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Sample GSM225342 Query DataSets for GSM225342
Status Public on Aug 27, 2008
Title Earthworm exposed to TNT_Rep5 vs TNT+RDX_Rep5
Sample type RNA
 
Channel 1
Source name mRNA from worm (Rep#5) 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#5) 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 3641.29646 2789.638274 323.622727 721.986364 1.405101031 0.96993959 0.5347 1.448647983
2 384.956858 727.567478 308.2 725.495455
3 361.054204 734.316372 309.090909 701.236364
4 1348.894912 1330.506637 319.354545 736.295455 0.43603089 0.278745638 0.6455 1.564260857
5 1546.147124 1673.388274 382.427273 725.5 0.492858579 0.44465626 0.1485 1.108403556
6 7776.043142 3769.454646 730.263636 922.109091 2.984028222 1.335695418 1.1597 2.234063382
7 11358.82301 4943.929204 354.468182 702.45 4.660563866 1.989686263 1.2280 2.342361181
8 830.441372 894.507743 436.813636 799.945455 0.166709201 0.044359356 1.9100 3.758151982
9 760.692478 885.063053 557.454545 788.363636 0.08607532 0.045361887 0.9241 1.897525113
10 2152.591814 1476.956858 366.25 733.713636 0.756551405 0.348656862 1.1176 2.169902526
11 3028.061947 1603.076327 291.4 741.590909 1.159030946 0.404124509 1.5200 2.868004585
12 2788.884956 1830.140487 327.409091 718.663636 1.042484149 0.521395984 0.9996 1.999409625
13 1512.965708 1242.887168 296.527273 736.236364 0.515185952 0.237670892 1.1161 2.167644291
14 814.618363 1208.740044 325.568182 705.054545 0.207122511 0.236279861 -0.1900 0.876598241
15 337.67146 741.262168 347.544118 723.681373
16 343.442478 719.960177 308.52451 729.333333
17 586.568584 786.275442 304.086364 693.677273 0.119636857 0.043437984 1.4616 2.754199132
18 1316.734513 1255.762168 285.786364 764.913636 0.436627114 0.230258015 0.9232 1.896251535
19 472.795354 826.609513 287.331818 735.563636 0.078547508 0.042709801 0.8790 1.839097994
20 418.692478 734.82854 326.104545 744.295455

Total number of rows: 8704

Table truncated, full table size 721 Kbytes.




Supplementary file Size Download File type/resource
GSM225342_slides_13436153_1.tif.gz 46.1 Mb (ftp)(http) TIFF
GSM225342_slides_13436153_2.tif.gz 49.6 Mb (ftp)(http) TIFF
Processed data included within Sample table

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