title: HCT116 1.3uM/48h

description: Cell culture and treatment: The human colon cancer derived cell line, HCT116 from (ATcc-CCL-247, Manassas, VA). The HCT116 cells were grown in cell culture flasks (Corning Inc., USA) in McCoy’s 5A medium with L-glutamine supplemented with 10% fetal calf serum and 1% penicillin-streptomycin mixture (Cambrex, Belgium). The cell line was grown at 37oC in a humidified atmosphere of 5% of CO2 in air. Cells were seeded in 100 mm cell culture dishes (Corning Inc, USA) and allowed to attach 24 h prior to cisplatin (Cis-Diamminedichloroplatinum(II) or CDDP, Sigma) treatment. Cells in exponential growth phase were exposed to cisplatin and the cells were harvested after 48 h of exposure and prepared for further analysis. RNA preparation: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Microarrays: 21K human oligonucleotide microarrays were printed at the Norwegian Microarray Consortium using OPERON hum oligo v2.0. The microarrays consist of 70 mer, oligos representing 21,329 genes from UniGene Database. cDNA synthesis and labeling:Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA). Briefly, 20 μg of total RNA (from cisplatin treated and control cell lines) in 13 μl of nuclease-free water was combined with 1 μl of 500 ng/μl oligo-d(T)12–18. The mixture was incubated at 70°C for 10 min and cooled on ice. For each reaction, 2 μl of 10X StrataScript reaction buffer, 1 μl of unlabeled 20X dNTP mix containing amino-allyl dUTP, 1.5 μl of 0.1 M dithiothreitol and 0.5 μl of RNase Block (40 U/μl) were prepared and mixed with the RNA sample and 1 μl of 50 U/μl StrataScript RT. After incubation at 48°C for 30 min an additional 1 μl of StrataScript RT was added and incubation was continued for 30 additional minutes. RNA was degraded by adding 10 μl of 1 M NaOH, followed by a 10-min incubation at 70°C and the mixture neutralized with 10 μl of 1 M HCl. Unincorporated nucleotides were removed by precipitation of the cDNA with 4 μl of 3 M sodium acetate, 1 μl of 20 mg/ml glycogen and 100 μl of 95% ethanol at -20°C for 1 h. After centrifugation and washing the pellet with 70% ethanol, it was resuspended in 5 μl of 2x coupling buffer provided in the kit. Cy3 or Cy5 dye (Amersham), resuspended in 45 ul of DMSO, was added and the reaction incubated for 2 h at room temperature in the dark. Dye-coupled cDNA was purified with a DNA-binding spin cup, combined and concentrated by vacuum drier.

source_name: HCT116 treated with 1.3uM cisplatin

treatment_protocol: Treatment of cell cultures: HCT116 cell line in exponential growth phase was exposed to 1.3uM (0.4ug/ml) cisplatin 48h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.

extract_protocol: GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA from at least three independent experiments was pooled together before labeling and hybridization to reduce possible bias for single treatment.


title: Ap 48 hr YE vs 48 hr YES Slide 11B

status: Public on Oct 01 2007

type: RNA

city: Mississippi State

first: Jeff

last: Wilkinson

state: MS

department: Biochemistry and Molecular Biology

country: USA

institute: Mississippi State University

description: The independent TIFF images from each channel were analyzed using TIGR Spotfinder software program.  After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values.

hyb_protocol: Pre-hybridization was performed according to TIGR’s protocols and washed according to post-hybridization instructions for the 3DNA Array 900MPXTM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900MPXTM Kit (Genisphere Inc.), according to the manufacturer’s protocol.  Each experiment consisted of one 48 hour YE sample coupled to either a 3, 6, 12, 24, or 48 hour sample from the YE to YES shift.  The 48 hour YE to 3, 6, 12 and 24 hour YES comparisons were repeated with duplicate biological replicates and with duplicate dye-flip; the 0 hour to 48 hour comparisons were done in triplicate each with a dye-flip.  Briefly, 3 µg of total RNA was used to generate cDNA using Genisphere’s random and MPX dT primers with Supercript II, dithiotreitol and 5X SuperScript II First Strand Buffer (Invitrogen Corp., Carlsbad, CA) as per Genisphere’s instructions.  The generated cDNA’s were purified using Qiagen MiniElute PCR Purification Kit (Qiagen Inc., Valencia, CA) as well as after terminal deoxynucleotidyl transferase tailing reaction and ligation to 3DNA capture sequence reactions. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA), unbound cDNA was removed by washing as per Genisphere’s instructions.  Hybridization of the 3DNA Capture reagent containing the fluorescent dyes were performed using the 2X Formamide-Based Hybridization Buffer at 49oC for 4 hours in Hybridization Cassette and washed as per Genisphere’s instructions to remove non-specific background.

scan_protocol: Hybridized slides were scanned using either a ScanArray5000XL (GSI Lumonics, Packard Biochip, Packard BioScience Company, Billerica, MA) or a GenePix 4000B (Axon Instruments, Molecular Devices, Sunnyvale, CA).

data_processing: To remove the non-specific background signals, the raw data was normalized using a local regression technique, LOWESS (LOcally WEighted Scatterplot Smoothing), using the MIDAS software tool.  The LOWESS normalized dye-flips were then combined to minimize any artifacts introduced by the Cy3 or Cy5 dyes.  The resulting data were averaged over duplicate gene features on each array for each replicate experiment.  Some genes are represented by two separate non-overlapping fragments, therefore since a gene may be detected by each fragment they are defined as features so that gene count will not be over reported.  All calculated gene expression ratios were log2-transformed when imported into TIGR MeV software [31].  Only genes that gave detectable signals in all replicate experiments were used for further analysis.

molecule: total RNA

organism: Aspergillus parasiticus

source_name: Aspergillus parasiticus SU-1 48 hr YE

growth_protocol:
A. parasiticus SRRC 143 ATCC 56775 (or SU-1), a wild type strain previously used for biochemical and genetic studies of both B group (B1 and B2) and G group (G1 and G2) aflatoxins, was selected for this study.  Fresh conidia were generated by plating 50 µl of 108 spore per ml onto Difco Potato-Dextrose Agar (PDA) (American Scientific Products, Charlotte, N.C.) and incubated at 30oC for 5 days.  The conidia were collected from 5-day cultures with sterile aqueous 0.05% Triton X-100.
A. parasiticus spores were inoculated to a final concentration of 105 spores/ml in 200 ml yeast extract (YE) liquid medium consisting of 25 g/L of yeast extract (DIFCO) and incubated for 48 hours at 30oC with constant shaking at 150 rpm.  The fungal mycelia were harvested by filtration in vacuo.  The harvested mycelia were divided into 1 gram aliquots.  Each aliquot was used to inoculate 100 ml of YES medium (60 g/L of sucrose and 25 g/L of yeast extract) for harvesting at different time points.  The cultures shifted from YE to YES were grown at 30oC with 150 rpm shaking until harvested at 3, 6, 12, 24, and 48 hours post-inoculation.  The harvested fungal mycelial samples were fresh frozen in liquid nitrogen and stored at -80oC for RNA preparation and aflatoxin extraction.

extract_protocol: The frozen fungal mycelia were ground to a fine powder in liquid nitrogen using mortar and pestle.  Total RNA was extracted from approximately 100 mg of ground mycelium in 1 ml of TRIZOL® (Molecular Research Center, Inc., Cincinnati, OH) according to manufacturer's instructions.  Total RNA was quantified using a ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and visualized by agarose gel electrophoresis to ensure quality.

tag: Aspergillus parasiticus SU-1 RNA collected from 48 hr YE cultures

source_name: Aspergillus parasiticus SU-1 48 hr YES

tag: Aspergillus parasiticus SU-1 RNA collected 48 hr post shift from 48 hr YE to YES


title: Ap 48 hr YE vs 24 hr YES Slide 7B

label_protocol: Pre-hybridization was performed according to TIGR’s protocols and washed according to post-hybridization instructions for the 3DNA Array 900MPXTM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900MPXTM Kit (Genisphere Inc.), according to the manufacturer’s protocol.  Each experiment consisted of one 48 hour YE sample coupled to either a 3, 6, 12, 24, or 48 hour sample from the YE to YES shift.  The 48 hour YE to 3, 6, 12 and 24 hour YES comparisons were repeated with duplicate biological replicates and with duplicate dye-flip; the 0 hour to 48 hour comparisons were done in triplicate each with a dye-flip.  Briefly, 3 µg of total RNA was used to generate cDNA using Genisphere’s random and MPX dT primers with Supercript II, dithiotreitol and 5X SuperScript II First Strand Buffer (Invitrogen Corp., Carlsbad, CA) as per Genisphere’s instructions.  The generated cDNA’s were purified using Qiagen MiniElute PCR Purification Kit (Qiagen Inc., Valencia, CA) as well as after terminal deoxynucleotidyl transferase tailing reaction and ligation to 3DNA capture sequence reactions. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA), unbound cDNA was removed by washing as per Genisphere’s instructions.  Hybridization of the 3DNA Capture reagent containing the fluorescent dyes were performed using the 2X Formamide-Based Hybridization Buffer at 49oC for 4 hours in Hybridization Cassette and washed as per Genisphere’s instructions to remove non-specific background.

