast cell, control (Cy5)


title: set2sir4_array2

status: Public on Jun 01 2006

city: San Francisco

first: Rachel

last: Tompa

department: Biochemistry

institute: UC San Francisco

description: set2∆sir4∆ vs. wild type

data_processing: log2 of set2sir4/WT ratio, normalized for total signal in each channel

tag: set2sir4, YPAD, log phase, 30C

source_name: WT

tag: WT, log phase, YPAD, 30C


title: Su(Hw)_IP-EmbryoChromatin1b

source_name: anti-Su(Hw)

tag: Chromatin purified from 0-20hr Drosophila melanogaster (Oregon R strain) embryos immunopurified with rabbit anti-Su(Hw)

tag: Chromatin purified from 0-20hr Drosophila melanogaster (Oregon R strain) embryos immunopurified with normal rabbit serum


title: Su(Hw)_IP-EmbryoChromatin2a

tag: Chromatin from 0-20 hr Drosophila melanogaster (Oregon R strain) Immunopurified with normal rabbit serum.

tag: Chromatin from 0-20 hr Drosophila melanogaster (Oregon R strain) Immunopurified with rabbit anti Su(Hw)


title: set2sir4_array4

description: set2∆sir4∆ vs. wild type


title: set2sir4_array1

description: set2∆sir4∆ vs. wild type


title: set2_array3

description: set2∆ vs. wild type

data_processing: log2 of set2/WT ratio, normalized for total signal in each channel

tag: set2∆, log phase, YPAD, 30C


title: Su(Hw)_IP-EmbryoChromatin1a


title: set2sir4_array3

description: set2∆sir4∆ vs. wild type


title: Su(Hw)_IP-EmbryoChromatin2b


title: set2_array1

description: set2∆ vs. wild type


title: biological rep3 sample b IAA

city: Napoli

first: Roberto

last: Defez

address: via Castellino 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

description: Gene expression data from late exponentially growing E. coli cells

hyb_protocol: After incubation for 2 h at 65 °C, the pre-hybridisation solution was replaced with 3 ml of hybridisation buffer containing the denatured radioactively labelled cDNA probes. Filter hybridisations were carried out for 16 h in a hybridisation oven. The filters were then washed three times, for 5 min each, at room temperature and then three times at 65 °C of warmed wash solution.

scan_protocol: The exposed phosphorimager screens were scanned at 100 mm resolution using a STORM 445 PhosphorImager (Molecular Dynamics).

data_processing: The  signal intensities were measured by Image-Quant (version 3.0) software (Molecular Dynamics). Background values were measured in the surrounding region of the four corner grids containing E. coli genomic DNA, as a positive control, and empty spots. To avoid extreme intensity ratio for genes close to or below the detection limit, signal intensity values corresponding to a signal-to-background (S/B) ratio < 2.0 were scaled up to a value corresponding to the normalised background means.

organism: Escherichia coli K-12

source_name: Escherichia coli K12 growing in exponential growth phase

label_protocol: 33P-labelled probes were prepared using E. coli gene-specific primers (Sigma-Genosys) following the protocol provided by the manufacturer, except that the reaction mixture contained 40 mCi of [a-33P]dCTP (1,000 to 3,000 Ci mmol-1;Amersham Pharmacia), and 200 U of Superscript II (Promega) in 30 ml volume. Unincorporated-radiolabelled nucleotides were removed by applying the reaction mixture to a Sephadex G-25 gel filtration spin column.

growth_protocol: E.coli cells were grown aerobically at 37 °C in M9 minimal medium containing: 20 mg l-1 uracil, 1 mg l-1 thiamine, 0.4 % L-arabinose as carbon source, and supplemented with 40 mg l-1 casein acid hydrolysate.

extract_protocol: Total RNA was purified from cells grown in M9 arabinose medium using the RNeasy Mini-Kit from QIAGEN by following the manufacturer’s instructions.

treatment_protocol: Exponentially growing E. coli K-12 (MG1655) cultures (OD600 = 0.6) was treated with an IAA solution to a final concentration of 0.5 mM. After two hours (OD600 = 1.2) different cell batches were aliquoted, frozen in liquid nitrogen for 5 min and stored at –80 °C for use in experiments.

tag: Genotype

value: wild type strain MG1655

tag: Age

value: 5 days old liquid colture, 4-times subcultivated


title: set2_array2

description: set2∆ vs. wild type

tag: set2, log phase, YPAD, 30C


title: biological rep1 sample a IAA


title: biological rep3 sample a IAA


title: biological rep1 sample b IAA


title: biological rep2 sample a IAA


title: biological rep2 sample b IAA


title: set2_array4

description: set2∆ vs. wild type


title: biological rep3 sample b

treatment_protocol: After two hours (OD600 = 1.2) different cell batches were aliquoted, frozen in liquid nitrogen for 5 min and stored at –80 °C for use in experiments.


title: biological rep1 sample b


title: biological rep2 sample b


title: biological rep3 sample a


title: Agilent_MRP1/MC_5

city: Boston

first: Winston

middle: Patrick

last: Kuo

state: MA

address: 188 Longwood Avenue

department: Genetics

institute: Harvard Medical School

description: MRP1/MC technical replicate 5

hyb_protocol: Hybridization of the Agilent oligonucleotide arrays for this study was carried out according to the Agilent Oligonucleotide Microarray Hybridization Protocol. For 2X cRNA target preparation, 0.75ug of cy3 and 0.75ug of cy5 labeled cRNA were combined with 50ul of 10X Control Targets and nuclease free H2O was added to bring the total volume of the target to 250ul. Prior to hybridizations, the 2X Target Solutions were fragmented by adding 10ul of 25X Fragmentation buffer and heating the reactions in the dark in a heat block at 60°C for 30 minutes. After the incubation, 250ul of 2X Hybridization Buffer were added to the reactions to stop the fragmentation process. The reagents for hybridization are included in the Agilent In Situ Hybridization Kit (Part No. 5184-3568). The arrays were hybridized with 500ul of hybridization solution in hybridization chambers in the hybridization oven on a rotating rack at 60°C for 17 hours.

