title: MO control zebrafish embryo 21hpf-2

status: Public on Oct 25 2007

type: RNA

city: Yokohama

first: Tadashi

last: Wada

state: Kanagawa

address: 4259 Nagatsuta-cho, Midori-ku

department: Bioscience and Biotechnology

country: Japan

institute: Tokyo Institute of Technology

description: A High-Resolution Transcriptome Map of the Control Morpholino Oligo Injected Zebrafish Embryo

hyb_protocol: Aliquots of cRNA (20 µg) of each sample were fragmented, hybridized to the Genechip Zebrafish Genome Array, and processed according to the manufacturer’s instructions.

scan_protocol: Fluidics Station 400 is used to wash and stain the probe arrays, and controlled by Affymetrix® Microarray Suite. The scanner is also controlled by Affymetrix® Microarray Suite. All the procedure was according to the manufacturer’s instructions.

data_processing: Scanned data were analyzed with the GC-RMA algorithm (REF) to estimate gene expression levels.

label: biotin

molecule: total RNA

organism: Danio rerio

source_name: Control MO injected Danio rerio embryo, 21 hours post-fertilization

label_protocol: In vitro synthesis of cDNA and target cRNA preparations were carried out with 5 µg of total RNA according to a One-Cycle Target Labeling protocol (Affymetrix). Label reaction was performed using the GeneChip IVT Labeling Kit.

growth_protocol: Embryos were maintained in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4) at 28.5 centigrade for 21 hours post-fertilization.

extract_protocol: Total RNA was extracted from embryos using Sepasol-RNA I super (Nacalai tesque), followed by further purification using an RNeasy mini protocol for RNA cleanup (Qiagen).

treatment_protocol: Embryos were injected at the one-cell or two-cell stages with approximately 2.5 pmol of commercially available standard control morpholino oligo with a 3’ carboxyfluorescein (Gene Tools, LLC).

tag: strain

value: TL;

tag: age

value: 21 hours post-fertilization;


title: 0.2 mM As(III) stressed YAP1 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 2

status: Public on Oct 18 2007

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

data_processing:
See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417
VALUEs represent log2 (test/control) ratios.

organism: Saccharomyces cerevisiae

source_name: Stressed YAP1 mutant at 0.2 mM As(III) after 1 h

source_name: Stressed wild-type at 0.2 mM As(III) after 1 h


title: 0.2 mM As(III) stressed MET4 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 6

description: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417

source_name: Stressed MET4 mutant at 0.2 mM As(III) after 1 h

tag: Stressed wild-type at 0.2 mM As(III) after 1 h


title: MO control zebrafish embryo 21hpf-1


title: Spt5 knockdown zebrafish embryo 21hpf-2

description: A High-Resolution Transcriptome Map of the Spt5 knockdown Zebrafish Embryo

source_name: Spt5-targeted MO injected Danio rerio embryo, 21 hours post-fertilization

treatment_protocol: Embryos were injected at the one-cell or two-cell stages with approximately 2.5 pmol of Spt5-targeted morpholino oligo (5’-GTTTCTCTACAGTCTGTCGCTCCTG-3’) with a 3’ carboxyfluorescein (Gene Tools, LLC).

tag: The transcription factor Spt5 is knocked down.


title: 0.2 mM As(III) stressed MET4 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 5

hyb_protocol: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417

tag: Stressed MET4 mutant at 0.2 mM As(III) after 1 h


title: 0.2 mM As(III) stressed MET4 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 3

scan_protocol: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417


title: Channel catfish Liver control 3d replicate1

status: Public on Oct 23 2007

city: Auburn

first: Eric

last: Peatman

state: AL

address: 203 Swingle Hall

department: Fisheries and Allied Aquacultures

country: USA

institute: Auburn University

description: During the challenge, symptomatic treatment fish and control fish were collected and confirmed to be infected with E. ictaluri and pathogen-free, respectively, at the Fish Disease Diagnostic Laboratory, Auburn University.

hyb_protocol: The microarrays were prehybridized with a solution of 2x MES hybridization buffer (100 mM 2-morpholinoethanesulfonic acid, 1.0 M Na+, 20 mM EDTA, 0.01% Tween 20), 50 µg of herring sperm DNA, and 250 µg of acetylated bovine serum albumin (BSA) at 45°C for 15 min followed by hybridization with 10 µg of denatured and fragmented cRNA per microarray, 3.5 µl of CPK6 control oligo, 35 µg of herring sperm DNA, 175 µg of acetylated BSA, and 2X MES buffer at 45°C for 16–20 h with constant rotation. After hybridization, the microarrays were washed twice with nonstringent buffer (6x SSPE, 0.01% Tween 20) at room temperature followed by two stringent washes (100 mM MES salt and free acid solution, 0.1 M Na+, 0.01% Tween 20) at 45°C for 15 min each. After a final one minute rinse with nonstringent buffer, the arrays were placed into a 1x stain solution (100 mM MES, 1 M Na+, 0.05% Tween 20, 50 mg/ml BSA, and 1 µg/µl Cy3-streptavidin) at room temperature for 15 min, agitating every few minutes. The microarrays were removed from the stain solution and placed in fresh nonstringent wash buffer for one minute.  They were then placed into Nimblegen’s proprietary final wash buffer for 30 s, and then immediately dried under a stream of argon gas.

scan_protocol: The microarrays were scanned with an Axon GenePix 4000B scanner (Molecular Devices Corp., Union City, CA) at 5 µM resolution.

data_processing: After extraction of data from raw images using the NimbleScan software (Nimblegen, Inc.), gene calls were generated using the Robust Multichip Average (RMA) algorithm (Irizarry et al. 2003) which takes into account only the PM oligos.  RMA takes a background adjustment on the raw intensity scale, carries out quantile normalization (Bolstad et al. 2003), takes the log2 of the normalized background adjusted PM values, and then uses a linear model to estimate expression values on the log scale.

label: Biotin

organism: Ictalurus punctatus

source_name: Channel catfish Liver 3d control

label_protocol: Total RNA was converted to double-stranded cDNA using a SuperScript II cDNA synthesis kit (Invitrogen) and an oligo-dT primer containing the T7 RNA polymerase promoter.   In vitro transcription (IVT) was carried out to produce biotin-labeled cRNA from cDNA using the MEGAscript T7 kit (Ambion).  Briefly, 3 μL double-stranded cDNA was incubated with 7.5 mM ATP and GTP, 5.6 mM UTP and CTP, 1.875 mM bio-11-CTP and bio-16 UTP (Enzo) and 1x T7 enzyme mix in 1x reaction buffer for 16 h at 37˚C.  The cRNA was then purified using an RNeasy mini kit (Qiagen, ).   Before hybridization, cRNA was fragmented to an average size of 50 to 200 bp by incubation in a buffer of 100 mM potassium acetate, 30 mM magnesium acetate, and 40mM tris-acetate for 35 min at 94˚C.  Fragmentation was measured using a Bioanalyzer 1000 (Agilent Technologies).

growth_protocol:
Fish were moved to challenge aquaria at least two weeks prior to
challenge and 30 channel catfish and 30 blue catfish were added to
each aquaria. Fish were fed a commercial diet to satiation prior to
challenge and all fish were fed lightly during the course of the
challenge.  Continuous water flowthrough and supplemental aeration
were provided.  At 3 d fish were killed by anesthesia overdose and
their livers dissected.  The livers of 25 fish were pooled for each
replicate, flash frozen in liquid nitrogen, and stored at -80°C until
RNA extraction.

extract_protocol: The livers for each replicate were ground in liquid nitrogen by mortar and pestle to a fine powder and thoroughly mixed.  Approximately 30 mg of tissue powder was homogenized in Buffer RLT Plus by passing the lysate several times through a 20-gauge needle fitted to a syringe according to the protocol of the RNeasy Plus Mini Kit (Qiagen).  Following the manufacturer’s instructions, approximately 35 μg of total RNA was obtained from each extraction.   RNA quality and concentration was checked by spectrophotometer analysis and gel electrophoresis.  All extracted samples had an A260/280 ratio of greater than 1.8, and were diluted to 1 μg/μL.

treatment_protocol:
Fish were mock challenged for 2 h by adding sterile BHI media in 30 L
aquaria with water turned off.  Water flowthrough was resumed after
challenge.

tag: Livers from ~15 cm long Kansas Random strain channel catfish


title: 0.2 mM As(III) stressed MET4 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 2

label_protocol: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417


title: 0.2 mM As(III) stressed MET4 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 1

growth_protocol: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417


title: Channel catfish Liver ESC-infection 3d replicate3

source_name: Channel catfish Liver 3d post ESC infection

treatment_protocol: Edwardsiella ictaluri bacteria were cultured from a single isolate (MS-S97-773) and used in a small test infection of several channel catfish.  Bacteria were re-isolated from a single symptomatic fish and biochemically confirmed to be E. ictaluri, before being inoculated into brain heart infusion (BHI) medium and incubated in a shaker incubator at 28 °C overnight. The bacterial concentration was determined using colony forming unit (CFU) per ml by plating 10 μl of 10-fold serial dilutions onto BHI agar plates. At the time of challenge, the bacterial culture was added to the aquaria to a concentration of 4X108 CFU/ml.  Water was turned off in the aquaria for 2 h of immersion exposure, and then continuous water flow-through resumed for the duration of the challenge.

tag: Liver from ~15 cm long Kansas Random strain channel catfish


title: 1.0 mM As(III) stressed YAP1 mutant vs 1.0 mM As(III) stressed wild-type after 1 hour replicate 1

source_name: Stressed wild-type at 1 mM As(III) after 1 h

extract_protocol: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417

source_name: Stressed YAP1 mutant at 1 mM As(III) after 1 h


title: Untreated zebrafish embryo 21hpf-1

description: A High-Resolution Transcriptome Map of the Zebrafish Embryo

source_name: Danio rerio embryo, 21 hours post-fertilization

growth_protocol: maintained in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4) at 28.5 centigrade for 21 hours post-fertilization

treatment_protocol: non-treatment

value: TL

value: 21 hours post-fertilization


title: Channel catfish Liver ESC-infection 3d replicate2


title: Spt5 knockdown zebrafish embryo 21hpf-1


title: 1.0 mM As(III) stressed YAP1 mutant vs 1.0 mM As(III) stressed wild-type after 1 hour replicate 2

treatment_protocol: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 16885417

tag: Stressed wild-type at 1 mM As(III) after 1 h

tag: Stressed YAP1 mutant at 1 mM As(III) after 1 h


title: Untreated zebrafish embryo 5hpf-1

source_name: Danio rerio embryo, 5 hours post-fertilization

growth_protocol: maintained in E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4) at 28.5 centigrade 5 hours post-fertilization

value: 5 hours post-fertilization


title: Channel catfish Liver ESC-infection 3d replicate1


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 18 hours replicate 3

source_name: Wild-type untreated

label_protocol: See 'The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast' Mol Biol Cell. 2006 Oct;17(10):4400-4410, PMID: 1688541

tag: Wild-type untreated

source_name: Stressed wild-type at 1 mM As(III) after 18 h


title: Channel catfish Liver control 3d replicate3


title: 0.2 mM As(III) stressed MET4 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 4


title: Channel catfish Liver control 3d replicate2


title: 0.2 mM As(III) stressed YAP1 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 3

tag: Stressed YAP1 mutant at 0.2 mM As(III) after 1 h


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 18 hours replicate 2

tag: Stressed wild-type at 1 mM As(III) after 18 h


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 15 min replicate 3

source_name: Stressed wild-type at 1.0 mM As(III) after 15 min


title: 0.2 mM As(III) stressed YAP1 mutant vs 0.2 mM As(III) stressed wild-type after 1 hour replicate 1


