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Sample GSM37439 Query DataSets for GSM37439
Status Public on Dec 15, 2005
Title (X;AA) B[s]Y; hs-tra carcass vs (X;AA) Male Carcass - 29
Sample type RNA
 
Channel 1
Source name (X;AA) B[s]Y; hs-tra carcass female
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Channel 2
Source name (X;AA) y[1] w[67c] Male Carcass
Organism Drosophila melanogaster
Extracted molecule total RNA
 
 
Description Drosophila melanogaster (X;AA) w/B[s]Y; P{w[+] hs-tra[83]}/+ sex transformed females and y[1] w[67c] male flies were grown at 25C on GIF medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. Gonadectomized carcasses 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 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 TrisHCl 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). 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 Dec 09, 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)
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
Probe1_signal Raw signal intensity data from Cy3 (Probe 1) channel
Probe2_signal Raw signal intensity data from Cy5 (Probe 2) channel
Probe1_SB Probe 1 signal minus background/ background
Probe2_SB Probe 1 signal minus background/ background

Data table
ID_REF Log2Cy3 Log2Cy5 VALUE Probe1_signal Probe2_signal Probe1_SB Probe2_SB
1 12.695 12.836 0.141 14841 12710 79.9 90.5
2 5431 2466 30.4 18.4
3 3155 1523 18.2 11.3
4 13941 7296 77.2 50.3
5 14527 13974 84 94.8
6 8931 8571 52.9 58.5
7 8576 7861 50.9 53.8
8 4140 4400 25.9 30.3
9 1967 1715 13.2 12.7
10 8.071 7.854 -0.218 693 767 4.6 6.8
11 7.573 7.758 0.185 504 705 4.3 7.8
12 7.38 7.346 -0.034 433 498 3.9 5.8
13 7.19 7.109 -0.08 367 412 3.6 4.8
14 8.423 8.533 0.11 869 1139 7 11.4
15 8.785 8.641 -0.144 1068 1209 8.5 12.1
16 9.407 9.327 -0.08 1504 1769 11.2 15.9
17 6.197 6.201 0.004 169 190 2.1 2.6
18 121 119 1.9 2
19 9.119 9.168 0.049 1286 1607 10.6 14.7
20 7.494 7.191 -0.303 477 437 4.6 4.8

Total number of rows: 31464

Table truncated, full table size 1173 Kbytes.




Supplementary data files not provided

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