scan_protocol: The arrays were washed the following morning in Wash 1 and Wash 2 solutions according to the Agilent protocol. They were scanned using the Agilent scanner at the default scan settings.

data_processing: LOWESS normalization

source_name: Adult mouse retina

label_protocol: We used the Shimadzu UV-1601 Spectrophotometer to quantify the labeled cRNA products. The spectrophotometer was baselined with 100ul of TE Buffer pH 8.0 and each sample was diluted 1:20 with TE Buffer pH8.0 to obtain readings at A260 and A280 for calculating the cRNA yield.

tag: The adult mouse retina samples were obtained from a pool of C57/B6 mice (n = 350), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA). All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.

source_name: Post-natal day 1 mouse cortex

tag: The mouse cortex samples were obtained from P1 C57/B6 mice (n = 19), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA).The mouse cortex was used as a reference sample. Universal mRNA reference was still being developed when the study started, so it was not utilized. All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.


title: Agilent_MRP1/MC_4

description: MRP1/MC technical replicate 4


title: Epe1_wt

status: Public on Jun 09 2006

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells, Epe1 ChIP(chromatin immunoprecipitation)-on-chip

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 7.5

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

organism: Schizosaccharomyces pombe

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

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

growth_protocol: asynchronous growing fission yeast cells at 30 C and cross-linked at 18C with paraformaldehyde for 30 minutes

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

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde/dimethyl adipimidate

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

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

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformaldehyde at 18C for 30 minutes

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Epe1-3xFLAG chromatin with anti-FLAG M2 mouse monoclonal antibody.


title: Agilent_MRP1/MC_1

description: MRP1/MC technical replicate 1


title: Agilent_MRP1/MC_2

description: MRP1/MC technical replicate 2


title: biological rep1 sample a


title: 8weeks v 20weeks, LSL04Ascan1.gpr

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
8 Weeks v 20 weeks comparison on cDNA microarrays with replication
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

data_processing: Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.

organism: Gossypium hirsutum

source_name: 8 weeks

tag: 8 weeks, Biological Repl

value: 1, Technical repl:1

source_name: 20 weeks

tag: 20 weeks, Biological Repl


title: 8weeks v 20weeks, LSL05Bscan1.gpr

description:
8 Weeks v 20 weeks comparison on cDNA microarrays with replication
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

value: 2, Technical repl:2


title: 8weeks v 14weeks, LSL03Bscan1.gpr

description:
8 Weeks v 14 weeks comparison on cDNA microarrays with replication
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true

source_name: 14 weeks

tag: 14 weeks, Biological Repl

value: 1, Technical repl:2


title: 8weeks v 10weeks, LSL02Ascan1.gpr

description:
8 Weeks v 10 weeks comparison on cDNA microarrays with replication
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

source_name: 10 weeks

tag: 10 weeks, Biological Repl


title: biological rep2 sample a


title: 8weeks v 20weeks, LSL04Bscan2.gpr

description:
8 Weeks v 20 weeks comparison on cDNA microarrays with replication
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: 8weeks v 20weeks, LSL05Ascan1.gpr

description:
8 Weeks v 20 weeks comparison on cDNA microarrays with replication
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false

value: 2, Technical repl:1


title: 8weeks v 14weeks, LSL03Ascan1.gpr

description:
8 Weeks v 14 weeks comparison on cDNA microarrays with replication
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: 8weeks v 22weeks, LSL06Bscan1.gpr

description:
8 Weeks v 2 weeks comparison on cDNA microarrays with replication
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true

source_name: 22 Weeks

tag: 22 Weeks, Biological Repl

source_name: 8 Weeks

tag: 8 Weeks, Biological Repl


title: Agilent_MRP1/MC_3

description: MRP1/MC technical replicate 3


title: 8weeks v 10weeks, LSL02Bscan1.gpr

description:
8 Weeks v 10 weeks comparison on cDNA microarrays with replication
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: 8weeks v 22weeks, LSL07Bscan1.gpr

description:
8 Weeks v 2 weeks comparison on cDNA microarrays with replication
Biological Replicate: 3, Technical Replicate: 2, Dye Swapped: true

value: 3, Technical repl:2


title: 8weeks v 22weeks, LSL06Ascan1.gpr

description:
8 Weeks v 2 weeks comparison on cDNA microarrays with replication
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: 8weeks v 22weeks, LSL07Ascan1.gpr

description:
8 Weeks v 2 weeks comparison on cDNA microarrays with replication
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false

value: 3, Technical repl:1


title: Amersham-MC-S2-1

description: MC technical replicate 1 (site 2)

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

data_processing: Signal intensities across microarrays were normalized using the quantile normalization (www.bioconductor.org).

