GSM8156200: BN1470, Rep2, Dam::EMR-1; Caenorhabditis elegans; ChIP-Seq
To purify genomic DNA, samples were lysed in 5 freeze/thaw cycles (1min in liquid nitrogen; 3min in 37C shaker) and processed with DNeasy Blood and Tissue Kit (QIAGEN #69504). DamID was performed on 200 ng genomic DNA  extracted from embryos cultured and collected as indicated above. Three replicates were performed as described (de la Cruz Ruiz et al. 2022), using primer AdR (5'-NNNNGTGGTCGCGGCCGAGGATC) and 24 PCR cycles. Successful amplification of Dam-methylated genomic DNA yielded a smear of ~400-~1500 bp fragments when analyzed on Agilent Bioanalyzer. 50 ng of PCR amplified fragments were used for library preparation as described (de la Cruz Ruiz et al. 2022), using E7370 NEBNext® Ultra™ DNA Library Prep Kit for Illumina. Library amplicons' size distribution was checked to be maintained as for PCR fragments indicated above followed by pooling, repurification and sequencing on a Illumina NextSeq2000 platform at EMBL GeneCore.