design: K562 and L1210 cells were pre-treated with drugs separately by seeding 150,000 (L1210) and 200,000 (K562) cells into 6-well plate wells (Corning). Cells were grown in 2mL of IMDM with 10% FBS, 1X Pen/Strep in the presence of no drugs (repeat 2 and 3) for 48 hours. Next, cells were collected and K562 and L1210 cell-lines were pooled based on the drug condition at a 1:1 ratio. Cell suspensions were encapsulated into CAGEs using a final cell concentration of 1.4e6 cells/mL. Each drug condition was encapsulated for 2 hours, collecting the droplets into four 30 min fractions. One fraction of each condition was sampled instantly by lysing the cells inside the CAGEs and freezing the lysate containing CAGEs at -80C in 3X SSCI with 10% DMSO and 0.05U/L Murine RNAse Inhibitor. Remaining fractions of packed hydrogel CAGEs were seeded into a different 24-well plate well into 1mL of IMDM with 10% FBS and 1x Pen/Strep, 0.1% F127 and 0.1% L31. 10,000 K562 and L1210 cells from appropriate drug conditions were seeded outside the CAGEs for the first two days. Every two days, media was exchanged with fresh media and one well of each condition was sampled for inC-RNA-seq by lysing the cells and freezing at -80C as described above.After all the time points were collected, CAGEs were thawed, washed, and treated with Turbo DNAse I and Proteinase K. Finally, CAGEs were washed three times with 3X SSCI buffer and three times with HI10. Resulting CAGEs were subjected to the inC-RNA-seq protocol. Resulting barcoded cDNA libraries were purified, fragmented and indexed with 48 indices as described above. 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).