treatment_protocol:
A. parasiticus SRRC 143 ATCC 56775 (or SU-1), a wild type strain previously used for biochemical and genetic studies of both B group (B1 and B2) and G group (G1 and G2) aflatoxins, was selected for this study.  Fresh conidia were generated by plating 50 µl of 108 spore per ml onto Difco Potato-Dextrose Agar (PDA) (American Scientific Products, Charlotte, N.C.) and incubated at 30oC for 5 days.  The conidia were collected from 5-day cultures with sterile aqueous 0.05% Triton X-100.
A. parasiticus spores were inoculated to a final concentration of 105 spores/ml in 200 ml yeast extract (YE) liquid medium consisting of 25 g/L of yeast extract (DIFCO) and incubated for 48 hours at 30oC with constant shaking at 150 rpm.  The fungal mycelia were harvested by filtration in vacuo.  The harvested mycelia were divided into 1 gram aliquots.  Each aliquot was used to inoculate 100 ml of YES medium (60 g/L of sucrose and 25 g/L of yeast extract) for harvesting at different time points.  The cultures shifted from YE to YES were grown at 30oC with 150 rpm shaking until harvested at 3, 6, 12, 24, and 48 hours post-inoculation.  The harvested fungal mycelial samples were fresh frozen in liquid nitrogen and stored at -80oC for RNA preparation and aflatoxin extraction.

source_name: Aspergillus parasiticus SU-1 24 hr YES

tag: Aspergillus parasiticus SU-1 RNA collected 24 hr post shift from 48 hr YE to YES


title: Ap 48 hr YE vs 48 hr YES Slide 9B


title: Ap 48 hr YE vs 12 hr YES Slide 5B

source_name: Aspergillus parasiticus SU-1 12 hr YES

tag: Aspergillus parasiticus SU-1 RNA collected 12 hr post shift from 48 hr YE to YES


title: HCT116 6.7uM/24h

city: Oslo

first: Nur

last: Duale

address: Lovisenbergg. 8, P.O.Box 4404 Nydalen,

department: Division of Climate and Environment Health

country: Norway

institute: Norwegian Institute of Public Health

description: Cell culture and treatment: The human colon cancer derived cell line, HCT116 from (ATcc-CCL-247, Manassas, VA). The HCT116 cells were grown in cell culture flasks (Corning Inc., USA) in McCoy’s 5A medium with L-glutamine supplemented with 10% fetal calf serum and 1% penicillin-streptomycin mixture (Cambrex, Belgium). The cell line was grown at 37oC in a humidified atmosphere of 5% of CO2 in air. Cells were seeded in 100 mm cell culture dishes (Corning Inc, USA) and allowed to attach 24 h prior to cisplatin (Cis-Diamminedichloroplatinum(II) or CDDP, Sigma) treatment. Cells in exponential growth phase were exposed to cisplatin and the cells were harvested after 24 h of exposure and prepared for further analysis. RNA preparation: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Microarrays: 21K human oligonucleotide microarrays were printed at the Norwegian Microarray Consortium using OPERON hum oligo v2.0. The microarrays consist of 70 mer, oligos representing 21,329 genes from UniGene Database. cDNA synthesis and labeling:Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA). Briefly, 20 μg of total RNA (from cisplatin treated and control cell lines) in 13 μl of nuclease-free water was combined with 1 μl of 500 ng/μl oligo-d(T)12–18. The mixture was incubated at 70°C for 10 min and cooled on ice. For each reaction, 2 μl of 10X StrataScript reaction buffer, 1 μl of unlabeled 20X dNTP mix containing amino-allyl dUTP, 1.5 μl of 0.1 M dithiothreitol and 0.5 μl of RNase Block (40 U/μl) were prepared and mixed with the RNA sample and 1 μl of 50 U/μl StrataScript RT. After incubation at 48°C for 30 min an additional 1 μl of StrataScript RT was added and incubation was continued for 30 additional minutes. RNA was degraded by adding 10 μl of 1 M NaOH, followed by a 10-min incubation at 70°C and the mixture neutralized with 10 μl of 1 M HCl. Unincorporated nucleotides were removed by precipitation of the cDNA with 4 μl of 3 M sodium acetate, 1 μl of 20 mg/ml glycogen and 100 μl of 95% ethanol at -20°C for 1 h. After centrifugation and washing the pellet with 70% ethanol, it was resuspended in 5 μl of 2x coupling buffer provided in the kit. Cy3 or Cy5 dye (Amersham), resuspended in 45 ul of DMSO, was added and the reaction incubated for 2 h at room temperature in the dark. Dye-coupled cDNA was purified with a DNA-binding spin cup, combined and concentrated by vacuum drier.

hyb_protocol: Microarray slides were prehybridized in buffer containing 5X SSC, 1% Bovine Serum Albumin and 0.1% SDS at 42°C for 1 h to block nonspecific binding and washed by dipping several times in double distilled water. The slides were then dipped in isopropanol and centrifuged to dry in 50 ml un-capped centrifuge tubes at 480 x g for 5 min. Labeled cDNAs were added to hybridization buffer (50% formamide, 5x SSC, 0.1% SDS, 4 µg/µl yeast tRNA, and 0.6 µg/µl human Cot-1 DNA), denatured for 5 min at 95°C, and applied to the arrays using a cover slip (LifterSlip, Erie Scientific). Arrays were placed in a hybridization chamber and the hybridization chamber was incubated overnight at 42°C water bath. After hybridization, washing was performed as follows: 5 min washing with  2×SSC, 0.1% SDS at 42°C, 10 min washing with  0.1x SSC, 0.1% SDS and 4x1 min washing with  0.1×SSC at room temperature. The slide was dried by centrifuging at 480x g for 5 min and scanned with an Agilent microarray laser Scanner (Agilent, Palo Alto, CA).

scan_protocol: According to the manufacturer's protocol, Agilent microarray laser Scanner (Agilent, Palo Alto, CA)

data_processing: Quality control of the scanned images (tiff-files) and conversion to numerical values were performed using the GenePix Pro 4.1 (Axon Instruments). The gpr-files obtained were further analyzed using J-Express Pro2.7 (http://www.molmine.com). Mean FG intensities were used as input values. Controls as well as flagged or empty spots were filtered away before Global Lowess Normalization. Further quality control was performed using the various Plot and Spot Image View options in J-Express. The relevant data were transferred to Excel. The average ratios, as well as average red and green intensities were calculated.

organism: Homo sapiens

source_name: HCT116 treated with 6.7uM cisplatin

extract_protocol: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA from at least three independent experiments was pooled together before labeling and hybridization to reduce possible bias for single treatment.

treatment_protocol: Treatment of cell cultures: HCT116 cell line in exponential growth phase was exposed to 6.7uM (0.4ug/ml) cisplatin 24h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.

tag: Human colon cancer derived cell line, HCT116 (ATcc-CCL-247, Manassas, VA)

source_name: HCT116 CTL


title: Ap 48 hr YE vs 12 hr YES Slide 6B


title: GCT27 1.3uM/48h

description: Cell culture and treatment: The human testis cancer cell lines GCT27 was generous gifts from Professor John R. W. Masters (University College London, UK). The GCT27 cells are derived from human primary embryonal carcinoma. The GCT27 cells were grown in cell culture flasks (Corning Inc., USA) in RPMI 1640 medium with L-glutamine supplemented with 10% fetal bovine serum and 1% penicillin -streptomycin mixture. All three cell lines were grown at 37oC in a humidified atmosphere of 5% of CO2 in air. Cells were seeded in 100 mm cell culture dishes (Corning Inc, USA) and allowed to attach 24 h prior to cisplatin (Cis-Diamminedichloroplatinum(II) or CDDP, Sigma) treatment. Cells in exponential growth phase were exposed to cisplatin and the cells were harvested after 48 h of exposure and prepared for further analysis. RNA preparation: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Microarrays: 21K human oligonucleotide microarrays were printed at the Norwegian Microarray Consortium using OPERON hum oligo v2.0. The microarrays consist of 70 mer, oligos representing 21,329 genes from UniGene Database. cDNA synthesis and labeling:Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA). Briefly, 20 μg of total RNA (from cisplatin treated and control cell lines) in 13 μl of nuclease-free water was combined with 1 μl of 500 ng/μl oligo-d(T)12–18. The mixture was incubated at 70°C for 10 min and cooled on ice. For each reaction, 2 μl of 10X StrataScript reaction buffer, 1 μl of unlabeled 20X dNTP mix containing amino-allyl dUTP, 1.5 μl of 0.1 M dithiothreitol and 0.5 μl of RNase Block (40 U/μl) were prepared and mixed with the RNA sample and 1 μl of 50 U/μl StrataScript RT. After incubation at 48°C for 30 min an additional 1 μl of StrataScript RT was added and incubation was continued for 30 additional minutes. RNA was degraded by adding 10 μl of 1 M NaOH, followed by a 10-min incubation at 70°C and the mixture neutralized with 10 μl of 1 M HCl. Unincorporated nucleotides were removed by precipitation of the cDNA with 4 μl of 3 M sodium acetate, 1 μl of 20 mg/ml glycogen and 100 μl of 95% ethanol at -20°C for 1 h. After centrifugation and washing the pellet with 70% ethanol, it was resuspended in 5 μl of 2x coupling buffer provided in the kit. Cy3 or Cy5 dye (Amersham), resuspended in 45 ul of DMSO, was added and the reaction incubated for 2 h at room temperature in the dark. Dye-coupled cDNA was purified with a DNA-binding spin cup, combined and concentrated by vacuum drier.

