ATAC-seq Profiling of Mixed Stage C. elegans Neuronal Nuclei

Using ATAC-seq, we aimed to identify regions of open chromatin in the developing C. elegans nervous system. This dataset was used to determine regions of chromatin and compare it to ChIP-seq data of TFs of interest, to assist us in identifying ChIP-seq peaks which are solely expressed in neurons (vs. general, total worm binding). Specifically, since EGL-43 is expressed in many tissues, including both neuronal and the somatic gonad, ATAC-seq was particularly helpful in identifying neuronal-specific ChIP-seq peaks and NanoDam peaks of interest (GSE227552). We utilized a strongly expressed pan-neuronal nuclear GFP strain, and grew worms to density as a mixed stage population, with the majority being larval animals. Then, we used standard homogenizing procedures using a stainless steel dounce and ChIP-seq buffers to isolate neuronal nuclei. Nuclei were sorted on a FACSAria Fusion with DAPI to stain for nuclei. Neuronal nuclei were gated as GFP+ and DAPI+; Total Nuclei were gated as DAPI+, and 50,000 nuclei were used for each sample. Nuclei were subjected immediately to Tn5 transposition and amplification.