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 15 min replicate 2

tag: Stressed wild-type at 1.0 mM As(III) after 15 min


title: 0.2 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 2


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 30 min replicate 1

source_name: Stressed wild-type at 1.0 mM As(III) after 30 min


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 15 min replicate 1


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 30 min replicate 2

tag: Stressed wild-type at 1.0 mM As(III) after 30 min


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 18 hours replicate 1


title: 0.2 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 3


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 3


title: 0.2 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 1


title: 1.0 mM As(III) stressed YAP1 mutant vs 1.0 mM As(III) stressed wild-type after 1 hour replicate 3


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 4


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 2


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 1


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 6


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 30 min replicate 3


title: Cochlea DBA2J 7 weeks 3

status: Public on Oct 16 2007

city: Madison

first: Shinichi

last: Someya

state: WI

address: 425 Henry Mall Dr

department: Medical Genetics

institute: University of Wisconsin-Madison

hyb_protocol: Hybridization (Affymetrix Hybridization oven 640), washing, and staining (Affymetrix Fluidics station 400) were accomplished according to the manufacture’s instructions.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000. Image analysis was performed using the Affymetrix software.

data_processing: Scaled to 1500 (Affymetrix software)

organism: Mus musculus

source_name: RNA

label_protocol: cDNA synthesis from total RNA (Invitrogen), cRNA amplification and labeling (Enzo BioArray IVT kit) were accomplished according to the manufacture’s instructions (Affymetrix).

growth_protocol: All mice were raised under 12:12 dark/light conditions, and housed in the the University of Tokyo-approved Animal Care Facility, and were provided a nonpurified diet and acidified water ad libitum.

extract_protocol: Total RNA was isolated from cochlea tissues using the TriZol reagent (Invitrogen) according to the manufacture’s instructions.

treatment_protocol: To identify genes associated with AHL, each 7-week-old sample (n = 3) was compared to each 36-week-old sample (n = 3), generating a total of nine pairwise comparisons.

tag: Strain

value: DBA/2J mice

tag: Gender

value: male

tag: Age

tag: Tissue

value: cochlea


title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour replicate 5


title: N1_biorep1

status: Public on Oct 17 2007

city: Stillwater

first: Patricia

middle: J

last: Ayoubi

state: OK

address: 246 NRC

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

description: Pre-processing of data obtained using GenePix Pro 4.0 was accomplished using R-project statistical environment (http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) and the LIMMA package (Smyth, 2005).   normalization using global Lowess intensity-dependent normalization.  Normalized ratio values obtained for each probe were averaged across four biological replicates and three or more technical replicates. Significant differences were defined as P-value ≤ 0.05 and displaying an expression fold change greater than 1.7-fold (log (base 2) ratio ≥ 0.8).

hyb_protocol: Labeled total RNA (1 µg) was was hybridized to the microarrays using the supplied formamide-based hybridization buffer and 24x60 mm LifterSlips slides (Erie Scientific, Portmouth, NH, USA) according to the manufacturer’s (Genisphere) instructions. Post-hybridization washes were done according to the manufacturer’s (Genisphere) instructions.

scan_protocol: Hybridization signals were measured using a ScanArray Express (PerkinElmer, Boston, MA, USA) and the images where processed using GenePix Pro version 4.0 (Axon, Union City, CA, USA).

organism: Cervus elaphus hispanicus

source_name: uninfected animal N1

label_protocol: Partially degraded total RNA (1 µg) was labeled using the 3DNA Array900MPX kit with Alexa Fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random primers, oligo-dT primers, and Superscript II Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s (Genisphere) instructions for partially degraded RNA samples.

extract_protocol: RNeasy (Quiagen, Valencia, CA, USA) according to manufacturer’s instructions.

tag: Mesenteric lymph node RNA of uninfected animal from Iberian red deer stags that were hunter-harvested, tissue retrieved 2-6 hrs after animal hunting.

source_name: M. bovis infected animals N8 and N9 (pooled)

label_protocol: Partially degraded total RNA (1 µg) pooled from two infected animals was labeled using the 3DNA Array900MPX kit with Alexa Fluor dyes (Genisphere, Hatfield, PA, USA), the supplied random primers, oligo-dT primers, and Superscript II Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s (Genisphere) instructions for partially degraded RNA samples.

tag: Mesenteric lymph node RNA pooled from two animals infected with Mycobacterium bovis from Iberian red deer stags that were hunter-harvested, tissue retrieved 2-6 hrs after animal hunting.


title: Cochlea DBA2J 36 weeks 3


title: N13_biorep3

data_processing: normalization using global Lowess intensity-dependent normalization

source_name: uninfected animal N13


title: Cochlea DBA2J 36 weeks 2


title: Cochlea DBA2J 7 weeks 2


title: HMEC/hTERT/eIF4E/Total RNA

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

description: Comparison of polysomal and total RNA between HMEC/hTERT and HMEC/hTERT/eIF4E cells.

data_processing: GCRMA using custom HS133P_HS_REFSEQ_6

organism: Homo sapiens

label_protocol: Affymetrix single round labelling

growth_protocol: Serum starvation for 24h, see manuscript

extract_protocol: Trizol

tag: Cell line

tag: Breast

tag: hTERT immortalized

tag: eIF4E expression


title: Cochlea DBA2J 7 weeks 1


title: N12+N14_biorep2

source_name: uninfected animals N12 and N14 (pooled)


title: HMEC/hTERT/Total RNA 2

source_name: HMEC/hTERT


title: HMEC/hTERT/Total RNA


title: Cochlea DBA2J 36 weeks 1


title: HMEC/hTERT/eIF4E/polysomal RNA 3

type: other

molecule: other

extract_protocol: Polysomal preparation, see manuscript

tag: eIF4E expresssion


title: HMEC/hTERT/eIF4E/Polysomal RNA 2


title: HMEC/hTERT/polysomal RNA 1


title: control Group, Line 2, Replicate 1, Male

status: Public on Oct 01 2007

city: Raleigh

first: Katherine

middle: W

last: Jordan

state: NC

address: Campus Box 7614

department: Genetics

institute: North Carolina State University

description: Gene expression data from adult male flies of the control group of an artificial selection experiment for locomotion.

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 500.

organism: Drosophila melanogaster

source_name: Male Drosophila adults, age 3-7 days

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

tag: artificially selected, wild-derived lines


title: Control Group, Line 1, Replicate 1, Male


title: Control Group, Line 1, Replicate 2, male

source_name: male Drosophila adults, age 3-7 days


title: HMEC/hTERT/polysomal RNA 2


title: low Group, Line 1, Replicate 2, male

description: Gene expression data from adult male flies of the low group of an artificial selection experiment for locomotion.


title: control Group, Line 2, Replicate 2, male


title: Low Group, Line 2, Replicate 2, male


title: low Group, Line 2, Replicate 2, Female

description: Gene expression data from adult female flies of the low group of an artificial selection experiment for locomotion.

source_name: Female Drosophila adults, age 3-7 days


title: Low Group, Line 2, Replicate 1, Male


title: high Group, Line 2, Replicate 2, male

description: Gene expression data from adult male flies of the high group of an artificial selection experiment for locomotion.


title: Low Group, Line 1, Replicate 2, female

source_name: female Drosophila adults, age 3-7 days


title: High Group, Line 2, Replicate 1, Male


title: Control Group, Line 2, Replicate 1, Female

description: Gene expression data from adult female flies of the control group of an artificial selection experiment for locomotion.


title: Low Group, Line 1, Replicate 1, Female


title: low Group, Line 2, Replicate 1, female


title: control Group, Line 1, Replicate 1, Female


title: HMEC/hTERT/eIF4E/Total RNA 2


title: Control Group, Line 2, Replicate 2, female


title: HMEC/hTERT/eIF4E/polysomal RNA 1

tag: eIF4E overexpressopm


title: control Group, Line 1, Replicate 2, female


title: low Group, Line 1, Replicate 1, Male


title: high Group, Line 2, Replicate 2, female

description: Gene expression data from adult female flies of the high group of an artificial selection experiment for locomotion.


title: High Group, Line 1, Replicate 2, male


title: high Group, Line 2, Replicate 1, Female


title: E. coli K1 BW25113 delta trpE LB glu 24 hr biofilm cells

status: Public on May 01 2007

city: College Station

first: Jintae

last: Lee

state: TX

department: Chemical Engineering

institute: Texas A&M University

description: RNA extracted from biofilm cell of E. coli K12 BW25113 delta trpE after 24 hours of growth in LB glu with glass wool

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli antisense array at 45°C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix).  Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: channel 1

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process.  The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel.  The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).


title: HighGroup, Line 1, Replicate 1, Male


title: E. coli K1 BW25113 wild type LB 24 hr biofilm cells

description: RNA extracted from biofilm cell of E. coli K12 BW25113 wild type after 24 hours of growth in LB with glass wool


title: E. coli K1 BW25113 wild type LB glu 24 hr biofilm cells

description: RNA extracted from biofilm cell of E. coli K12 BW25113 wild type after 24 hours of growth in LB glu with glass wool


title: HighGroup, Line 1, Replicate 2, Female

description: Gene expression data from adult female flies of the high group of an artificial selection experiment for locomotion


title: 16Mm.148

status: Public on Jul 06 2007

city: Indianapolis

first: Hosein

last: Kouros-Mehr

state: IN

address: 533 Merrill St.

department: Oncology

institute: Eli Lilly

description: Total RNA from GATA-3 infected tumor compared to empty vector infected tumor

data_processing: Lowess print-tip normalization (Acuity 4.0)

source_name: GATA-3 infected tumor

tag: Tumor outgrowth retrovirally over-expressing GATA-3

source_name: Control infected tumor

tag: Tumor outgrowth retrovirally over-expressing empty vector


title: HP1021 Regulon 2

status: Public on Apr 01 2007

city: Wuerzburg

first: Dagmar

last: Beier

address: Am Hubland

country: Germany

institute: Universität Wuerzburg

description:
scanning software: ScanArray express
sofware version 3.0

data_processing: value: log2 transformed ratio of normalized channel 2 median to channel 1 median; normalization method: LOWESS algorithm

organism: Helicobacter pylori

source_name: 20 µg of total RNA, WT

tag: strain

source_name: 20 µg of total RNA, 1021Delta


title: 15Mm.175

description: Total RNA from Adenoma (5 week outgrowth) compared to Late Caricinoma (18 week outgrowth) in MMTV-PyMT hyperplasia transplant model

source_name: Adenoma

tag: Adenoma (5 week outgrowth)

source_name: Late carcinoma

tag: Late carcinoma (18 week outgrowth)


title: 24h BQ hepatotoxicity R2

status: Public on Feb 27 2007

city: Lucknow

first: Sanjeev

last: Noel

state: Uttar Pradesh

address: M G Marg

department: Toxicology

country: India

institute: Central Drug Research Institute

description: Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent(Sigma).25 ug of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit(Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were resuspended in Cyscribe Hyb buffer(Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml yeast tRNA.The samples were heated at 95 degree C for 3 minutes and immediately chilled to avoid secondary structures. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C. The arrays were washed with 1xSSC + 0.2% SDS and 0.1xSSC + 0.2SDS at 42 degree C and 0.1xSSC at room temperature for 15 minutes each. The arrays were dried immediately at 1000rpm for 2 minutes.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with Molecular dynamics III scanner supported with ImageQuant v5.0 at default settings.

