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Sample GSM225321 Query DataSets for GSM225321
Status Public on Aug 27, 2008
Title Earthworm exposed to TNT_Rep3 vs TNT+RDX_Rep4
Sample type RNA
 
Channel 1
Source name mRNA from worm (Rep#3) treated with 50 ppm of TNT labeled with Cyanine-3 (green)
Organism Eisenia fetida
Characteristics Adult earthowrms exposed in soil for 28 days.
Worms were snap frozen in liquid nitrogen.
Worm tissue was fixed in RNAlater-ICE (Ambion).
Extracted molecule polyA RNA
Extraction protocol RNeasy kit (Qiagen) and NucleoTrap Nucleic Acid Purification Kit (BD Biosciences)
Label Cy3
Label protocol 30 ng mRNA was reverse-transcribed into cDNA and labeled using Genisphere 3DNA 900 Expression Array Detection Cy3 kit.
 
Channel 2
Source name mRNA from worm (Rep#4) treated with 50 ppm of TNT and 30 ppm of RDX labeled with Alex Fluor 647 (red)
Organism Eisenia fetida
Characteristics Adult earthowrms exposed in soil for 28 days.
Worms were snap frozen in liquid nitrogen.
Worm tissue was fixed in RNAlater-ICe (Ambion).
Extracted molecule polyA RNA
Extraction protocol RNeasy kit (Qiagen) and NucleoTrap Nucleic Acid Purification Kit (BD Biosciences)
Label A647
Label protocol 30 ng mRNA was reverse transcribed into cDNA and labeled using Genisphere 3DNA 900 Expression Array Detection Alex Fluor 647 kit.
 
 
Hybridization protocol Labeled cDNA probes for both channels (Genisphere) were added to the array, covered with a glass cover slip, which was then placed in a 50-ml tube. A few drops of water was also added into the tube to keep the air moisture. The capped tube was incubated at 55oC in a hybridization oven without rotation overnight (ca. 16 hr). Arrays were post-hyb washed according to manufacture's instruction (Genisphere).
Scan protocol Arrays were scanned at 5-um resolution using VersArray ChipReader (Bio-Rad).
Description A RNAlater-ICE fixed worm was chopped into 8-10 pieces in equal length. Total RNA was isolated using Qiagen RNeasy Mini Kit from each of the 8-10 pieces and was pooled as one biological replicate representing each individual earthworm. The pooled total RNA was purified to obtain mRNA using NucleoTrap Nucleic Acid Purification Kit (BD Biosciences).
Data processing A spot was flagged out if its raw signal intensity was below its background level or the mean + 2x standard deviation of the 256 blank spots. The filtered spot intensity data were normalized by (1) subtraction of background intensity, and (2) centering to the mean spot signal intensity of each channel.
 
Submission date Aug 28, 2007
Last update date Aug 14, 2011
Contact name Ping Gong
E-mail(s) ping.gong@us.army.mil
Phone (601) 634-3521
Organization name US Army ERDC
Department Environmental Laboratory
Lab Environmental Genomics and Genetics
Street address 3909 Halls Ferry Road
City Vicksburg
State/province MS
ZIP/Postal code 39180
Country USA
 
Platform ID GPL5776
Series (1)
GSE8909 Profiling differentially expressed earthworm genes in response to TNT, RDX, or TNT+RDX exposure.

Data table header descriptions
ID_REF spot number
Raw_Cy3 Spot raw signal intensity (mean value) of the Cy3 channel
Raw_A647 Spot raw signal intensity (mean value) of the A647 channel
Raw_Cy3back Spot raw local background intensity (mean value) of the Cy3 channel
Raw_A647back Spot raw local background intensity (mean value) of the A647 channel
Cy3_value processed Cy3 channel signal
A647_value processed A647 channel signal
VALUE log2 of PRE_VALUE
PRE_VALUE (Cy3-signal/A647-signal) per feature (processed signals used)

Data table
ID_REF Raw_Cy3 Raw_A647 Raw_Cy3back Raw_A647back Cy3_value A647_value VALUE PRE_VALUE
1 2412.575221 2230.81969 354.122727 723.377273 1.069665599 0.836814191 0.3542 1.278259392
2 366.310841 738.393805 299.895455 695.322727
3 346.25885 736.362832 297.85 696.227273
4 956.498894 958.547566 318.968182 719.086364 0.331289973 0.13293014 1.3174 2.492211113
5 714.040929 782.037611 270.654545 722.295455 0.230403744 0.033164175 2.7965 6.947368513
6 3549.818584 2139.160398 400.309091 759.545455 1.636628472 0.76585437 1.0956 2.136996975
7 5953.030973 3043.868363 327.959091 727.918182 2.923043356 1.2856345 1.1850 2.273619257
8 865.988938 787.738938 323.013636 713.672727 0.282154679 0.04111577 2.7787 6.862444148
9 403.267699 787.357301 341.754545 729.836364 0.031965034 0.031931128 0.0015 1.001061868
10 862.664823 893.125 294.177273 724.25 0.295412004 0.093746199 1.6559 3.151189142
11 1056.574115 867.070796 272.145455 682.068182 0.407624832 0.102698989 1.9888 3.969122138
12 1241.266593 1433.914823 297.686364 723.645455 0.490327231 0.39428603 0.3145 1.243582559
13 521.963496 780.306416 275.354545 723.9 0.128149235 0.031312433 2.0330 4.092599107
14 761.42146 924.015487 297.413636 711.336364 0.241119583 0.118062824 1.0302 2.042298969
15 336.905973 724.71792 292.55 687.7
16 296.840708 713.579646 240.818182 692.381818
17 521.362832 775.70354 340.481818 761.118182 0.093994007 0.008096651 3.5372 11.60899879
18 857.50885 966.504425 423.263636 719.486364 0.225653576 0.137125118 0.7186 1.64560352
19 345.143805 760.727876 304.122727 690.918182
20 326.914823 749.831858 330.136364 722.5

Total number of rows: 8704

Table truncated, full table size 684 Kbytes.




Supplementary file Size Download File type/resource
GSM225321_slides_13436149_1.tif.gz 46.0 Mb (ftp)(http) TIFF
GSM225321_slides_13436149_2.tif.gz 49.4 Mb (ftp)(http) TIFF
Processed data included within Sample table

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