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Sample GSM154766 Query DataSets for GSM154766
Status Public on Jan 19, 2007
Title Cholesterol 3rdCholcy5Pycy3
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 11, 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 (1)
GSE6709 Effects of cholesterol 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 82.36 80.92657 132.68 199.10033
2 0.64083 266.81579 77.69408 278.2439 129.64333 1.55923
3 0.55715 319.13953 89.61624 322.62791 133.30072 1.47136
4 0.78949 187.875 85.04902 206.71006 129.07656 1.72846
5 102.56 96.14381 134.24 135.64548
6 166.30631 72.98122 145.89583 146.88827
7 124.07907 116.1133 154.04206 161.98529
8 142.82609 102.50667 127.54545 130.4094
9 1.79794 139.89119 110.87023 150.68912 137.70866 3.47723
10 -0.35792 112.54118 106.06316 143.4152 130.80952 0.78029
11 1.99146 138.68 103.37183 145.08 131.23099 3.97641
12 0.56594 110.63115 96.815 139 124.62814 1.48035
13 0.44531 117.32 85.08358 147.44 112.35522 1.36161
14 0.72163 87.32 65.1828 126.88 105.93548 1.64904
15 1.40288 80.64 66.90221 117.24 109.26183 2.6443
16 2.5371 110.36 67.79848 121.13043 109.69318 5.80419
17 4.78337 92.88 68.57867 121.05 119.744 27.53827
18 0.61286 82.91667 64.39661 133.58333 114.79322 1.52929
19 0.50266 67.18333 63.45729 116.184 112.28934 1.41682
20 83.52 89 124.6 128.54511

Total number of rows: 22080

Table truncated, full table size 1237 Kbytes.




Supplementary data files not provided

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