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background corrected raw data was LOWESS normalized using Avadis v4. Normalized data was analysed to find differentially expressed genes.

source_name: Mice Liver

label_protocol: CyScribe First Strand cDNA Labelling Kit Protocol

growth_protocol: Mice were kept under control temparature and humidity conditions. Food and water was allowed ad libitum.

extract_protocol: TRI Reagent Protocol

treatment_protocol: Vehicle Treatment

tag: Mus musculus, Male, 10-12 weeks, Liver

label_protocol: CyScribe First Strand cDNA Labeling Kit Protocol

treatment_protocol: Mice were sacrificed 24h after drug administration


title: 16Mm.147


title: E. coli K1 BW25113 delta yceP LB glu 24 hr biofilm cells with 0.06% DMF

description: RNA extracted from biofilm cells of E. coli K12 BW25113 delta yceP grown in LB glu for 24 hr with 0.06% DMF with glass wool

hyb_protocol: he biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli antisense array at 45°C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.


title: 24h PQ hepatotoxicity 22.4K F


title: High Group, Line 1, Replicate 1, Female


title: 24h BQ hepatotoxicity F2


title: 2nd BW25113 yceP 600 uM indole LB glu 24hr biofilm cells

description: RNA extracted from biofilm cells of E. coli K12 yceP mutants after24 hours of growth in LB glu with 600 uM indole with glass wool.

source_name: Channel 1


title: E. coli K1 BW25113 delta tnaA LB 24 hr biofilm cells

description: RNA extracted from biofilm cell of E. coli K12 BW25113 delta tnaA after 24 hours of growth in LB with glass wool


title: 24h PQ hepatotoxicity F

description: Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent(Sigma).25 ug of total RNA was converted into labelled cDNA using CyScribe first strand cDNA labelling kit(Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background corrected raw data was LOWESS normalized using Avadis V4. Normalized data was analysed to find differentially expressed genes.

treatment_protocol: Vehicle Treated

treatment_protocol: Mice were sacrificed 12h after drug administration


title: 15Mm.131


title: HP1021 Regulon 3


title: 15Mm.95


title: 12h PQ hepatotoxicity R


title: E. coli K1 BW25113 delta yceP LB glu 24 hr biofilm cells with 600 microM indole

description: RNA extracted from biofilm cell of E. coli K12 BW25113 delta yceP after 24 hours of growth in LB glu with glass wool with 600 microM indole


title: HP1021 Regulon 1


title: HP1021 Regulon 4


title: 12h PQ hepatotoxicity F


title: 24h PQ hepatotoxicity 22.4K R


title: 6h PQ hepatotoxicity F

treatment_protocol: Mice were sacrificed 6h after drug administration


title: 24h BQ hepatotoxicity R1


title: 12h BQ hepatotoxicity F1


title: Liver LIV1

status: Public on Feb 01 2007

city: Chicago

first: Omar

last: De la Cruz

state: IL

address: 5734 S University Ave

department: Department of Statistics

institute: University of Chicago

description: Characterizing the expression of human olfactory receptor genes

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: RMA summary expression value, no background adjustment, quantile normalization, adjustment based on housekeeping genes

label: Standard Affymetrix label

source_name: Liver

label_protocol: Standard Affymetrix Protocol

extract_protocol: Trizol extraction

tag: From autopsy


title: Lung 1a

label: Affymetrix standard labeling

source_name: Lung


title: 6h BQ hepatotoxicity R2


title: 6h BQ hepatotoxicity R1


title: 15Mm.127


title: Heart 1b

source_name: Heart


title: Kidney 1b

source_name: Kidney


title: 6h BQ hepatotoxicity F1

tag: Mus musculus, Mice, 10-12 weeks, Liver


title: 12h BQ hepatotoxicity F2


title: Kidney 1a


title: 24h BQ hepatotoxicity F1


title: 6h BQ hepatotoxicity F2

tag: Mus musculus


title: Liver 1


title: 12h BQ hepatotoxicity R1


title: Olfactory epithelium OE4a

label: Standard Affymetrix Protocol

source_name: Olfactory epithelium

tag: Human olfactory epithelium, from autopsy


title: Olfactory epithelium OE2

source_name: Human olfactory epithelium

tag: Second sample of human olfactory epithelium, from autopsy


title: Olfactory epithelium OE5a


title: Heart 1a


title: Olfactory epithelium OE5b

data_processing: RMA expression values, no background corrections, quantile normalization, adjusted using housekeeping genes


title: 12h BQ hepatotoxicity R2


title: Lung 1b


title: 6h PQ hepatotoxicity R


title: Testis 1b

source_name: Testis


title: Olfactory epithelium OE


title: Testis 1a


title: Olfactory epithelium OE4b


title: UCB-MSC_UCB2_rep1B

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

data_processing: RMA method implemented in BioConductor

source_name: human umbilical cord blood-derived mesenchymal stem cell population 2, replicate 1

label_protocol: Microarray target was prepared following the Affymetrix protocol.  In brief, cDNA was synthesized from total RNA using the SuperScript II double-stranded cDNA synthesis kit (Invitrogen), followed by in vitro transcription, where labeled cRNA was generated (Enzo).

extract_protocol: Total RNA was isolated from cells in culture using the RNAeasy Mini Kit (Qiagen), according to manufacturer's protocol

tag: Tissue

value: umbilical cord blood-derived mesenchymal stem/stromal cell


title: BM-MSC_rep2B

source_name: human bone marrow-derived mesenchymal stem cell

value: bone marrow-derived mesenchymal stem cell (Cambrex Lot#4F0312)


title: UCB-MSC_UCB1_rep3B

source_name: human umbilical cord blood-derived mesenchymal stem cell population 1, replicate 3


title: UCB-MSC_UCB2_rep2B

source_name: human umbilical cord blood-derived mesenchymal stem cell population 2, replicate 2


title: UCB-MSC_UCB1_rep2A

hyb_protocol: Hybridization was carried out according to Affymetrix protocol.

data_processing: RMA method normalization implemented in BioConductor

source_name: human umbilical cord blood-derived mesenchymal stem cell population 1, replicate 2


title: UCB-MSC_UCB2_rep3B

source_name: human umbilical cord blood-derived mesenchymal stem cell population 2, replicate 3


title: BM-MSC_rep1A


title: UCB-MSC_UCB2_rep1A


title: BM-MSC_rep3B

source_name: human bone marrow-derived mesenchymal stem cell replicate 3


title: UCB-MSC_UCB1_rep1B

source_name: human umbilical cord blood-derived mesenchymal stem cell population 1, replicate 1


title: BM-MSC_rep1B


title: UCB-MSC_UCB1_rep2B


title: BM-MSC_rep3A


title: Interference of PTS with PrfA in L.monocytogenes - Hpr 2

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

description: scanning software: ScanArray express software version: 3.0

hyb_protocol: Hybridization performed exactly as described in Marr et al., J Bacteriol. 2006 Jun;188(11):3887-901

scan_protocol: not provided

data_processing: VALUE: log2 transformed ratio of normalized medians (mutant/wild type); normalization method: LOWESS algorithm

label: Cyanine 3

organism: Listeria monocytogenes

source_name: Wild type L.monocytogenes EGDe

label_protocol: Labeling performed exactly as described in Marr et al., J Bacteriol. 2006 Jun;188(11):3887-901

growth_protocol: Overnight cultures of the respective strains - Wild type L.monocytogenes EGDe, ccpA mutant of L.monocytogenes EGDe and hpr K/P mutant in Brain heart infusion broth (BHI) were diluted and allowed to grow to a late log phase (OD 600 nm 1.0) in the same medium, and the cells were harvested.

extract_protocol: RNA was isolated using RNeasy kit from Qiagen according to the manufacturers protocol.

tag: Wild type L.monocytogenes EGDe grown in BHI to an OF 600 nm of 1.0

label: cyanine 5

source_name: Hpr KP mutant of L.monocytogenes EGDe

tag: Hpr KP mutant of L.monocytogenes EGDe grown in BHI to OD 600 nm 1.0


title: BM-MSC_rep2A


title: IMR32_WT_rep2

city: London

first: Sandeep

middle: K

last: Gill

state: Ontario

address: 100 Perth Drive

department: Molecular Medicine

country: Canada

institute: Robarts Research Institute

data_processing: RMA

label: Streptavidin Phycoerythrin (SAPE)

source_name: IMR32 human neuroblastoma cell line

tag: IMR32 human neuroblastoma cell line


title: Interference of PTS with PrfA in L.monocytogenes - Hpr KP 4

label: Cyanine 5

tag: Wild type L.monocytogenes EGDe grown in BHI to OD 600 nm 1.0


title: UCB-MSC_UCB2_rep2A


title: UCB-MSC_UCB2_rep3A


title: IMR32_82CHAT_rep3


title: UCB-MSC_UCB1_rep1A


title: UCB-MSC_UCB1_rep3A


title: Interference of PTS with PrfA of L.monocytogenes CcpA 5

source_name: Wild type L.monocytogenes EGDe grown in BHI to an OF 600 nm of 1.0

source_name: CcpA mutant of L.monocytogenes EGDe

tag: CcpA mutant of L.monocytogenes EGDe grown in BHI to OD 600 nm 1.0


title: Interference of PTS with PrfA of L.monocytogenes CcpA 6


title: IMR32_82CHAT_rep2


title: IMR32_WT_rep3


title: IMR32_82CHAT_rep1


title: IMR32_WT_rep1


title: Interference of PTS with PrfA in L.monocytogenes - Hpr KP 3


title: Interference of PTS with PrfA of L.monocytogenes Hpr KP 1


title: Interference of PTS with PrfA of L.monocytogenes CcpA1


title: HE140 CMglu 1

status: Public on Jan 01 2007

city: Marburg

first: Britta

last: Winterberg

address: Karl-von-Frisch-Str.

department: Orgnaismische Interaktionen

institute: Max-Planck-Institut für terrestrische Mikrobiologie

description: Experiment to measure the efects of Adr1 induction in U. maydis. Free Adr1 signals a high level of cAMP.

hyb_protocol: Affymetrix EukEG-WS2 on a GeneChip Fluidics Station 400

scan_protocol: Affymetrix GCS2500

label: biotin/ phycoerythrin

organism: Mycosarcoma maydis

source_name: Ustilago maydis

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, except a reaction temperature of 50°C for first strand cDNA synthesis.

growth_protocol: HE140 was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer´s instructions. RNA samples were further column purified (Qiagen RNeasy) and the quality checked using a Bioanalyser with a RNA6000 Nano LabChip Kit (Agilent).

tag: Strain HE140 is a derivative of FB1 carrying the adr1 gene under the control of the arabinose inducible crg1 promotor in single copy in the Cbx locus of U. maydis.


title: Interference of PTS with PrfA in L.monocytogenes - CcpA2


title: FB1 plusFe 1

description: Experiment to identify iron regulated genes in U. maydis.

growth_protocol: wt (FB1) was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose in the presence of 10 mM FeSO4.

