title: sitter_mutants_4

description:
Array Number:  12906620
Total RNA was extracted from Drosophila third instar larvae using Trizol Reagent (Invitrogen). Please refer to Osborne et al. 1997 (PMID: 9242616) for information on the fly strains.  80ug of RNA, quantified by A260 using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), was used in each direct labeling reaction (see <http://www.flyarrays.com>) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 17.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-73, Cy5(633 nm) 100-68 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Lot batch = D12K_300404

source_name: Untreated sitter third instar larvae

source_name: Untreated DGCalpha1[3] sitter third instar larvae


title: sitter_mutants_1

status: Public on May 01 2005

type: RNA

city: Mississauga

first: Zak

last: Razak

state: ON

address: 3359 Mississauga Road

department: Zoology Department

country: Canada

institute: University of Toronto

description:
Array Number:  12695449
Total RNA was extracted from Drosophila third instar larvae using Trizol Reagent (Invitrogen). Please refer to Osborne et al. 1997 (PMID: 9242616) for information on the fly strains.  80ug of RNA, quantified by A260 using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), was used in each direct labeling reaction (see <http://www.flyarrays.com>) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 15.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-73, Cy5(633 nm) 100-68 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Lot batch = D12K_130104

molecule: total RNA

organism: Drosophila melanogaster


title: sitter_mutants_3

description:
Array Number:  12906622
Total RNA was extracted from Drosophila third instar larvae using Trizol Reagent (Invitrogen). Please refer to Osborne et al. 1997 (PMID: 9242616) for information on the fly strains.  80ug of RNA, quantified by A260 using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), was used in each direct labeling reaction (see <http://www.flyarrays.com>) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 17.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-73, Cy5(633 nm) 100-64 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Lot batch = D12K_300404


title: 24_Hr_No_MGd_3

city: Los Angeles

first: Mazen

last: Karaman

state: CA

address: 2250 Alcazar St IGM/CSC 240

department: Institute for Genetic Medicine

country: USA

institute: University of Southern California

description: A549 cells control treatment (Mannitol) for 24hrs.  Replicate #3

organism: Homo sapiens

source_name: A549 cultured cell


title: Rover_mutants_3

description:
Array Number:  12906625
Total RNA was extracted from Drosophila third instar larvae using Trizol Reagent (Invitrogen). Please refer to Osborne et al. 1997 (PMID: 9242616) for information on the fly strains.  80ug of RNA, quantified by A260 using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), was used in each direct labeling reaction (see <http://www.flyarrays.com>) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 17.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-74, Cy5(633 nm) 100-64 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Lot batch = D12K_300404

source_name: Untreated Rover third instar larvae

source_name: Untreated DGCalpha1[3] Rover third instar larvae


title: Rover_mutants_1

description:
Array Number:  12695448
Total RNA was extracted from Drosophila third instar larvae using Trizol Reagent (Invitrogen). Please refer to Osborne et al. 1997 (PMID: 9242616) for information on the fly strains.  80ug of RNA, quantified by A260 using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), was used in each direct labeling reaction (see <http://www.flyarrays.com>) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 15.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-73, Cy5(633 nm) 100-67 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Lot batch = D12k1_130104


title: S.cerevisiae S288C, about one doubling time after treatment with imazalil, rep 3

city: University

first: Isabelle

middle: Ann

last: Kagan

state: MS

address: University Ave.

department: US Department of Agriculture

institute: National Center for Natural Products Research

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Imazalil, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Imazalil-Cy3=control, ch2=Imazalil-Cy5=treatment with imazalil
Ontario Cancer Inst. Bar Code no. 12314410

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae treated with I50 concentration of imazalil

source_name: S. cerevisiae treated with solvent (DMSO)


title: 24_Hr_+MGd_3

description: A549 cells treated with 50uM MGd for 24hrs.  Replicate #3


title: 24_Hr_No_MGd_2

description: A549 cells control treatment (Mannitol) for 24hrs.  Replicate #2


title: S.cerevisiae S288C, about one doubling time after treatment with imazalil, rep 4

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Imazalil, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Imazalil-Cy5=control, ch2=Imazalil-Cy3=treatment with imazalil
Ontario Cancer Inst. Bar Code no. 12314377


title: S.cerevisiae S288C, about one doubling time after treatment with fenbuconazole

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenbuconazole, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenbuconazole-Cy3=control, ch2=Fenbuconazole-Cy5=treatment with fenbuconazole
Ontario Cancer Inst. Bar Code no. 12278977

source_name: S. cerevisiae treated with I50 concentration of fenbuconazole


title: 24_Hr_No_MGd_1

description: A549 cells control treatment (Mannitol) for 24hrs.  Replicate #1


title: S.cerevisiae S288C, about one doubling time after treatment with triadimefon, rep 3

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Triadimefon, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Triadimefon-Cy5=control, ch2=Triadimefon-Cy3=treatment with triadimefon
Ontario Cancer Inst. Bar Code no. 12256989

source_name: S. cerevisiae treated with I50 concentration of triadimefon


title: S.cerevisiae S288C, about one doubling time after treatment with imazalil

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Imazalil, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Imazalil-Cy3=control, ch2=Imazalil-Cy5=treatment with imazalil
Ontario Cancer Inst. Bar Code no. 12314409


title: S.cerevisiae S288C, about one doubling time after treatment with triadimefon

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Triadimefon, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Triadimefon-Cy3=control, ch2=Triadimefon-Cy5=treatment with triadimefon
Ontario Cancer Inst. Bar Code no. 12314465


title: 24_Hr_+MGd_1

description: A549 cells treated with 50uM MGd for 24hrs.  Replicate #1


title: CEA_SGF:ABU004

city: Villejuif

first: Ali G.

last: Turhan

country: France

institute: institut Gustave Roussy

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured without doxycycline to activate Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy3 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy5.

organism: Mus musculus

source_name: Parental Ba/F3 cells


title: S.cerevisiae S288C, about one doubling time after treatment with imazalil, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Imazalil, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Imazalil-Cy5=control, ch2=Imazalil-Cy3=treatment with imazalil
Ontario Cancer Inst. Bar Code no. 12279000


title: S.cerevisiae S288C, about one doubling time after treatment with triadimefon, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Triadimefon, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Triadimefon-Cy5=control, ch2=Triadimefon-Cy3=treatment with triadimefon
Ontario Cancer Inst. Bar Code no. 12256914


title: S.cerevisiae S288C, about one doubling time after treatment with fenhexamid, rep 3

