title: RNA-seq of MAPS experiment L. paracasei
design: RNA sequencing was performed to investigate the interacting RNAs co-purified with tracrRNA in Lacticaseibacillus paracasei under four conditions: (1) cells transformed with an empty vector control (EV), (2) tracrRNA without an aptamer (ptrRNA01), (3) tracrRNA tagged with MS2 aptamer for RNA pulldown (ptrRNA01_MS2), and (4) an MS2 aptamer-only control (pMS2). RNA samples were fragmented by ultrasound, and 3' oligonucleotide adapters were ligated to the RNA. First-strand cDNA synthesis was carried out using M-MLV reverse transcriptase, followed by adapter ligation to the 5' end of the antisense cDNA. The cDNA was PCR-amplified, purified with the Agencourt AMPure XP kit, and analyzed by capillary electrophoresis. Equimolar cDNA libraries (200600 bp) were pooled, size-fractionated on agarose gels, and sequenced on an Illumina NextSeq 500 platform with 75 bp single-end reads.