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Sample GSM693915 Query DataSets for GSM693915
Status Public on Mar 29, 2011
Title Cholic acid 1st, Chol-Cy5 Py-Cy3
Sample type RNA
 
Channel 1
Source name R. jostii RHA1, cholic acid
Organism Rhodococcus jostii RHA1
Characteristics strain: RHA1
condition: grown on cholic acid
sample type: 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 R. jostii RHA1, pyruvate
Organism Rhodococcus jostii RHA1
Characteristics strain: RHA1
condition: grown on pyruvate
sample type: 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 were 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 (experiment/control) were calculated for each gene and tested for significant variation between treatments (ANOVA p < 0.05).
 
Submission date Mar 21, 2011
Last update date Mar 29, 2011
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)
GSE28048 Effects of cholic acid on Rhodococcus sp. RHA1

Data table header descriptions
ID_REF
VALUE Log2 ratio of means defined as CH1 divided by CH2 (log2(CH1/CH2))
CH1_SIG_MEAN Experiment signal mean
CH1_BKD_MEAN Experiment background mean
CH2_SIG_MEAN Control signal mean
CH2_BKD_MEAN Control background mean
RATIO Normalized ratio of means after background subtraction (CH1/CH2)

Data table
ID_REF VALUE CH1_SIG_MEAN CH1_BKD_MEAN CH2_SIG_MEAN CH2_BKD_MEAN RATIO
1 64 60 55 51
2 64 58 63 52
3 68 58 61 54
4 69 62 54 53
5 69 62 57 53
6 71 66 57 55.5
7 74 67 60 55
8 70 64 56 55
9 67 62 57 55
10 62 61 56.5 55
11 67 61 59 56
12 71 60 63 57
13 70 62 60 57
14 73.5 63 60.5 58
15 74 64 59 57
16 69 61 61 56
17 66 62 59 57
18 71 62 60 57
19 65 59 60 57
20 64 60 59 56

Total number of rows: 22080

Table truncated, full table size 726 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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