tag: FB1 is a Ustilago maydis wildtype strain of a1b1 matingtype.


title: HE140 CMara 180min 3

growth_protocol: HE140 was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose. Subsequently, cells were shifted to CM medium containing 1 % (w/v) arabinose instead of glucose as a carbon source and incubated for 180 min.


title: IMR32_69CHAT_rep2

tag: IM32 human neuroblastoma cell line


title: HE140 CMara 75min 2

growth_protocol: HE140 was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose. Subsequently, cells were shifted to CM medium containing 1 % (w/v) arabinose instead of glucose as a carbon source and incubated for 75 min.


title: IMR32_69CHAT_rep1

source_name: human neuroblastoma IMR32 cell line


title: FB1 minusFe 1

growth_protocol: wt (FB1) was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose in the absence FeSO4.


title: FB1 plusFe 2


title: FB1 minusFe 2


title: FB1 CMara 75min 3

growth_protocol: wt (FB1) was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose. Subsequently, cells were shifted to CM medium containing 1 % (w/v) arabinose instead of glucose as a carbon source and incubated for 75 min.


title: BW12 plusFe 2

growth_protocol: BW12 was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose in the presence of 10 mM FeSO4.

tag: BW12 is a derivative of FB1 with a deletion of the urbs1 open reading frame.


title: FB1 CMglu 1

growth_protocol: wt (FB1) was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose.


title: BW12 plusFe 1


title: IMR32_69CHAT_rep3


title: Interference of PTS with PrfA of L.monocytogenes CcpA 4


title: FB1 CMara 180min 3

growth_protocol: wt (FB1) was grown to a OD600 of 0.5 at 28°C in CM medium (Holliday, 1974) containing 1 % (w/v) glucose. Subsequently, cells were shifted to CM medium containing 1 % (w/v) arabinose instead of glucose as a carbon source and incubated for 180 min.

tag: FB1 is a Ustilago maydis wildtype strain of a1b1 matingtype


title: HE140 CMglu 2


title: FB1 CMara 180min 2


title: Interference of PTS with PrfA of L.monocytogenes CcpA 3


title: HE140 CMara 75min 1


title: HE140 CMara 75min 3


title: HE140 CMara 180min 2


title: HE140 CMara 180min 1


title: FB1 CMara 75min 1


title: FB1 CMara 75min 2


title: Heart_DOCA_High_vs._Low_Salt_M17ka_859

first: Andrea

middle: A.

last: Domenighetti

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

description: In the present study, microarray slides were produced at the DNA Array Facility (DAF) in Lausanne – Switzerland - by 32-pin robotic printing (http://www.unil.ch/dafl). PCR amplified cDNA clones were arrayed at high density in 1.5 M betaine, 3xSSC on NexterionTM glass Slide AL (Schott Nexterion, Mainz, Germany). The specific clone set printed onto the slides was the NIA 15K mouse embryonic clone set (National Institute of Aging, NIH - USA- http://lgsun.grc.nia.nih.gov/cDNA/15k.html), to which an additional 1563 custom clone set was added (GAL file: GPL4371). For post-experimental normalization of data, each microarray slide also possessed a subset of control spots including spikes, ‘housekeeping’ genes, blocking controls and negative controls.

hyb_protocol: For each slide, a hybridization mixture was prepared (volume 30 ul) containing 0.6 ug/ul poly-A (Sigma), 0.6 ug/ul yeast tRNA (Sigma), 0.6 ug/ul mouse Cot1 DNA (Invitrogen) and two purified Cy5- and Cy3-labeled cDNA samples to be compared. After heating (98 Celsius), the entire hybridization mixture was pipetted on the microarray slide and a 60x25 mm cover-slip was placed over the marked array region. The hybridization mixture was allowed to move by capillary action across the surface of the array. The slide was then placed horizontally in hybridization chambers (Corning), sealed and placed at the bottom of a 64 Celsius water bath where they incubated overnight in the dark.

scan_protocol: Following incubation, the array slides were removed from chambers, rinsed in SSC 20x, SDS 10% and Triton 10% solutions of different concentration and spun dry in a plate centrifuge. The microarray slides were placed in slide mailers and kept in a dark, desiccated environment prior to scanning. Each slide was imaged by an Agilent Technologies laser scanner which acquired two gray-scaled 16-bit single image TIFF files corresponding to the Cy5 and Cy3 fluorescence emission channels (argon laser operating at ~650 nm and ~550 nm excitation wavelengths respectively). The gray-scaled images were ‘pseudo colored’ (red intensities for Cy5, green intensities for Cy3) and merged to give one single picture for dual color (red/green) differential microarray analysis. The GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, USA) extracted foreground and background intensities for individual spots on a microarray image, producing a matrix containing Cy5 (red) and Cy3 (green) intensities for each spot on the microarray.

data_processing: Raw data were normalized by print tip lowess normalization (Yang et al., Nucleic Acids Res. 2002,30(4):e15). Significantly changing genes (p≤ 0.05) were identified by t-test

source_name: Ventricles from DOCA-salt mouse, High-salt treatment

label_protocol: A total of 50 ug total RNA per dye labeling reaction was used for each ‘sample versus sample’ comparison, giving a total of 100 ug total RNA per array (2 labeling reactions per array). RNA was reverse transcribed (RT) into cDNA using oligo(dT) 21-mer (Invitrogen) to avoid transcription of non-messenger RNA populations. Several control spikes were added to the RT reactions, including SpotReport Alien and Arabidopsis Spikes (Stratagene). During each RT reaction, Cy3- or Cy5-labelled dCTP (Amersham) were incorporated into the cDNA population. After reverse transcription, the RNA template was hydrolyzed and each Cy-labeled cDNA was purified using the Qiagen’s MiniElute PCR Purification kit.

growth_protocol:
The DOCA/salt model was induced and grown as published in:
Wang Q, Hummler E, Nussberger J, Clement S, Gabbiani G, Brunner HR,
Burnier M. Blood pressure, cardiac, and renal responses to salt and
deoxycorticosterone acetate in mice: role of renin genes. J Am Soc
Nephrol. 2002;13:1509 –1516.

extract_protocol: Total RNA was purified from heart tissue by Trizol reagent (Invitrogen), according to manufacturer’s protocol. The first step involved homogenizing ventricular mouse tissue samples using a Polytron Homogenizer (Kinematica AG) in a buffer containing Trizol (1 ml/50 mg of cardiac tissue). Total RNA was precipitated in isopropanol, washed in 80% ethanol, re-suspended in sterile RNase-free water and allowed to dissolve overnight at 4 Celsius. Samples were subsequently analyzed by spectrophotometry using a Nanodrop ND-100 UV-Vis Spectrophotometer (Nanodrop Technologies), where measurements of 220-750 nm absorbance were recorded. From these measurements, concentration (A260 nm) and quality (A260/A280) of each RNA sample was estimated. As a further check of RNA quality and quantity, each RNA sample was electrophoresed using a microfluidic Bioanalyzer 2100 (Agilent Technologies). Results were visualized for expression of and integrity of 21S and 18S rRNA bands.

treatment_protocol:
LS + Nx + DOCA35 + 1%NaCl 5w
(LS= 0.5mg Na/g food; Nx= uninephrectomized; DOCA35= deoxycorticosterone acetate-treated; 1%NaCl 5w= 1%NaCl in drinking water for 5 weeks)

tag: Strain

value: wild-type backcross N5–6(129Ola/C57BL/6J), 1-renin

tag: Mouse ID

tag: Gender

tag: Age

value: 12-13 weeks

value: right and left ventricles and septum

tag: Body weight

tag: Heart weight

tag: Cardiac weight index

source_name: Ventricles from DOCA-salt mouse, Low-salt treatment

treatment_protocol:
LS + Nx + DOCA35 + tap
(LS= 0.5mg Na/g food; Nx= uninephrectomized; DOCA35= deoxycorticosterone acetate-treated; tap= normal drinking water)


title: FB1 CMara 180min 1


title: FB1 CMglu 2


title: Heart_DOCA_High_vs._Low_Salt_M17ka_862

tag: Tissue


title: Heart_DOCA_High_vs._Low_Salt_M17ka_861


title: Heart_DOCA_High_vs._Low_Salt_M17ka_860


title: Stomach, biological rep2

city: Menlo Park

first: Tyson

middle: A

last: Clark

state: CA

address: 1380 Willow Rd.

institute: Pacific Biosciences

description: Exon Level Gene Expression data from one of three biological replicates of normal adult stomach tissue

hyb_protocol: 20 ug of labeled ds cDNA was hybridized to the arrays for 16 hours at 50deg C in a hybridization solution containing 7% DMSO.  The same hybridization cocktail was hybridized to the 4 arrays in the set serially over 4 consecutive days.

scan_protocol: GeneChips were scanned using a GCS3000 scanner with 1.09um pixelation

data_processing: .CEL files were quantile normalized within tissues and median scaled across tissues using probesets from a set of housekeeping genes to a median value of 700.  Probeset values were summarized using SEA.

label: DLR-1a (biotin)

source_name: normal adult stomach tissue

label_protocol: ds cDNA was generated using the Affymetrix WT labeling reagents, cDNA was fragmented using DNase1 digestion, and end labeled with DLR-1a using terminal transferase

extract_protocol: unknown

value: Male

tag: RNA Conc (ug/ul)

tag: Lot #


title: Stomach, biological rep3


title: Testis, biological rep2

description: Exon Level Gene Expression data from one of three biological replicates of normal adult testis tissue

source_name: normal adult testis tissue


title: Ovary, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult ovary tissue

source_name: normal adult ovary tissue

value: Female


title: Kidney, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult kidney tissue

source_name: normal adult kidney tissue


title: Stomach, biological rep1


title: Liver, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult liver tissue

source_name: normal adult liver tissue


title: Testis, biological rep3


title: Spinal Cord, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult spinal cord tissue

source_name: normal adult spinal cord tissue


title: Spinal Cord, biological rep1


title: Heart, biological rep1

description: Exon Level Gene Expression data from one of three biological replicates of normal adult heart tissue

source_name: normal adult heart tissue


title: Skeletal Muscle, biological rep2

description: Exon Level Gene Expression data from one of three biological replicates of normal adult skeletal muscle tissue

source_name: normal adult skeletal muscle tissue


title: Brain-Temporal Lobe, biological rep2

description: Exon Level Gene Expression data from one of three biological replicates of normal adult temporal lobe tissue

source_name: normal adult temporal lobe tissue


title: Ovary, biological rep1


title: Kidney, biological rep2


title: Spinal Cord, biological rep2


title: Heart, biological rep2


title: Brain-Temporal Lobe, biological rep3


title: Kidney, biological rep1


title: Skeletal Muscle, biological rep3


title: Liver, biological rep2


title: Brain-Parietal Lobe, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult parietal lobe tissue

source_name: normal adult parietal lobe tissue


title: Ovary, biological rep2


title: Brain-Temporal Lobe, biological rep1


title: proband 3 Tcells, past exercise

status: Public on Dec 31 2006

city: Jena

first: Sandy

last: Mosig

address: Bachstrasse 18

department: Molecular Hemostaseology - Institute of Vascular Medicine

institute: University Hospital Jena

description: proband 3 Tcells, past exercise

hyb_protocol: 6.5 µg biotinylated RNA were hybridised for 16h at 45°C on geneChip human U133 A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics station 400.

