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Sample GSM161855 Query DataSets for GSM161855
Status Public on Oct 15, 2007
Title TNT_0ppm_Rep4 vs TNT_35ppm_Rep4
Sample type RNA
 
Channel 1
Source name mRNA from worm (Rep#4) treated with 0 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)
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 35 ppm of TNT 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)
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 (1) its raw signal intensity was below its background level, (2) it overlapped with other spots, or (3) it was stained or over-saturated. The filtered spot intensity data were normalized by (1) subtraction of background intensity, (2) cross-channel LOWESS (local regression), and (3) centering to each channel's median spot intensity.
 
Submission date Feb 12, 2007
Last update date Oct 02, 2007
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 GPL4859
Series (1)
GSE7024 Profiling differentially expressed earthworm genes in response to TNT exposure.

Data table header descriptions
ID_REF
VALUE log(Cy3-signal/A647-signal) per feature (processed signals used)
Cy3_value processed Cy3 channel signal
A647_value processed A647 channel signal

Data table
ID_REF VALUE Cy3_value A647_value
1 0.228711941 6.43319954 3.799400547
2 0.121397185 0.328210211 0.248173213
3 0.069171072 0.131677465 0.11228982
4 0.158868561 0.20325761 0.140986735
5 0.113833418 0.780856904 0.600811222
6 0.175730726 0.272355524 0.181721144
7 0.076454072 3.494034347 2.930036954
8 0.01598932 0.360612402 0.347577247
9 0.104638025 0.464428851 0.364990168
10 -0.029518095 1.695488721 1.814734101
11 -0.020730216 1.950791168 2.046166625
12 0.235985149 1.686257363 0.979351764
13 0.146641833 0.901837724 0.643408161
14 0.151555865 0.580356332 0.409391539
15 0.018030403 0.035952267 0.034490213
16 0.158931489 4.125443626 2.861140385
17 -0.014034142 0.085974291 0.08879791
18 0.213150146 0.859556453 0.52616779
19 0.115333178 0.155575666 0.119291223
20 0.195717272 0.067042662 0.042720269

Total number of rows: 8704

Table truncated, full table size 312 Kbytes.




Supplementary file Size Download File type/resource
GSM161855_Slide13170412_1.tif.gz 48.2 Mb (ftp)(http) TIFF
GSM161855_Slide13170412_2.tif.gz 49.6 Mb (ftp)(http) TIFF

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