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenhexamid, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenhexamid-Cy5=control, ch2=Fenhexamid-Cy3=treatment with fenhexamid
Ontario Cancer Inst. Bar Code no. 12256996

source_name: S. cerevisiae treated with I50 concentration of fenhexamid


title: 24_Hr_+MGd_2

description: A549 cells treated with 50uM MGd for 24hrs.  Replicate #2


title: S.cerevisiae S288C, about one doubling time after treatment with prochloraz

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Prochloraz, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Prochloraz-Cy3=control, ch2=Prochloraz-Cy5=treatment with prochloraz
Ontario Cancer Inst. Bar Code no. 12314419

source_name: S. cerevisiae treated with I50 concentration of prochloraz


title: S.cerevisiae S288C, about one doubling time after treatment with fenarimol, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenarimol, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenarimol-Cy5=control, ch2=Fenarimol-Cy3=treatment with fenarimol
Ontario Cancer Inst. Bar Code no. 12257170

source_name: S. cerevisiae treated with I50 concentration of fenarimol


title: S.cerevisiae S288C, about one doubling time after treatment with prochloraz, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Prochloraz, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Prochloraz-Cy5=control, ch2=Prochloraz-Cy3=treatment with prochloraz
Ontario Cancer Inst. Bar Code no. 12279473


title: sitter_mutants_2

description:
Array Number:  12906624
Total RNA was extracted from Drosophila third instar larvae using Trizol Reagent (Invitrogen). Please refer to Osborne et al. 1997 (PMID: 9242616) for information on the fly strains.  80ug of RNA, quantified by A260 using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), was used in each direct labeling reaction (see <http://www.flyarrays.com>) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 17.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-74, Cy5(633 nm) 100-64 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Lot batch = D12K_300404


title: CEA_SGF:ABU007

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured in the presence of doxycycline to inhibit Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy5 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy3.


title: S.cerevisiae S288C, about one doubling time after treatment with fenarimol

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenarimol, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenarimol-Cy3=control, ch2=Fenarimol-Cy5=treatment with fenarimol
Ontario Cancer Inst. Bar Code no. 12314417


title: S.cerevisiae S288C, about one doubling time after treatment with fenbuconazole, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenbuconazole, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenbuconazole-Cy5=control, ch2=Fenbuconazole-Cy3=treatment with fenbuconazole
Ontario Cancer Inst. Bar Code no. 12314394


title: Rover_mutants_2

description:
Array Number:  12906627
Total RNA was extracted from Drosophila third instar larvae using Trizol Reagent (Invitrogen). Please refer to Osborne et al. 1997 (PMID: 9242616) for information on the fly strains.  80ug of RNA, quantified by A260 using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE), was used in each direct labeling reaction (see <http://www.flyarrays.com>) to generate fluorescently labeled cDNA. The respective Cy3 and Cy5 targets were suspended in 75 uL DIG EasyHyb solution (Roche, Mississauga, ON) and were competitively hybridized to the array for 17.75 hours in a CMT-GAPS hybridization chamber (Corning, Acton, MA). Scanning was performed with a ScanArray 4000 system (Perkin Elmer, Boston, MA) using the following settings: 10uM scan: Cy3(543 nm) 100-74, Cy5(633 nm) 100-64 (laser power-PMT Gain). Quantification was performed using QuantArray v3 software (Perkin Elmer) using the adaptive algorithm without background subtraction. The data in the file is not normalized. The ratio in the Value column was derived from normalized data (not shown) as discussed in the manuscript.
Keywords = Drosophila
Keywords = foraging
Keywords = behavior
Keywords = cGMP
Keywords = guanylyl cyclase
Keywords = genetic background
Lot batch = D12K_300404


title: S.cerevisiae S288C, about one doubling time after treatment with fenhexamid, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenhexamid, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenhexamid-Cy3=control, ch2=Fenhexamid-Cy5=treatment with fenhexamid
Ontario Cancer Inst. Bar Code no. 12257491


title: S.cerevisiae S288C, about one doubling time after treatment with fenhexamid

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenhexamid, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenhexamid-Cy3=control, ch2=Fenhexamid-Cy5=treatment with fenhexamid
Ontario Cancer Inst. Bar Code no. 12257497


title: CEA_SGF:ABU003

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured without doxycycline to activate Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy5 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy3.


title: CEA_SGF:ABU011

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured in the presence of doxycycline to inhibit Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy3 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy5.


title: 12_Hr_No_MGd_1

description: A549 cells control treatment (Mannitol) for 12hrs.  Replicate #1


title: S.cerevisiae S288C, about one doubling time after treatment with fenpropimorph

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenpropimorph, diluted in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenpropimorph-Cy5=control, ch2=Fenpropimorph-Cy3=treatment with fenpropimorph
Ontario Cancer Inst. Bar Code no. 12262556

source_name: S. cerevisiae treated with I50 concentration of fenpropimorph


title: 12_Hr_No_MGd_2

description: A549 cells control treatment (Mannitol) for 12hrs.  Replicate #2


title: S.cerevisiae S288C, about one doubling time after treatment with dodemorph, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Dodemorph, dissolved in ethanol, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of ethanol.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Dodemorph-Cy3=control, ch2=Dodemorph-Cy5=treatment with dodemorph
Ontario Cancer Inst. Bar Code no. 12257524

source_name: S. cerevisiae treated with I50 concentration of dodemorph

source_name: S. cerevisiae treated with solvent (ethanol)


title: 12_Hr_+MGd_1

description: A549 cells treated with 50uM MGd for 12hrs.  Replicate #1


title: CEA_SGF:ACI003

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured without doxycycline to activate Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy3 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy5.


title: S.cerevisiae S288C, about one doubling time after treatment with dodemorph

