S series

TAPIN-generated nuclear RNA was treated with DNase and purified by the Arcturus PicoPure system. Purified RNA was amplified to cDNA via Nugen Ovation v2 system (Nugen: 7102–32) and was then fragmented with a Covaris s-series to 200bp. Fragmented cDNA was repaired and underwent second strand synthesis before being ligated to barcoded linkers (Nugen: 0319–32, 0320–32). Libraries were quantified via KAPA qPCR before being sequenced on Illumina NextSeq to 76bp read length.

Genomic DNA was sheared using Covaris S series (Covaris, MS, USA). The sheared DNA was end-repaired, A-tailed, and ligated to pair-end adapters, in accordance with the manufacturer’s protocol (Pair End Library Preparation Kit, Illumina, San Diego, CA, USA). Adapter-ligated fragments were purified and dissolved in 30 μl of elution buffer, and 1 μl of the mixture was used as a template for 12 cycles of PCR amplification. The PCR product was gel-purified using the QIAquick Gel Extraction Kit (Qiagen). Library quality and concentration were determined using an Agilent 2100 BioAnalyzer (Agilent). Libraries were quantified using a SYBR green qPCR protocol on a LightCycler 480 (Roche, Indianapolis, IN, USA), in accordance with Illumina’s library quantification protocol. Based on the qPCR quantification, libraries were normalized to 2 nM, and then denatured using 0.1 N NaOH. Cluster amplification of denatured templates was performed in flow cells, in accordance with the manufacturer’s protocol (Illumina). Flow cells were paired-end sequenced on an Illumina HiSeq 2000 using HiSeq Sequencing kits. A base-calling pipeline (Sequencing Control Software (SCS), Illumina) was used to process the raw fluorescent images and the called sequences.