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Sample GSM154764 Query DataSets for GSM154764
Status Public on Jan 19, 2007
Title Cholesterol 1stCholcy5Pycy3
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 10, 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 -0.20065 130.2 108.408 106.12 100.712 0.87016
2 0.93709 169.15556 108.26567 112.51111 99.14627 1.91466
3 0.48965 161.16667 102.8135 117 98.00635 1.40411
4 -0.35596 136.4 114.71237 98.76 92.30435 0.78135
5 -0.85104 141.44 124.90141 95.44 89.46197 0.55439
6 -0.48487 136.28125 114.66954 96.75 89.25862 0.71456
7 0.4969 115.72 100.04348 85.96 84.95652 1.41117
8 1.33116 131.33333 95.97603 83.68 80.8495 2.51604
9 0.82136 117.12 91.70986 82.8 80.48169 1.76707
10 0.46551 100.28 79.68061 80.76 78.64259 1.3808
11 0.20011 109.96 84.03679 85.4 80.26421 1.14879
12 1.704 122.16667 86.74843 85.78261 83.96226 3.25804
13 -1.22886 100.88 85.87382 91.8 84.39117 0.42666
14 0.77116 114.6 87.04101 90.68 87.67823 1.70664
15 -3.44585 89.38624 86.10811 88.72539 86.43243 0.09177
16 -0.19575 113.84 88.06355 93.44 85.23077 0.87312
17 -0.32574 115.16 91.51839 91.6 83.86288 0.79789
18 -1.11499 113.84375 94.00862 99.45161 86.47414 0.46169
19 2.6944 121.5625 93.44073 91.46875 91.17933 6.47283
20 -0.79431 109.36 89.94314 94.56 86.21739 0.57662

Total number of rows: 22080

Table truncated, full table size 1259 Kbytes.




Supplementary data files not provided

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