Er. As illustrated in Fig 1, the LO was administered orally for the rats, including the sham, and 14 days following treatment, the intestine, spleen, and liver had been dissected out to examine the differentially expressed genes. The cause for picking the time point and dose was depending on a preliminary trial exactly where LO was administrated to male Fischer rats at a dose of 0, 5 mg/kg, or 500 mg/kg. At 1 or six hours soon after the oral administration, we collected the liver and investigated in to the PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19877681 genome-wide gene expression profiles on a rat entire genome 444-K DNA microarray chip. For the 5 mg/kg LO dose, only 11 & 12 up and down regulated genes have been found at a single hour soon after administration, and 27 & 22 up and down regulated genes at six hours right after LO administration. For the 500 mg/kg LO dose, 44 & 17 up and down regulated genes have been found at 1 hour after administration, and 111 & 49 up and down regulated genes at six hours after LO administration. These low number of gene expression changes had been insufficient to discuss about the influence of the oral administration of LO. In traditional way of use, usually 10 to 20 days of continuous daily administration of essential oils is used or recommended, followed by one-week interval prior towards the next round. Keeping this time of administration and the preliminary data on 7 / 29 Positive Effects of Lavender Oil Genome Wide in a Rat Model five mg/kg over 500 mg/kg LO administration in mind, we focused on a two-week experiment using the low-dose, as described in Materials and Methods section, for determining the influence of LO on the body of rat. Total RNA extraction and confirmation of Gapdh gene expression by RT-PCR To investigate global changes in gene expression in the small intestine, spleen, and liver, we first optimized a protocol for total RNA extraction, HC-067047 price especially for the small intestine, for the first time in our research. The quantity and quality of the total RNA had been confirmed, and this RNA was then used to synthesize cDNA. Prior to DNA microarray analysis, we examined of commonly used house-keeping gene Gapdh in the small intestine, spleen, and liver, allowing us to subsequently use this gene as a positive control rather than by simply loading or using internal controls. This simple test of gene expression showed that the mRNAs for Gapdh had been expressed almost uniformly across conditions; i.e., primarily to check its mRNA abundance in all samples and not as a mathematical adjustment or denominator for gene expression calculations. Recently, we showed similar expression levels for the Gapdh gene with Cy3 and Cy5 labels in a microarray experiment on the ischemic brain. Using the 
same order Luteolin 7-O-β-D-glucoside analysis approach, we found that the Cy3 and Cy5 label associated expression for all the 10 Gapdh is similar across all probes plotted on the microarray chip. Results showed a good correlation between the Cy3 and Cy5 labels expression points across the 1.5-fold change ratio. Following this preliminary analysis of sample quantity and quality depending on the total RNA check, we conducted a DNA microarray analysis with a dye-swap method using the small intestine, spleen, and liver samples; pooled samples have been used as detailed above in the Materials and Methods section. The cause for multiple checks as mentioned above is important in any gene expression analysis experiment and is especially true for a DNA microarray-based approach. The resulting data on gene expression changes can be easily misinterpreted if any of the above.Er. As illustrated in Fig 1, the LO was administered orally for the rats, like the sham, and 14 days just after remedy, the intestine, spleen, and liver have been dissected out to examine the differentially expressed genes. The cause for picking the time point and dose was depending on a preliminary trial where LO was administrated to male Fischer rats at a dose of 0, five mg/kg, or 500 mg/kg. At 1 or six hours immediately after the oral administration, we collected the liver and investigated in to the PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19877681 genome-wide gene expression profiles on a rat complete genome 444-K DNA microarray chip. For the five mg/kg LO dose, only 11 & 12 up and down regulated genes were found at one particular hour right after administration, and 27 & 22 up and down regulated genes at six hours after LO administration. For the 500 mg/kg LO dose, 44 & 17 up and down regulated genes have been found at one particular hour after administration, and 111 & 49 up and down regulated genes at six hours just after LO administration. These low number of gene expression changes have been insufficient to discuss about the influence of the oral administration of LO. In traditional way of use, usually 10 to 20 days of continuous daily administration of essential oils is used or recommended, followed by one-week interval prior to the next round. Keeping this time of administration and the preliminary data on 7 / 29 Positive Effects of Lavender Oil Genome Wide in a Rat Model 5 mg/kg over 500 mg/kg LO administration in mind, we focused on a two-week experiment using the low-dose, as described in Materials and Methods section, for determining the influence of LO on the body of rat. Total RNA extraction and confirmation of Gapdh gene expression by RT-PCR To investigate global changes in gene expression in the small intestine, spleen, and liver, we first optimized a protocol for total RNA extraction, especially for the small intestine, for the first time in our research. The quantity and quality of the total RNA have been confirmed, and this RNA was then used to synthesize cDNA. Prior to DNA microarray analysis, we examined of commonly used house-keeping gene Gapdh in the small intestine, spleen, and liver, allowing us to subsequently use this gene as a positive control rather than by simply loading or using internal controls. This simple test of gene expression showed that the mRNAs for Gapdh have been expressed almost uniformly across conditions; i.e., primarily to check its mRNA abundance in all samples and not as a mathematical adjustment or denominator for gene expression calculations. Recently, we showed similar expression levels for the Gapdh gene with Cy3 and Cy5 labels in a microarray experiment on the ischemic brain. Using the same analysis approach, we found that the Cy3 and Cy5 label associated expression for all the 10 Gapdh is similar across all probes plotted on the microarray chip. Results showed a good correlation between the Cy3 and Cy5 labels expression points across the 1.5-fold change ratio. Following this preliminary analysis of sample quantity and quality depending on the total RNA check, we conducted a DNA microarray analysis with a dye-swap method using the small intestine, spleen, and liver 
samples; pooled samples had been used as detailed above in the Materials and Methods section. The explanation for multiple checks as mentioned above is important in any gene expression analysis experiment and is especially true for a DNA microarray-based approach. The resulting data on gene expression changes can be easily misinterpreted if any of the above.