label: Biotin

label_protocol: CodeLink Expression Assay protocol


title: Amersham-MC-S2-5

description: MC technical replicate 5 (site 2)


title: 8weeks v 22weeks, LSL01Bscan1.gpr

description:
8 Weeks v 2 weeks comparison on cDNA microarrays with replication
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true


title: Amersham-MRP1-S2-2

description: MRP1 technical replicate 2 (site 2)


title: Amersham-MC-S2-3

description: MC technical replicate 3 (site 2)


title: Amersham-MC-S2-2

description: MC technical replicate 2 (site 2)


title: Amersham-MRP1-S2-3

description: MRP1 technical replicate 3 (site 2)


title: Amersham-MC-3

description: MC technical replicate 3


title: Amersham-MC-S2-4

description: MC technical replicate 4 (site 2)


title: Amersham-MRP1-S2-4

description: MRP1 technical replicate 4 (site 2)


title: Amersham-MC-4

description: MC technical replicate 4


title: Amersham-MC-2

description: MC technical replicate 2


title: Amersham-MC-5

description: MC technical replicate 5


title: Amersham-MRP1-3

description: MRP1 technical replicate 3


title: Amersham-MRP1-S2-1

description: MRP1 technical replicate 1 (site 2)


title: Amersham-MRP1-5

description: MRP1 technical replicate 5


title: Amersham-MRP1-2

description: MRP1 technical replicate 2


title: Amersham-MRP1-4

description: MRP1 technical replicate 4


title: Amersham-MRP1-1

description: MRP1 technical replicate 1

scan_protocol: CodeLink Expression Assay protocol CodeLink Expression Analysis


title: Amersham-MRP1-S2-5

description: MRP1 technical replicate 5 (site 2)


