Samples from of all (pooled) colonies per well, were collected by resuspending the MethoCult Optimum media (and colonies) in 3mL of standard culture media (IMDM or RPMI), centrifuging at 200xg for 5 mins, and resuspending the cell pellet in 20-50µL RLT PLUS buffer, before storage at −80°C. TEM-seq of pooled colonies was performed as previously described using 5-10µL of cell lysate as input for bisulphite conversion, and 29 cycles for SINE Alu amplification. [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)] [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]