Simultaneous quantifications of protein-DNA contacts and transcriptomics in single cells (mESC data)

Here we present a new version of the DamID method that allows efficient capturing of protein-DNA interactions and mRNA output from the same single cell. With this protocol, we have measured the direct impact of spatial genome positioning and chromatin accessibility on mRNA output in mouse embryonic stem cells Overall design: (i) 7 libraries with a total of 336 single-cell mESC samples expressing Dam-LMNB1, in two separate clonal lines (ii) 5 libraries with a total of 288 single-cell mESC samples expressing Dam (untethered) in serum, 2i and differentiated conditions, (iii) 2 libraries with a total of 192 single-cell mESC samples expressing Dam-RING1B in serum and differentiated conditions and (iv) 2 libraries with a total of 96 single-cell mESC samples (clone expressing untethered Dam), where AluI digestion is performed, instead of DpnI digestion