title: Amersham-MC-1

description: MC technical replicate 1


title: MGH_MRP1/MC_5

description: MRP1/MC technical replicate 5

hyb_protocol: 1.  Initial Setup 1. Make sure all floppy disks are removed from machine, for they will prevent program from booting up. 2. Turn on hybridization station by switch on back right side of machine. 3. Place all manifold extension tubes (1-10) in appropriate containers. Tube 1 goes into wash 1, tube 2 in wash 2, etc. Tubes 9 and 10 are in waste 1 and 2, respectively. Make sure that wash buffers and tubes correspond with correct location in hybridization method design. 2. Preparing Sample 1. Pool Cy3 and Cy5 labeled cDNA samples. 2. Add 12 µL competitive DNA mix. 3. Add water to a final volume of 62 µL. 4. Heat samples 3 min at 95°C. Heat 2X Hybridization Buffer for 5 min at 95°C 5. Add 62 µL (1x vol) of 2X hybridization buffer to pooled template and pipette gently to mix. 6. Spin prepared samples for 5 min at 16,000 g. 7. Keep samples at 42°C until ready to load into hybridization chambers. 3. Loading Slides 1. Before loading slides into hybridization cassettes, they must be numbered with their corresponding order in print run with the diamond pen in the upper left corner of the back of the slide. 2. Boil slides in distilled H2O for 10 minutes and dry one at a time with compressed air. 3. Clean hybridization cassette pieces with ethanol. Do NOT spray ethanol into holes in cassette top. 4. Dry cassette pieces completely with Kimwipe. If the holes contain liquid, dry them as best possible using tip of Kimwipe. 5. Fit two clean o-rings into slots on cassette top. 6. Place slides face up on cassette back. For all print runs before 9/4/02, place "MOTOROLA" at top of cassette (away from you). For all print runs on 9/4/02 and after, place "MOTOROLA" at bottom of cassette. 7. Slowly place top of cassette on bottom and slides so that slot of the top fits over the projection of the bottom. Once the top of the cassette touches the slides, do not shift either cassette piece. Once the two pieces are together, keep constant pressure on the cassette to prevent slides from moving because shifting may cause slide breakage. 8. Continuing to keep pressure on the cassette, load it into the desired module platform on the hybridization station. Slide central hole at top edge of cassette onto post at top of platform. Settle cassette onto platform block and lower cassette holder onto cassette while maintaining pressure on cassette. 9. Tighten screw at bottom of holder until it is as tight as possible without forcing the screw ("finger tight"). 10. Place one port plug in each of the small ports at the bottom of the upward cassette face. 11. Repeat steps 3.3-3.10 for all cassettes needed in hybridization.  Note: If using an uneven number of slides, load a blank slide into unoccupied slide position. All cassettes must contain two slides before they are loaded onto the station. 4. Initiating Hybridization 1. Make sure all port plugs are in and all manifold tubes are in the proper wash solutions. 2. On computer screen of hybridization station, press "Start a Run." 3. The Load a Method screen will appear. Make sure that disk with methods is inserted in disk drive. Then select "Floppy Disk." 4. Select desired method from resulting list by touching it. A small box will appear by selected method. When correct method is selected, press "Load." 5. Select appropriate slide locations on screen corresponding to loaded slide positions. Arrows on this screen will indicate recommended positions based on maintaining evenly spread use of all modules. If desired, steps 4.2-4.5 can be performed before slide cassettes are loaded, and the recommended positions can thus be used. If this tool is not used, make sure that use of modules is rotated evenly. Also, if one cassette contains a blank slide, due to uneven numbers of slides in the experiment, this blank slide position does NOT need to be selected for the run. This saves time and wash solution. 6. Press "Start." 7. After ensuring that all equipment is ready to begin the run, press "Continue." 5. Loading Sample 1. After o-rings are conditioned by machine, the computer will prompt for loading of samples. 2. Draw up all of prepared sample (124 µL) using standard, non-barrier 10µL-200µL pipette tips. Make sure that there are no bubbles in the tip. 3. Press "Probe" for first slide in indicated module. 4. Remove port plug from first slide chamber in indicated module. Fit pipette tip into port so that a seal is formed, and then slowly load sample into chamber. If possible, direct flow of sample so that the bubble at the top will enter into tube at the top of the chamber. 5. Withdraw tip and replace immediately with port plug. 6. Press "Finished" for that chamber. Repeat steps 5.2-5.5 for second chamber in cassette. 7. Press the large "Finished" at the bottom of the computer screen. 8. Repeat steps 5.2-5.7 for all cassettes on the hybridization station, waiting for each until prompted. 9. After all samples are loaded, the hybridization station will carry out the hybridization steps for the indicated amount of time. 6. Removing Slides 1. When the hybridization reaches the first wash cycle, the station will wash one cassette at a time while holding the others in hybridization buffer at the final hybridization temperature. Thus, the cassettes will be finished one at a time. 2. When a module completes the wash cycle, that module will be denoted as "Finished" on the computer screen. 3. Immediately and carefully remove cassette by first removing port plugs and then unscrewing the cassette holder. Lift cassette off the module platform. At this point it is ok to separate the cassette pieces as long as the slides are not moved. 4. Slowly and carefully remove slides from the top cassette piece, being sure not to touch the front of the slide. 5. Place each slide directly into a 50 mL conical tube filled with 0.06X SSC. 6. Agitate slides in tubes using forceps, then transfer to new tubes filled with 0.06X SSC. 7. Agitate in tube again, and then transfer each to a third tube of 0.06X SSC. 8. Prepare a 50 mL conical tube with a Kimwipe packed into the bottom. Remove slides from 0.06X SSC, blot bottom of slides on a paper towel or Kimwipe, and then place into prepared centrifuge tubes, leaving tubes uncapped. 9. Immediately centrifuge slides for 3 minutes at 1000 rpm to dry. 10. Repeat steps 6.3-6.9 for all cassettes as they finish. 11. After slides have been dried by centrifugation, they should be scanned within the next 24 hours. 7. Cleaning Post-hybridization 1. Make sure o-rings are seated properly in cassette tops. 2. Place blank slides in all cassettes used for hybridization. 3. Put cassette pieces together as before, and replace onto hybridization station in modules used for hybridization. 4. Replace port plugs in ports at the bottom of the upward cassette face. 5. Move all manifold tubes used for wash solutions to a container of distilled or deionized water. 6. On computer screen, select "Machine Maintenance." 7. Choose "Valve." This will result in a screen listing all of the valves on the hybridization station. Pressing a valve name on the screen will open the valve on the station and show a check mark by the name on the screen. Each opening should produce an audible click. Pressing the valve name again closes the valve and removes the check mark. 8. Check each valve by opening and closing it once. A failure to produce a click upon opening indicates a potentially faulty valve. If a second check again fails to produce a click, this valve may need to be replaced. 9. When all valves have been checked, press "Close." 10. Select "Machine Cleaning Cycle." 11. Select on the screen those chambers corresponding with the cassettes loaded on the hybridization station. Press "Continue." 12. Make sure manifold tubes are in water, and then press "Continue." 13. After the hybridization station has finished this cleaning cycle, remove all chambers from the module platforms as before. This should be done as soon as possible after cleaning finishes. 14. Remove slides from chambers. 15. Remove o-rings from cassettes and place these and port plugs in a "used" container. 16. Blow 100% EtOH through holes in cassette top to clean out chamber tubes. 17. Rinse both cassette pieces in EtOH and dry with Kimwipe. 18. Wash blank slides with Alconox. Rinse first with dI water and then with EtOH. Dry with Kimwipe. 19. Turn off hybridization station. 8. General Maintenance 1. Empty waste containers when or before they reach 3/4 full. Unscrew cap, leaving all tubes in place, and dispose contents in appropriate containers. Waste container for wash buffers can be emptied in the sink. 2. Wash and refill distilled water container once a week, or when half empty during times of little station usage. 3. O-rings and port plugs must be cleaned after every use. To do this, boil in distilled water for 10 minutes and remove to dry. 4. Replace wash buffers on station when needed and record date of replacement. If a wash buffer becomes cloudy or starts showing crystalline precipitation, heat until clear and crystals dissolve. Refilter buffer.