source_name: GCT27 treated with 1.3uM cisplatin

growth_protocol: The GCT27 cells were grown in cell culture flasks (Corning Inc., USA) in RPMI 1640 medium with L-glutamine supplemented with 10% fetal bovine serum and 1% penicillin -streptomycin mixture (Cambrex, Belgium). The cell line was grown at 37oC in a humidified atmosphere of 5% of CO2 in air.

treatment_protocol: Treatment of cell cultures: GCT27cell line in exponential growth phase was exposed to 1.3uM (0.4ug/ml) cisplatin 48h after plating. Cells were harvested after 48h of exposure and prepared for further analysis.

tag: The testis cancer cell lines GCT27 (primary embryonal carcinoma, nonseminomatous germ cell tumour).

source_name: GCT27 CTL


title: HCT116 1.3uM/24h

label_protocol: Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA).

growth_protocol: The HCT116 cells were grown in cell culture flasks (Corning Inc., USA) in McCoy’s 5A medium with L-glutamine supplemented with 10% fetal calf serum and 1% penicillin-streptomycin mixture (Cambrex, Belgium). The cell line was grown at 37oC in a humidified atmosphere of 5% of CO2 in air.

treatment_protocol: Treatment of cell cultures: HCT116 cell line in exponential growth phase was exposed to 1.3uM (0.4ug/ml) cisplatin 24h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.


title: GCT27 0.3uM/24h

description:
Cell culture and treatment: The human testis cancer cell lines GCT27 was generous gifts from Professor John R. W. Masters (University College London, UK). The GCT27 cells are derived from human primary  embryonal carcinoma. The GCT27 cells were grown in cell culture flasks (Corning Inc., USA) in RPMI 1640 medium with L-glutamine supplemented with 10% fetal bovine serum and 1% penicillin -streptomycin mixture.  All three cell lines were grown at 37oC in a humidified atmosphere of 5% of CO2 in air.
Cells were seeded in 100 mm cell culture dishes (Corning Inc, USA) and allowed to attach 24 h prior to cisplatin (Cis-Diamminedichloroplatinum(II) or CDDP, Sigma) treatment. Cells in exponential growth phase were exposed to cisplatin and the cells were harvested after 24 h  of exposure and prepared for further analysis.
RNA preparation: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Microarrays: 21K human oligonucleotide microarrays were printed at the Norwegian Microarray Consortium using OPERON hum oligo v2.0. The microarrays consist of 70 mer, oligos representing 21,329 genes from UniGene Database.
cDNA synthesis and labeling:Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA). Briefly, 20 μg of total RNA (from cisplatin treated and control cell lines) in 13 μl of nuclease-free water was combined with 1 μl of 500 ng/μl oligo-d(T)12–18. The mixture was incubated at 70°C for 10 min and cooled on ice. For each reaction, 2 μl of 10X StrataScript reaction buffer, 1 μl of unlabeled 20X dNTP mix containing amino-allyl dUTP, 1.5 μl of 0.1 M dithiothreitol and 0.5 μl of RNase Block (40 U/μl) were prepared and mixed with the RNA sample and 1 μl of 50 U/μl StrataScript RT. After incubation at 48°C for 30 min an additional 1 μl of StrataScript RT was added and incubation was continued for 30 additional minutes. RNA was degraded by adding 10 μl of 1 M NaOH, followed by a 10-min incubation at 70°C and the mixture neutralized with 10 μl of 1 M HCl. Unincorporated nucleotides were removed by precipitation of the cDNA with 4 μl of 3 M sodium acetate, 1 μl of 20 mg/ml glycogen and 100 μl of 95% ethanol at -20°C for 1 h. After centrifugation and washing the pellet with 70% ethanol, it was resuspended in 5 μl of 2x coupling buffer provided in the kit. Cy3 or Cy5 dye (Amersham), resuspended in 45 ul of DMSO, was added and the reaction incubated for 2 h at room temperature in the dark. Dye-coupled cDNA was purified with a DNA-binding spin cup, combined and concentrated by vacuum drier.

source_name: GCT27 treated with 0.3uM cisplatin

treatment_protocol: Treatment of cell cultures: GCT27 cell line in exponential growth phase was exposed to 0.3uM (0.4ug/ml) cisplatin 24h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.


title: Ap 48 hr YE vs 6 hr YES Slide 3B

source_name: Aspergillus parasiticus SU-1 6 hr YES

tag: Aspergillus parasiticus SU-1 RNA collected 6 hr post shift from 48 hr YE to YES


title: 833K 1.3uM/48h

description:
Cell culture and treatment: The human testis cancer cell lines 833K was generous gifts from Professor John R. W. Masters (University College London, UK). The 833K cells are derived from human metastatic  embryonal carcinoma. The 833K cells were grown in cell culture flasks (Corning Inc., USA) in RPMI 1640 medium with L-glutamine supplemented with 10% fetal bovine serum and 1% penicillin -streptomycin mixture.  All three cell lines were grown at 37oC in a humidified atmosphere of 5% of CO2 in air.
Cells were seeded in 100 mm cell culture dishes (Corning Inc, USA) and allowed to attach 24 h prior to cisplatin (Cis-Diamminedichloroplatinum(II) or CDDP, Sigma) treatment. Cells in exponential growth phase were exposed to cisplatin and the cells were harvested after 24 h  of exposure and prepared for further analysis.
RNA preparation: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Microarrays: 21K human oligonucleotide microarrays were printed at the Norwegian Microarray Consortium using OPERON hum oligo v2.0. The microarrays consist of 70 mer, oligos representing 21,329 genes from UniGene Database.
cDNA synthesis and labeling:Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA). Briefly, 20 μg of total RNA (from cisplatin treated and control cell lines) in 13 μl of nuclease-free water was combined with 1 μl of 500 ng/μl oligo-d(T)12–18. The mixture was incubated at 70°C for 10 min and cooled on ice. For each reaction, 2 μl of 10X StrataScript reaction buffer, 1 μl of unlabeled 20X dNTP mix containing amino-allyl dUTP, 1.5 μl of 0.1 M dithiothreitol and 0.5 μl of RNase Block (40 U/μl) were prepared and mixed with the RNA sample and 1 μl of 50 U/μl StrataScript RT. After incubation at 48°C for 30 min an additional 1 μl of StrataScript RT was added and incubation was continued for 30 additional minutes. RNA was degraded by adding 10 μl of 1 M NaOH, followed by a 10-min incubation at 70°C and the mixture neutralized with 10 μl of 1 M HCl. Unincorporated nucleotides were removed by precipitation of the cDNA with 4 μl of 3 M sodium acetate, 1 μl of 20 mg/ml glycogen and 100 μl of 95% ethanol at -20°C for 1 h. After centrifugation and washing the pellet with 70% ethanol, it was resuspended in 5 μl of 2x coupling buffer provided in the kit. Cy3 or Cy5 dye (Amersham), resuspended in 45 ul of DMSO, was added and the reaction incubated for 2 h at room temperature in the dark. Dye-coupled cDNA was purified with a DNA-binding spin cup, combined and concentrated by vacuum drier.

source_name: 833K treated with 1.3uM cisplatin

growth_protocol: The 833K cells were grown in cell culture flasks (Corning Inc., USA) in RPMI 1640 medium with L-glutamine supplemented with 10% fetal bovine serum and 1% penicillin -streptomycin mixture (Cambrex, Belgium). The cell line was grown at 37oC in a humidified atmosphere of 5% of CO2 in air.

treatment_protocol: Treatment of cell cultures: 833K cell line in exponential growth phase was exposed to 1.3uM (0.4ug/ml) cisplatin 48h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.

