RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells (second batch)
RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells (second batch)
For control and semi-extractability samples: naive pluripotent stem cells (nPSCs) were washed twice with PBS, then lysed by adding TRIzol to the plate and scraping the cells off. The samples were snap frozen on dry ice and stored at -80°C prior isolation.  Naive mESC (nPSCs) were grown in 2i conditions (PMID: 18497825). For control: TRIzol samples were thawed and RNA was extracted from the aqueous phase, following manufacturer's instructions.  For semi: TRIzol samples were thawed and heated for 10 min at 55°C and also passed 40 times through a 20G needle (PMID: 28404604).  For OOPS: RNA was isolated from the interphase following published protocol (PMID: 30607034, PMID: 32651564).  Libraries for sequencing were prepared using CORALL Total RNA-Seq with RiboCop rRNA depletion version 2 (Lexogen) with 1000 ng DNase-treated RNA as input.