scan_protocol: Axon GenePix 3.0


title: MGH_MRP1/MC_4

description: MRP1/MC technical replicate 4

hyb_protocol: 1.  Initial Setup 1. Make sure all floppy disks are removed from machine, for they will prevent program from booting up. 2. Turn on hybridization station by switch on back right side of machine. 3. Place all manifold extension tubes (1-10) in appropriate containers. Tube 1 goes into wash 1, tube 2 in wash 2, etc. Tubes 9 and 10 are in waste 1 and 2, respectively. Make sure that wash buffers and tubes correspond with correct location in hybridization method design. 2. Preparing Sample 1. Pool Cy3 and Cy5 labeled cDNA samples. 2. Add 12 µL competitive DNA mix. 3. Add water to a final volume of 62 µL. 4. Heat samples 3 min at 95°C. Heat 2X Hybridization Buffer for 5 min at 95°C 5. Add 62 µL (1x vol) of 2X hybridization buffer to pooled template and pipette gently to mix. 6. Spin prepared samples for 5 min at 16,000 g. 7. Keep samples at 42°C until ready to load into hybridization chambers. 3. Loading Slides 1. Before loading slides into hybridization cassettes, they must be numbered with their corresponding order in print run with the diamond pen in the upper left corner of the back of the slide. 2. Boil slides in distilled H2O for 10 minutes and dry one at a time with compressed air. 3. Clean hybridization cassette pieces with ethanol. Do NOT spray ethanol into holes in cassette top. 4. Dry cassette pieces completely with Kimwipe. If the holes contain liquid, dry them as best possible using tip of Kimwipe. 5. Fit two clean o-rings into slots on cassette top. 6. Place slides face up on cassette back. For all print runs before 9/4/02, place "MOTOROLA" at top of cassette (away from you). For all print runs on 9/4/02 and after, place "MOTOROLA" at bottom of cassette. 7. Slowly place top of cassette on bottom and slides so that slot of the top fits over the projection of the bottom. Once the top of the cassette touches the slides, do not shift either cassette piece. Once the two pieces are together, keep constant pressure on the cassette to prevent slides from moving because shifting may cause slide breakage. 8. Continuing to keep pressure on the cassette, load it into the desired module platform on the hybridization station. Slide central hole at top edge of cassette onto post at top of platform. Settle cassette onto platform block and lower cassette holder onto cassette while maintaining pressure on cassette. 9. Tighten screw at bottom of holder until it is as tight as possible without forcing the screw ("finger tight").  10. Place one port plug in each of the small ports at the bottom of the upward cassette face. 11. Repeat steps 3.3-3.10 for all cassettes needed in hybridization.  Note: If using an uneven number of slides, load a blank slide into unoccupied slide position. All cassettes must contain two slides before they are loaded onto the station. 4. Initiating Hybridization 1. Make sure all port plugs are in and all manifold tubes are in the proper wash solutions. 2. On computer screen of hybridization station, press "Start a Run." 3. The Load a Method screen will appear. Make sure that disk with methods is inserted in disk drive. Then select "Floppy Disk." 4. Select desired method from resulting list by touching it. A small box will appear by selected method. When correct method is selected, press "Load." 5. Select appropriate slide locations on screen corresponding to loaded slide positions. Arrows on this screen will indicate recommended positions based on maintaining evenly spread use of all modules. If desired, steps 4.2-4.5 can be performed before slide cassettes are loaded, and the recommended positions can thus be used. If this tool is not used, make sure that use of modules is rotated evenly. Also, if one cassette contains a blank slide, due to uneven numbers of slides in the experiment, this blank slide position does NOT need to be selected for the run. This saves time and wash solution. 6. Press "Start." 7. After ensuring that all equipment is ready to begin the run, press "Continue." 5. Loading Sample 1. After o-rings are conditioned by machine, the computer will prompt for loading of samples. 2. Draw up all of prepared sample (124 µL) using standard, non-barrier 10µL-200µL pipette tips. Make sure that there are no bubbles in the tip. 3. Press "Probe" for first slide in indicated module. 4. Remove port plug from first slide chamber in indicated module. Fit pipette tip into port so that a seal is formed, and then slowly load sample into chamber. If possible, direct flow of sample so that the bubble at the top will enter into tube at the top of the chamber. 5. Withdraw tip and replace immediately with port plug. 6. Press "Finished" for that chamber. Repeat steps 5.2-5.5 for second chamber in cassette. 7. Press the large "Finished" at the bottom of the computer screen. 8. Repeat steps 5.2-5.7 for all cassettes on the hybridization station, waiting for each until prompted. 9. After all samples are loaded, the hybridization station will carry out the hybridization steps for the indicated amount of time. 6. Removing Slides 1. When the hybridization reaches the first wash cycle, the station will wash one cassette at a time while holding the others in hybridization buffer at the final hybridization temperature. Thus, the cassettes will be finished one at a time. 2. When a module completes the wash cycle, that module will be denoted as "Finished" on the computer screen. 3. Immediately and carefully remove cassette by first removing port plugs and then unscrewing the cassette holder. Lift cassette off the module platform. At this point it is ok to separate the cassette pieces as long as the slides are not moved. 4. Slowly and carefully remove slides from the top cassette piece, being sure not to touch the front of the slide. 5. Place each slide directly into a 50 mL conical tube filled with 0.06X SSC. 6. Agitate slides in tubes using forceps, then transfer to new tubes filled with 0.06X SSC. 7. Agitate in tube again, and then transfer each to a third tube of 0.06X SSC. 8. Prepare a 50 mL conical tube with a Kimwipe packed into the bottom. Remove slides from 0.06X SSC, blot bottom of slides on a paper towel or Kimwipe, and then place into prepared centrifuge tubes, leaving tubes uncapped. 9. Immediately centrifuge slides for 3 minutes at 1000 rpm to dry. 10. Repeat steps 6.3-6.9 for all cassettes as they finish. 11. After slides have been dried by centrifugation, they should be scanned within the next 24 hours. 7. Cleaning Post-hybridization 1. Make sure o-rings are seated properly in cassette tops. 2. Place blank slides in all cassettes used for hybridization. 3. Put cassette pieces together as before, and replace onto hybridization station in modules used for hybridization. 4. Replace port plugs in ports at the bottom of the upward cassette face. 5. Move all manifold tubes used for wash solutions to a container of distilled or deionized water. 6. On computer screen, select "Machine Maintenance." 7. Choose "Valve." This will result in a screen listing all of the valves on the hybridization station. Pressing a valve name on the screen will open the valve on the station and show a check mark by the name on the screen. Each opening should produce an audible click. Pressing the valve name again closes the valve and removes the check mark. 8. Check each valve by opening and closing it once. A failure to produce a click upon opening indicates a potentially faulty valve. If a second check again fails to produce a click, this valve may need to be replaced. 9. When all valves have been checked, press "Close." 10. Select "Machine Cleaning Cycle." 11. Select on the screen those chambers corresponding with the cassettes loaded on the hybridization station. Press "Continue." 12. Make sure manifold tubes are in water, and then press "Continue." 13. After the hybridization station has finished this cleaning cycle, remove all chambers from the module platforms as before. This should be done as soon as possible after cleaning finishes. 14. Remove slides from chambers. 15. Remove o-rings from cassettes and place these and port plugs in a "used" container. 16. Blow 100% EtOH through holes in cassette top to clean out chamber tubes. 17. Rinse both cassette pieces in EtOH and dry with Kimwipe. 18. Wash blank slides with Alconox. Rinse first with dI water and then with EtOH. Dry with Kimwipe. 19. Turn off hybridization station. 8. General Maintenance 1. Empty waste containers when or before they reach 3/4 full. Unscrew cap, leaving all tubes in place, and dispose contents in appropriate containers. Waste container for wash buffers can be emptied in the sink. 2. Wash and refill distilled water container once a week, or when half empty during times of little station usage. 3. O-rings and port plugs must be cleaned after every use. To do this, boil in distilled water for 10 minutes and remove to dry. 4. Replace wash buffers on station when needed and record date of replacement. If a wash buffer becomes cloudy or starts showing crystalline precipitation, heat until clear and crystals dissolve. Refilter buffer.


