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Sample GSM16587 Query DataSets for GSM16587
Status Public on Jun 28, 2004
Title tudor male vs ovaries-19b
Sample type RNA
 
Channel 1
Source name Adult tud[1] bw[1]sp[1] Male
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Channel 2
Source name Adult y[1]w[67c] Ovaries
Organism Drosophila melanogaster
Extracted molecule total RNA
 
 
Description Germlineless adult Drosophila melanogaster tud[1] bw[1]sp[1] progeny of tud[1] bw[1]sp[1] mothers and adult y[1]w[67c] flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. Whole flies (tudor males) and dissected y[1]w[67c] ovaries 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 Feb 06, 2004
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 1 Signal Raw signal intensity data from Cy3 (Probe 1) channel
Probe 1S/B 1 signal minus background/background
Probe 1 Area% Percentage of area read from element spot
Probe 2 BalancedSignal 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 2 Signal Raw signal intensity data from Cy5 (Probe 2) channel
Probe 2 S/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 1 Signal Probe 1S/B Probe 1 Area% Probe 2 BalancedSignal Probe 2 Signal Probe 2 S/B Probe 2 Area%
1 2.86 2.94 -0.08 1 1.4 17118 80.6 100 12126 17079 156.3 100
2 1.39 0.74 0.65 2.2 3 4009 19.6 100 1322 1862 17.3 100
3 0.97 0.61 0.36 1.6 2.2 2628 12.5 100 1181 1664 14.6 100
4 2.4 1.98 0.42 1.8 2.5 11406 48.1 100 4515 6359 51.1 100
5 2.37 2.54 -0.17 -1.1 1.3 10598 45.9 100 8311 11706 93.9 100
6 1.69 1.92 -0.23 -1.2 1.2 5419 26.6 100 4484 6315 53.6 100
7 1.57 1.64 -0.06 -1 1.4 4676 24.4 100 3462 4876 42 100
8 1.01 1.18 -0.16 -1.2 1.2 2648 15.2 100 2219 3125 28.4 100
9 0.17 0.25 -0.08 -1 1.3 1170 7.5 100 868 1222 12.2 100
10 -0.75 -0.7 -0.04 1.1 1.6 429 3.2 100 266 374 4.7 100
11 -0.95 -0.67 -0.28 -1.1 1.3 349 3.4 100 277 390 6 100
12 -0.94 -0.54 -0.39 -1.3 1.1 350 3.2 100 319 449 6.3 100
13 -1.14 -1.24 0.1 1.3 1.9 293 2.8 100 156 220 3.5 100
14 -0.34 -0.34 0 1.1 1.5 624 4.9 100 404 569 7.7 100
15 -0.16 -0.14 -0.02 1.1 1.5 746 5.8 100 498 702 9 100
16 0.36 -0.27 0.64 2 2.8 1239 8.6 100 448 631 7.6 100
17 180 2 98 80 112 2.1 98
18 151 1.9 91 48 67 1.7 91
19 -0.39 -0.23 -0.16 -1.1 1.3 590 4.8 100 467 658 8 100
20 -1.19 -1.27 0.07 1.2 1.7 273 2.8 100 162 228 3.6 100

Total number of rows: 31464

Table truncated, full table size 1612 Kbytes.




Supplementary data files not provided

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