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Sample GSM16609 Query DataSets for GSM16609
Status Public on Jun 28, 2004
Title tudor Female vs ovaries-21b
Sample type RNA
 
Channel 1
Source name Adult tud[1] bw[1]sp[1] Female
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 females) 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 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 Probe 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 2.57 2.55 0.02 1.2 1.2 19769 98.4 100 16773 15824 70.4 100
2 1.91 1.13 0.77 2.3 2.2 9749 49 100 4410 4160 19.2 100
3 1.42 0.79 0.62 2.1 2 6169 31.1 100 3091 2916 13.5 100
4 2.58 2.03 0.54 1.9 1.8 19659 98.8 100 11060 10434 46 100
5 2.43 2.55 -0.11 1 -1 17793 91.3 100 18069 17046 74.5 100
6 2 2.2 -0.2 -1 -1.1 11704 60.7 100 12873 12144 52.5 100
7 1.91 1.87 0.04 1.2 1.1 10776 56.5 100 9576 9034 39.1 100
8 1.22 1.27 -0.04 -1 -1.1 5204 27.4 100 5598 5281 23.2 100
9 0.38 0.3 0.08 1.1 1.1 2300 12.9 100 2122 2002 9.3 100
10 -0.23 -0.41 0.18 1.3 1.2 952 5.8 100 795 750 4.7 100
11 -0.56 -0.38 -0.18 -1.2 -1.3 676 5.5 100 852 804 6.2 100
12 -0.71 -0.34 -0.37 -1.3 -1.4 609 4.9 100 871 822 5.9 100
13 -0.77 -0.93 0.15 1.3 1.2 583 4.8 100 494 466 3.8 100
14 -0.12 -0.16 0.04 1 -1 1088 8 100 1117 1054 7.2 100
15 0.09 -0.03 0.13 1.1 1 1342 9.7 100 1320 1245 8.3 100
16 0.45 -0.19 0.65 2 1.9 2081 13.8 100 1092 1030 6.6 100
17 206 2.3 100 196 185 2 100
18 193 2.3 100 139 131 1.7 100
19 0.02 0.11 -0.08 -1.1 -1.2 1365 10.4 100 1582 1492 9.6 100
20 -0.75 -1.09 0.34 1.5 1.4 652 5.4 100 469 442 3.5 100

Total number of rows: 31464

Table truncated, full table size 1682 Kbytes.




Supplementary data files not provided

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