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Sample GSM2456 Query DataSets for GSM2456
Status Public on Dec 25, 2002
Title Female vs Male-1a
Sample type RNA
 
Channel 1
Source name Adult Drosophila female, whole fly
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Channel 2
Source name Adult Drosophila male, whole fly
Organism Drosophila melanogaster
Extracted molecule total RNA
 
 
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).
 
Submission date Oct 03, 2002
Last update date Apr 25, 2012
Contact name Brian Oliver
E-mail(s) briano@nih.gov
Phone 301-204-9463
Organization name NIDDK, NIH
Department LBG
Lab Developmental Genomics
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL20
Series (1)
GSE442 Sex-biased gene expression

Data table header descriptions
ID_REF
LnCy3DA2 Natural log transformed intensity signal from Cy3 channel. Values are corrected using Qualifier software by taking a moving average across the entire signal range.
LnCy5DA2 Natural log transformed intensity signal from Cy5 channel. Values are corrected using Qualifier software by taking a moving average across the entire signal range.
VALUE Natural log transformed ratio of corrected Cy3/Cy5 signal calculated by taking the corrected LnCy3DA2 signal value and subtracting the LnCy5DA2 signal value for each array element.
DiffExpr Ratio of uncorrected Probe 1/Probe 2 signal intensity.
BalancedDiffExpr Ratio of uncorrected Probe 1/balanced Probe 2 signal intensity
Probe 1Signal Raw signal intensity data from Cy3 (Probe 1) channel.
Probe 1S/B Probe 1 signal minus background/background.
Probe 1Area% Percentage of area read from element spot.
Probe 2BalancedSignal Raw signal intensity data from Cy5 channel balanced against Probe 1 signal. Intensity is adjusted by a balancing coefficient that takes the average Cy3 signal on an array/the average Cy5 signal on the array.
Probe 2Signal Raw signal intensity data from Cy5 (Probe 2) channel.
Probe 2S/B Probe 2 signal-background/background.
Probe 2 %Area Percentage of area read from element spot.

Data table
ID_REF LnCy3DA2 LnCy5DA2 VALUE DiffExpr BalancedDiffExpr Probe 1Signal Probe 1S/B Probe 1Area% Probe 2BalancedSignal Probe 2Signal Probe 2S/B Probe 2 %Area
1 2.985519864 2.654778591 0.330741273 1.3 -1.1 10707 88.8 68 11420 8042 83.9 68
2 1.322760822 1.289936704 0.032824118 1.8 1.3 2770 23.7 86 2195 1546 16.6 86
3 0.862971697 0.87604791 -0.013076213 2 1.4 1894 15.9 93 1370 965 10.5 93
4 2.622352458 1.901686046 0.720666412 1.7 1.2 7075 55.8 73 6046 4258 41.2 73
5 2.20094507 2.222537812 -0.021592742 -1.3 -1.8 4623 36.6 68 8371 5895 55.1 68
6 1.44231023 2.258529093 -0.816218863 -1.5 -2.1 3029 24.3 76 6305 4440 42.5 76
7 1.982540687 2.221124957 -0.23858427 -1.2 -1.8 4289 35.6 44 7550 5317 53.6 44
8 0.791178271 1.467520142 -0.676341871 -1.2 -1.7 1658 14.7 61 2850 2007 21.9 61
9 -0.788267776 -0.267022986 -0.521244789 -1.1 -1.5 339 3.8 80 518 365 4.8 80
10 154 2.4 94 162 114 2.3 94
11 -1.540984659 -0.776938665 -0.764045994 1.1 -1.3 159 2.8 100 212 149 3 100
12 -0.514530483 -0.984811245 0.470280762 2.8 2 399 5.5 100 200 141 2.8 100
13 -0.932220833 -0.938953523 0.00673269 2 1.4 280 4.2 100 199 140 2.9 100
14 -1.094467253 -0.861538931 -0.232928322 1.8 1.3 260 4 94 200 141 3 94
15 -1.225312623 -1.222382995 -0.002929628 2.2 1.5 223 3.6 100 146 103 2.5 100
16 0.072488438 0.563731352 -0.491242914 1.2 -1.2 779 9.7 89 920 648 10.4 89
17 80 1.9 100 68 48 1.7 100
18 -2.325858208 -0.784286153 -1.541572055 -1.7 -2.4 85 1.9 100 203 143 2.8 100
19 -0.904503841 -0.672701028 -0.231802813 1.3 -1.1 277 3.9 100 301 212 3.6 100
20 105 2.2 100 98 69 1.9 100

Total number of rows: 31464

Table truncated, full table size 2140 Kbytes.




Supplementary data files not provided

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