Global miRNA expression profiling of domestic cat livers following acute Toxoplasma gondii infection

Cong, Wei; Zhang, Xiao-Xuan; He, Jun-Jun; Li, Fa-Cai; Elsheikha, Hany M.; Zhu, Xing-Quan

RNA samples from T. gondii-infected and noninfected livers collected at 7 dpi were sent to Beijing Novogene Bioinformatics Institute for Illumina sequencing. To analyze miRNAs by sequencing, a total of 3 μg RNAs of three pooled samples from each group were used for the construction of four small RNA (sRNA) libraries, which were subjected to sequencing on a Hi-seq 2500 platform. Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean reads were obtained by removing reads containing ploy-N, with 5' adapter contaminants, without 3' adapter or the insert tag, containing ploy A or T, or G or C and low quality reads from raw data. At the same time, Q20, Q30 and GC-content of the raw data were calculated. Then, we chose a certain range of length from clean reads to do all downstream analyses. Next, the small RNA tags were mapped to the feline reference genome sequence using Bowtie software [55] . The following parameters were used: -k [valid alignments per read], 1; -m [number of possible alignments], 10; -l [seed length], 25; --best [optimal alignments]).