| 1 |
GSM37438 |
(X;AA) hs-tra carcass vs (XX;AA) pi[[2]]/ y w - 28 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
 |
unclassified |
source_name:(X;AA) B[s]Y; hs-tra carcass female (XX;AA) pi[[2]]/ y w title:(X;AA) hs-tra carcass vs (XX;AA) pi[[2]]/ y w - 28 description:Drosophila melanogaster (X;AA) B[s]Y; P{w[+] hs-tra[83]}/+ sex transformed females and pi[[2]]/ y w female flies that show hybrid dysgenesis in the germline were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. The whole fly in pi[[2]]/ y w and the gonadectomized carcass of hs-tra flies were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using RiboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations (determined by absorbance at 260 nm) ranging from 1 to 5000 ng/ml. A Millennium RNA size ladder (Ambion, Austin, TX) was used to generate standard curves and unknown samples were diluted as necessary. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 200 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using a custom labeling kit (Incyte Genomics). Each reaction contained 50 mM TrisHCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially stored and analyzed using GEMTools software (Incyte Genomics, Palo Alto CA). Background corrections were done by calculating the average Cy3/Cy5 signal to produce a balanced coefficient (Yue et al., 2001) Further corrections for non-uniform conditions during array printing and/or hybridization were performed using Qualifier software (Novation Bioscience, Palo Alto CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 2 |
GSM37439 |
(X;AA) B[s]Y; hs-tra carcass vs (X;AA) Male Carcass - 29 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:(X;AA) B[s]Y; hs-tra carcass female (X;AA) y[1] w[67c] Male Carcass title:(X;AA) B[s]Y; hs-tra carcass vs (X;AA) Male Carcass - 29 description:Drosophila melanogaster (X;AA) w/B[s]Y; P{w[+] hs-tra[83]}/+ sex transformed females and y[1] w[67c] male flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. Gonadectomized carcasses were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using RiboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations (determined by absorbance at 260 nm) ranging from 1 to 5000 ng/ml. A Millennium RNA size ladder (Ambion, Austin, TX) was used to generate standard curves and unknown samples were diluted as necessary. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 200 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using a custom labeling kit (Incyte Genomics). Each reaction contained 50 mM TrisHCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially stored and analyzed using GEMTools software (Incyte Genomics, Palo Alto CA). Background corrections were done by calculating the average Cy3/Cy5 signal to produce a balanced coefficient (Yue et al., 2001) Further corrections for non-uniform conditions during array printing and/or hybridization were performed using Qualifier software (Novation Bioscience, Palo Alto CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 3 |
GSM37440 |
(X;AA) B[s]Y; hs-tra carcass vs (XX;AA) Female Carcass - 34 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:(X;AA) B[s]Y; hs-tra carcass female (XX;AA) y[1] w[67c] Female Carcass title:(X;AA) B[s]Y; hs-tra carcass vs (XX;AA) Female Carcass - 34 description:Drosophila melanogaster (X;AA) B[s]Y; Df(3L)st[j7] Ki roe p[p] P{hs-tra}/+ sex transformed females and y[1] w[67c] female flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. Gonadectomized carcasses were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using RiboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations (determined by absorbance at 260 nm) ranging from 1 to 5000 ng/ml. A Millennium RNA size ladder (Ambion, Austin, TX) was used to generate standard curves and unknown samples were diluted as necessary. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 200 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using a custom labeling kit (Incyte Genomics). Each reaction contained 50 mM TrisHCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially stored and analyzed using GEMTools software (Incyte Genomics, Palo Alto CA). Background corrections were done by calculating the average Cy3/Cy5 signal to produce a balanced coefficient (Yue et al., 2001) Further corrections for non-uniform conditions during array printing and/or hybridization were performed using Qualifier software (Novation Bioscience, Palo Alto CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 4 |
