Sixteen Sprague-Dawley rats, were either exposed to ECS for 4 weeks or kept in filtered air for the same period of time (sham)
Extracted molecule
total RNA
Extraction protocol
The lungs were collected, immersed in an RNA stabilizing buffer and frozen at -80°C
Label
Biotin
Label protocol
Five µg of total RNA was reverse-transcribed using a reaction mix containing 1µg of (3'(N)8-(A)12-biotin-(A)12-biotin 5') oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. Four µl of 5X first-strand buffer, 2 volumes of DTT 0,1M, 1µl of 10 mM dNTPs mix and 1µl Superscript II RNaseH reverse transcriptase (200 U/µl) were added. The samples were incubated for 90 min at 37°C. To denature the RNA/DNA hybrids and degrade RNA templates a mixture of 3,5 µl of 0,5M NaOH/ 50mM EDTA were added to 20 µl of first reaction mix. Five µl of 1M Tris-HCl pH7,6 were added to neutralize the reaction mix, and the labeled targets were stored at -80°C until hybridization.
Hybridization protocol
Microarray were hybridized in 6X SSPE/30% formamide at 25°C for 18h, washed in 0,75XTNT buffer at 37 for 40 min, and processed using direct detection of the biotin-containing transcript by streptavidin-Alexa647 conjugate. T
Scan protocol
The processed slides were scanned by using an Axon 4000B microarray Scanner, with the laser set at 635 nm and Power 80% and the photomultiplier set at 70% with a scan resolution of 10 µm
Description
none
Data processing
After local background subtraction, raw data were log transformed normalized and analyzed by GeneSpring software version 7.2. Expression data were median centered using the GeneSpring normalization option, which normalizes both per gene and per array. Comparison between ECS and sham were done by evaluating the fold variation of the mean value of quadruplicate data generated for each miRNA. In addition, the statistical significance of the differences was evaluated by using the GeneSpring ANOVA tool and Bonferroni multiple testing correction. Correlations between rodent and human miRNA were evaluated by simple regression analysis using the StatView software.