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Dodemorph, dissolved in ethanol, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of ethanol.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Dodemorph-Cy5=control, ch2=Dodemorph-Cy3=treatment with dodemorph
Ontario Cancer Inst. Bar Code no. 12256977


title: 12_Hr_+MGd_3

description: A549 cells treated with 50uM MGd for 12hrs.  Replicate #3


title: DD035.048 Oct 20 Coho Salmon GH Transgenic Study

city: Milwaukee

first: Matthew

middle: Lawrence

last: Rise

state: WI

address: 600 E. Greenfield Ave.

department: Great Lakes WATER Institute

institute: University of Wisconsin - Milwaukee

description:
Total RNA, prepared from flash-frozen adult coho salmon liver tissues using TRIzol reagent and methods (Invitrogen), was quantified and quality-checked by spectrophotometer and agarose gel. The microarray experiment used pooled RNA templates: pooled control non-transgenic (C) contained equal quantities from 5 individual C fish, pooled ration-fed transgenic (R) contained equal quantities from 5 individual R fish, and pooled full ration transgenic (T) contained equal quantities from 5 individual T fish. Microarray experimental design involved 3 comparisons (C vs. R, C vs. T, R vs. T), each run in triplicate (2 replicates and 1 dye flip). To minimize technical variability, all targets were synthesized in one round, and all hybridizations were conducted simultaneously on slides from a single batch (DD035). Validating quantitative RT-PCR (QPCR) used RNA templates from individual fish rather than pooled samples. Microarray hybridizations were performed using the Genisphere Array50 kit and instructions. Briefly, 20 ug total RNA (pooled C, pooled R, or pooled T) were reverse transcribed using oligo d(T) primers with 3-prime or 5-prime unique sequence overhangs for the Cy3 or Cy5 labeling reactions, respectively. Microarrays were prepared for hybridization by washing 2 X 5 min in 0.1% SDS, washing 5 X 1 min in MilliQ water, immersing 3 min in 95 degrees C MilliQ water, and drying by centrifugation (5 min 2000 rpm in 50 ml conical tube). Microarray hybridizations were run in the dark under HybriSlips hybridization covers (Grace Biolabs) in slide hybridization chambers (Corning) submerged in a 48 degrees C water bath. The coho salmon liver cDNAs were hybridized to the salmonid cDNA microarray (GEO platform GPL966) in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 16 h at 48 degrees C. Coverslips were floated off in 48 degrees C (2X SSC, 0.1% SDS), and arrays were washed 1 X 10 min in 48 degrees C (2X SSC, 0.1% SDS), 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature (RT), 2 X 5 min in 1X SSC at RT, and 2 X 5 min in 0.1X SSC at RT, and dried by centrifugation as before. The Cy3 and Cy5 3-dimensional fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized to the bound cDNA on the microarray in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 3 h at 48 degrees C, and washed and dried as before.
Keywords = salmon
Keywords = transgenic
Keywords = growth hormone
Keywords = microarray
Keywords = caloric restriction
Keywords = gene expression
Lot batch = DD035

organism: Oncorhynchus kisutch

source_name: Cy3 ration-fed transgenic (R)

source_name: Cy5 control non-transgenic (C)


title: 4_Hr_No_MGd_2

description: A549 cells control treatment (Mannitol) for 4hrs.  Replicate #2


title: CEA_SGF:ACI004

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured in the presence of doxycycline to inhibit Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy5 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy3.


title: CEA_SGF:ACI002

source_name: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus


title: 4_Hr_No_MGd_3

description: A549 cells control treatment (Mannitol) for 4hrs.  Replicate #3

source_name: A549 cultured cell


title: S.cerevisiae S288C, about one doubling time after treatment with cyprodinil

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Cyprodinil, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Cyprodinil-Cy5=control, ch2=Cyprodinil-Cy3=treatment with cyprodinil
Ontario Cancer Inst. Bar Code no. 12256904

source_name: S. cerevisiae treated with I50 concentration of cyprodinil


title: S.cerevisiae S288C, about one doubling time after treatment with fenpropimorph, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Fenpropimorph, diluted in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Fenpropimorph-Cy3=control, ch2=Fenpropimorph-Cy5=treatment with fenpropimorph
Ontario Cancer Inst. Bar Code no. 12257528


title: 12_Hr_+MGd_2

description: A549 cells treated with 50uM MGd for 12hrs.  Replicate #2


title: Dd2 8 days:pooled rep 2

city: Rockville

first: Tetsuya

last: Furuya

state: MD

institute: National Institutes of Health

description:
mAdb experiment ID: 56739
Dd2 cells 8 days gametocytes versus pooled RNA as a common reference
cell_type: P. falciparum gametocytes
cell_line: Dd2

organism: Plasmodium falciparum

source_name: Dd2 8 days gametocytes

source_name: W2+Dd2 gametocytes day 2 to day 10 pooled sample


title: CEA_SGF:ACI005

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured in the presence of doxycycline to inhibit Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy3 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy5.


title: Dd2 8 days:pooled rep 3

description:
mAdb experiment ID: 59566
Dd2 cells 8 days gametocytes versus pooled RNA as a common reference
cell_type: P. falciparum gametocytes
cell_line: Dd2


title: CEA_SGF:AFU024


title: 4_Hr_No_MGd_1

description: A549 cells control treatment (Mannitol) for 4hrs.  Replicate #1


title: DD035.046 Oct 20 Coho Salmon GH Transgenic Study

source_name: Cy3 control non-transgenic (C)

source_name: Cy5 ration-fed transgenic (R)


title: DD035.044 Oct 20 Coho Salmon GH Transgenic Study

source_name: Cy3 full ration transgenic (T)


title: 4_Hr_+MGd_3

description: A549 cells treated with 50uM MGd for 4hrs.  Replicate #3


title: DD035.047 Oct 20 Coho Salmon GH Transgenic Study


title: DD035.043 Oct 20 Coho Salmon GH Transgenic Study

source_name: Cy5 full ration transgenic (T)


title: CEA_SGF:AFU025

source_name: Parental Ba/F3 cells


title: X29.2

status: Public on Apr 30 2005

city: Boston

first: Penelope

middle: Lyn

last: Miron

state: MA

department: Cancer Biology

institute: Dana Farber Cancer Institute

description:
Rat mammary tumors induced by N-methyl-N-nitrosurea (NMU)
Keywords = breast cancer
Keywords = rat mammary tumor
Keywords = NMU
Keywords = animal model

organism: Rattus norvegicus

source_name: Frozen rat mammary tumors


title: X29.1


title: X28


title: X32


title: X21


title: CEA_SGF:AFU022

description: Ba/F3 cells transduced by the SIN-Tet-p210/Bcr-Abl retrovirus were cultured without doxycycline to activate Bcr-Abl expression for 48 hours. RNA sample was extracted, labeled with Cy5 and hybridized against RNA sample from parental Ba/F3 cells labeled in Cy3.