tag: The testis cancer cell lines 833K (metastasis, nonseminomatous germ cell tumour).

source_name: 833K CTL


title: GCT27 1.3uM/24h

treatment_protocol: Treatment of cell cultures: GCT27 cell line in exponential growth phase was exposed to 1.3uM (0.4ug/ml) cisplatin 24h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.

label_protocol: Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA). Briefly, 20 μg of total RNA (from cisplatin treated and control cell lines) in 13 μl of nuclease-free water was combined with 1 μl of 500 ng/μl oligo-d(T)12–18. The mixture was incubated at 70°C for 10 min and cooled on ice. For each reaction, 2 μl of 10X StrataScript reaction buffer, 1 μl of unlabeled 20X dNTP mix containing amino-allyl dUTP, 1.5 μl of 0.1 M dithiothreitol and 0.5 μl of RNase Block (40 U/μl) were prepared and mixed with the RNA sample and 1 μl of 50 U/μl StrataScript RT. After incubation at 48°C for 30 min an additional 1 μl of StrataScript RT was added and incubation was continued for 30 additional minutes. RNA was degraded by adding 10 μl of 1 M NaOH, followed by a 10-min incubation at 70°C and the mixture neutralized with 10 μl of 1 M HCl. Unincorporated nucleotides were removed by precipitation of the cDNA with 4 μl of 3 M sodium acetate, 1 μl of 20 mg/ml glycogen and 100 μl of 95% ethanol at -20°C for 1 h. After centrifugation and washing the pellet with 70% ethanol, it was resuspended in 5 μl of 2x coupling buffer provided in the kit. Cy3 or Cy5 dye (Amersham), resuspended in 45 ul of DMSO, was added and the reaction incubated for 2 h at room temperature in the dark. Dye-coupled cDNA was purified with a DNA-binding spin cup, combined and concentrated by vacuum drier.


title: Ap 48 hr YE vs 6 hr YES Slide 4B


title: Ap 48 hr YE vs 3 hr YES Slide 2B

source_name: Aspergillus parasiticus SU-1 3 hr YES

tag: Aspergillus parasiticus SU-1 RNA collected 3 hr post shift from 48 hr YE to YES


title: GCT27 0.3uM/48h

treatment_protocol: Treatment of cell cultures: GCT27cell line in exponential growth phase was exposed to 0.3uM (0.1ug/ml) cisplatin 48h after plating. Cells were harvested after 48h of exposure and prepared for further analysis.


title: Ap 48 hr YE vs 24 hr YES Slide 8B


title: 833K 0.3uM/48h

source_name: 833K treated with 0.3uM cisplatin

treatment_protocol: Treatment of cell cultures: 833K cell line in exponential growth phase was exposed to 0.3uM (0.4ug/ml) cisplatin 48h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.


title: 833K 0.3uM/24h

treatment_protocol: Treatment of cell cultures: 833K cell line in exponential growth phase was exposed to 0.3uM (0.1ug/ml) cisplatin 24h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.


title: Ap 48 hr YE vs 3 hr YES Slide 1B


title: Ap 24 hr YES vs 48 hr YE Slide 8A


title: Ap 48 hr YES vs 48 hr YE Slide 9A


title: Ap 48 hr YES vs 48 hr YE Slide 10A


title: Ap 48 hr YES vs 48 hr YE Slide 11A


title: Ap 3 hr YES vs 48 hr YE Slide 2A


title: Never Smoker, Sample 318

status: Public on Oct 02 2007

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

description: RNA isolated from Bronchial Epithelial cells obtained from the large airway during time of bronchosocpy

hyb_protocol: Affymetrix Suggest Protocol

scan_protocol: Affymetrix Suggest Protocol

data_processing: GCRMA generated expression value

label: Biotin

source_name: Bronchial Epithelium

label_protocol: Affymetrix Suggest Protocol

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

tag: Never Smoker


title: 833K 1.3uM/24h

treatment_protocol: Treatment of cell cultures: 833K cell line in exponential growth phase was exposed to 1.3uM (0.4ug/ml) cisplatin 24h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.


title: Relapsed MM_M315

status: Public on Apr 01 2007

city: Scottsdale

first: Rafael

last: Fonseca

state: AZ

address: 13400 E Shea Blvd

department: Hematology-Oncology

institute: Mayo Clinic

description: Gene expression data from newly diagnosed myeloma.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on HG-U133A GeneChip.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

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

label: biotin

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

tag: Hyperdiploid

tag: Normal Chromosome 13


title: N2 (wt) worms at L1 stage, third replicate

status: Public on Apr 27 2007

city: Laramie

first: David

last: Fay

state: WY

address: 1000 E. University Dept. 3944

department: MOLB

institute: University of Wyoming

description: L1 stage N2 hermaphrodites

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: expression values were generated using RMA

organism: Caenorhabditis elegans

source_name: RNA from synchronized at L1 stage C. elegans population

label_protocol: 2.5 ug total RNA were used for cDNA synthesis. cDNA synthesis, cRNA synthesis, fragmentation and labeling were performed according to Affymetrix protocol.

growth_protocol: Worms were grown on NGM plates spotted with OP50 at 20 oC.

extract_protocol: Total RNA was extracted with phenol, cleaned with phenol:chlorophorm:isoamyl alcohol (25:24:1), and then with chlorophorm:isoamyl alcohol (24:1). Total RNA was precipitated overnight at 4 oC with 4M lithium acetate and DNAseI treated before purification on RNEasy minicolumns from Qiagen.

tag: L1 stage N2 hermaphrodites


title: Ap 12 hr YES vs 48 hr YE Slide 5A

source_name: Aspergillus parasiticus SU-1 48 hr YE


title: N2 (wt) worms at L1 stage, second replicate

description: L1 stage N2 hermaphrodites

label_protocol:
2.5 ug total RNA were used for cDNA synthesis.
cDNA synthesis, cRNA synthesis, fragmentation and labeling were performed according to Affymetrix protocol.


title: Ap 6 hr YES vs 48 hr YE Slide 3A


title: Ap 12 hr YES vs 48 hr YE Slide 6A


title: NA19201

status: Public on Feb 09 2007

city: Geneva

first: Emmanouil

middle: T

last: Dermitzakis

address: 1 Rue Michel-Servet

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

description: HapMap YRI_parent Female

hyb_protocol: 1.5ug cRNA as as per Gene expression on Sentrix® Arrays direct hybridization system manual (Illumina Doc. #11161707, Rev. B). Arrays were hybridized for 18 hours and stained with Cy3-Streptavidin.

scan_protocol: Standard Illumina protocol, PMT 638

data_processing: background-corrected values for each single bead type (raw data) were normalised on a log scale using a quantile normalization method (Bolstad et al. Bioinformatics, 2003. 19(2): p. 185-93) across replicates of a single individual, followed by a median normalisation across individuals of a single population.

source_name: lymphoblastoid cell line

label_protocol: One-quarter scale Message Amp II reactions (Ambion) were performed for each RNA extraction using 200 ng of total RNA. Biotin-16-UTP (Perkin Elmer) made up half of the UTP used in the in vitro transcription (IVT) reaction (37 Celsius for 18 hours).

growth_protocol: RPMI 1640 with Glutamax I medium (Invitrogen Corporation) supplemented with 10% fetal calf serum and 1% penicillin and streptomycin mix (Invitrogen Corporation). Cells lines were harvested at a density of 0.6 ~ 1 x 10^6 cells/ml and at least 80 % viability. Cultures were spun for 5 min at 1000 g, and the resulting pellets were washed once in PBS and lysed by adding 2 ml of micro glass beads (Sigma) and vortexing in 1 ml lysis solution containing beta-mercaptoethanol (Qiagen, RNeasy kit). Cell lysates were stored at -80°C.

extract_protocol: RNAs were extracted using RNeasy mini kits with on-column DNAse I digestion (Qiagen).

