Scalable co-sequencing of RNA and DNA from individual nuclei

We present DEFND-seq (DNA and Expression From Nucleosome Depletion), a scalable method for co-sequencing RNA and DNA from single nuclei. In DEFND-seq we treat nuclei with lithium diiodosalicylate to disrupt chromatin and expose genoimc DNA. The nuclei are then tagmented with Tn5 transposase, which fragments and tags gDNA. Tagmented nuclei are loaded into a microfluidic droplet generator which combines nuclei, beads containing transcriptomic and genomic barcodes, and reverse transcription reagents into single droplets. Ultimately two libraries are created, one for nuclear mRNA and one for genomic DNA, with each library containing barcodes linking it to its nuclei of origin, thus allowing simultaneous analysis of single nuclei transcriptomes and genomes. Once nuclei have been depleted of nucleosomes, all steps can be performed using a 10x Chromium Controller and 10x Multiome Kit without further experimental modification. Overall design: DEFND-seq (snRNA/DNA-seq), snATAC-seq, snDNA-seq