GSM37441 |
(XX;AA) dsx male vs (X:AA) tudor male - 35 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:(XX;AA) dsx[swe]/Df(3R)dsx[M+15] sex transformed male (X:AA) tud[1] bw[1] sp[1] male title:(XX;AA) dsx male vs (X:AA) tudor male - 35 description:Drosophila melanogaster dsx[swe]/Df(3R)dsx[M+15] and tud[1] bw[1] sp[1] male progeny of tud[1] bw[1] sp[1] mothers were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. Whole flies were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using RiboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations (determined by absorbance at 260 nm) ranging from 1 to 5000 ng/ml. A Millennium RNA size ladder (Ambion, Austin, TX) was used to generate standard curves and unknown samples were diluted as necessary. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 200 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using a custom labeling kit (Incyte Genomics). Each reaction contained 50 mM TrisHCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially stored and analyzed using GEMTools software (Incyte Genomics, Palo Alto CA). Background corrections were done by calculating the average Cy3/Cy5 signal to produce a balanced coefficient (Yue et al., 2001) Further corrections for non-uniform conditions during array printing and/or hybridization were performed using Qualifier software (Novation Bioscience, Palo Alto CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 5 |
GSM37442 |
(XX;AA) otu ovarian tumor vs (X;AA) hstra ovarian tumor- 212 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
ovary |
(XX;AA) otu[1]/ otu[17] ovarian tumors (X;AA) hs-tra ovarian tumors |
| 6 |
GSM37443 |
(X;AA) hstra ovarian tumor / (XX;AA) otu ovarian tumor - 217 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
ovary |
(X;AA) hs-tra ovarian tumor (XX;AA) otu[1]/otu[17] ovarian tumor |
| 7 |
GSM37444 |
Df(2L)J-H/+ vs Dp(2;2)Cam3/+ female - 221 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Df(2L)J-H/+ female adult Dp(2;2)Cam3/+ female adult title:Df(2L)J-H/+ vs Dp(2;2)Cam3/+ female - 221 description:Drosophila melanogaster y[1] w[67c] /+; Df(2L)JH/+ female adult flies and y[1] w[67c] /+; Dp(2;2)Cam3/+ female adult flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Whole flies were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 8 |
GSM37445 |
Dp(2;2)Cam3/+ vs Df(2L)JH/+ female - 222 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Dp(2;2)Cam3/+ female adult Df(2L)JH/+ female adult title:Dp(2;2)Cam3/+ vs Df(2L)JH/+ female - 222 description:Drosophila melanogaster y[1] w[67c] /+; Dp(2;2)Cam3/+ and y[1] w[67c] /+; Df(2L)JH/+ female adult flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Whole flies were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using iboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 9 |
GSM37446 |
(XX;AA) Sxl ovarian tumor vs (X;AA) hs-tra ovarian tumor - 225 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
ovary |
(XX;AA) y Sxl[fs3] / y cm Sxl[7BO] ovarian tumors (X;AA) w/B[s]Y; P{w[+] hs-tra[83]}/+ ovarian tumors |
| 10 |
GSM37447 |
Df(2L)JH/+ male vs Dp(2;2)Cam3/+ male - 230 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Df(2L)JH/+ male adult flies Dp(2;2)Cam3/+ male adult flies title:Df(2L)JH/+ male vs Dp(2;2)Cam3/+ male - 230 description:Drosophila melanogaster y[1] w[67c] /Y; Df(2L)JH/Y male adult flies and y[1] w[67c] /+;Dp(2;2)Cam3/+ male adult flies flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Whole flies were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using RiboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 11 |
GSM37448 |
Dp(2;2)Cam3/+ male vs Df(2L)JH/+ male - 231 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Dp(2;2)Cam3/+ male adult flies Df(2L)JH/+ male adult flies title:Dp(2;2)Cam3/+ male vs Df(2L)JH/+ male - 231 description:Whole adult Drosophila melanogaster y[1] w[67c]/Y; Dp(2;2)Cam3/+ male adult flies and y[1] w[67c]/Y; Df(2L)JH/+ male adult flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Whole flies were quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD). Probes were labeled with Cy3 or Cy5. To synthesize probes, RNA was isolated by a single round of poly(A) selection using Oligotex resin (Qiagen, Valencia, CA). The purified mRNA was quantified using RiboGreen dye (Molecular Probes) in a fluorescent assay. RiboGreen dye was diluted 1:200 (v/v final) and mixed with known RNA concentrations determined by absorbance at 260 nm) ranging from 1 to 10,000 ng/ml. Fluorescence was measured in 96-well plates with a FLUOstar fluorometer (BMG Lab Technologies, Germany) fitted with 485 nm (excitation) and 520 nm (emission) filters. Between 25 and 100 ng mRNA were separated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), to examine the mRNA size distribution. 