tag: HapMap YRI_parent, Female


title: NA19204

description: HapMap YRI_parent Female


title: N2 (wt) worms at L1 stage, first replicate

description: L1 stage N2 hermaphrodites


title: NA19223

description: HapMap YRI_parent Male

tag: HapMap YRI_parent, Male


title: NA19192

description: HapMap YRI_parent Male


title: NA19207

description: HapMap YRI_parent Male


title: Ap 24 hr YES vs 48 hr YE Slide 7A

source_name: Aspergillus parasiticus SU-1 24 hr YES


title: Ap 3 hr YES vs 48 hr YE Slide 1A


title: NA19239

description: HapMap YRI_parent Male


title: NA19203

description: HapMap YRI_parent Male


title: NA19238

description: HapMap YRI_parent Female


title: Ap 6 hr YES vs 48 hr YE Slide 4A


title: NA19193

description: HapMap YRI_parent Female


title: NA19209

description: HapMap YRI_parent Female


title: NA19206

description: HapMap YRI_parent Female


title: NA19222

description: HapMap YRI_parent Female


title: NA19172

description: HapMap YRI_parent Female


title: NA19200

description: HapMap YRI_parent Male


title: NA19171

description: HapMap YRI_parent Male


title: NA19143

description: HapMap YRI_parent Female


title: NA19153

description: HapMap YRI_parent Male


title: NA19144

description: HapMap YRI_parent Male


title: NA19159

description: HapMap YRI_parent Female


title: NA19140

description: HapMap YRI_parent Female


title: NA19138

description: HapMap YRI_parent Male


title: NA19141

description: HapMap YRI_parent Male


title: NA19152

description: HapMap YRI_parent Female


title: NA19160

description: HapMap YRI_parent Male


title: NA19210

description: HapMap YRI_parent Male


title: NA19102

description: HapMap YRI_parent Female


title: NA19127

description: HapMap YRI_parent Female


title: NA19131

description: HapMap YRI_parent Female


title: NA19119

description: HapMap YRI_parent Male


title: NA19098

description: HapMap YRI_parent Male


title: NA19099

description: HapMap YRI_parent Female


title: NA19116

description: HapMap YRI_parent Female


title: NA19137

description: HapMap YRI_parent Female


title: NA19128

description: HapMap YRI_parent Male


title: NA19092

description: HapMap YRI_parent Male


title: NA19130

description: HapMap YRI_parent Male


title: NA19093

description: HapMap YRI_parent Female


title: NA18862

description: HapMap YRI_parent Male


title: NA18912

description: HapMap YRI_parent Female


title: NA19101

description: HapMap YRI_parent Male


title: NA18858

description: HapMap YRI_parent Female


title: NA18913

description: HapMap YRI_parent Male


title: NA18870

description: HapMap YRI_parent Female


title: NA18855

description: HapMap YRI_parent Female


title: NA18861

description: HapMap YRI_parent Female


title: NA18871

description: HapMap YRI_parent Male


title: NA18859

description: HapMap YRI_parent Male


title: NA18852

description: HapMap YRI_parent Female


title: NA18856

description: HapMap YRI_parent Male


title: NA18523

description: HapMap YRI_parent Female


title: NA18853

description: HapMap YRI_parent Male


title: NA18517

description: HapMap YRI_parent Female


title: NA18507

description: HapMap YRI_parent Male


title: NA18505

description: HapMap YRI_parent Female


title: NA18516

description: HapMap YRI_parent Male


title: NA19007

description: HapMap JPT Male

tag: HapMap JPT, Male


title: NA18504

description: HapMap YRI_parent Male


title: NA18508

description: HapMap YRI_parent Female


title: NA18522

description: HapMap YRI_parent Male


title: NA18502

description: HapMap YRI_parent Female


title: NA18501

description: HapMap YRI_parent Male


title: NA18999

description: HapMap JPT Female

tag: HapMap JPT, Female


title: NA18998

description: HapMap JPT Female


title: NA19012

description: HapMap JPT Male


title: NA19005

description: HapMap JPT Male


title: NA18997

description: HapMap JPT Female


title: NA19000

description: HapMap JPT Male


title: NA18990

description: HapMap JPT Male


title: NA18980

description: HapMap JPT Female


title: NA19003

description: HapMap JPT Female


title: NA18995

description: HapMap JPT Male


title: NA18991

description: HapMap JPT Female


title: NA18994

description: HapMap JPT Male


title: NA18992

description: HapMap JPT Female


title: NA18973

description: HapMap JPT Female


title: NA18981

description: HapMap JPT Female


title: NA18976

description: HapMap JPT Female


title: NA18978

description: HapMap JPT Female


title: NA18965

description: HapMap JPT Male


title: NA18968

description: HapMap JPT Female


title: NA18987

description: HapMap JPT Female


title: NA18974

description: HapMap JPT Male


title: NA18975

description: HapMap JPT Female


title: NA18961

description: HapMap JPT Male


title: NA18969

description: HapMap JPT Female


title: NA18972

description: HapMap JPT Female


title: NA18971

description: HapMap JPT Male


title: NA18966

description: HapMap JPT Male


title: NA18964

description: HapMap JPT Female


title: NA18970

description: HapMap JPT Male


title: NA18967

description: HapMap JPT Male


title: NA18952

description: HapMap JPT Male


title: NA18956

description: HapMap JPT Female


title: NA18948

description: HapMap JPT Male


title: NA18951

description: HapMap JPT Female


title: NA18953

description: HapMap JPT Male


title: NA18949

description: HapMap JPT Female


title: NA18945

description: HapMap JPT Male


title: NA18940

description: HapMap JPT Male


title: NA18943

description: HapMap JPT Male


title: NA18960

description: HapMap JPT Male


title: NA18959

description: HapMap JPT Male


title: NA18944

description: HapMap JPT Male


title: NA18947

description: HapMap JPT Female


title: NA18942

description: HapMap JPT Female


title: NA18637

description: HapMap CHB Male

tag: HapMap CHB, Male


title: NA18633

description: HapMap CHB Male


title: NA18623

description: HapMap CHB Male


title: NA18622

description: HapMap CHB Male


title: NA18636

description: HapMap CHB Male


title: NA18612

description: HapMap CHB Male


title: NA18620

description: HapMap CHB Male


title: NA18621

description: HapMap CHB Male


title: NA18605

description: HapMap CHB Male


title: NA18571

description: HapMap CHB Female

tag: HapMap CHB, Female


title: NA18577

description: HapMap CHB Female


title: NA18594

description: HapMap CHB Female


title: NA18624

description: HapMap CHB Male


title: NA18635

description: HapMap CHB Male


title: NA18611

description: HapMap CHB Male


title: NA18579

description: HapMap CHB Female


title: NA18593

description: HapMap CHB Female


title: NA18582

description: HapMap CHB Female


title: NA18603

description: HapMap CHB Male


title: NA18608

description: HapMap CHB Male


title: NA18570

description: HapMap CHB Female


title: NA18566

description: HapMap CHB Female


title: NA18576

description: HapMap CHB Female


title: NA18609

description: HapMap CHB Male


title: NA18564

description: HapMap CHB Female


title: NA18572

description: HapMap CHB Male


title: NA18592

description: HapMap CHB Female


title: NA18573

description: HapMap CHB Female


title: NA18563

description: HapMap CHB Male


title: NA18555

description: HapMap CHB Female


title: NA18558

description: HapMap CHB Male


title: NA18561

description: HapMap CHB Male


title: NA18562

description: HapMap CHB Male


title: NA18547

description: HapMap CHB Female


title: NA18550

description: HapMap CHB Female


title: NA18552

description: HapMap CHB Female


title: NA12892

description: HapMap CEU_parent Female

tag: HapMap CEU_parent, Female


title: NA18545

description: HapMap CHB Female


title: NA18529

description: HapMap CHB Female


title: NA18542

description: HapMap CHB Female


title: NA18532

description: HapMap CHB Female


title: NA18540

description: HapMap CHB Female


title: NA18526

description: HapMap CHB Female


title: NA12891

description: HapMap CEU_parent Male

tag: HapMap CEU_parent, Male


title: NA18524

description: HapMap CHB Male


title: NA18537

description: HapMap CHB Female


title: NA12762

description: HapMap CEU_parent Male


title: NA12872

description: HapMap CEU_parent Male


title: NA12763

description: HapMap CEU_parent Female


title: NA12874

description: HapMap CEU_parent Male


title: NA12812

description: HapMap CEU_parent Male


title: NA12873

description: HapMap CEU_parent Female


title: NA12814

description: HapMap CEU_parent Male


title: NA12815

description: HapMap CEU_parent Female


title: NA12875

description: HapMap CEU_parent Female


title: NA12813

description: HapMap CEU_parent Female


title: NA12760

description: HapMap CEU_parent Male


title: NA12761

description: HapMap CEU_parent Female


title: NA12751

description: HapMap CEU_parent Female


title: NA12716

description: HapMap CEU_parent Male


title: NA12264

description: HapMap CEU_parent Male


title: NA12717

description: HapMap CEU_parent Female


title: NA12249

description: HapMap CEU_parent Female


title: NA12750

description: HapMap CEU_parent Male


title: NA12156

description: HapMap CEU_parent Female


title: NA12145

description: HapMap CEU_parent Female


title: NA12236

description: HapMap CEU_parent Female


title: NA12155

description: HapMap CEU_parent Male


title: NA12248

description: HapMap CEU_parent Male


title: NA12239

description: HapMap CEU_parent Female


title: NA12146

description: HapMap CEU_parent Male


title: NA12006

description: HapMap CEU_parent Female


title: NA11994

description: HapMap CEU_parent Male


title: NA12144

description: HapMap CEU_parent Male


title: NA12154

description: HapMap CEU_parent Male


title: NA12043

description: HapMap CEU_parent Male


title: NA12004

description: HapMap CEU_parent Female


title: NA12057

description: HapMap CEU_parent Female


title: NA12056

description: HapMap CEU_parent Male


title: NA12234

description: HapMap CEU_parent Female


title: NA12044

description: HapMap CEU_parent Female


title: NA12005

description: HapMap CEU_parent Male


title: NA11995

description: HapMap CEU_parent Female


title: NA11992

description: HapMap CEU_parent Male


title: NA12003

description: HapMap CEU_parent Male


title: NA11993

description: HapMap CEU_parent Female


title: NA11882

