Expression analysis of Pleurotus pulmonarius LBM 105 during PCBs degradation
These files represent an early stage of the expression analysis of the white rot fungi Pleurotus pulmonarius LBM 105 during PCBs degradation in liquid culture. We have already proven that this fungal strain is capable of achiving high percentages of PCBs removal in nitrogen-limited liquid media (doi: doi.org/10.1016/j.chemosphere.2020.129093). The data we present here was obtained by mapping the RNA reads of the strain LBM 105 obtained from two different conditions (a PCBs-containing condition and a control one) against the GCA_2979565.1 genome. For the mapping and the read count regarding each gene we used the Geneious software V 8.0.
Steps to reproduce
The total RNA extraction was made from fresh mycelium of P. pulmonairus LBM 105 obtained from a nitrogen limited liquid media (see: doi.org/10.1016/j.chemosphere.2020.129093). The mycelium was then homogenized using liquid nitrogen. The homogenate was then suspended on 500 μl of buffer (Tris 0.1 M, EDTA 0.02M, Guanidinium thiocyanate 4 M, Tritón X-100 1% ). The homogenate was then centrifugated at 12000 rpm for 10 min at 4 °C and the supernatant was resuspended in a same volume of Phenol. After Centrifugation (12000 rpm for 2 min at 4 °C) 300 μl of chloroform was added. After another step of centrifugation (12000 rpm for 2 min at 4 °C) the supernatant was recovered and 150 μl of Potassium Acetate 3 M was added. After centrifugation (12000 rpm for 5 min at 4 °C) a same volume of isopropanol was used for precipitation of the supernatant. After 1 hour at -4 °C the sample was centrifugated (12000 rpm for 10 min at 4 °C) and the pellet was recovered and washed using 500 μl abosulte ethanol. The pellet was resuspended in sterile water. The RNA library was then made using Illumina TruSeq stranded total RNA with Ribo-Zero Gold and the sequencing plataform was Illumina NovaSeq6000, 100PE. The obtained reads were assessed for quality with FastQC. The reads were then mapped to each conting of the GCA_2979565.1 genome using the Geneious V 8.0 software using three iterations. Finally, using the same software, for each gene the total read count was obtained as well as the normalization of those counts.