RNA-seq Analysis of Induced Cell Lines

Cells were collected in duplicates at 48 h and 9 days after doxycycline induction. We combined new iA RNA-seq with those published (Aydin et al., 2019 (link)) to make an n of 5. TRIzol (Invitrogen, 15596026) reagent was used to isolate RNA. Isolated RNA was purified with RNeasy mini kit (Qiagen, 74106). RNA integrity was measured using Agilent High Sensitivity RNA Screentape (Agilent Tech, 5067–5080). 500 ng RNA was spiked (1:100) with ERCC Exfold Spike-in mixes (Thermo Fisher Scientific, 4456739) for accurate comparison across samples. RNA-seq libraries were prepared with Illumina TruSeq LS kit v2 (RS-122–2001; RS-122–2002). KAPA library amplification kit was used for the final quantification of the library before pooling (Roche Lightcycler 480). The libraries were sequenced on an Illumina Next-Seq 500 using V2 and V2.5 chemistry for 50 cycles (single-end) at NYU Genomics Core facility.