title: DD035.042 Oct 20 Coho Salmon GH Transgenic Study


title: 4_Hr_+MGd_2

description: A549 cells treated with 50uM MGd for 4hrs.  Replicate #2


title: Dd2 8 days:pooled rep 1

description:
mAdb experiment ID: 57326
Dd2 cells 8 days gametocytes versus pooled RNA as a common reference
cell_type: P. falciparum gametocytes
cell_line: Dd2


title: W2 8 days:pooled rep 3

description:
mAdb experiment ID: 59565
W2 cells 8 days gametocytes versus pooled RNA as a common reference
cell_type: P. falciparum gametocytes
cell_line: W2

source_name: W2 8 days gametocytes


title: X26


title: 4_Hr_+MGd_1

description: A549 cells treated with 50uM MGd for 4hrs.  Replicate #1


title: W2 8 days:pooled rep 1

description:
mAdb experiment ID: 57476
W2 cells 8 days gametocytes versus pooled RNA as a common reference
cell_type: P. falciparum gametocytes
cell_line: W2


title: W2 8 days:pooled rep 2

description:
mAdb experiment ID: 56733
W2 cells 8 days gametocytes versus pooled RNA as a common reference
cell_type: P. falciparum gametocytes
cell_line: W2


title: X25L


title: CEA_SGF:AFU026


title: X27


title: DD035.041 Oct 20 Coho Salmon GH Transgenic Study

description:
Total RNA, prepared from flash-frozen adult coho salmon liver tissues using TRIzol reagent and methods (Invitrogen), was quantified and quality-checked by spectrophotometer and agarose gel.  The microarray experiment used pooled RNA templates:  pooled control non-transgenic (C) contained equal quantities from 5 individual C fish, pooled ration-fed transgenic (R) contained equal quantities from 5 individual R fish, and pooled full ration transgenic (T) contained equal quantities from 5 individual T fish.  Microarray experimental design involved 3 comparisons (C vs. R, C vs. T, R vs. T), each run in triplicate (2 replicates and 1 dye flip).  To minimize technical variability, all targets were synthesized in one round, and all hybridizations were conducted simultaneously on slides from a single batch (DD035).  Validating quantitative RT-PCR (QPCR) used RNA templates from individual fish rather than pooled samples.  Microarray hybridizations were performed using the Genisphere Array50 kit and instructions.  Briefly, 20 ug total RNA (pooled C, pooled R, or pooled T) were reverse transcribed using oligo d(T) primers with 3-prime or 5-prime unique sequence overhangs for the Cy3 or Cy5 labeling reactions, respectively.  Microarrays were prepared for hybridization by washing 2 X 5 min in 0.1% SDS, washing 5 X 1 min in MilliQ water, immersing 3 min in 95 degrees C MilliQ water, and drying by centrifugation (5 min 2000 rpm in 50 ml conical tube).  Microarray hybridizations were run in the dark under HybriSlips hybridization covers (Grace Biolabs) in slide hybridization chambers (Corning) submerged in a 48 degrees C water bath.  The coho salmon liver cDNAs were hybridized to the salmonid cDNA microarray (GEO platform GPL966) in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 16 h at 48 degrees C.  Coverslips were floated off in 48 degrees C (2X SSC, 0.1% SDS), and arrays were washed 1 X 10 min in 48 degrees C (2X SSC, 0.1% SDS), 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature (RT), 2 X 5 min in 1X SSC at RT, and 2 X 5 min in 0.1X SSC at RT, and dried by centrifugation as before.  The Cy3 and Cy5 3-dimensional fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized to the bound cDNA on the microarray in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 3 h at 48 degrees C, and washed and dried as before.
Keywords = salmon
Keywords = transgenic
Keywords = growth hormone
Keywords = microarray
Keywords = caloric restriction
Keywords = gene expression
Lot batch = DD035


title: DD035.038 Oct 20 Coho Salmon GH Transgenic Study

description:
Total RNA, prepared from flash-frozen adult coho salmon liver tissues using TRIzol reagent and methods (Invitrogen), was quantified and quality-checked by spectrophotometer and agarose gel.  The microarray experiment used pooled RNA templates:  pooled control non-transgenic (C) contained equal quantities from 5 individual C fish, pooled ration-fed transgenic (R) contained equal quantities from 5 individual R fish, and pooled full ration transgenic (T) contained equal quantities from 5 individual T fish.  Microarray experimental design involved 3 comparisons (C vs. R, C vs. T, R vs. T), each run in triplicate (2 replicates and 1 dye flip).  To minimize technical variability, all targets were synthesized in one round, and all hybridizations were conducted simultaneously on slides from a single batch (DD035).  Validating quantitative RT-PCR (QPCR) used RNA templates from individual fish rather than pooled samples.  Microarray hybridizations were performed using the Genisphere Array50 kit and instructions.  Briefly, 20 ug total RNA (pooled C, pooled R, or pooled T) were reverse transcribed using oligo d(T) primers with 3-prime or 5-prime unique sequence overhangs for the Cy3 or Cy5 labeling reactions, respectively.  Microarrays were prepared for hybridization by washing 2 X 5 min in 0.1% SDS, washing 5 X 1 min in MilliQ water, immersing 3 min in 95 degrees C MilliQ water, and drying by centrifugation (5 min 2000 rpm in 50 ml conical tube).  Microarray hybridizations were run in the dark under HybriSlips hybridization covers (Grace Biolabs) in slide hybridization chambers (Corning) submerged in a 48 degrees C water bath.  The coho salmon liver cDNAs were hybridized to the salmonid cDNA microarray (GEO platform GPL966) in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 16 h at 48 degrees C.  Coverslips were floated off in 48 degrees C (2X SSC, 0.1% SDS), and arrays were washed 1 X 10 min in 48 degrees C (2X SSC, 0.1% SDS), 2 X 5 min in (2X SSC, 0.1% SDS) at room temperature (RT), 2 X 5 min in 1X SSC at RT, and 2 X 5 min in 0.1X SSC at RT, and dried by centrifugation as before.  The Cy3 and Cy5 3-dimensional fluorescent molecules (3DNA capture reagent, Genisphere) were hybridized to the bound cDNA on the microarray in a formamide based buffer (25% formamide, 4X SSC, 0.5% SDS, 2X Denhardt's solution) 3 h at 48 degrees C, and washed and dried as before.

