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Sample GSM154397 Query DataSets for GSM154397
Status Public on Jan 19, 2007
Title Phthalate 1stPTHcy5Pycy3
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 08, 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 -1.11 66.5555 45.4708 141 92.5656 0.4633
2 0.51432 108.0545 47.1764 131.2432 93.108 1.42832
3 0.66389 126.4385 45.5417 135.2407 91.8895 1.58435
4 -0.5718 45.1599 42.6889 105.5999 89.4581 0.67278
5 0.23284 44.0366 43.2988 95.3853 89.4502 1.17514
6 -1.28886 45.4399 44.5317 105.5999 90.4835 0.40928
7 -0.3443 47 45.2307 101.8399 89.2575 0.78769
8 45.6399 46.1558 103.1666 91.711
9 -1.85154 46.7599 45.1672 116.4117 91.2149 0.2771
10 -0.48953 48.5999 44.9698 108.5199 90.3444 0.71226
11 44.5833 44.7123 105.48 91.5284
12 43.9599 43.964 100.8799 89.6387
13 -1.37329 45.68 44.6776 104.2399 87.794 0.38601
14 -1.09464 46.5999 45.1352 107.76 90.9436 0.46825
15 -1.1618 46.7999 45.5384 107.5999 91.2793 0.44696
16 -0.38393 46.4666 45.2222 101.6666 90.6128 0.76635
17 -1.86349 46.1199 45.6107 106.2399 91.0434 0.27481
18 0.3932 48.5999 45.5389 104.36 93.3645 1.3133
19 45.2 45.6844 100.8799 90.8973
20 -1.47535 59.56 45.9641 133.3 86.0358 0.35965

Total number of rows: 22080

Table truncated, full table size 1181 Kbytes.




Supplementary data files not provided

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