title: GSM1184616: RNA-Seq in tet1-/-T, biological rep 2, differentiation day 6; Mus musculus; RNA-Seq
library_construction_protocol: Total RNA from 2 million cells was extracted with TRIZOL (Invitrogen, Carlsbad, CA) using manufacturer's instructions Total RNA was subjected to mRNA purification with Dynabeads Oligo (dT)25 (Invitrogen, Carlsbad, CA). First strand synthesis was performed with SuperScript® III First-Strand Synthesis System (Invitrogen, Carlsbad, CA), followed by purification with Sephadex G50 beads (medium) (GE Healthcare, UK) and second strand synthesis with dUNTPs. cDNA was sonicated with a Bioruptor (Diagenode, Woburn, MA) followed by end repair, addition of a 3' base, and ligation of adaptors. Fragments were purified on a 2% agarose gel and the second strand was degraded with AmpErase UNG (Applied Biosystems, Foster City, CA). Samples were amplified with between 7 and 10 cycles of PCR, followed by gel purification.