title: MGH_MRP1/MC_1

description: MRP1/MC technical replicate 1


title: cDNA_MRP1_MC_4

description: MRP1/MC Technical replicate 4

hyb_protocol: cDNA microarrays were constructed at the BioDiscovery Center at Biogen Idec (Cambridge, MA). RNA samples were reverse transcribed and cDNAs were amplified for 16-20 cycles using the SMART system (Clontech). Previous studies have shown that expression data generated by this approach are comparable to results obtained by other results (ref). To generate probes for array hybridization, 10ug cDNA was labeled by incorporation of either Cy5 or Cy3-dCTP (Amersham-Pharmacia) during oligo-dT-primed or random hexamer-primed primer extension in the presence of Klenow DNA polymerase (Roche). Arrays were pre-hybridized with poly-adenylic acid (Sigma) and mouse Cot-1 DNA (Life Technologies) before overnight hybridization with paired Cy3 and Cy5-labeled probes in the presence of poly-adenylic acid and mouse Cot-1 DNA. Pairs of labeled probes were hybridized at 42 overnight. Arrays were washed at room temperature in 0.2 × SSC, 0.1%SDS for 2 min, followed by 2 washes in 0.2 × SSC for 2 min each.


title: MGH_MRP1/MC_3

description: MRP1/MC technical replicate 3


title: MGH_MRP1/MC_2

description: MRP1/MC technical replicate 2


title: cDNA_MRP1_MC_5

description: MRP1/MC Technical replicate 5


title: cDNA_MRP1_MC_2

description: MRP1/MC Technical replicate 2


title: 8h1

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

description: cDNAs were generated from 5ug of total RNA per sample by reverse transcription (RT) for two hours at 42oC using the 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA) and Superscript II (Invitrogen, Carlsbad, CA). For each microarray chip two consecutive hybridizations were performed with cDNAs and the fluorescent probes following the manufacture’s specifications. Briefly, in the first hybridization reaction the solution containing the mixture of cDNAs obtained from control and treated cells was loaded onto the CAG Human 19K array and incubated overnight at 55oC in a hybridization chamber (Genemachines, San Carlos, CA). The human 19K array (www.cag.icph.org/microarray_facility.htm) contains 60-mer oligonucleotides (Compugen, San Jose, CA) representing 18,861 human genes spotted onto poly-l-lysine coated glass microscope slides. In the second hybridization reaction Cy3 (green) and Cy5 (red) fluorescent probes were used to label the cDNAs from control and PGJ2-treated cells, respectively. The second hybridization was carried out for 3 hours at 65oC in the hybridization chambers. The arrays were scanned using an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) with laser intensities adjusted to bring the brightest spot just below saturation and the data extracted with the Axon GenePix Pro software.

scan_protocol: Scanned with a GenePix 4000B scanner, and gridded with GenePix Pro 4.0 software

data_processing: The data was filtered so that only spots with a signal intensity of two-fold above background in at least one channel, flagged good (0) and with a diameter above 70 were given a relative expression value: PGJ2-treated vs. control.  The data was then normalized globally so the median log ratios for each experiment were equal to zero.

growth_protocol: Human neuroblastoma SK-N-SH cells were maintained at 37oC and 5% CO2 in minimal essential media (MEM) with Eagle's salts containing 2mM L-glutamine, 1mM sodium pyruvate, 0.4% MEM vitamins, 0.4% MEM nonessential amino acids, 100 units/ml penicillin, 100μg/ml streptomycin and 5% normal fetal bovine serum. These cells are derived from peripheral tissue.

extract_protocol: Quiagen RNeasy Mini kit (Valencia, CA)

treatment_protocol: Cells were treated at 37oC for 8 hours with 20uM of PGJ2 (Cayman Chemical Co., Ann Arbor, Michigan) in DMSO. The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.

tag: Human neuroblastoma SK-N-SH cells treated with 20uM PGJ2 for 8 hours

source_name: untreated SK-N-SH cells

treatment_protocol: Cells were treated at 37oC for 8 hours with vehicle (0.5% DMSO).  The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.

