| 1 |
GSM2456 |
Female vs Male-1a |
31,464 |
NIDDK, NIH |
2002-10-03 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
 |
unclassified |
source_name:Adult Drosophila female, whole fly Adult Drosophila male, whole fly title:Female vs Male-1a description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 2 |
GSM2457 |
Female vs Male-1b |
31,464 |
NIDDK, NIH |
2002-10-03 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Adult Drosophila female, whole fly Adult Drosophila male, whole fly title:Female vs Male-1b description:Adult Drosophila melanogaster strain y1w67c flies were grown at 25oC on GIFmedium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 3 |
GSM2458 |
Male vs Female-2a |
31,464 |
NIDDK, NIH |
2002-10-03 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Adult Drosophila male, whole fly Adult Drosophila female , whole fly title:Male vs Female-2a description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25oC on GIFmedium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 4 |
GSM2459 |
Male vs Female-2b |
31,464 |
NIDDK, NIH |
2002-10-03 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Adult Drosophila male, whole fly Adult Drosophila female , whole fly title:Male vs Female-2b description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIFmedium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 5 |
GSM2460 |
Female Carcass vs Male Carcass-3a |
31,464 |
NIDDK, NIH |
2002-10-04 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Adult Drosophila female, gonadectomized Adult Drosophila male, gonadectomized title:Female Carcass vs Male Carcass-3a description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIFmedium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 6 |
GSM2461 |
Female Carcass vs Male Carcass-3b |
31,464 |
NIDDK, NIH |
2002-10-04 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Adult Drosophila female, gonadectomized Adult Drosophila male, gonadectomized title:Female Carcass vs Male Carcass-3b description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 7 |
GSM2462 |
Male Carcass vs Female Carcass-4a |
31,464 |
NIDDK, NIH |
2002-10-04 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Adult Drosophila male, gonadectomized Adult Drosophila female, gonadectomized title:Male Carcass vs Female Carcass-4a description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 8 |
GSM2463 |
Male Carcass vs Female Carcass-4b |
31,464 |
NIDDK, NIH |
2002-10-04 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Adult Drosophila male, gonadectomized Adult Drosophila female, gonadectomized title:Male Carcass vs Female Carcass-4b description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 9 |
GSM2468 |
Drosophila Adult Whole Fly, Mixed Sexes-27a |
31,464 |
NIDDK, NIH |
2002-10-05 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Drosophila Adult Whole Fly, Mixed Sexes title:Drosophila Adult Whole Fly, Mixed Sexes-27a description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. A mixed sex collection of adult 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 10 |
GSM2469 |
Drosophila Adult Whole Fly, Mixed Sexes-27b |
31,464 |
NIDDK, NIH |
2002-10-05 |
[cDNA Array] Incyte Drosophila LifeArray v1.0 (GPL20) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:Drosophila Adult Whole Fly, Mixed Sexes title:Drosophila Adult Whole Fly, Mixed Sexes-27b description:Adult Drosophila melanogaster strain y[1]w[67c] flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. A mixed sex collection of adult 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 (Probe 1) or Cy5 (Probe 2). To synthesize probes, mRNA 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 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 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). |
| 11 |
GSM3244 |
KS-48 |
21,482 |
Academic Medical Centre, University of Amsterdam |
2002-12-17 |
[SAGE NlaIII] SAGE:10:NlaIII:Homo sapiens (GPL4) |
SAGE |
Homo sapiens
 |
unclassified |
source_name:AIDS-KS lesion title:KS-48 description:SAGE library generated grom a KS lesion from an AIDS-KS patient. Biopsy was taken 48 hours after chemotherapy with adriamycine, bleomycine, and vincristine. |
| 12 |
GSM3243 |
KS-24 |
20,807 |
Academic Medical Centre, University of Amsterdam |
2002-12-17 |
[SAGE NlaIII] SAGE:10:NlaIII:Homo sapiens (GPL4) |
SAGE |
Homo sapiens
|
unclassified |
source_name:AIDS-KS lesion title:KS-24 description:SAGE library generated from a KS lesion from an AIDS-KS patient. Biopsy was taken 24 hours after treatment with adriamycine, bleomycine, and vincristine. |
| 13 |
GSM3241 |
AIDS-KSb |
16,881 |
Academic Medical Centre, University of Amsterdam |
2002-12-17 |
[SAGE NlaIII] SAGE:10:NlaIII:Homo sapiens (GPL4) |
SAGE |
Homo sapiens
|
unclassified |
source_name:AIDS-KS nodular lesion title:AIDS-KSb description:SAGE library derived from a nodular KS lesion of an AIDS-KS patient. Sample was taken at autopsy (1986). Patient died of AIDS-KS, and received vinblastine therapy till two weeks before death. |
| 14 |
GSM2583 |
body wall 1 |
14,010 |
Ohio State University |
2002-11-08 |
[GeneChip] [DrosGenome1] Affymetrix Drosophila Genome Array (GPL72) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:imaginal wing disc title:body wall 1 description:Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as NOTUM 2. Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts |
| 15 |
GSM2584 |
body wall 2 |
14,010 |
Ohio State University |
2002-11-08 |
[GeneChip] [DrosGenome1] Affymetrix Drosophila Genome Array (GPL72) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:imaginal wing disc title:body wall 2 description:Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as NOTUM 2R. |
| 16 |
GSM2585 |
body wall 3 |
14,010 |
Ohio State University |
2002-11-08 |
[GeneChip] [DrosGenome1] Affymetrix Drosophila Genome Array (GPL72) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:imaginal wing disc title:body wall 3 description:Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as NOTUM 3. Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts |
| 17 |
GSM2586 |
wing/hinge 1 |
14,010 |
Ohio State University |
2002-11-08 |
[GeneChip] [DrosGenome1] Affymetrix Drosophila Genome Array (GPL72) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:wing imaginal disc title:wing/hinge 1 description:Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as POUCH 1. Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts |
| 18 |
GSM2587 |
wing/hinge 2 |
14,010 |
Ohio State University |
2002-11-08 |
[GeneChip] [DrosGenome1] Affymetrix Drosophila Genome Array (GPL72) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:wing imaginal disc title:wing/hinge 2 description:Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as POUCH 2 Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts |
| 19 |
GSM2588 |
wing/hinge 3 |
14,010 |
Ohio State University |
2002-11-08 |
[GeneChip] [DrosGenome1] Affymetrix Drosophila Genome Array (GPL72) |
RNA |
Drosophila melanogaster
|
unclassified |
source_name:imaginal wing disc title:wing/hinge 3 description:Wild type third instar imaginal wing discs were dissected to produce body wall and wing/hinge fragments. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA. 3 body wall and 3 wing hinge biological replicates were analyzed. This sample is also known as POUCH 3. Keywords = Drosophila, imaginal wing disc, molecular screen for spatially restricted transcripts |
| 20 |
GSM2996 |
zzMex67IP_v_zzIP 060701 slide 3 scan 3 |
12,801 |
Harvard Medical School and Dana-Farber Cancer Institute |
2002-11-25 |
[cDNA Array] Ontario Cancer Institute full-genome S. cerevisiae ORF array (GPL221) |
RNA |
Saccharomyces cerevisiae
 |
unclassified |
source_name:zzMex67 IP zz IP title:zzMex67IP_v_zzIP 060701 slide 3 scan 3 description:Comparison of cDNA from RNA IPed with zzMez67 IP to that IPed with the zz tag alone (control IP) |
|