library_construction_protocol: Aggregates were unencapsulated from agarose by washing in sodium citrate, then all aggregates were dissociated in Accutase for 30 minutes. Cells for each condition were barcoded using the MuliSeq protocol (Mcginnis et al 2018). Individual GEMs were then generated using the 10x genomics V2 library construction kit with additional anchor specific primers for Multi-Seq. Barcode libraries were generated with KAPA HiFi Hotstart protocol to functionalize with the P5 sequencing adapter and library-specific RPIX barcode. Sample libraries were sequenced on an Illumina NovaSeq 6000 to a depth of >30k reads/cell. Barcode libraries were sequenced on an Illumina NextSeq 500 to an average depth of ~10k reads/barcode.