600 ng of purified mRNA were converted to either a Cy3- or Cy5-labeled cDNA probe using 50 mM Tris-HCl pH 8.3, 75 mM KCl, 15 mM MgCl2, 4 mM DTT, 2 mM dNTPs (0.5 mM each), 2 µg Cy3 or Cy5 random 9mer (Trilink, San Diego, CA), 20 U RNase inhibitor (Ambion), 200 U MMLV RNase H-free reverse transcriptase (Promega, Madison, WI) and mRNA. Correspondingly labeled Cy3 and Cy5 cDNA products were combined and purified on a size exclusion column, concentrated by ethanol precipitation and resuspended in hybridization buffer. Probes were added between two subarray slides and developed as described (Yue et al.2001, NAR. 29:e41). Microarrays were scanned on a GenePix 4000A scanner (Axon Instruments, Foster City, CA) at 535 nm. Signal intensities were initially captured using GenePix Pro 4.1 (Axon Instruments, Foster City CA). Normalization by within -slide print tip loess and between-slide quantile, along with subsequent analyses, were performed using the bioconductor package LIMMA (v.1.6.7) (Smyth et.al, 2004). |
| 12 |
GSM37449 |
(XX;AA) Sxl ovarian tumor vs (X;AA) hs-tra ovarian tumor - 232 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
ovary |
(XX;AA) y Sxl[fs3] / y cm Sxl[7BO] ovarian tumors (X;AA) y[1] w[67c]/Y; Df(3L)st[j7] Ki roe p[p] P{hs-tra}/+ ovarian tumors |
| 13 |
GSM37450 |
(XX;AA) otu ovarian tumor vs (X;AA) hs-tra ovarian tumor - 237 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
ovary |
(XX;AA) otu[1]/ otu[17] ovarian tumors (X;AA) hs-tra ovarian tumors |
| 14 |
GSM37451 |
(X;AA) hstra ovarian tumor / (XX;AA) otu ovarian tumor - 238 |
31,464 |
NIDDK, NIH |
2004-12-09 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
ovary |
(X;AA) hs-tra ovarian tumor (XX;AA) otu[1]/otu[17] ovarian tumor |
| 15 |
GSM37582 |
dmyc overexpression 7h-1 |
6,637 |
Fred Hutchinson Cancer Research Center |
2004-12-14 |
[cDNA Array] dmyc overexpression (GPL1748) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:ywhs-FLP122; Act-GAL4, UAS-GFP; + hs-FLP122; Act-GAL4, UAS-GFP; UAS-dMyc title:dmyc overexpression 7h-1 description:Total RNA was isolated 7h after 2h of heat shock. |
| 16 |
GSM37583 |
dmyc overexpression 7h-2 |
6,637 |
Fred Hutchinson Cancer Research Center |
2004-12-14 |
[cDNA Array] dmyc overexpression (GPL1748) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:yw, hs-FLP122; Act-GAL4, UAS-GFP; + yw, hs-FLP122; Act-GAL4, UAS-GFP; UAS-dMyc title:dmyc overexpression 7h-2 description:Total RNA was isolated 7h after 2h of heat shock. |
| 17 |
GSM37584 |
dmyc 7-3 |
6,637 |
Fred Hutchinson Cancer Research Center |
2004-12-14 |
[cDNA Array] dmyc overexpression (GPL1748) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:yw, hs-FLP122; Act-GAL4, UAS-GFP; + yw, hs-FLP122; Act-GAL4, UAS-GFP; UAS-dMyc title:dmyc 7-3 description:Total RNA was isolated 7h after 2h of heat shock. |
| 18 |
GSM37585 |
dmyc overexpression 7h-4 |
6,637 |
Fred Hutchinson Cancer Research Center |
2004-12-14 |
[cDNA Array] dmyc overexpression (GPL1748) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:yw, hs-FLP122; Act-GAL4, UAS-GFP; UAS-dMyc yw, hs-FLP122; Act-GAL4, UAS-GFP; + title:dmyc overexpression 7h-4 description:Total RNA was isolated 7h after 2h of heat shock. |
| 19 |
GSM37586 |
dmyc overexpression 7h-5 |
6,637 |
Fred Hutchinson Cancer Research Center |
2004-12-14 |
[cDNA Array] dmyc overexpression (GPL1748) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:yw, hs-FLP122; Act-GAL4, UAS-GFP; UAS-dMyc yw, hs-FLP122; Act-GAL4, UAS-GFP; + title:dmyc overexpression 7h-5 description:Total RNA was isolated 7h after 2h of heat shock. |
| 20 |
GSM37593 |
dmyc overexpression 14h-1 |
6,637 |
Fred Hutchinson Cancer Research Center |
2004-12-14 |
[cDNA Array] dmyc overexpression (GPL1748) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:yw, hs-FLP122; Act-GAL4, UAS-GFP; + yw, hs-FLP122; Act-GAL4, UAS-GFP; UAS-dMyc title:dmyc overexpression 14h-1 description:Total RNA was isolated 14h after 2h of heat shock. |
|