scan_protocol: GeneChips were scanned with the Affymetrix Scanner 3000.

data_processing: The data were first analysed with Affymetrix GCOS 1.2 using default analysis settings.

source_name: human peripheral T-lymphocytes

label_protocol: biotinylated RNA was prepared from 3 µg total RNA according to the Affymetrix manual (2003)

extract_protocol: RNA was extracted from Trizol through addition of chloroform and phase separation using PLG tubes. Additionally RNA was cleaned up using the Rneasy Micro Kit with a Dnase step.

treatment_protocol: 8ml of whole blood were collected in BD Vacutainer CPT tubes. 400 µl of RosetteSep Tcell Enrichment cocktail were added immediately following the blood withdrawal. Tubes were inverted five times and incubated for 20 minutes at room temperature. Tubes were next centrifuged for 20 minutes at 1850g at room temperature. The cells were washed two times in icecold (4°C) PBS/ 2mM EDTA once in a volume of 50ml and the second time with a final volume of 5ml, spun down for 10 minutes at 500g at 4°C, the supernatant was removed by vacuum suction and the final pellet was lysed with Trizol.

tag: human peripheral T-lymphocytes


title: proband 3 Tcells, before exercise

description: proband 3 Tcells, before exercise


title: Brain-Parietal Lobe, biological rep2


title: Liver, biological rep1


title: Testis, biological rep1


title: proband 3 PBMC, past exercise

description: proband 3 PBMC, past exercise

source_name: human PBMC

treatment_protocol: 8ml of whole blood were collected in BD Vacutainer CPT tubes. Tubes were next centrifuged for 20 minutes at 1850g at room temperature. The cells were washed two times in icecold (4°C) PBS/ 2mM EDTA once in a volume of 50ml and the second time with a final volume of 5ml, spun down for 10 minutes at 500g at 4°C, the supernatant was removed by vacuum suction and the final pellet was lysed with Trizol.

tag: human PBMC


title: proband 2 Tcells, past exercise

description: proband 2 Tcells, past exercise


title: proband 2 PBMC, past exercise

description: proband 2 PBMC, past exercise


title: proband 2 PBMC, before exercise

description: proband 2 PBMC, before exercise


title: proband 2 Tcells, before exercise

description: proband 2 Tcells, before exercise


title: proband 1 PBMC, past exercise

description: proband 1 PBMC, past exercise


title: proband 1 PBMC, before exercise

description: proband 1 PBMC, before exercise


title: Brain-Parietal Lobe, biological rep1


title: Brain-Occipital Lobe, biological rep2

description: Exon Level Gene Expression data from one of three biological replicates of normal adult occipital lobe tissue

source_name: normal adult occipital lobe tissue


title: proband 1 Tcells, before exercise

description: proband 1 Tcells, before exercise


title: DBA/2J 1-22

status: Public on Dec 02 2006

city: Baltimore

first: Alexander

last: Balbir

state: MD

address: 615 N. Wolfe St.  Room E7610

department: Environmental Health Sciences

institute: Johns Hopkins Bloomberg School of Public Health

description: DBA/2J carotid body gene expression

hyb_protocol: Following fragmentation, 1 200 ul of hybridization cocktail containing 10 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

scan_protocol: Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

data_processing: Data extraction was processed by Affy GeneChip? Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets A/J x 3 sets DBA/2J comparison (1.5 fold cutoff, Mann-Whitney test < 0.05, 6 out of 9 comparisons)

source_name: DBA/2J Caroitd body

label_protocol: cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module,cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)-Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

growth_protocol: no growth protocol

treatment_protocol: no treatment

tag: DBA/2J mouse strain (Jackson Lab)  gender- male, age- 28 days, n = 19, # of tissue = 38 tissue

value: carotid body


title: Brain-Occipital Lobe, biological rep1


title: Brain-Cerebellum, biological rep1

description: Exon Level Gene Expression data from one of three biological replicates of normal adult cerebellum tissue

source_name: normal adult cerebellum tissue


title: DBA2/J 4-16

description: DBA/2J carotid body gene expression

label: ENZO BioArray HighYield RNA Transcript Labeling Kit

tag: DBA/2J mouse strain (Jackson Lab)  gender- male, age- 28 days, n = 18, # of tissue = 36 tissue


title: AJ 4-23

description: A/J carotid body gene expression

source_name: AJ 3 Caroitd body

tag: A/J mouse strain (Jackson Lab)  gender- male, age- 28 days, n = 19, # of tissue = 38 tissue


title: Brain-Occipital Lobe, biological rep3


title: Brain-Frontal Lobe, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult frontal lobe tissue

source_name: normal adult frontal lobe tissue


title: Brain-Frontal Lobe, biological rep2


title: proband 1 Tcells, past exercise

description: proband 1 Tcells, past exercise


title: AJ4-16

description: A/J carotid body gene expression

source_name: AJ 2 Caroitd body

tag: A/J mouse strain (Jackson Lab)  gender- male, age- 28 days, n = 21, # of tissue = 42 tissue


title: AJ 2-10

description: A/J carotid body gene expression

source_name: AJ 1 Caroitd body

tag: A/J mouse strain (Jackson Lab)  gender- male, age- 28 days, n = 20, # of tissue = 40 tissue


title: Caco2_OspF complementation infected_Rep2

status: Public on Nov 19 2006

city: Paris

first: Thierry

last: Pedron

address: 28 rue du Docteur Roux

department: Biologie cellulaire et Infection

country: France

institute: Pasteur Institute

description: RNA and labeled fragmentated cRNA qualities were checked with the Agilent BioAnalyseur

hyb_protocol: Following Affymetrix protocol: PE-streptavidin

scan_protocol: Using scanner « GCS 3000 » with the software GeneChip®Operating (GCOS) v1.1.1.

data_processing: RMA normalization was used

source_name: Caco-2 intestinal epithelial cell line

label_protocol: Following Affymetrix protocol, using 5 microgrammes of total RNA

extract_protocol: The RNA was prepared using Qiagen RNeasy Mini Kit

treatment_protocol: Semi confluent cells were growth on petri dish plate in culture medium

tag: Infection with a strain complementated for OspF expression


title: E8.5 mDom-/- embryo proper

status: Public on Nov 20 2006

city: Suita

first: Rikiro

last: Fukunaga

state: Osaka

address: 2-2 Yamadaoka

department: Grad School Frontier Biosciences

institute: Osaka University

description: The array image was analyzed using CodeLinkTM System Software (Amersham Biosciences).

hyb_protocol: CodeLink Expression Bioarray System protocol

scan_protocol: The arrays were scanned using an arrayWoRx Biochip Reader (Applied Precision).

data_processing: KURABO CodeLink Expression Analysis

label: biotin-UTP

source_name: E8.5 mDom-/- whole embryo proper

extract_protocol: RNeasy extraction kit (QIAGEN)

tag: Total RNA was extracted from a mixture of male and female mDom-/- embryos (C57BL/6_129/sv) at embryonic day 8.5.


title: Caco2_OspF complementation infected_Rep1


title: E8.5 Wild-type embryo proper

source_name: E8.5 Wild-type whole embryo proper

label_protocol: CodeLink Expression Bioarray System protocol

tag: Total RNA was extracted from a mixture of male and female wild-type embryos (C57BL/6_129/sv) at embryonic day 8.5.


title: Brain-Cerebellum, biological rep2

tag: Gender

tag: Age


title: Caco2_M90T wild type infected_Rep2

tag: Intestinal cell line infected 2 hours with M90T, the wild type strain of Shigella flexneri 5a


title: proband 3 PBMC, before exercise

description: proband 3 PBMC, before exercise


title: Heart, biological rep3


title: Caco2_M90T wild type infected_Rep1


title: Caco2_OspF mutant infected_Rep2

tag: Infection with the bacterial mutant deleted for Ospf expression


title: Caco2_OspF mutant infected_Rep1

tag: Infection with the bacterial mutant deleted for OspF expression


title: Brain-Corpus Callusom, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult corpus callosum tissue

source_name: normal adult corpus callosum tissue

tag: RNA Conc (ug/ul)


title: Caco2_Non infected_Rep1

tag: Intestinal cell line


title: Brain-Corpus Callusom, biological rep2

tag: Lot #


title: Appendix, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult appendix tissue

source_name: normal adult appendix tissue


title: Caco2_Non infected_Rep2


title: Brain-Frontal Lobe, biological rep1


title: Brain-Corpus Callusom, biological rep1


title: HepG2 Heat Inactived Heat Inactived TSV01_V_72_repeated 2 68

status: Public on Nov 16 2006

city: Singapore

first: Martin

last: Hibberd

state: Singapore

address: 60, Biopolis Street

department: Population Genetics

country: Singapore

institute: Genome Institute of Singapore

description: HepG2 cells were collected 72 hours after  Heat Inactived Dengue 2 virus (TSV01) infection

hyb_protocol: Labeled cDNA were pooled, concentrated, resuspended in DIG EasyHyb (Roche, Basel, Switzerland) buffer and Hybridizated overnight (14-16h) in the MAUI Hybridization chamber( BioMicro, Salt Lake City, UT)

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner in the two channels (Cy3 and Cy5) at the same time. The GenePix Pro 6.0 software was used to grid the microarrays and to calculate the signals for each spot

data_processing: Lowess normalized ratio value ( Ch1/Ch2 )

source_name: HepG2 cell  and dengue virus serotype2 HepG2 cell  and dengue virus serotype2

label_protocol: 20µg of total RNA from experiment samples were reverse transcribed in the presence of Cy3-dUTP  (Amersham Biosciences, Little Chalfont, UK) by using the Superscript?reverse transcription kit (Invitrogen,USA). Resuspend cDNA in the cy3 dye thoroughly, incubate for 1 hour at room temperature in the dark. Mix every 15 minutes

extract_protocol: standard  QIAGEN  Rneasy Mini Protocol for isolation total RNA from Animal Cells

tag: Human hepatoma cell line (HepG2)

source_name: Universal Human Reference (Strategene. USA)

label_protocol: 20µg of total RNA from universal human reference (Strategene. USA)  were reverse transcribed in the presence of Cy5-dUTP  (Amersham Biosciences, Little Chalfont, UK) by using the Superscript?reverse transcription kit (Invitrogen,USA). Resuspend cDNA in the cy5 dye thoroughly, incubate for 1 hour at room temperature in the dark. Mix every 15 minutes

tag: Total RNA prepared from 10 different human cell lines


title: HepG2 Heat Inactived Heat Inactived TSV01_V_72_repeated 1 67


title: Appendix, biological rep1


title: HepG2 Heat Inactived Heat Inactived TSV01_V_72_repeated 3 69


title: HepG2 Heat Inactived Heat Inactived TSV01_V_48_repeated 3 66

description: HepG2 cells were collected 48 hours after  Heat Inactived Dengue 2 virus (TSV01) infection


title: HepG2 Heat Inactived Heat Inactived TSV01_V_24_repeated 3 63

description: HepG2 cells were collected 24 hours after  Heat Inactived Dengue 2 virus (TSV01) infection


title: HepG2 Heat Inactived Heat Inactived TSV01_V_48_repeated 1 64


title: Adipose, biological rep2

description: Exon Level Gene Expression data from one of three biological replicates of normal adult adipose tissue

