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Sample GSM154399 Query DataSets for GSM154399
Status Public on Jan 19, 2007
Title Phthalate 3rdPTHcy5Pycy3
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)
GSE6683 Effects of phthalate 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 -1.02875 70.5599 56.9373 132.32 104.3373 0.49013
2 0.04584 184.8181 64.6912 212.0238 111.9633 1.03229
3 0.17278 165.5882 68.2048 187.0232 110.5566 1.12723
4 -0.77023 66.6136 65.9816 114.7045 111.641 0.58632
5 0.68578 64.1555 59.4881 113.3111 108.3491 1.60857
6 -0.56813 65.9833 63.9202 112.8499 106.8837 0.67449
7 0.95618 68.4375 66.2583 111.5625 108.9878 1.94016
8 -1.41693 59.7599 58.4604 114.8 107.6309 0.37451
9 -0.77016 69.029 65.2592 118.7151 108.7724 0.58635
10 -0.63368 65.1136 62.3082 112.8 105.2222 0.64453
11 66.2916 70.8388 113.36 107.7343
12 0.06117 118.15 64.6308 179.4825 139.0879 1.04331
13 72.5999 65.4416 107.1999 108.4447
14 -0.40794 73.68 66.1549 120.16 107.2338 0.7537
15 -0.51462 78.3199 73.5431 116.6399 106.6056 0.69998
16 69.1415 69.7606 111.1481 104.472
17 -2.13283 68.875 67.914 113.625 104.756 0.22801
18 -2.26788 66.6923 65.7768 111.1724 101.8888 0.20764
19 -1.83831 69.1574 67.3813 116.9166 105.7069 0.27965
20 -1.22111 81.6666 70.1749 133.16 105.3193 0.42895

Total number of rows: 22080

Table truncated, full table size 1192 Kbytes.




Supplementary data files not provided

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