Simultaneous quantifications of protein-DNA contacts and transcriptomics in single cells (KBM7 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 human haploid cells Overall design: (i) 5 libraries with a total of 240 single-cell samples of KBM7 clone 14, expressing Dam-LMNB1, generated with 2 different DamID adapter concentrations, (ii) 3 libraries with a total of 144 single-cell samples of KBM7 clone 5.5, also expressing Dam-LMNB1, (iii) 2 libraries with a total of 96 single-cell samples of KBM7 clone 5.8, expressing Dam (untethered) and (iv) a single library with 24 single-cell samples of wild-type KBM7, digested with the AluI restriction enzyme, processed without combined transcriptomic measurements