description: HapMap CEU_parent Female


title: NA11840

description: HapMap CEU_parent Female


title: NA11881

description: HapMap CEU_parent Male


title: NA11839

description: HapMap CEU_parent Male


title: NA11829

description: HapMap CEU_parent Male


title: NA07357

description: HapMap CEU_parent Male


title: NA11830

description: HapMap CEU_parent Female


title: NA11832

description: HapMap CEU_parent Female


title: NA11831

description: HapMap CEU_parent Male


title: NA07034

description: HapMap CEU_parent Male


title: NA07345

description: HapMap CEU_parent Female


title: 518-75-2 Citrinin 2nd-3

status: Public on Nov 01 2006

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Citrinin 2nd-3

hyb_protocol: Hybridized for 16 h at 42 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array (Hitachi Software Engineering Co., Ltd.).

data_processing: GeneSpring ver 7.3.1 (Agilent Technologies Inc.)

organism: Saccharomyces cerevisiae

source_name: citrinin treated for 2 h, Cy5

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in 50 ml YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 300 ppm (final concentration).

extract_protocol: Hot-phenol

treatment_protocol: Citrinin was purchased from MP Biochemicals and dissolved with 100% DMSO. (stock solution = 20,000 ppm)

tag: strain S288C

source_name: control (solvent treated for 2h), Cy3

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in 50 ml YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. DMSO as  the solvent were added into OD=1 (exponential growing) culture with 1.5% (750 ul).

treatment_protocol: 100% DMSO


title: NA07056

description: HapMap CEU_parent Female


title: NA07000

description: HapMap CEU_parent Female


title: NA07022

description: HapMap CEU_parent Male


title: NA07055

description: HapMap CEU_parent Female


title: 518-75-2 Citrinin 1st-3

description: Citrinin 1st-3

source_name: citrinin treated for 2 h, Cy3

source_name: control (solvent treated for 2h), Cy5


title: 518-75-2 Citrinin 3rd-3

description: Citrinin 3rd-3


title: 518-75-2 Citrinin 3rd-1

description: Citrinin 3rd-1


title: 518-75-2 Citrinin 3rd-2

description: Citrinin 3rd-2


title: NA06994

description: HapMap CEU_parent Male


title: 518-75-2 Citrinin 2nd-1

description: Citrinin 2nd-1


title: NA06985

description: HapMap CEU_parent Female

hyb_protocol: 1.5ug cRNA as lumina Doc. #11161707, Rev. B). Arrays were hybridized for 18 hours and stained with Cy3-Streptavidin.


title: NA06993

description: HapMap CEU_parent Male


title: 518-75-2 Citrinin 1st-1

description: Citrinin 1st-1


title: 518-75-2 Citrinin 3rd-H

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning.  Data with flag value 0 were used for LOWESS normalization processing. Merging high and low scanned data were done on the GeneSpring and represented as "AVG_VALUE".

hyb_protocol: Hybridized for 16-18 h at 65 C

scan_protocol: Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).

label_protocol: Cyscribe first-strand cDNA labelling kit (Amersham Biosciences)


title: 518-75-2 Citrinin 1st-2

description: Citrinin 1st-2


title: 518-75-2 Citrinin 3rd-L

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from low power scanning.  Data with flag value 0 were used for LOWESS normalization processing. Merging high and low scanned data were done on the GeneSpring and represented as "AVG_VALUE".


title: 518-75-2 Citrinin 2nd-H


title: 518-75-2 Citrinin 2nd-L


title: 518-75-2 Citrinin 1st-H


title: 518-75-2 Citrinin 1st-L


title: met1_RNA_expression_A

status: Public on Nov 26 2006

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Expression profiling of met1-6 mutant plants compared to wild type (two biological replicates).  The values are log2 signal ratios of met1-6 cDNA / wild type cDNA.  RNA from each sample was converted into double-stranded cDNA using an oligo d(T) primer according to the instructions for the SuperScript Double-Stranded cDNA Sythesis kit (Invitrogen).  The cDNA samples were then labeled and hybridized.

hyb_protocol: Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Set MAUI hybridization unit to 42 deg C and allow time for the temperature to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to completely dissolve the sample. Spin the tube down briefly to collect the contents in the bottom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5 microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microliter Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are included in the hybridization as controls that hybridize to alignment features on the NimbleGen arrays. They are required for proper extraction of array data from the scanned image. Mix the tube briefly then spin down to collect the contents in the bottom and place at 95 deg C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at this temperature until you are are ready for sample loading. Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disassembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put the array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up to temperature. Load the sample using the pipet supplied with the MAUI Station and following manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sample may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If there are, very gently massage any bubbles to either of the ends, away from the center of the array. Avoid applying too much pressure since this will force liquid out of the ports. Place the loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Close the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm that the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours. Prior to removing the array from the MAUI Hybridization Station, prepare the following solutions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One dish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works well. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften the adhesive on the hybridization chamber; this will help prevent braking the array. Place the remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I: 225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C. Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not let the surface of the slide dry out at any point during washing. While the chip is submerged, carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfer the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agitation. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wash over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation. Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dark desiccator.

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Axon Scanner (model 4000B). Turn on the power of the scanner. The switch is on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow lasers to warm. Open the scanner door and open the side carriage. Place chip in carriage so that array is face down and barcode end is closest to you. Move the black lever on the left side of the carriage left until the array is lying flat in the carriage. Release the lever so that the arry is pushed over gently to the right side of the carriage and held firmly. Close the carriage (you should hear a click) and slide the scanner door shut. Open the hardware settings. Select the following settings for scanning: Wavelength (532=Cy3, 635=Cy5). Set the 532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750. Power=100%. Pixel Size=5m. Lines to average=1. Focus position=0micrometer. Select Image/Ratio to view both channels simultaneously. Perform a preview scan by clicking on the fast-forward icon. Stop scan once the full arry is in view by pressing the stop icon. Switch to zoom mode by clicking on the array image and pressing Z. Click and drag the mouse on the area in which you want to zoom. Center the image of the entire array area within the viewing window. Under Tools on the left side of the screen, click the Scan Area icon. Click and drag to define a box that bounds the visibile array area. The box dimensions should be stretched to create a box just slightly larger than the array area. It is critical to include all of the corner probes within the scan image. Scan chip by clicking the play icon. While scanning, set the zoom level to view the whole image and adjust the brightness and contrast of the displayed image to eliminate visible saturation. Based on the appearance of the array features, adjust the PMT setting as appropriate. The features should be mostly yellow. If your features are mostly green, either decrease the 532 PMT or raise the 635 PMT. If the features are mostly red or orange, either raise the 532 PMT or decrease the 635 PMT. Zoom the view to a region scanned under the most recent PMT settings and click on the Histogram tab at the top of the left side of the screen to check global intensity of the features. On the top left side of the screen make sure you have the 532 and 635 wavelength boxes checked so both wavelength histograms are displayed. Make sure the Log Axis box is checked. You want the red and green curves to be as close as possible to one another. If the red curve is above the green, lower the red PMT setting or raise the green PMT setting. You want the curve to have 1e-5 normalized counts at the 65,000 intensity level (saturation). This means that you have about 1% of the features saturated. The position of the two curves on top of each other is more important than hitting the 1% saturation mark.  The histogram only graphs the area of the image that is viewable in the screen on the image tab. If the histogram is no longer changing then either the chip is done scanning or the area that you can see on the image screen has been scanned. After the PMT settings are properly adjusted, stop the current scan, do not save this image. Restart the scan under the new settings and wait until the scan has completed. Save the images. Make sure you save both the 532nm and 635nm images as separate single image tif files.

data_processing: Log base 2 (ch_635/ch_532) ratios were bi-weight mean centered

organism: Arabidopsis thaliana

source_name: Arabidopsis, ecotype Col-gl, adult plants

label_protocol: Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol: Methods are described in publication available at http://dx.doi.org/10.1038/ng1929.