source_name: normal adult adipose tissue


title: Appendix, biological rep2


title: HepG2 Heat Inactived Heat Inactived TSV01_V_48_repeated 2 65


title: HepG2 Heat Inactived Heat Inactived TSV01_V_24_repeated 2 62


title: DBA/2J 4-23

description: DBA/2J carotid body gene expression

tag: DBA/2J mouse strain (Jackson Lab)  gender- male, age- 28 days, n = 19, # of tissue = 38 tissue


title: HepG2 Heat Inactived Heat Inactived TSV01_V_6_repeated 3 57

description: HepG2 cells were collected 6 hours after  Heat Inactived Dengue 2 virus (TSV01) infection


title: HepG2 Heat Inactived Heat Inactived TSV01_V_6_repeated 1 55


title: HepG2 Heat Inactived Heat Inactived TSV01_V_24_repeated 1 61


title: HepG2 Heat Inactived Heat Inactived TSV01_V_6_repeated 2 56


title: HepG2 Heat Inactived Heat Inactived TSV01_V_3_repeated 3 54

description: HepG2 cells were collected 3 hours after  Heat Inactived Dengue 2 virus (TSV01) infection


title: HepG2 Heat Inactived Heat Inactived TSV01_V_12_repeated 1 58

description: HepG2 cells were collected 12 hours after  Heat Inactived Dengue 2 virus (TSV01) infection


title: HepG2 Heat Inactived Heat Inactived TSV01_V_3_repeated 2 53


title: HepG2 Heat Inactived Heat Inactived TSV01_V_12_repeated 3 60


title: HepG2 TSV01_V_72_repeated 2 51

description: HepG2 cells were collected 72 hours after Dengue 2 live virus (TSV01) infection

source_name: HepG2 cell  and dengue virus serotype2 TSV01


title: HepG2 TSV01_V_24_repeated 1 45

description: HepG2 cells were collected 24 hours after Dengue 2 live virus (TSV01) infection


title: HepG2 TSV01_V_48_repeated 2 49

description: HepG2 cells were collected 48 hours after Dengue 2 live virus (TSV01) infection


title: HepG2 TSV01_V_24_repeated 3 47


title: Adipose, biological rep1


title: HepG2 TSV01_V_48_repeated 1 48


title: HepG2 TSV01_V_48_repeated 3 50


title: HepG2 TSV01_V_12_repeated 3 44

description: HepG2 cells were collected 12 hours after Dengue 2 live virus (TSV01) infection


title: HepG2 TSV01_V_72_repeated 3 52


title: HepG2 Heat Inactived Heat Inactived TSV01_V_12_repeated 2 59


title: HepG2 TSV01_V_12_repeated 2 43


title: HepG2 TSV01_V_6_repeated 1 39

description: HepG2 cells were collected 6 hours after Dengue 2 live virus (TSV01) infection


title: HepG2 TSV01_V_12_repeated 1 42


title: HepG2 TSV01_V_6_repeated 2 40


title: HepG2 TSV01_V_24_repeated 2 46


title: HepG2 TSV01_V_6_repeated 3 41


title: HepG2 Heat Inactived Heat Inactived TSV01_V_72_repeated 3 36


title: HepG2 Heat Inactived Heat Inactived TSV01_V_72_repeated 1 34


title: HepG2 Heat Inactived Heat Inactived TSV01_V_72_repeated 2 35


title: HepG2 TSV01_V_3_repeated 2 37

description: HepG2 cells were collected 3 hours after Dengue 2 live virus (TSV01) infection


title: HepG2 TSV01_V_3_repeated 3 38


title: HepG2 Heat Inactived Heat Inactived TSV01_V_48_repeated 2 32


title: HepG2 Heat Inactived Heat Inactived TSV01_V_48_repeated 3 33


title: Adipose, biological rep3


title: HepG2 Heat Inactived Heat Inactived TSV01_V_24_repeated 1 28


title: HepG2 Heat Inactived Heat Inactived TSV01_V_12_repeated 1 25


title: HepG2 Heat Inactived Heat Inactived TSV01_V_12_repeated 2 26


title: HepG2 Heat Inactived Heat Inactived TSV01_V_24_repeated 2 29


title: HepG2 Heat Inactived Heat Inactived TSV01_V_6_repeated 1 22


title: HepG2 Heat Inactived Heat Inactived TSV01_V_3_repeated 1 19


title: HepG2 Heat Inactived Heat Inactived TSV01_V_6_repeated 2 23


title: HepG2 Heat Inactived Heat Inactived TSV01_V_12_repeated 3 27


title: HepG2 Heat Inactived Heat Inactived TSV01_V_48_repeated 1 31


title: HepG2 Heat Inactived Heat Inactived TSV01_V_3_repeated 3 21


title: Brain-Cerebellum, biological rep3

description: Exon Level Gene Expression data from one of three biological replicates of normal adult cerebellum tissue


title: HepG2 TSV01_V_48_repeated 3 15


title: HepG2 TSV01_V_72_repeated 2 17


title: HepG2 TSV01_V_72_repeated 1 16


title: HepG2 TSV01_V_72_repeated 3 18


title: HepG2 TSV01_V_12_repeated 2 8


title: HepG2 TSV01_V_24_repeated 3 12


title: HepG2 TSV01_V_24_repeated 2 11


title: HepG2 TSV01_V_24_repeated 1 10


title: HepG2 TSV01_V_12_repeated 1 7


title: HepG2 TSV01_V_48_repeated 1 13


title: HepG2 TSV01_V_48_repeated 2 14


title: HepG2 Heat Inactived Heat Inactived TSV01_V_6_repeated 3 24


title: Folate deficient growth, biological rep2

status: Public on Nov 15 2006

city: Boston

first: Carmen

last: Marsit

state: MA

address: 665 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

description: Gene expression data from cells grown for 6 days in folate deficient media.

hyb_protocol: Labelled miRNA were hybridized for 16 hr at 42C on miRVANA Bioarrays. Following hybridization, bioarrays were washed 3x and dried.

scan_protocol: Bioarrays were scanned using the GenePix 4200AL scanner.

data_processing: The fluorescent signal associated with the probes and local background was extracted using GenePix Pro and background adjusted fluorescent values were normalized for each microRNA using a variation stabilization transformation method described by Huber et al

source_name: TK6 cells 6day folate-deficient media

label_protocol: The 3’ ends of the RNA molecules were tailed and labeled using the mirVana™ miRNA Labeling Kit (Ambion) according to the manufacturer’s instructions. Amine-modified nucleotides were incorporated during the poly (A) polymerase mediated tailing reaction, and Cy5 succinimide esters (Amersham Biosciences (GE Healthcare)) were conjugated to the amine moieties on the microRNAs

extract_protocol: Ambion miRVANA RNA isolation kit according to manufacturer's protocol

tag: normal human diploid lymphoblast immortalized cell line


title: Cells grown in normal media control for folate deficiency, biological rep2

description: Gene expression data from cells grown in normal media for 6 days as controls for folate deficiency

source_name: TK6 grown in normal growth media for 6 days as control for folate deficiency experiment


title: Folate deficient growth, biological rep3


title: Cells grown in normal media control for folate deficiency, biological rep3


title: Folate deficient growth, biological rep1


title: HepG2 TSV01_V_6_repeated 2 5


title: Cells grown in normal media control for folate deficiency, biological rep1


title: HepG2 TSV01_V_6_repeated 3 6


title: HepG2 TSV01_V_12_repeated 3 9


title: HepG2 Heat Inactived Heat Inactived TSV01_V_24_repeated 3 30


title: HepG2 Heat Inactived Heat Inactived TSV01_V_3_repeated 2 20


title: HepG2 TSV01_V_3_repeated 2 2


title: HepG2 TSV01_V_3_repeated 3 3


title: HepG2 TSV01_V_3_repeated 1 1


title: HepG2 TSV01_V_6_repeated 1 4


title: No treatment control for As and IR 6d, biological rep3

description: Gene expression data from mock treated cells collected after 6 days used as controls for As and IR treatment.

source_name: TK6 cells mock treated 6 day


title: As treatment, biological rep3

description: Gene expression data from cells treated for 6 days in 2 uM sodium arsenite.

source_name: TK6 cells 6day As treat


title: IR treatment 6d timepoint, biological rep3

description: Gene expression data from cells treated with 2.5 Gy g-IR and collected after 6days.

source_name: TK6 cells 6hour IR treat


title: No treatment control 4h, biological rep2

description: Gene expression data from mock treated cells collected at 4 h.

source_name: TK6 cells mock treated 4 hours


title: No treatment control for As and IR 6d, biological rep1


title: No treatment control for As and IR 6d, biological rep2


title: IR treatment 4h timepoint, biological rep1

description: Gene expression data from cells treated with 2.5 Gy g-IR and collected at 4h.

source_name: TK6 cells 4hour IR treat

label_protocol: The 3� ends of the RNA molecules were tailed and labeled using the mirVana� miRNA Labeling Kit (Ambion) according to the manufacturer�s instructions. Amine-modified nucleotides were incorporated during the poly (A) polymerase mediated tailing reaction, and Cy5 succinimide esters (Amersham Biosciences (GE Healthcare)) were conjugated to the amine moieties on the microRNAs


title: IR treatment 6d timepoint, biological rep1


title: IR treatment 6d timepoint, biological rep2


title: No treatment control 4h, biological rep1


title: No treatment control 4h, biological rep3


title: As treatment, biological rep2


title: IR treatment 4h timepoint, biological rep3


title: IR treatment 4h timepoint, biological rep2


title: As treatment, biological rep1


title: Adenocarcinoma therapy T6

status: Public on Nov 01 2006

city: Duesseldorf

first: Michael

last: Rosskopf

address: Universitaetsstrasse 1

department: Bioinformatics

institute: University of Duesseldorf

description: Laser captured primary lung cancer cells

hyb_protocol: Arrays were prehybridizised for 10 minutes using 140µl MES- hybridization buffer (70,4g MES free acid monohydrate, 193.3g MES Sodium Salt, 800ml accugen water, pH 6.5 – 6.7) and 140µl aqua dest. at 45°C and 60rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix). After removal of the pre-hybridizing solution, the array is loaded with 250 µl of the hybridizing solution (30µl fragmented aRNA, 5µl control-oligo B2, 15µl 20x Eukaryotic hybridizing control, 3µl salmon sperm-DNA, 3µl azetylic BSA, 150µl 2x MES- Hybridizing buffer and 94µl aqua dest.). Following 16-hour incubation at 45°C with permanent rotation, the hybridizing solution is removed. The array is loaded with 280µl of washing buffer A (300ml 20x SSPE, 1ml 10% Tween 20, 698ml accugen water) and a maximum of 4 hybridized arrays are put into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B (83.3ml 12x MES, 5.2ml 5M NaCl, 1ml 10% Tween 20, 910.5ml accugen water) using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus Oligonukleotid- Arrays = Midi-euk2v3). During washing procedure the staining solution is prepared: Staining solution: 600µl 2x Staining Buffer 540µl dH2O 48µl BSA 12µl Streptavidine- Phycoerythrin- Conjugate Array is incubated with 600µl of the staining solution after washing for 40 minutes followed by incubation with the antibody solution for 10 minutes: Antibody solution: 300µl 2x Staining Buffer 266 4µl dH2O 24µl BSA 6µl Goat IgG 3.6µl biotinylated Anti- Streptavidin- AB After removal of the antibody solution 600µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.

scan_protocol: The scanning of the array is performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome phycoerythrin at a wave length of 488nm with an emission at 570nm.

