design: K562 cell suspensions were centrifuged at 400g for 3 mins and the pellet was resuspended in 1mL of 4% PFA in DPBS. The solution was incubated at room temperature for 15 mins, followed by 3 washes with 1x DPBS + 0.1% BSA. The fixed cells were encapsulated into CAGEs by adding the cells to ~1.2e6 cells/mL into the core solution. Fixed cells were reverse cross-linked in CAGEs by washing the CAGEs twice with 3x SSCI + 0.01U/L RiboLock RNAse Inhibitor (ThermoFisher, EO0381). Next, CAGEs were washed three times with 100mM Tris (pH 7.5) with 10mM EDTA, 0.1% Igepal CA-630 (Millipore Sigma, I8896-50ML), 0.1% SDS. Finally, CAGEs were resuspended in the same solution to a volume of 1 mL and 50 L of proteinase K (NEB, P8107S) was added followed by incubation at 56C for 30 min. After the reverse crosslinking, CAGEs were washed three times with 3X SSCI, three times with HI10 and were used in a reverse transcription reaction . Detailed protocol for CAGE generation, inC-RNAseq and library construction described in "Mazelis et al., Multi-step genomics on single cells and live cultures in sub-nanoliter capsules, bioRxiv, doi.org/10.1101/2025.03.14.642839 (2025)."