Project description:To study the mechanisms of Ni resistance in the metal resistant Acidiphilium sp. PM, the transcriptome of Acidiphilium sp. PM was studied 5min and 30 min after the addition of 10mM Ni and compared to the transcriptome in untreated cells.
Project description:To study the mechanisms of Ni resistance in the metal resistant Acidiphilium sp. PM, the transcriptome of Acidiphilium sp. PM was studied 5min and 30 min after the addition of 10mM Ni and compared to the transcriptome in untreated cells. Two-condition hybridization experiments: untreated cells vs cells treated with 10mM Ni (for either 5 or 30 minutes). Eighteen 100ml-cultures: 6 untreated control cultures (not exposed to Ni), 6 cultures exposed to 10mM Ni for 5min, and 6 cultures exposed to 10mM Ni for 30 min. Cultures were independently grown and harvested. Gene expression levels of one untreated replicate were compared separately with one 5min-exposed replicate and with one 30min-exposed replicate (yielding two microarray data sets. One for each hybridization).
Project description:Acidiphilium sp. C61 cultures were cultivated in APPW+YE+Glucose medium with 0 µM or 10 µM PEA. RNA was extracted and library preparation was done using the NEBNext Ultra II directional RNA library prep kit for Illumina. Data was demultiplied by GATC sequencing company and adaptor was trimmed by Trimgalore. After trimming, data was processed quality control by sickle and mRNA was sorted by SortmeRNA. mRNA transcripts were mapped to the assembled genome of Acidiphilium sp. C61 and read counts table was produced by featurecounts. Differential gene expression analysis was done by edgeR package.
