GSM6603406: Hypodermal RAPID rep1; Caenorhabditis elegans; OTHER
To purify genomic DNA, samples were lysed in 5 freeze/thaw cycles (1 min in liquid nitrogen; 3 min in 37°C shaker) and processed with DNeasy Blood and Tissue Kit (QIAGEN #69504). Two hundred ng of genomic DNA was used as input in the DamID protocol that included an improved pool of AdR primers as described (doi: 10.1007/978-1-0716-2337-4_11). Dam-methylated fragments were amplified with 14 PCR cycles and quality checked on an Agilent Bioanalyzer 2100. Libraries were prepared using 50 ng of PCR-amplified fragments and NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S). Library amplicons size range distribution was checked as before, pooled and re-purified with 1x volume SpeedBeads (doi: 10.1007/978-1-0716-2337-4_11) followed by sequencing at EMBL GeneCore using a NextSeq 500 (Illumina).