Fluorescent images of hybridized arrays were acquired immediately at 10 um resolution using ScanArray Express (PerkinElmer).  The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm respectively, and the same laser power (90%) and photomultiplier tube (PMT) settings were used for all slides in the study (PMT 75 Cy3, PMT 65-67 Cy5).  Fluorescent intensity data were extracted from TIFF images using Imagene 5.5 software (Biodiscovery).
Keywords = salmon
Keywords = transgenic
Keywords = growth hormone
Keywords = microarray
Keywords = caloric restriction
Keywords = gene expression
Lot batch = DD035


title: X25R


title: S.cerevisiae S288C, about one doubling time after treatment with cyprodinil, rep 2

description:
Cultures were grown in synthetic dextrose medium, pH 7.0.  Cultures were started from an overnight culture diluted to A600=0.10.  Cyprodinil, dissolved in DMSO, was added when the A600 was 0.20, and the amount added was such that the final concentration would be the I50 value determined previously in growth curves.  Controls received an equivalent amount of DMSO.  Cells were harvested about 2 hours after treatment (about one doubling time).
cDNA containing aminoallyl-dUTP was synthesized from mRNA.  The indirect coupling of cDNA to Cy3 or Cy5 (dye swapping done for each fungicide) was based largely on a protocol from TIGR (SOP Moo4).  Hybridization to microarrays, based largely on the Corning GAPS II protocol, was done in a GeneTAC Hybridization Station from Genomic Solutions.
Array scanning was done on a ScanArray 5000, at 10 micron resolution.
Raw intensity values for ch1 and ch2 were background-subtracted and normalized (LOWESS sub-grid normalization) using GeneTraffic Multi software (Iobion Informatics).  The background-subtracted and normalized values are not shown here because the tables obtained in GeneTraffic displayed combinations of biological replicates instead of showing each replicate as a separate sample.
ch1=Cyprodinil-Cy3=control, ch2=Cyprodinil-Cy5=treatment with cyprodinil
Ontario Cancer Inst. Bar Code no. 12256908

source_name: S. cerevisiae treated with solvent (DMSO)


title: X22L


title: 12_Hr_No_MGd_3

description: A549 cells control treatment (Mannitol) for 12hrs.  Replicate #3


title: X20


title: DD035.040 Oct 20 Coho Salmon GH Transgenic Study


title: X19


title: X14


title: X18


title: X13


title: X8


title: X2


title: X17


title: NewN4

description:
Rat normal mammary gland
Keywords = breast cancer
Keywords = rat mammary tumor
Keywords = NMU
Keywords = animal model

source_name: rat normal mammary glands


title: Young


title: NewN6


title: X9


title: X27.1N


title: NewN8


title: X6


title: NewN5


title: X15


title: X28.1N


title: X10


title: NewN3


title: X11


title: NewN2


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_36

status: Public on Apr 29 2005

city: Duarte

first: Robert

middle: R

last: Klevecz

address: 1450 E. Duarte Rd.

department: Biology

institute: Beckman Research Institute of the City of Hope

description:
Time series , cycle 3, sample 36, phase 81.2 degrees
This sample is also known as AFFY3_36.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,

source_name: time series sampling continuous gated synchrony yeast culture


title: NewN1


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_35

description:
Time series , cycle 3, sample 35, phase 48.7 degrees
This sample is also known as AFFY3_35.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: NewN7


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_29

description:
Time series , cycle 3, sample 29, phase 213.8 degrees
This sample is also known as AFFY3_29.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_34

description:
Time series , cycle 3, sample 34, phase 16.2 degrees
This sample is also known as AFFY3_34.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_21

description:
Time series , cycle 3, sample 21, phase 314.0 degrees
This sample is also known as AFFY3_21.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_27

description:
Time series , cycle 3, sample 27, phase 148.9 degrees
This sample is also known as AFFY3_27.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_26

description:
Time series , cycle 3, sample 26, phase 116.4 degrees
This sample is also known as AFFY3_26.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_17

description:
Time series , cycle 3, sample 17, phase 184.1 degrees
This sample is also known as AFFY3_17.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_15

description:
Time series , cycle 2, sample 15, phase 119.1 degrees
This sample is also known as AFFY2_15.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_20

description:
Time series , cycle 3, sample 20, phase 281.5 degrees
This sample is also known as AFFY3_20.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_9

description:
Time series , cycle 2, sample 9, phase 284.2 degrees
This sample is also known as AFFY2_9.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_11

description:
Time series , cycle 2, sample 11, phase 349.2 degrees
This sample is also known as AFFY2_11.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_13

description:
Time series , cycle 2, sample 13, phase 54.1 degrees
This sample is also known as AFFY2_13.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_22

description:
Time series , cycle 3, sample 22, phase 346.5 degrees
This sample is also known as AFFY3_22.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_7

description:
Time series , cycle 2, sample 7, phase 219.2 degrees
This sample is also known as AFFY2_7.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_8

description:
Time series , cycle 2, sample 8, phase 251.7 degrees
This sample is also known as AFFY2_8.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_12

description:
Time series , cycle 2, sample 12, phase 21.72 degrees
This sample is also known as AFFY2_12.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_8

description:
Time series , cycle 1, sample 8, phase 115.0 degrees
This sample is also known as AFFY1_8.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_5

description:
Time series , cycle 2, sample 5, phase 154.3 degrees
This sample is also known as AFFY2_5.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_6

description:
Time series , cycle 2, sample 6, phase 186.8 degrees
This sample is also known as AFFY2_6.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_9

