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Sample GSM50903 Query DataSets for GSM50903
Status Public on Dec 15, 2005
Title (XX;AA) otu ovarian tumor / (XX;AA) Sxl ovarian tumors - 211
Sample type RNA
 
Channel 1
Source name (XX;AA) otu ovarian tumor
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Channel 2
Source name (XX;AA) Sxl ovarian tumor
Organism Drosophila melanogaster
Extracted molecule total RNA
 
 
Description Whole adult Drosophila melanogaster ct otu[1] v[24]/y w otu[17] and y Sxl[fs3]/y cm Sxl[7BO] flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected ovarian tumors 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).
 
Submission date May 12, 2005
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)
GSE2119 Global analysis of X chromosome dosage compensation

Data table header descriptions
ID_REF ID to link data back to GPL20 platform
Log2Cy3 Log2 transformed intensity signal from Cy3 channel. Values are normalized within each array by print tip Loess and across the series using quantile normalization in Bioconductor.
Log2Cy5 Log2 transformed intensity signal from Cy5 channel. Values are normalized within each array by print tip Loess and across the series using quantile normalization in Bioconductor.
VALUE Log2 transformed ratio of corrected Cy3/Cy5 signal calculated by taking the corrected Log2Cy5 signal value and subtracting the Log2Cy3 signal value for each element
Cy3_SIGNAL Raw median signal intensity data from from Cy3 channel acquired by Genepix
Cy5_SIGNAL Raw median signal intensity data from from Cy5 channel acquired by Genepix
BCy3 Median background intensity signal from Cy3 channel acquired by Genepix
BCy5 Median background intensity signal from Cy5 channel acquired by Genepix

Data table
ID_REF Log2Cy3 Log2Cy5 VALUE Cy3_SIGNAL Cy5_SIGNAL BCy3 BCy5
1 14.297 14.338 0.042 20244 26630 393 158
2 15287 4196 392 157
3 8969 2663 399 159
4 32383 9852 398 160
5 23106 15050 401 161
6 16851 9946 403 175
7 13554 8749 392 161
8 6078 3198 396 163
9 2589 1597 402 166
10 8.492 8.621 0.129 526 341 394 154
11 8.868 8.824 -0.043 608 402 394 154
12 10.453 10.191 -0.261 1363 1089 396 156
13 9.102 9.426 0.324 646 608 399 155
14 9.098 9.002 -0.096 666 461 401 156
15 9.21 9.097 -0.113 698 496 400 151
16 9.919 10.047 0.128 989 960 399 160
17 498 261 401 159
18 474 209 393 154
19 9.467 9.387 -0.08 791 600 396 160
20 541 302 401 158

Total number of rows: 31464

Table truncated, full table size 1135 Kbytes.




Supplementary data files not provided

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