tag: Human neuroblastoma SK-N-SH cells untreated


title: cDNA_MRP1_MC_3

description: MRP1/MC Technical replicate 3


title: 4h2

hyb_protocol: 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA)

treatment_protocol: Cells were treated at 37oC for 4 hours with 20uM of PGJ2 (Cayman Chemical Co., Ann Arbor, Michigan) in DMSO. The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.

tag: Human neuroblastoma SK-N-SH cells treated with 20uM PGJ2 for 4 hours

treatment_protocol: Cells were treated at 37oC for 4 hours with vehicle (0.5% DMSO).  The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.


title: reptest2_rep_4_67_PMTexport

city: Charleston

first: MarineGenomics

last: Project

state: SC

address: 331 Fort Johnson Rd

hyb_protocol: 33% formamide, 2.6X SSPE, 2.4% SDS, 1.7X Denhardts

data_processing: Ch1 Intensities read directly from the Microarray scanner.

organism: Penaeus vannamei

tag: biosecure recirculating artificial seawater, adult, muscle, KONA


title: reptest2_rep_5_67_PMTexport


title: MWG_MRP1_MC_4

description: MPR1/MC technical replicate 4

hyb_protocol: Briefly, RNA was prepared using the RNeasy Midi kit according to the manufacturer's instructions (Qiagen). First-strand complementary DNA synthesis from 5ug total RNA was done at 42oC for 1h, followed by second-strand cDNA synthesis at 16oC for 2h. RNase I digestion was followed by proteinase K treatment. The resulting double-stranded cDNA was purified using the RNeasy Mini Kit according to the manufacturer's instructions (Qiagen). Fluorescence-labeled RNA was generated by carrying out an in vitro transcription reaction (40 mM Tris-HCl, pH 7.5, 7 mM MgCl2, 10 mM NaCl, 2 mM spermidine, 5 mM ditihothreitol, 7.5 mM each of ATP, CTP and GTP, 5 mM UTP, 20 units RNase inhibitor and 1,000 units T7 polymerase) at 37oC for 4h. This reaction was done in the presence of fluorescence-labeled nucleotide (Amersham Pharmacia Biotech) to generate Cy3- or Cy5-labelled RNA. The labeled RNA was subsequently purified (Qiagen RNeasy Mini kit) and chemically fragmented at 94oC for 15 min in fragmentation buffer (20 mM Tris-acetate, pH8.1, 50 mM potassium acetate, 15 mM magnesium acetate). The fragmented, Cy3- or Cy5-labelled complementary RNA (20ug) was lyophilized, resolubilized in hybridization buffer (50% formamide, 50mM sodium phosphate, pH8.0, 6X SSC, 5X Denhardt's Solution, 0.5% SDS), and hybridized to oligonucleotide mouse 11K microarrays (Macrogen) at 42oC for 24h. T7 RNA polymerase was purchased from Ambion: primers, RNase inhibitors and all other enzymes were purchased from Roche Molecular Biochemicals.


title: MWG_MRP1_MC_3

description: MPR1/MC technical replicate 3


title: MWG_MRP1_MC_2

description: MPR1/MC technical replicate 2

hyb_protocol: Briefly, RNA was prepared using the RNeasy Midi kit according to the manufacturer's instructions (Qiagen). First-strand complementary DNA synthesis from 5ug total RNA was done at 42oC for 1h, followed by second-strand cDNA synthesis at 16oC for 2h. RNase I digestion was followed by proteinase K treatment. The resulting double-stranded cDNA was purified using the RNeasy Mini Kit according to the manufacturer's instructions (Qiagen). Fluorescence-labeled RNA was generated by carrying out an in vitro transcription reaction (40 mM Tris-HCl, pH 7.5, 7 mM MgCl2, 10 mM NaCl, 2 mM spermidine, 5 mM ditihothreitol, 7.5 mM each of ATP, CTP and GTP, 5 mM UTP, 20 units RNase inhibitor and 1,000 units T7 polymerase) at 37oC for 4h. This reaction was done in the presence of fluorescence-labeled nucleotide (Amersham Pharmacia Biotech) to generate Cy3- or Cy5-labelled RNA. The labeled RNA was subsequently purified (Qiagen RNeasy Mini kit) and chemically fragmented at 94oC for 15 min in fragmentation buffer (20 mM Tris-acetate, pH8.1, 50 mM potassium acetate, 15 mM magnesium acetate). The fragmented, Cy3- or Cy5-labelled complementary RNA (20ug) was lyophilized, resolubilized in hybridization buffer (50% formamide, 50mM sodium phosphate, pH8.0, 6X SSC, 5X Denhardt's Solution, 0.5% SDS), and hybridized to oligonucleotide mouse 11K microarrays at 42oC for 24h. T7 RNA polymerase was purchased from Ambion: primers, RNase inhibitors and all other enzymes were purchased from Roche Molecular Biochemicals.

tag: The mouse cortex samples were obtained from P1 C57/B6 mice (n = 19), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA).The mouse cortex was used as a reference sample. Universal mRNA reference was still being developed when the study started, so it was not utilized. All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation


title: 8h2

source_name: SK-N-SH cells treated with 20uM PGJ2 for 8 hours

label_protocol: 3DNA SubmicroTM Oligo Expression Array Detection Kit (Genisphere, Hatfield, PA)


title: 16h2

treatment_protocol: Cells were treated at 37oC for 16 hours with 20uM of PGJ2 (Cayman Chemical Co., Ann Arbor, Michigan) in DMSO. The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.