description:
Time series , cycle 1, sample 9, phase 147.5 degrees
This sample is also known as AFFY1_9.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_4

description:
Time series , cycle 1, sample 4, phase 311.3 degrees
This sample is also known as AFFY1_4.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: X4

description:
Rat mammary tumors induced by N-methyl-N-nitrosurea (NMU)
Keywords = breast cancer
Keywords = rat mammary tumor
Keywords = NMU
Keywords = animal model


title: Genome wide transcriptional oscillation gates DNA replication AFFY3_19

description:
Time series , cycle 3, sample 19, phase 249.0 degrees
This sample is also known as AFFY3_19.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_10

description:
Time series , cycle 2, sample 10, phase 316.7 degrees
This sample is also known as AFFY2_10.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_5

description:
Time series , cycle 1, sample 5, phase 343.8 degrees
This sample is also known as AFFY1_5.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY2_3

description:
Time series , cycle 2, sample 3, phase 89.3 degrees
This sample is also known as AFFY2_3.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_29

description:
Time series , cycle 1, sample 29, phase 161.1 degrees
This sample is also known as AFFY1_29.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_6

description:
Time series , cycle 1, sample 6, phase 16.2 degrees
This sample is also known as AFFY1_6.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_7

description:
Time series , cycle 1, sample 7, phase 48.7 degrees
This sample is also known as AFFY1_7.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_3

description:
Time series , cycle 1, sample 3, phase 278.8 degrees
This sample is also known as AFFY1_3.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_2

description:
Time series , cycle 1, sample 2, phase 246.3 degrees
This sample is also known as AFFY1_2.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: Genome wide transcriptional oscillation gates DNA replication AFFY1_1

description:
Time series , cycle 1, sample 1, phase 205.7 degrees
This sample is also known as AFFY1_1.
Sample_strain: IFO 0233 diploid
Keywords = oscillation, attractor, DNA-replication, redox gating, quantized,


title: WT-tMPh-sample2

status: Public on Apr 28 2005

city: Heidelberg

first: Benedikt

last: Brors

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
thymic macrophages from wild type mice were FACS-sorted
Keywords = thymus
Keywords = macrophage
Keywords = promiscuous gene expression

source_name: WT thymic-macrophage sample2


title: WT-tMPh-sample1

source_name: WT thymic-macrophage sample1


title: WT-tDC-sample2

description:
thymic dendritic cells from wild type mice were FACS-sorted
Keywords = thymus
Keywords = DC
Keywords = promiscuous gene expression

source_name: WT thymic-DC sample2


title: WT-CD80lo-mTEC-sample2

description:
medullary thymic epithelial cells from wild type mice were FACS-sorted by low CD80 expression
Keywords = thymus
Keywords = mTEC
Keywords = promiscuous gene expression

source_name: WT CD80lo mTEC sample2


title: AIRE-ko-CD80hi-mTEC-sample1

description:
medullary thymic epithelial cells from AIRE k/o mice were FACS-sorted by high CD80 expression
Keywords = thymus
Keywords = mTEC
Keywords = promiscuous gene expression

source_name: AIRE ko CD80hi mTEC sample1


title: WT-mTEC-sample2

description:
medullary thymic epithelial cells from wild type mice were FACS-sorted
Keywords = thymus
Keywords = mTEC
Keywords = promiscuous gene expression

source_name: WT mTEC sample2


title: WT-cTEC-sample1

description:
cortical thymic epithelial cells from wild type mice were FACS-sorted
Keywords = thymus
Keywords = cTEC
Keywords = promiscuous gene expression

source_name: WT cTEC sample1


title: WT-CD80hi-mTEC-sample2

description:
medullary thymic epithelial cells from wild type mice were FACS-sorted by high CD80 expression
Keywords = thymus
Keywords = mTEC
Keywords = promiscuous gene expression

source_name: WT CD80hi mTEC sample2


title: AIRE-ko-CD80hi-mTEC-sample2

source_name: AIRE ko CD80hi mTEC sample2


title: Nullvirus_compound_rep 2

city: Research Triangle Park

first: Sujoy

last: GHOSH

state: NC

institute: GLAXOSMITHKLINE

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 2

source_name: Rat pancreatic islets


title: AIRE-ko-CD80lo-mTEC-sample2

description:
medullary thymic epithelial cells from AIRE k/o mice were FACS-sorted by low CD80 expression
Keywords = thymus
Keywords = mTEC
Keywords = promiscuous gene expression

source_name: AIRE ko CD80lo mTEC sample2


title: PPARgamma_adenovirus_replicate 4

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization. Replicate 4


title: WT-tDC-sample1

source_name: WT thymic-DC sample1


title: PPARgamma_compound_replicate 1

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 1


title: PPARgamma_compound_replicate 3

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 3


title: PPARgamma_compound_replicate 2

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 2


title: AIRE-ko-CD80lo-mTEC-sample1

source_name: AIRE ko CD80lo mTEC sample1


title: PPARgamma_compound_replicate 4

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 4


title: WT-cTEC-sample2

source_name: WT cTEC sample2


title: Nullvirus_compound_rep4

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 4


title: WT-mTEC-sample1

source_name: WT mTEC sample1


title: WT-CD80lo-mTEC-sample1

source_name: WT CD80lo mTEC sample1


title: PPARgamma_adenovirus_replicate 2

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization. Replicate 2


title: PPARgamma_adenovirus_replicate 1

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization. Replicate 1


title: Nullvirus_compound_rep1

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 1


title: Nullvirus_compound_rep3

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in compound (GW347845 at 200 nM) for 16h before use for microarray hybridization. Replicate 3


title: Null_replicate 2

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization - replicate 2


title: WT-CD80hi-mTEC-sample1

source_name: WT CD80hi mTEC sample1


title: Null_replicate 3

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization - replicate 3


title: Z5_Cont_TA

city: Tuebingen

first: Antje

last: Bornemann

institute: Institute of Brain Research

description: Three male 8-week-old Wistar rats were used. The peroneal nerve of the animals was transected and sutured to the biceps femoris muscle. Four weeks later, the proximal stump was sutured to the distal stump. The animals survived for 8 weeks.

