Numbers over peaks and next to ladder bands refer to nucleotide size.
The approach differentiates the nucleotide size fractions that are stained with SYBR Gold to show only those associated with Viral DNA and RNA.
Interestingly, in contrast to down-regulated transcripts, we noticed that up-regulated ones rather exhibit a small nucleotide size, most of them being exclusive for the spotted fever group rickettsiae.
Using primers specific to the conserved regions flanking the rickA gene in several rickettsial genomes and with genomic R. raoultii DNA as the template, we successfully amplified a PCR fragment with a nucleotide size comparable to that obtained with R. conorii.
Table 1 categorizes the number of predictions by nucleotide size and rickettsial strain.
Firstly, the 20-22 nucleotide and 23-27 nucleotide size classes were detected for both conserved and novel miRNA families.
Among the newly identified miRNAs, 9 were the most abundant in the 22 nucleotide size category (see Additional file 1: Table S3).
Additional file 14: Nucleotide size distribution of reads from Anopheles antisense (grey) and sense (red) TEs using reads from the various samples (A-G).
A 200-300 nucleotide size selection was performed and the RNA was then converted into an Illumina sequencing library according to the manufacturer's protocol (TruSeq, Illumina).