tag: Ecotype

value: Col-gl, Age:adult plant, Tissue:whole plant

source_name: Arabidopsis, ecotype Col-gl with met1-6 mutation, adult plants

label_protocol: Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

value: met1-6 mutantion in the Col-gl background, Age:adult plant, Tissue:whole plant


title: HF1113_Xba

status: Public on Oct 24 2006

type: genomic

city: Bethesda

first: Howard

last: Fine

state: MD

address: 9030 Old Georgetown Rd

department: Neurological Disorders and Stroke

institute: National Cancer Institute

description: Snap-frozen sections of areas immediately adjacent to the region used for the histopathologic diagnosis

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner 3000, GCOS 1.2

data_processing: DAT and CEL files were processed by Affymetrix GCOS 1.2 with default analysis settings. Calls generated by GDAS 3.0 with confidence threshold 0.25. Copy numbers were generated by Affymetrix Chromosome Copy Number Tool, which uses reference set of 145 normal individuals.

molecule: genomic DNA

source_name: Brain tissue (snap-frozen sections) from glioma patient of Henry Ford Hospital

label_protocol: Standard Affymetrix procedures

extract_protocol: Extraction of genomic DNA with high molecular weight was performed using QIamp micro DNA extraction kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: Tissue

value: brain tumor, Histopathological diagnosis:mixed , grade 2


title: HF1313_Xba

value: brain tumor, Histopathological diagnosis:astrocytoma, grade 2


title: HF1510_Xba

value: brain tumor, Histopathological diagnosis:glioblastoma, grade 4


title: HF1708_Xba

value: brain tumor, Histopathological diagnosis:astrocytoma , grade 2


title: methylation_IP/total_DNA 60930

description: Antibody-based methylation mapping of the Arabidopsis genome.  The DNA was extracted from a line in the Colombia background.  The values are log2 signal ratios of immunoprecipitated DNA / input DNA.  This dataset was used for all the analyses in the manuscript.

source_name: sonicated total genomic DNA

label_protocol: Sample labeling protocol provided by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

tag: Ecotype:Columbia, Age

source_name: Immunoprecipitated methylated genomic DNA

label_protocol: Sample labeling protocol provided by NimbleGen (http://www.nimblegen.com/products/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

value: Columbia, Age 25 days old, Tissue:whole plant without roots


title: HF1628_Xba


title: HF1702_Xba


title: met1_RNA_expression_B


title: HF1671_Xba


title: HF1667_Xba


title: HF0118_Xba

value: brain tumor, Histopathological diagnosis:mixed , grade 3


title: HF1677_Xba

value: brain tumor, Histopathological diagnosis:oligodendroglioma, grade 2


title: HF1618_Xba


title: HF1114_Xba

value: brain tumor, Histopathological diagnosis:astrocytoma, grade 3


title: HF1640_Xba


title: methylation_IP/total_DNA 60935

description: Antibody-based methylation mapping of the Arabidopsis genome.  The DNA was extracted from a line in the Colombia background that is different from the one in sample 60930.  Because this Arabidopsis line contained some chromosomal regions different from the Ws background, it was used only for validation.

value: Columbia, Age:25 days old, Tissue:whole plants without roots

value: Columbia, Age 25 days old, Tissue:whole plants without roots


title: HF1606_Xba


title: HF1568_Xba


title: HF1588_Xba


title: HF1589_Xba


title: HF1581_Xba

value: brain tumor, Histopathological diagnosis:astrocytoma , grade 3


title: HF1608_Xba


title: HF1560_Xba


title: HF1585_Xba


title: HF1613_Xba


title: HF1553_Xba


title: HF1538_Xba


title: HF1534_Xba


title: HF1540_Xba


title: HF1494_Xba


title: HF1511_Xba


title: HF1493_Xba

value: brain tumor, Histopathological diagnosis:oligodendroglioma, grade 3


title: HF1502_Xba


title: HF1517_Xba


title: HF1551_Xba


title: HF1469_Xba


title: HF1489_Xba


title: HF1381_Xba


title: HF1433_Xba


title: HF1442_Xba


title: HF1458_Xba


title: HF1380_Xba


title: HF1382_Xba


title: HF1397_Xba


title: HF1407_Xba


title: HF1490_Xba


title: HF1409_Xba


title: HF1366_Xba


title: HF1487_Xba


title: HF1463_Xba


title: HF1398_Xba


title: HF1357_Xba


title: HF1356_Xba


title: HF1338_Xba


title: HF1348_Xba


title: HF1345_Xba


title: HF1318_Xba


title: HF1334_Xba


title: HF1255_Xba


title: HF1325_Xba


title: HF1344_Xba


title: HF1269_Xba


title: HF1246_Xba


title: HF1232_Xba


title: HF1242_Xba


title: HF1286_Xba


title: HF1264_Xba


title: HF1297_Xba


title: HF1295_Xba


title: HF1262_Xba


title: HF1326_Xba_2


title: HF1220_Xba


title: HF1235_Xba


title: HF1219_Xba


title: HF1227_Xba


title: HF1280_Xba


title: HF1186_Xba


title: HF1178_Xba


title: HF1185_Xba


title: HF1167_Xba


title: HF1139_Xba


title: HF1122_Xba


title: HF1150_Xba


title: HF1156_Xba


title: HF1137_Xba


title: HF1136_Xba


title: HF1090_Xba


title: HF1097_Xba


title: HF1077_Xba


title: HF1071_Xba


title: HF1057_Xba


title: HF1087_Xba


title: HF1191_Xba


title: HF1000_Xba


title: HF0992_Xba


title: HF0975_Xba


title: HF0996_Xba


title: HF0963_Xba


title: HF1059_Xba


title: HF0966_Xba


title: HF0982_Xba


title: HF1032_Xba


title: HF1058_Xba


title: HF0990_Xba


title: HF0954-2_Xba

source_name: Brain tissue (snap-frozen sections) from  patient of Henry Ford Hospital

value: brain tumor, Histopathological diagnosis:


