"RNA-Seq Comparing TRIZOL and XRNAX Extracted RNA"

For interrogating the RNA content of UV254nm XRNAX extracts MCF7 cells were UV254nm crosslinked and extracted with XRNAX. For comparison non-crosslinked cells were extracted with conventional TRIZOL. Both extracts were digested with proteinase K and cleaned up with silica spin columns. Resulting RNA was prepared into sequencing libraries before and after RiboZero rRNA depletion using the TruSeq RNA Library Prep Kit v2 (Illumina, not stranded). For interrogating the RNA content of UV365nm XRNAX extracts MCF7 cells were grown in the presence of 100 µM 4-thiouridine (4-SU) for 16 hours before crosslinking at UV365nm and extraction with XRNAX. For comparison identically treated but non-crosslinked cells were extracted with conventional TRIZOL. Both extracts were digested with proteinase K and cleaned up with silica spin columns. Resulting RNA was prepared into sequencing libraries after RiboZero rRNA depletion using the TruSeq Stranded Total RNA kit (Illumina, stranded).