title: GSM7635379: SMC1_CA1200_1hrauxin_L3_rep1 [JK159b]; Caenorhabditis elegans; ChIP-Seq
library_construction_protocol: ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP. Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima High Coverage Hi-C kit, which uses four 4-base cutters. The Arima manufacturer's protocol was followed. ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified. Hi-C: Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.