Lamina Associated Domains in MEFs depleted of specific lamin isotypes

Purpose: To compare the effects on Lamina Associated Domains (LADs) of shRNA treatment against lamin isotypes. Results: Using an optimized data analysis workflow (LADetector, available at https://github.com/thereddylab/LADetector), We found near identical sequences within the genome-wide maps indicating that ensemble methods are not effective for measuring random perturbations - perturbations that vary from cell to cell. Overall design: LAD profiles, of MEFs, corresponding to LmnB1 at the nuclear periphery were generated following the DamID protocol (L.Guelen et al, Nature 2008), library randomization and sequencing preparation using the NEBNext Ultra DNA library prep kit for Illumina (NEB, E7370S) and sequenced on the Illumina HiSeq 2500.