RNA-seq for identifying semi-extractable and OOPS RNAs in naive mouse embryonic stem cells after thapsigargin stress

Total RNA-seq data from samples produced using conventional TRIzol RNA extraction (control), using the semi-extractability assay (PMID: 28404604) or Orthogonal Organic Phase Separation (OOPS; PMID: 30607034, PMID: 32651564) in naive mESCs (nPSCs) after the cells were exposed to 10 μM thapsigargin for 30 minutes. Control samples RNA was extracted from the aqueous phase of non-heated and non-sheared TRIzol samples. The semi-extractability assay samples were prepared by heating and needle-shearing TRIzol samples prior to extraction. For OOPS, the RNA was extracted from the TRIzol interphase of UV-crosslinked cells (254 nm, 400 mJ/cm2). Total RNA-seq libraries were prepared using the CORALL Total RNA-Seq Kit with RiboCop (Dual Indexing, UDI12A) - version 2.