source_name: Skeletal muscle


title: Z5_TA


title: Z6_TA


title: Z4_Cont_TA

description:
Three male 8-week-old Wistar rats were used. The peroneal nerve of the animals was transected and sutured to the biceps femoris muscle. Four weeks later, the proximal stump was sutured to the distal stump. The animals survived for 8 weeks.
All experiments were performed under Ketanest (ketamine hydrochloride, Essex Pharma GmbH, Munich, Germany; 100 mg/kg) and Rompun (xylazine hydrochloride, Bayer, Leverkusen, Germany; 10 mg/kg) anesthesia. Both substances were injected intraperitoneally. RNA was extracted from the ipsilateral and contralateral tibialis anterior muscles of each animal. The gene array analysis compared the ipsilateral muscle with the contralateral muscle of each animal.


title: Z4_TA


title: R-3-C1-3

status: Public on Apr 21 2005

first: Kenneth

middle: Lyon

last: Phillips

institute: Paradigm Array Labs

description: Each laboratory was provided with aliquots of two different RNA samples that were prepared in one of the Consortium laboratories - a sample prepared from mouse livers (Liver RNA), and a sample prepared from equal amounts of RNA isolated from five mouse tissues (liver, kidney, lung, brain and spleen: Pooled RNA).

source_name: Pool


title: R-2-C1-4


title: Null_replicate 1

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization


title: R-3-C1-2


title: R-2-C1-3


title: R-3-C1-4


title: R-2-C1-1


title: underreplication 3

status: Public on Apr 22 2005

type: genomic

city: Novosibirsk

first: Stepan

last: Belyakin

country: Russia

institute: Institute of Cytology and Genetics

description: Genomic DNA from salivary glands of 4xSu(UR)+ and Su(UR)- strains were hybridized with the microarray to determine underreplicated areas in the drosophila polytene chromosomes

molecule: genomic DNA

source_name: genomic DNA from Su(UR)- drosophila larvae salivary glands

source_name: genomic DNA from 4xSu(UR)+ drosophila larvae salivary glands


title: Null_replicate 4

description: Islets infected with null adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization - replicate 4


title: R-2-C1-2


title: underreplication 1


title: underreplication 2


title: Exp103Neg on 74A

city: Farmington

first: Baikang

last: Pei

state: CT

institute: University of Connecticut

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp103Neg were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp103Neg, total_rna, cell culture, sorted calvarial osteoblast GFP negative


title: Exp106Neg on 74C

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp106Neg were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp106Neg, total_rna, calvaria, sorted calvarial osteoblast GFP negative


title: Exp106Neg on 74A


title: Exp106Pos on 74C

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp106Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp106Pos, total_rna, calvaria, sorted calvarial osteoblast GFP positive


title: Exp105Neg on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp105Neg were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp105Neg, total_rna, cell culture, sorted calvarial osteoblast GFP negative


title: Exp106Un on 74C

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid bGP.
10ug Exp106Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp106Un, total_rna, calvaria, unsorted calvarial osteoblast


title: Exp105Pos on 74C

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp105Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp105Pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: R-3-C1-1


title: Exp100Neg on 74A

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day 17.
Grow on 37 celsius.
Addition of Asc acid and bGP.
10ug Exp100Neg were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp100Neg, total_rna, cell culture, sorted calvarial osteoblast GFP negative


title: Exp99Neg on 74A

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp99Neg were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp99Neg, total_rna, cell culture, sorted calvarial osteoblast GFP negative


title: Exp105Neg on 74C


title: Exp101neg on 74A

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Cells harvested with trypsin, washed, declumped and sent for fac sorting.
Grow on 37 celsius.
Without any additions.
10ug Exp101neg were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp101neg, total_rna, calvaria, sorted calvarial osteoblast GFP negative


title: Exp100Neg on 74C


title: Exp103pos on 74C

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp103pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp103pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: PPARgamma_adenovirus_replicate 3

description: Islets infected with PPARgamma encoding adenovirus at multiplicity of infection of 50 viral particles/cell for 32h and further incubated in 0.004% DMSO for 16h before use for microarray hybridization. Replicate 3

source_name: Rat pancreatic islets


title: Exp100Pos on 74C

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Adiition of Asc acid and bGP.
10ug EXp100Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: EXp100Pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: Exp106Pos on 74B


title: Exp103Neg on 74C


title: Exp101neg on 74C


title: Exp101pos on 74C

description:
7 day new born mice.
Cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp101pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp101pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: Exp106Neg on 74B


title: Murine CD8+ Pmel Lymphocytes IL-2 vs. IL-15

status: Public on Apr 27 2005

city: Bethesda

first: Keith

last: Kerstann

department: Surgery Branch

description:
Central memory tumor-reactive CD8+ T cells confer superior
antitumor immunity compared to effector memory T cells

source_name: pmel CD8+ IL-15

source_name: pmel CD8+ IL-2


title: Exp99Neg on 74C


title: Exp99Pos on 74C

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp99Pos were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp99Pos, total_rna, cell culture, sorted calvarial osteoblast GFP positive


title: R-7-cDNA-7

description: Each laboratory was provided with aliquots of two different RNA samples that were prepared in one of the Consortium laboratories - a sample prepared from mouse livers (Liver RNA), and a sample prepared from equal amounts of RNA isolated from five mouse tissues (liver, kidney, lung, brain and spleen: Pooled RNA).

source_name: cy3 Liver5

source_name: cy5 Liver3


title: Z6_Cont_TA

description: Three male 8-week-old Wistar rats were used. The peroneal nerve of the animals was transected and sutured to the biceps femoris muscle. Four weeks later, the proximal stump was sutured to the distal stump. The animals survived for 8 weeks.

