Next generation sequencing analysis of potential target genes of lncRNA BLACAT2. Homo sapiens

Next generation sequencing analysis was performed to identify potential target genes of lncRNA BLACAT2. Purified total RNA (3 μg) was used to deplete ribosomal RNA with Ribo-Zero rRNA Removal Kits (MRZMB126,Epicentre). Poly(A)+ RNA was purified with oligo(dT) magnetic beads and fragmented into short sequences. The library was prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Cat. No.15032612,Illumina) according to manufacturer’s instructions. Each library was sequenced on an Illumina Hiseq2500 in 125PE mode (Illumina, San Diego, CA, USA). These data provided transcriptional changes in bladder cancer cell line UM-UC-3 after BLACAT2 depletion. Overall design: BLACAT2 was depleted with lentiviral vectors expressing two independent short hairpin RNA specifically targeting BLACAT2 in human bladder cancer cell line UM-UC-3, and knockdown efficiency was quantified by quantitative RT-PCR before library construction. A scramble shRNA sequence was used as a negative control.