title: HF0931_Xba


title: HF0962_Xba


title: HF0953_Xba


title: HF0899_Xba


title: HF0960_Xba


title: HF0986_Xba


title: HF0897_Xba


title: HF0831_Xba


title: HF0844_Xba


title: HF0850_Xba


title: HF0855_Xba


title: HF0828_Xba


title: HF0914_Xba


title: HF0813_Xba


title: HF0802_Xba


title: HF0822_Xba


title: HF0749_Xba


title: HF0666_Xba


title: HF0790_Xba


title: HF0778_Xba


title: HF0894_Xba


title: HF0702_Xba


title: HF0627_Xba


title: HF0606_Xba


title: HF0639_Xba


title: HF0652-4_Xba


title: HF0583_Xba


title: HF0757_Xba


title: HF0816_Xba


title: HF0615_Xba


title: HF0936_Xba


title: HF0543_Xba_2


title: HF0599_Xba


title: HF0510_Xba


title: HF0505_Xba


title: HF0491_Xba


title: HF0608_Xba


title: HF0488_Xba


title: HF0471_Xba


title: HF0520_Xba


title: HF0654_Xba


title: HF0450_Xba


title: HF0445_Xba


title: HF0442-5_Xba


title: HF0453_Xba


title: HF0350_Xba


title: HF0460_Xba


title: HF0291_Xba


title: HF0434_Xba


title: HF0184_Xba


title: HF0252_Xba


title: HF0244_Xba


title: HF0332_Xba


title: HF0435_Xba


title: HF0212_Xba


title: HF0285_Xba


title: HF0251_Xba


title: HF0152_Xba


title: HF0223_Xba


title: HF0108_Xba


title: HF0189_Xba


title: HF0180_Xba


title: HF0089_Xba


title: HF0300-3_Xba


title: HF0218_Xba


title: HF0066_Xba


title: HF0017_Xba


title: HF0408_Xba


title: HF0138_Xba


title: HF1510_Hind


title: HF0026_Xba


title: HF1114_Hind


title: HF1113_Hind


title: HF0024_Xba_2


title: HF0118_Hind


title: HF1708_Hind


title: HF0031_Xba


title: HF1677_Hind


title: HF1640_Hind


title: HF1613_Hind


title: HF1608_Hind


title: HF1313_Hind


title: HF1628_Hind


title: HF1667_Hind


title: HF1618_Hind


title: HF0087_Xba


title: HF0050_Xba


title: HF1671_Hind


title: HF1702_Hind


title: HF1568_Hind


title: HF1588_Hind


title: HF0329_Xba


title: HF1553_Hind


title: HF1581_Hind


title: HF1551_Hind


title: HF1560_Hind


title: HF1538_Hind


title: HF1589_Hind


title: HF1534_Hind


title: HF1540_Hind


title: HF1585_Hind


title: HF1606_Hind


title: HF1487_Hind


title: HF1494_Hind


title: HF0022_Xba


title: HF1511_Hind


title: HF1502_Hind


title: HF1493_Hind


title: HF1489_Hind


title: HF1490_Hind


title: HF1517_Hind


title: HF1407_Hind


title: HF1398_Hind


title: HF1397_Hind


title: HF1433_Hind


title: HF1442_Hind_3


title: HF1463_Hind


title: HF1409_Hind


title: HF1382_Hind


title: HF1458_Hind


title: HF1366_Hind


title: HF1381_Hind_2


title: HF1380_Hind


title: HF1357_Hind_2


title: HF1356_Hind


title: HF1348_Hind


title: HF1334_Hind_2


title: HF1345_Hind


title: HF1297_Hind


title: HF1326_Hind


title: HF1325_Hind


title: HF1318_Hind


title: HF1264_Hind


title: HF1242_Hind


title: HF1280_Hind


title: HF1262_Hind


title: HF1338_Hind


title: HF1235_Hind


title: HF1255_Hind


title: HF1246_Hind


title: HF1219_Hind


title: HF1269_Hind


title: HF1186_Hind


title: HF1178_Hind


title: HF1191_Hind


title: HF1150_Hind


title: HF1156_Hind


title: HF1469_Hind_2


title: HF1232_Hind


title: HF1227_Hind


title: HF1220_Hind


title: HF1139_Hind_2


title: HF1137_Hind


title: HF1122_Hind


title: HF1087_Hind


title: HF1185_Hind


title: HF1167_Hind


title: HF1077_Hind_2


title: HF1097_Hind_3


title: HF1344_Hind


title: HF1071_Hind


title: HF1058_Hind


title: HF1136_Hind


title: HF1059_Hind


title: HF1090_Hind


title: HF1032_Hind


title: HF0982_Hind


title: HF0966_Hind


title: HF1000_Hind


title: HF0996_Hind


title: HF0990_Hind


title: HF0986_Hind


title: HF1057_Hind


title: HF0975_Hind


title: HF0954-2_Hind


title: HF0992_Hind_3


title: HF0953_Hind


title: HF1295_Hind


title: HF0963_Hind


title: HF0899_Hind


title: HF0936_Hind


title: HF0962_Hind


title: HF0931_Hind


title: HF0960_Hind


title: HF0850_Hind


title: HF0897_Hind


title: HF0844_Hind


title: HF0855_Hind


title: HF0894_Hind


title: HF0822_Hind


title: HF0816_Hind


title: HF0831_Hind


title: HF0813_Hind


title: HF0790_Hind


title: HF0828_Hind


title: HF0778_Hind


title: HF0702_Hind


title: HF0914_Hind


title: HF0802_Hind


title: HF0654_Hind


title: HF0627_Hind


title: HF0599_Hind


title: HF0639_Hind


title: HF0749_Hind


title: HF0757_Hind


title: HF0583_Hind


title: HF0505_Hind


title: HF0543_Hind


title: HF0520_Hind


title: HF0510_Hind


title: HF0488_Hind


title: HF0615_Hind


title: HF0450_Hind


title: HF0445_Hind


title: HF0666_Hind


title: HF0471_Hind


title: HF0608_Hind


title: HF0453_Hind


title: HF0491_Hind


title: HF0652-4_Hind


title: HF0350_Hind_2


title: HF0332_Hind


title: HF0460_Hind


title: HF0329_Hind


title: HF0435_Hind


title: HF0434_Hind


title: HF0291_Hind


title: HF0442-5_Hind


title: HF0252_Hind_2


title: HF0606_Hind


title: HF0184_Hind


title: HF0251_Hind


title: HF0108_Hind


title: HF0189_Hind


title: HF0152_Hind


title: HF0300-3_Hind


title: HF0223_Hind


title: HF0218_Hind


title: HF0212_Hind


title: HF0244_Hind


title: HF0180_Hind


title: HF0285_Hind


title: HF0087_Hind


title: HF0138_Hind


title: HF0066_Hind


title: HF0408_Hind


title: 149-29-1 patulin 3 (low power scan)

status: Public on Jul 13 2005

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from low power scanning. Additional flags were not responsible for the normalization.

hyb_protocol: Hybridized for 24-36 h at 65 C

scan_protocol: Scan Array 4000 (GSI Lunomics) was used for scanning. Array images were analyzed with Gene Pix (Inter Medical).

data_processing: GeneSpring ver 7.2 (Agilent technologies)

molecule: polyA RNA

source_name: patulin treated (2 h), Cy5

growth_protocol: Saccharomyces cerevisiae strain S288C was grown in YPD medium (2% polypeptone, 1% yeast extract, 2% glucose) at 25 C with shaking. Chemical solution were added into OD=1 (exponential growing) culture with 50 ppm (final concentration).

extract_protocol: Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)

treatment_protocol: Patulin was purchased from MP Biochemicals and dissolved with 100% DMSO.

source_name: control (before treatment), Cy3

growth_protocol: cells at OD=1


title: 149-29-1 patulin 3 (high power scan)

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning. Additional flags were not responsible for the normalization.


title: HF0050_Hind


title: HF0026_Hind


title: HF0031_Hind


title: HF0017_Hind


title: 149-29-1 patulin 1 (low power scan)


title: HF0089_Hind


title: 149-29-1 patulin 2 (high power scan)


title: HF0024_Hind_2


title: 149-29-1 patulin 2 (low power scan)


title: HF0022_Hind_2


title: 149-29-1 patulin 1 (high power scan)

description: In order to rescue data that had a higher intensity than the scanning range, the array were scanned twice with different laser power. This data were result from high power scanning.

data_processing: GeneSpring (Agilent technologies)


title: 12m x Guy11 48h-3

status: Public on Nov 01 2007

first: Tomoaki

last: Kato

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

description:
Keyword : Oryza sativa
Keyword : Magnaporthe grisea
Guy11 is a wild type of the Magnaporthe grisea.

hyb_protocol: Kit : in situ hybridization kit plus Manufacture : Agilent Technologies

scan_protocol: Scanner : Agilent DNA microarray scanner Manufacture: Agilent Technologies

data_processing: Feature Extraction ver 9.1 (Agilent Technologies)

organism: Oryza sativa

source_name: Mock infection

label_protocol:
kit : Low input RNA linear amplification kit
Manufacture : Agilent Technologies

growth_protocol: Ten rice seeds (Oryza sativa L. cv. IRBL12-M) were sown in a pot that has been filled with a commercial soil mixture (Bonsol type 1; Sumitomo Chemical, Osaka, Japan). The pot was then submerged in water inside a container and was kept in a greenhouse at 28 degreeC under natural sunlight for 14 days.

extract_protocol:
kit : RNeasy mini kit
Manufacture : Qiagen

treatment_protocol: Fourteen days old rice plants were sprayed with conidia-free water and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 48hpi.

tag: cultivar

tag: Age

value: 14 days

value: Leaf

source_name: Guy11 infection

treatment_protocol: Fourteen days old rice plants were sprayed with Guy11 conidia suspension (100,000/mL) and inoculated in a dew chamber at 25 degreeC for 16 h then transferred to a greenhouse.  Total RNAs were isolated from fourth leaves at 48hpi.

value: A wild type of the Magnaporthe grisea.


title: FEC100_0020_A

status: Public on Oct 18 2007

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Patients included in clinical trials (PACS01 / PEGASE01).

hyb_protocol: Labelled cDNAs were then hybridized in 0.3 ml hybridization mix in scintillation vials for 48 h at 68° C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68° C for 90 min.

scan_protocol: DNA microarrays were scanned at 25-µm resolution using a Fuji BAS 5000 image plate system (Raytest, Paris, France). The hybridization signals were quantified using ArrayGauge software v.1.3 (Fuji, Ltd, Tokyo, Japan).

data_processing: Data were background noise subtracted (negative controls ± 6 SD), then normalized by original global intensity of hybridization and finally log2-transformed. Only genes well measured for 70% of patients were retained. Data have been normalized with an expression data correction by the amount of PCR product spotted onto the membrane (ratio : Patient probe / Testing probe).

source_name: FEC100_0020_A Breast tumor tissue

label_protocol: Between 0.4 and one µg of total RNA was used as template to generate cDNA bearing T7 promoter, then antisense RNA (aRNA) was generated by in vitro transcription using MEGAscript technology according to the Ambion protocol (Ambion Inc., Austin TX). An aliquot of 2µg of labelled aRNA was then primed with random hexaprimers and reverse transcribed with a mix of cold dNTPs and [a-33P]dCTP.

extract_protocol: All RNA was prepared on the same platform by the CsCl-cushion, as described (Chirgwin, 1979, Biochemistry, 18, 5294-5299.). The quality and the quantity of RNA samples were evaluated by Agilent 2100 Bioanalyser RNA LabChip kit (Agilent Technologies, Palo Alto, CA, USA).

tag: Breast tumor tissue


title: NA18632

description: HapMap CHB Male

source_name: lymphoblastoid cell line


title: 518-75-2 Citrinin 2nd-2

description: Citrinin 2nd-2


title: HF1286_Hind