source_name: Skeletal muscle


title: R-7-cDNA-8


title: Exp105Neg on 74B


title: Exp105Pos on 74B


title: R-7-cDNA-6

source_name: cy3 Liver3

source_name: cy5 Liver5


title: Exp103pos on 74B


title: Exp101neg on 74B


title: Exp103Neg on 74B

description:
7 day new born mice.
Cells were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
Grow on 37 celsius.
Without any additions.
10ug Exp103Neg were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp103Neg, total_rna, cell culture, sorted calvarial osteoblast GFP negative


title: Exp101pos on 74B


title: R-7-cDNA-2

source_name: cy5 Pool


title: R-7-cDNA-1


title: Exp99Pos on 74B


title: R-7-C3-3

source_name: Pool


title: Exp100Pos on 74B


title: R-7-cDNA-3

source_name: cy3 Pool


title: R-7-cDNA-5


title: R-7-C3-2


title: Exp99Neg on 74B

source_name: Exp99Neg, total_rna, cell culture, sorted calvarial osteoblast GFP negative


title: Exp100Neg on 74B

source_name: Exp100Neg, total_rna, cell culture, sorted calvarial osteoblast GFP negative


title: R-7-C3-6


title: R-7-C3-5


title: R-7-C3-7


title: R-7-C3-9


title: R-7-C3-4


title: Infected roots 4dpi, r92brn.gpr

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
cotton roots 4 days after infection with fusarium wilt compared to roots 4 days after mock inoculation with water
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes

organism: Gossypium hirsutum

source_name: Uninfected roots 4dpi

source_name: Infected roots 4dpi


title: R-7-C3-11


title: Fusarium hybridisation, FUSR92.3.gpr

description:
Saprophytically grown mycelium, 4days growth, hybridised with infected cotton root tissue 4dpi.
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes

source_name: Fov Infected cotton root tissue 4dpi

source_name: Saprophytically grown Fusarium (Fov)


title: R-7-C3-10


title: R-7-C3-12


title: Fusarium hybridisation, FUSR92.3r.gpr

description:
Saprophytically grown mycelium, 4days growth, hybridised with infected cotton root tissue 4dpi.
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: R-7-C3-8


title: Infected roots 4dpi, r92bn.gpr

description:
cotton roots 4 days after infection with fusarium wilt compared to roots 4 days after mock inoculation with water
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Fusarium hybridisation, FUSR92.2r.gpr

description:
Saprophytically grown mycelium, 4days growth, hybridised with infected cotton root tissue 4dpi.
Biological Replicate: 1, Technical Replicate: 3, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: R-7-C3-1


title: Infected roots 3dpi, r68bn.gpr

description:
cotton roots 3 days after infection with fusarium wilt compared to roots  3 days after mock inoculation with water
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes

source_name: Infected roots 3dpi

source_name: Uninfected roots 3dpi


title: Infected roots 3dpi, r68cn.gpr

description:
cotton roots 3 days after infection with fusarium wilt compared to roots  3 days after mock inoculation with water
Biological Replicate: 5, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected roots 4dpi, r92cn.gpr

description:
cotton roots 4 days after infection with fusarium wilt compared to roots 4 days after mock inoculation with water
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected roots 3dpi, r68an.gpr

description:
cotton roots 3 days after infection with fusarium wilt compared to roots  3 days after mock inoculation with water
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Exp106Un on 74B

description:
7 day new born mice.
cell were grown in DMEM/10%FCS for 7 days, media exchanged on day 2 and day 5.
From day 7 cells were grown in presence of Asc acid and bGP until day17.
Grow on 37 celsius.
Addition of Asc acid bGP.
10ug Exp106Un were diluted in n/a solution.
Hybridized under 45oC in Affymetrix hyb oven for 16 h.
This work was sponsored by BMS.

source_name: Exp106Un, total_rna, calvaria, unsorted calvarial osteoblast


title: R-7-cDNA-4


title: Infected roots 3dpi, r68.1n.gpr

description:
cotton roots 3 days after infection with fusarium wilt compared to roots  3 days after mock inoculation with water
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected roots 2dpi, r40cn.gpr

description:
cotton roots 2 days post infection with fusarium wilt compared to root tissue 2 days after mock inoculation
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes

source_name: Infected roots 2 dpi

source_name: Uninfected roots 2dpi


title: Infected roots 3dpi, r68dn.gpr

description:
cotton roots 3 days after infection with fusarium wilt compared to roots  3 days after mock inoculation with water
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected roots 2dpi, r40.2n.gpr

description:
cotton roots 2 days post infection with fusarium wilt compared to root tissue 2 days after mock inoculation
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected roots 3dpi, r68rn.gpr

description:
cotton roots 3 days after infection with fusarium wilt compared to roots  3 days after mock inoculation with water
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected roots 2dpi, r40rn.gpr

description:
cotton roots 2 days post infection with fusarium wilt compared to root tissue 2 days after mock inoculation
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected root 1dpi, r24.1rn.gpr

description:
cotton roots  1 day post infection with fusarium wilt compared to  root tissue 1 day after mock inoculation
Biological Replicate: 4, Technical Replicate: 2, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes

source_name: Infected roots 1 dpi

source_name: Uninfected roots 1dpi


title: Infected roots 2dpi, r40an.gpr

description:
cotton roots 2 days post infection with fusarium wilt compared to root tissue 2 days after mock inoculation
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: D-8-8

description: Each laboratory was provided with aliquots of two different RNA samples that were prepared in one of the Consortium laboratories - a sample prepared from mouse livers (Liver RNA), and a sample prepared from equal amounts of RNA isolated from five mouse tissues (liver, kidney, lung, brain and spleen: Pooled RNA).

source_name: cy3 Liver5

source_name: cy5 Liver3


title: Infected root 1dpi, r24.1n.gpr

description:
cotton roots  1 day post infection with fusarium wilt compared to  root tissue 1 day after mock inoculation
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected root 1dpi, r24bn.gpr

description:
cotton roots  1 day post infection with fusarium wilt compared to  root tissue 1 day after mock inoculation
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected root 1dpi, r24cn.gpr

description:
cotton roots  1 day post infection with fusarium wilt compared to  root tissue 1 day after mock inoculation
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: Infected root 14 hpi, n14.2.gpr

description:
cotton roots 14 hours post infection with fusarium wilt compared to uninfected roots 14 hours after mock inoculation
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes

source_name: Infected root 14hpi

source_name: Uninfected root 14hpi


title: D-8-3

source_name: cy3 Pool

source_name: cy5 Liver5


title: Infected root 1dpi, r24an.gpr

description:
cotton roots  1 day post infection with fusarium wilt compared to  root tissue 1 day after mock inoculation
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = cotton, Fusarium wilt, AtsC, virulence, in planta expressed genes


title: D-8-6

source_name: cy3 Liver3