data_processing: Using the affy package of functions of statistical scripting language 'R' integrated into the Bioconductor project data from cel files of each sample were normalized by variance stabilizing transformations (VSN) Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics 2002;18:96-104.

label: Biotin/Streptavidin-PE

source_name: Primary lung cancer samples

label_protocol:
Amplification, reverse transcription and labelling of the sample.
For amplification of micro-dissected RNA, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used.
Between 200-500ng of isolated RNA were transcribed into cDNA.
First strand cDNA- Synthesis:
11µl (RNA or RNA and dH2O) Sample
1µl Oligo(dT)Primer
70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
Reaction kit:
2µl 10x First Strand Buffer
1µl Ribonuclease Inhibitor
4µl dNTP Mix
Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
Second strand cDNA- Synthese:
63µl Nuclease-free Water
10µl 10x Second Strand Buffer
4µl dNTP Mix
1µl RNase H
For second strand sythesis 2µl der DNA- Polymerase are added followed by a 2 h incubation at 42°C.
Purification of cDNA:
Final elution volume = 16 µl and storage for 12 h at -20°C
Labelling with in vitro transcription using biotin labelled nucleotides:
Labeling mix:
4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit, Enzo Life Sciences, Farmingdale)
4µl T7 10x reaction buffer
12µl RNase free water
The labelling mix is incubated with the sample and 4µl of the enzyme mix is added followed by an incubation period of 5 hours at 37°C. The amplified RNA is
purified and is eluted in a final volume of 96 µl.
Quality control of aRNA:
The concentration and purity of aRNA is measured using the NanoDrop ND-1000 (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
The OD 260/OD 280 aRNA was between 1.7 and 2. To exclude the possibility of degradation and/or contamination RNA was analyzed again using a Agilent 2100
Bioanalyzer (Agilent Technologies, Palo Alto CA).
Fragmentation:
For optimal hybridization with the complementary oligonucleodid sequences, a fragmentation of the amplified RNA was performed.
24µl of the sample were added to 6µl of fragmentation buffer (200mM TRIS-Acetat, ph 8.2, 500mM KOAc, 150mM MgOAc, Affymetrix) and incubated at 94°C for 35
minutes.

extract_protocol:
RNA of LCM-tumor cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the
kit and were applied according to the manufacturer’s instructions.
In brief:
LCM tumor cells suspended in 350µl lysis buffer were incubated with 350µl 70% ethanol.
700µl suspension was put on RNeasy MinElute- column and spun down for one minute with 10,000 rpm.
DNase- digestion (10µl DNase+70µl RDD buffer-> 80µl) for 15 at 30°C.
2 washing steps with 350µl RW1- buffer and 500µl RPE- buffer.
500µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2 minutes with 10,000 rpm.
Removal of ethanol: column was spun down for 5 minutes with 30,000 rpm.
Elution of RNA with 14µl of RNAse free water.
Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
GmbH, Erlangen). Purified RNA was stored at -80°C.

tag: age

tag: gender

value: w

tag: disease

value: Adenocarcinoma

tag: received platinum-based therapy with progression

value: yes


title: Adenocarcinoma therapy T7

value: m


title: Adenocarcinoma therapy T5


title: Primary lung cancer therapy T4

tag: disease:


title: Squamous Cell Carcinoma therapy T10

value: Squamous Cell Carcinoma


title: Squamous Cell Carcinoma therapy T9


title: Squamous Cell Carcinoma therapy T13


title: Adenocarcinoma therapy T8


title: Squamous Cell Carcinoma therapy T11


title: Adenocarcinoma therapy T3


title: Squamous Cell Carcinoma therapy T12


title: Small RNAs from rosette leaves

status: Public on Nov 02 2006

city: Cambridge

first: Ramya

last: Rajagopalan

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research, MIT Department of Biology

description: Rosette-derived total RNA fractionation by polyacrylamide gel electrophoresis, ligation to adaptors, reverse transcription, and pyrosequencing of the small RNA cDNA library was performed as described in Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006) A two-hit trigger for siRNA biogensis in plants.  Cell 127:565-577.

data_processing: Sequences of small RNAs were BLAST-matched to the Version 6.0 build of the A. thaliana genome

organism: Arabidopsis thaliana

source_name: rosette leaves, Arabidopsis thaliana, wild-type Col-0

growth_protocol: Wild-type Col-0 plants were grown under standard greenhouse conditions.  Rosette leaves were harvested six weeks after planting.

extract_protocol: Rosette leaves were ground to a fine powder in liquid nitrogen, and thawed in five volumes of buffer (0.1 M NaCl, 2% SDS, 50 mM Tris/HCl, pH 9.0, 10 mM EDTA, and 20 mM ß-mercaptoethanol).  Total RNA was isolated from the sample by phenol/chloroform extraction and ethanol precipitation.


title: Adenocarcinoma therapy T2


title: Squamous Cell Carcinoma P9

value: Squamous Cell Cancer

value: no


title: Squamous Cell Carcinoma P6


title: Primary lung cancer therapy T1


title: Squamous Cell Carcinoma P5


title: Small RNAs from whole seedlings

description: Seedling-derived total RNA fractionation by polyacrylamide gel electrophoresis, ligation to adaptors, reverse transcription, and pyrosequencing of the small RNA cDNA library was performed as described in Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006) A two-hit trigger for siRNA biogensis in plants.  Cell 127:565-577.

source_name: seedlings, Arabidopsis thaliana, wild-type Col-0

growth_protocol: Col-0 Arabidopsis seedlings were grown on agar-based medium overlaid with filter paper and harvested after 6 days.

extract_protocol: Total RNA from seedlings was extracted using Trizol (GIBCO BRL) and ethanol precipitated.


title: Squamous Cell Carcinoma P10


title: Small RNAs from whole flowers

description: Flower-derived total RNA fractionation by polyacrylamide gel electrophoresis, ligation to adaptors, reverse transcription, and pyrosequencing of the small RNA cDNA library was performed as described in Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006) A two-hit trigger for siRNA biogensis in plants.  Cell 127:565-577.

source_name: whole flowers, Arabidopsis thaliana, wild-type Col-0

growth_protocol: Wild-type Col-0 plants were grown under standard greenhouse conditions (long-day, 16h light/8h dark). Flowers were harvested four weeks after planting.

extract_protocol: Total RNA from whole flowers was extracted using Trizol (GIBCO BRL) and ethanol precipitated.


title: Squamous Cell Carcinoma P7


title: Squamous Cell Carcinoma P4


title: Squamous Cell Carcinoma P2


title: Squamous Cell Carcinoma P3


title: Squamous Cell Carcinoma P8


title: Small RNAs from whole siliques

description: Silique total RNA fractionation by polyacrylamide gel electrophoresis, ligation to adaptors, reverse transcription, and pyrosequencing of the small RNA cDNA library was performed as described in Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006) A two-hit trigger for siRNA biogensis in plants.  Cell 127:565-577.

source_name: siliques, Arabidopsis thaliana, wild-type Col-0

growth_protocol: Wild-type Col-0 plants were grown under standard greenhouse conditions (long-day, 16h light/8h dark).   Siliques were harvested two months after planting.

extract_protocol: Whole siliques were ground to a fine powder in liquid nitrogen, and thawed in five volumes of buffer (0.1 M NaCl, 2% SDS, 50 mM Tris/HCl, pH 9.0, 10 mM EDTA, and 20 mM ß-mercaptoethanol).  Total RNA was isolated from the sample by phenol/chloroform extraction and ethanol precipitation.


title: Squamous Cell Carcinoma P1


title: Normal Lung Tissue N4

source_name: Lung samples

value: Normal Lung Tissue


title: Normal Lung Tissue N5


title: Normal Lung Tissue N2


title: Normal Lung Tissue N3


title: Small Cell Lung Cancer K8

value: Small Cell Lung Cancer


title: Normal Lung Tissue N1


title: Small Cell Lung Cancer K9


title: Small Cell Lung Cancer K3


title: Adenocarcinoma A7


title: Adenocarcinoma A3


title: Adenocarcinoma A4


title: Adenocarcinoma A2


title: Small Cell Lung Cancer K4


title: Small Cell Lung Cancer K2


title: Adenocarcinoma A6


title: Adenocarcinoma A5


title: Adenocarcinoma A8


title: Small Cell Lung Cancer K5


title: Small Cell Lung Cancer K6


title: Small Cell Lung Cancer K7


title: Adenocarcinoma A1


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part2 replicate 4

city: Halifax

first: George

middle: S

last: Robertson

state: Nova Scotia

address: 5850 College Street

department: Departments of Psychiatry and Pharmacology

institute: Dalhousie University

description: The scans were saved as image files in TIFF format, and imported into the QuantArrayTM version 3.0 (Perkin-Elmer) microarray analysis software, for spot identification and quantification, and background estimation.

hyb_protocol: The labeled cDNA samples were hybridized to the SAMF Human 14K microarray slides (GEO Accession numbers GPL3963 and GPL3964), printed at the University of Calgary. These arrays contain 13,972 70-mer oligos designed against the UniGene database (Operon V1.0) spotted in duplicate. For more information on the microarray chips used in these experiments, please see the SAMF website (www.microarrays.ucalgary.ca). The hybridization was carried out at 37°C for 18 hrs in a Boekel InSlide OutTM hybridization oven. The post-hybridization washes were performed as follows: 2 x SSC, 0.2% SDS for 3-4 min, 0.2 x SSC for 1 min followed by 0.1 x SSC for 1 min.

scan_protocol: The slides were scanned using ScanArray500 at of 550 nm and 649 nm for Cy3 and Cy5, respectively.

data_processing: The quantification and image files were then loaded into Gene Traffic DuoTM (Iobion) for microarray data management and analysis. The data were filtered to flag spots with intensities less than 100 units, or less than twice the average background. The data were normalized according to the Lowess method (Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15) resident in the Gene Traffic software.

label: Cy 5

source_name: SH-SY5Y cells treated with Q3G for 6 hours then H2O2

label_protocol: cDNA labeling was carried out using the FairPlay Microarray Labeling Kit II with modifications (Stratagene, Cat. #252006). The first step involved preparation of cDNA. 10 µg of DNase treated total RNA from Q3G and vehicle treated SH-SY5Y cells were reverse transcribed using StrataScript Reverse transcriptase (150.0U) at 42°C for 1h. The second step involved a dye coupling reaction and purification of the labeled cDNA. The cyanine mono-reactive dyes (Cy3 or Cy5; Amersham) were incubated with the cDNAs for 1h at RT in the dark.

extract_protocol: Total RNA was extracted using the RNeasy mini column (Qiagen). The integrity of total RNA was confirmed by gel electrophoresis (1% formaldehyde agarose). Absorbance of RNA was measured at 260/280 nm using a spectrophotometer and RNA samples having a 260/280 ratio > than 1.9 were subsequently used for microarray analysis.

