title: GSM6205395: CUT&RUNseq_H3K36me3_F2_K27me3_GMpGPm_hermaphrodite_germline_rep1; Caenorhabditis elegans; OTHER
library_construction_protocol: For germline collections, worms were selected at the L4 stage and allowed to develop 1 day at 20˚C to reach the 1st day of adulthood. Worms were decapitated to extrude the germlines. The distal halves of the germlines were collected by cutting the germline at the bend and transferring to ice-cold TRIzol reagent to reach a total of 30-50 germlines. Biological replicates of germlines in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation.  2-4 biological replicates were collected for each genotype.   For L1 collections, gravid mothers were allowed to lay eggs overnight at 20˚C. The next day, late-stage embryos along with some bacteria were transferred to 50 uL drops of S Basal on gelatin chrom alum-coated slides. After 2 hours at room temperature, newly hatched L1 larvae were transferred to ice-cold TRIzol. This process of transferring embryos to S basal, incubating 2 hours, and transferring newly hatched L1 larvae to TRizol was repeated throughout the day to reach a final collection of ~100 newly hatched larvae per replicate. Biological replicates of L1 larvae in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation. 3 biological replicates were collected for each genotype. Libraries were prepared according to manufacturer's instructions.  For transcript analysis, RNA was polyA-selected (NEB #E7490) and libraries prepared (NEB #E7530). For CUT&RUN library preparation, DNA associated with H3K27me3 and H3K36me3 was collected via CUT&RUN method (Skene and Henikoff 2017; Skene et al. 2018) and libraries prepared (Tecan Genomics #0344NB-32).