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Sample GSM77751 Query DataSets for GSM77751
Status Public on Dec 15, 2005
Title Df(2L)JH/+ ovaries / Dp(2;2)Cam3/+ ovaries - 300
Sample type RNA
 
Channel 1
Source name Df(2L)JH/+ ovaries
Organism Drosophila melanogaster
Characteristics Df(2L)JH/+ ovaries
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Dp(2;2)Cam3/+ ovaries
Organism Drosophila melanogaster
Characteristics Dp(2;2)Cam3/+ ovaries
Extracted molecule total RNA
Label Cy5
 
 
Description Whole adult Drosophila melanogaster Df(2L)JH/+ and Dp(2;2)Cam3/+ female flies were grown at 25C on PB medium (KD Medical, Columbia, MD) for 5 to 7 days post eclosion. Dissected 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 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 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 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).
Data processing 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 Oct 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
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 10836.312 22457.625 1.051 8380 40550 423 166
2 438 337 419 160
3 481 398 417 162
4 858 1321 418 170
5 473 412 418 173
6 420 327 421 177
7 475 441 421 175
8 520 485 425 174
9 488 459 423 181
10 879.949 916.353 0.058 776 1158 417 152
11 702.093 747.669 0.091 647 878 415 153
12 994.42 970.474 -0.035 869 1254 419 154
13 654.893 653.384 -0.003 626 729 416 158
14 1665.766 1789.128 0.103 1386 2531 418 160
15 1713.478 1747.93 0.029 1426 2473 418 160
16 2509.588 2276.082 -0.141 2074 3318 422 164
17 532.539 522.557 -0.027 544 528 418 170
18 399.084 414.493 0.055 463 366 419 172
19 1292.484 1337.786 0.05 1093 1839 423 174
20 697.979 719.363 0.044 648 837 424 176

Total number of rows: 31464

Table truncated, full table size 1368 Kbytes.




Supplementary data files not provided

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