tag: Human neuroblastoma SK-N-SH cells treated with 20uM PGJ2 for 16 hours

treatment_protocol: Cells were treated at 37oC for 16 hours with vehicle (0.5% DMSO).  The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.


title: cDNA_MRP1_MC_1

description: MRP1/MC Technical replicate 1


title: reptest2_rep_1_67_PMTexport

tag: muscle, biosecure recirculating artificial seawater, adult, KONA


title: 16h1

source_name: SK-N-SH cells treated with 20uM PGJ2 for 16 hours


title: reptest2_rep_2_67_PMTexport


title: reptest2_rep_3_67_PMTexport


title: 4h1

source_name: SK-N-SH cells treated with 20uM PGJ2 for 4 hours

extract_protocol: Qiagen RNeasy Mini kit (Valencia, CA)

tag: untreated SK-N-SH cells


title: MWG_MRP1_MC_5

description: MPR1/MC technical replicate 5

tag: The adult mouse retina samples were obtained from a pool of C57/B6 mice (n = 350), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA). All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.


title: BA82_40_WS1_75_export

treatment_protocol: treated

tag: hepatopancreas, biosecure recirculating artificial seawater, adult, hepatopancreas, KONA


title: BA82_40_WS7_75_export


title: MWG_MRP1_MC_1

description: MPR1/MC technical replicate 1

tag: The mouse cortex samples were obtained from P1 C57/B6 mice (n = 19), which were purchased from Charles River Laboratories (Charles River Laboratories, Inc., Willmington, MA).The mouse cortex was used as a reference sample. Universal mRNA reference was still being developed when the study started, so it was not utilized. All samples were placed in TRIzol reagent (Invitrogen, Carlsbad, CA) and stored at -80ºC before RNA extraction. Total RNA was extracted with TRIzol reagent according to the manufacturer's instructions. For a quality control measure of the samples, total RNA was ran through a 1% agarose gel and using the 2100 Agilent BioAnalyzer System (Agilent Technologies, Palo Alto, CA) to check for possible contamination and degradation.


title: BA82_40_WS8_75_export


title: 24h1

treatment_protocol: Cells were treated at 37oC for 24h with 20uM of PGJ2 (Cayman Chemical Co., Ann Arbor, Michigan) in DMSO. The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.

tag: Human neuroblastoma SK-N-SH cells treated with 20uM PGJ2 for 24 hours

treatment_protocol: Cells were treated at 37oC for 24 hours with vehicle (0.5% DMSO). The drug was added drop wise directly into serum-containing medium with a gentle swirl of the culture plate. At the end of the indicated incubation times, the cultures were washed twice with PBS and the cells were harvested. Cell washes removed unattached cells, hence subsequent assays were performed on adherent cells only.


title: BA82_40_WS6_75_export


title: BA82_40_WS3_75_export


title: BA82_40_U8_75_export

treatment_protocol: untreated control


title: BA82_40_WS2_75_export


title: BA82_40_WS4_75_export


title: BA82_40_U7_75_export


title: BA82_40_WS5_75_export


title: Operon_Compugen_MRP1_MC_4

description: Operon-Compugen MRP1/MC technical replicate 4

hyb_protocol: The Agilent Fluorescent Linear Amplification Kit (Agilent Technologies) was used for the preparation of fluorescently labeled target samples. Briefly, both first and second strand cDNAs were synthesized by incubating 3 µg of total RNA with T7 promoter primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3') using SuperScript II (Invitrogen, Carlsbad, CA). Fluorescently labeled complementary RNA (cRNA) was amplified by adding 4 ?l of cyanine 3-dCTP (6 mM) or 4 µl of cyanine 5-dCTP (4 mM) (PerkinElmer, Inc., Boston, MA) to the 20 ul of cDNA template and mixing with 56 µl of reaction mixture containing, in the following order: 20.1 µl of nuclease-free water, 20 µl of 4X transcription buffer, 6 µl of 0.1 M DTT, 8 µl of NTP mix, 0.5 µl of RNaseOUT, 0.6 µl of inorganic pyrophosphatase, and 0.8 µl of T7 RNA polymerase. After incubating at 40°C for 3 hr, cRNAs were cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA). Five ug of each labeled cRNA target were used for hybridization on the oligonucleotide-arrayed slide after being fragmented by fragmentation buffer (Agilent Technologies). After overnight hybridization at 65°C, the oligonucleotide arrays were washed and scanned by the Agilent Scanner G2505A (Agilent Technologies).

scan_protocol: Agilent Scanner G2505A


title: Operon_Compugen_MRP1_MC_1

description: Operon-Compugen MRP1/MC technical replicate 1


title: BA82_40_U4_75_export


title: Operon_Compugen_MRP1_MC_3

description: Operon-Compugen MRP1/MC technical replicate 3


title: BA82_40_U2_75_export


title: Operon_Compugen_MRP1_MC_5

description: Operon-Compugen MRP1/MC technical replicate 5


title: BA82_40_U1_75_export


title: Operon_Compugen_MRP1_MC_2

description: Operon-Compugen MRP1/MC technical replicate 2


title: diff_tiss_muscle_1_67_PMT


title: diff_tiss_muscle_2_67_PMT


title: diff_tiss_hemo_3_67_PMT

tag: biosecure recirculating artificial seawater, adult, hemolymph, KONA


title: BA82_40_U5_75_export


title: diff_tiss_muscle_3_67_PMT