INTACT nuclei were typically prepared from 100 to 500 frozen fly heads. TAPIN nuclei were prepared from 100 to 3000 frozen fly heads.

Nuclear RNA was DNAse I treated, purified, and amplified and the cDNA was then blunted and ligated to barcoded linkers.

RNA-seq libraries were sequenced on an Illumina Hiseq 2500 to 50-bp read length.

Reads were aligned to the reference genome of ENSEMBL release 91 using kallisto v0.43.1. ERCC, INTACT tag constructs, and rRNA genes were removed from the abundance tables and the estimated abundances of the remaining genes were normalised to one million total transcripts.