tag: Refers to RNA extracted from the second batch of cells treated with 10 uM Quercetin-3-glucoside for 6 hr and then 500 uM H2O2 for 15 min

label: Cy 3

source_name: SH-SY5Y cells treated with DMSO for 6 hours then H2O2

tag: Refers to RNA extracted from the second batch of cells treated with 0.05 % DMSO for 6 hr and then 500 uM H2O2 for 15 min


title: Adenocarcinoma A9


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part2 replicate 2

tag: Refers to RNA extracted from the first batch of cells treated with 10 uM Quercetin-3-glucoside for 6 hr and then 500 uM H2O2 for 15 min

label_protocol: cDNA labeling was carried out using the FairPlay Microarray Labeling Kit II with modifications (Stratagene, Cat. #252006).  The first step involved preparation of cDNA. 10 µg of DNase treated total RNA from Q3G and vehicle treated SH-SY5Y cells were reverse transcribed using StrataScript Reverse transcriptase (150.0U) at 42°C for 1h. The second step involved a dye coupling reaction and purification of the labeled cDNA. The cyanine mono-reactive dyes (Cy3 or Cy5; Amersham) were incubated with the cDNAs for 1h at RT in the dark.

tag: Refers to RNA extracted from the first batch of cells treated with 0.05 % DMSO for 6 hr and then 500 uM H2O2 for 15 min


title: Adenocarcinoma A10


title: Quercetin-3-glucoside vs vehicle on SAMF H14k part2 replicate 4

source_name: SH-SY5Y cells treated with Q3G for 6 hours

growth_protocol: SH-SY5Y cells were maintained in DMEM supplemented with 10% Foetal Bovine Serum, 2 mM L-glutamine, 1 mM sodium pyruvate, penicillin (100 U/ml) and streptomycin (100µg/ml) at 37°C in a humidified atmosphere of 5% CO2. SH-SY5Y cells were seeded at an initial density of 5x10E5 cells per ml in a 75 cm2 flask and passaged every fourth day.

treatment_protocol: The cells were treated with Q3G (10 μM) for 6h.

tag: Refers to RNA extracted from the second batch of SH-SY5Y cells treated with Quercetin-3-glucoside for 6 hr. The human neuroblastoma cell line, SH-SY5Y was obtained from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). SH-SY5Y cells are epithelial cells derived from the metastatic bone tumor of a female patient.

source_name: SH-SY5Y cells treated with DMSO for 6 hours

label_protocol: cDNA labeling was carried out using the FairPlay Microarray Labeling Kit II with modifications (Stratagene, Cat. #252006). The procedure involved three main steps. The first involved preparation of cDNA. 10 µg of DNase treated total RNA from Q3G and vehicle treated SH-SY5Y cells were reverse transcribed using StrataScript Reverse transcriptase (150.0U) at 42°C for 1h. The second step involved a dye coupling reaction and purification of the labeled cDNA. The cyanine mono-reactive dyes (Cy3 or Cy5; Amersham) were incubated with the cDNAs for 1h at RT in the dark. In a separate experiment, a reciprocal labeling reaction was carried by incorporating Cy5 into the Q3G treated sample and Cy3 into vehicle treated sample. As a result, two separate reactions were completed per sample. Following several washes, dye coupled cDNA purification was performed using microspin cup and cDNA was eluted from the column. Following dye incorporation, cDNAs from the control and Q3G samples were combined. These reciprocal labeling reactions were performed twice on two independent experimental samples to yield four replicates. These dye-switching experiments were performed in order to minimize any bias associated with cDNA synthesis.

treatment_protocol: SH-SY5Y cells were treated with DMSO (0.05%).

tag: Refers to RNA extracted from the second batch of cells treated with vehicle (DMSO) for 6 hr


title: Quercetin-3-glucoside vs vehicle on SAMF H14k part2 replicate 2

hyb_protocol: The labeled cDNA samples were hybridized to the SAMF Human 14K  microarray slides (GEO Accession numbers GPL3963 and GPL3964), printed at the University of Calgary. These arrays contain 13,972 70-mer oligos designed against the UniGene database (Operon V1.0) spotted in duplicate. For more information on the microarray chips used in these experiments, please see the SAMF website (www.microarrays.ucalgary.ca). The hybridization was carried out at 37°C for 18 hrs in a Boekel InSlide OutTM hybridization oven. The post-hybridization washes were performed as follows: 2 x SSC, 0.2% SDS for 3-4 min, 0.2 x SSC for 1 min followed by 0.1 x SSC for 1 min.

label_protocol: cDNA labeling was carried out using the FairPlay Microarray Labeling Kit II with modifications (Stratagene, Cat. #252006). The procedure involved three main steps. The first involved preparation of cDNA. 10 µg of DNase treated total RNA from Q3G and vehicle treated SH-SY5Y cells were reverse transcribed using StrataScript Reverse transcriptase (150.0U) at 42°C for 1h. The second step involved a dye coupling reaction and purification of the labeled cDNA. The cyanine mono-reactive dyes (Cy3 or Cy5; Amersham) were incubated with the cDNAs for 1h at RT in the dark. In a separate experiment, a reciprocal labeling reaction was carried by incorporating Cy5 into the Q3G treated sample and Cy3 into vehicle treated sample. As a result, two separate reactions were completed per sample. Following several washes, dye coupled cDNA purification was performed using microspin cup and cDNA was eluted from the column. Following dye incorporation, cDNAs from the control and Q3G samples were combined. These reciprocal labeling reactions were performed twice on two independent experimental samples to yield four replicates. These dye-switching experiments were performed in order to minimize any bias associated with cDNA synthesis

treatment_protocol: The cells were treated with Q3G (10 μM) for 6h

tag: Refers to RNA extracted from the first batch of SH-SY5Y cells treated with Quercetin-3-glucoside for 6 hr. The human neuroblastoma cell line, SH-SY5Y was obtained from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). SH-SY5Y cells are epithelial cells derived from the metastatic bone tumor of a female patient.

treatment_protocol: SH-SY5Y cells were treated with DMSO (0.05%)

tag: Refers to RNA extracted from the first batch of cells treated with vehicle (DMSO) for 6 hr


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part2 replicate 3


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part2 replicate 1

label_protocol: cDNA labeling was carried out using the FairPlay Microarray Labeling Kit II with modifications (Stratagene, Cat. #252006). The procedure involved three main steps. The first involved preparation of cDNA. 10 µg of DNase treated total RNA from Q3G and vehicle treated SH-SY5Y cells were reverse transcribed using StrataScript Reverse transcriptase (150.0U) at 42°C for 1h. The second step involved a dye coupling reaction and purification of the labeled cDNA. The cyanine mono-reactive dyes (Cy3 or Cy5; Amersham) were incubated with the cDNAs for 1h at RT in the dark.


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part1 replicate 1


title: Quercetin-3-glucoside vs vehicle on SAMF H14k part1 replicate 3


title: Small Cell Lung Cancer K1


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part1 replicate 3


title: Quercetin-3-glucoside vs vehicle on SAMF H14k part2 replicate 1


title: Quercetin-3-glucoside vs vehicle on SAMF H14k part2 replicate 3


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part1 replicate 4


title: Quercetin-3-glucoside vs vehicle on SAMF H14k part1 replicate 4


title: Quercetin-3-glucoside plus H2O2 vs vehicle plus H2O2 on SAMF H14k part1 replicate 2


title: Quercetin-3-glucoside vs vehicle on SAMF H14k part1 replicate 2


title: 514_Carcinoma_BAC_par

type: genomic

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Copy number analysis of colorectal tumors

hyb_protocol: Labelled test and reference samples were pooled and precipitated in the presence of Cot1 DNA (Invitrogen, Breda, The Netherlands). DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA, Giesen, The Netherlands).

scan_protocol: Scanned with a GenePix 4100A scanner (Axon Instruments, Westburg BV, Leusden, The Netherlands)

data_processing: limma

molecule: genomic DNA

source_name: Tumor DNA from patient 514 on BAC platform

label_protocol: overnight random prime labelling reaction (BioPrime Random Prime labelling Kit, Invitrogen, Breda, The Netherlands).

extract_protocol: DNA was extracted with the Chelex extraction method. Briefly, three tissue punches (diameter 0.6 mm) were obtained by a tissue microarrayer (Beecher Instruments, Sun Prairie, WI). DNA was isolated with Chelex and proteinase K. FFPE DNA was subsequently cleaned up using the Genomic Wizard kit (Promega).

tag: Tumor DNA of female patient with colorectal carcinoma

source_name: male reference DNA

extract_protocol: Commercially available pooled DNA (Promega)

tag: Gender mismatched pooled reference DNA


title: T95-2575 DNA 2ug red Vs nDNA 2ug green 150302

status: Public on Oct 31 2006

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: Slides were hybridised at 65C for 1 hour then 47C for 3 nights.

hyb_protocol: slides were rinsed in 4 x SSPE and 10mM EDTA, transferred to a fresh wash solution (4 x SSPE, 10mM EDTA) and gently agitated until the cover slip detached, and then in a third wash solution (4 x SSPE, 10mM EDTA) for 1 minute, all solution were pre warmed to 42ºC. Slides were then transferred a 42ºC wash containing 6 x SSPE and 50% formamide for 5 – 15 seconds, and finally washed for 30 seconds each in 2 x SSPE and 10mM EDTA, and 0.1 x SSPE. Finally slides were rinsed in HPLC grade water and excess solution removed with canned air.

scan_protocol: Hybridised microarray slides were scanned with a GenePix 4000B scanner (Axon Instruments), and images visualised by GenePix software (version 3). Slides were scanned with laser power levels at 100% PMT (Photomultiplyer Tube) voltage levels were altered in order to provide an average Cy5:Cy3 hybridisation ratio across the slide of 1:1.  Individual fluoresce intensities rations (Cy5:Cy3) for each cDNA were determined by the software, with the hybridisation signal for each clone being calculated as the median fluorescence of pixels within a defined area of array spot.  Spots from cDNA clones representing mitochondrial sequences and spots, which didn’t respond, were removed at this point of data analysis.  Data was normalised using Lowess Normalisation.

data_processing: Data were filtered for quality by automated spot flagging and manual inspection in GenePix software and the normalised using a lowess algorithm. Each clone was normalized according to its position on the array to adjust for regional variations in relative signal intensity on the slides. The data set was renormalized to a Log2 ratio of 0.

source_name: T95-2575(Primary Seminoma Testicular Germ Cell Tumour Sample)

label_protocol: DNA was Labelled using a Bioprime labelling kit (Invitrogen) according to the manufacturer’s instructions, except that 2 µg of DNA was labelled in a 40 µl reaction with 75 µM Cy5-dCTP (or Cy3-dCTP) [NEN, Boston, MA], plus 60 µM dCTP, and 120 µM dGTP, dATP, dTTP and 40units of Klenow large fragment DNA polymerase. Samples were then incubated over night at 37ºC. The labelling reaction was terminated by the addition of 90mM EDTA, unincorporated nucleotides were removed by the addition of 32µg of COT-1 DNA and 80mM NaOH and heated to 70ºC for 10 minutes. Samples were clean up and volume reduced by first adding 0.5 x SSPE (5mM Phosphate, pH 7.4, 0.5mM EDTA) to a total volume of 500µl, this was then filtered through a 0.1µm Ultrafree-MC filter column (Millipore) and centrifuged 6500rpm. The volume was then reduced to 3µl/2µg of labelled sample by filtering through a Microcon YM-30 filtration unit (Millipore) at 13K rpm.

extract_protocol: Tumour samples were ground in a pestle and mortar.  DNA was extracted using standard methods ie. cell lysis, proteinase K digestion, phenol extraction followed by precipitation (Sambrook and Russell,2001).

value: male

tag: tissue type

value: tumor

source_name: Genomic Male DNA(Genomic Male blood DNA)

value: normal