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Sample GSM154400 Query DataSets for GSM154400
Status Public on Jan 19, 2007
Title Terephthalate 1stTPAcy5Pycy3
Sample type RNA
 
Channel 1
Source name experiment
Organism Rhodococcus jostii RHA1
Characteristics experiment
Extracted molecule total RNA
Extraction protocol Total RNA isolation involved vortexing with glass beads, hot phenol plus SDS, precipitation of debris with acetate, phenol plus chloroform, precipitation of nucleic acids with acetate plus isopropanol, DNase treatment and purification with an RNeasy mini column (Qiagen).
Label Cy5
Label protocol Cy5 labeled cDNA were prepared by indirect labeling.
 
Channel 2
Source name control
Organism Rhodococcus jostii RHA1
Characteristics control
Extracted molecule total RNA
Extraction protocol Total RNA isolation involved vortexing with glass beads, hot phenol plus SDS, precipitation of debris with acetate, phenol plus chloroform, precipitation of nucleic acids with acetate plus isopropanol, DNase treatment and purification with an RNeasy mini column (Qiagen).
Label Cy3
Label protocol Cy3 labeled cDNA were prepared by indirect labeling.
 
 
Hybridization protocol The microarray slides were pre-hybridized using 5x SSC containing 0.1% SDS and 0.2% BSA for 45 minutes at 48oC and used immediately for hybridization in a GeneTac HybStation (Genomic Solution). The hybridization was carried out at 42oC for 18 hours with mixing using 120 μL per slide of SlideHyb#1 hybridization solution (Ambion). The post hybridization washing consisted of 3 cycles of 20 second incubations with each of the following solutions: 2x SSC plus 0.1% SDS (medium stringency) at 42oC; 0.1x SSC plus 0.05% SDS (high stringency) at 25oC; and 0.1x SSC (low stringency) at 25oC.
Scan protocol The slides scanned with a GenePix 4000B scanner (Axon Instruments). The spot intensities were quantified using Imagene 5.6 (BioDiscovery, Inc.).
Description To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.
Data processing Expression ratios were normalized using the LOWESS method. Average normalized expression ratios (treatment/control) were calculated for each gene and tested for significant variation between treatments (ANOVA p < 0.05).
 
Submission date Jan 09, 2007
Last update date Jan 18, 2007
Contact name Hirofumi Hara
E-mail(s) hara2950@mac.com
Organization name University of British Columbia
Department Microbilogy and Immunology
Lab Mohn
Street address 2350 Health Science Mall
City Vancouver
State/province BC
ZIP/Postal code V6T1Z3
Country Canada
 
Platform ID GPL3918
Series (2)
GSE6684 Effects of terephthalate on Rhodococcus sp. RHA1
GSE6685 Effect of phthalate and terephthalate on Rhodococcus sp. RHA1

Data table header descriptions
ID_REF
VALUE log2 ratio of means defined as CH1 divided by CH2 log(CH1/CH2)
Experiment Signal Mean
Experiment Background
Control Signal Mean
Control Background Mean
RATIO Normalized ratio of means after background subtraction (CH1-BG1)/(CH2-BG2)

Data table
ID_REF VALUE Experiment Signal Mean Experiment Background Control Signal Mean Control Background Mean RATIO
1 -0.63295 74.68 60.3791 142.9199 112.2358 0.64486
2 0.05775 122.8775 59.9063 173.72 115.3221 1.04084
3 0.08984 118.5777 58.6253 167.3265 113.0707 1.06425
4 -0.10542 60.4799 58.4121 120.8 110.3584 0.92954
5 -0.5924 59.1599 56.2675 122.72 107.4983 0.66324
6 0.13859 61.9599 58.5633 121.6399 110.2535 1.10083
7 -0.44569 60.9599 58.5425 120.9199 107.7097 0.73423
8 0.27646 68.3199 58.2699 125.6399 109.0152 1.21122
9 -0.21019 63.04 58.3992 121.8799 106.5817 0.86442
10 -0.49547 62.72 57.7223 123.8799 105.7552 0.70933
11 -1.14475 58.2799 57.1146 118.76 105.1872 0.45227
12 0.22104 65.48 59.3438 119.12 105.2302 1.16557
13 0.64498 61.8837 59.0112 112.0227 103.7183 1.56372
14 -0.09765 62.2812 59.8265 114.1935 102.971 0.93455
15 0.42744 63.4 58.612 115.16 103.8026 1.34485
16 -0.83483 60 58.369 118 104.4605 0.56065
17 60.84 61.1197 114.2399 107.1482
18 -0.38703 62.84 61.0725 118.04 106.8328 0.7647
19 -5.28907 58.9062 58.8941 118.5 104.4742 0.02558
20 -1.77902 65.8399 62.5484 135.0399 106.4414 0.29138

Total number of rows: 22080

Table truncated, full table size 1199 Kbytes.




Supplementary data files not provided

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