HGPS167 SAMMY-seq S3, late passage replicate 2
For DNA fractionation, we took an aliquot corresponding to 30% of volume of S2, S3, S4 fractions and added TE buffer to reach a final volume of 300L. After incubation with RNAse A (Roche) (90 minutes at 37) and Proteinase K (Sigma) (150 minutes at 55), DNA was extracted from beads by standard phenol/chloroform extraction, precipitated and resuspended in 25l milliQ H2O. After Nanodrop (260/280 = 1,7-1,9; 260/230  2) and Qubit HS DNA quantification, we added H2O to a final volume of 105L. Then samples were sonicated using a Bioruptor or Covarissonicator to reach a fragment dimension range of 100-500 bps. All the samples were quantified using Qubit HS DNA kit (Life Technologies) and library prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) using Unique Dual Index NEBNext Multiplex Oligos for Illumina (NEB). Library were quantified using Qubit HS DNA kit (Life Technologies) and profiles were checked by capillary electrophoresis on a Agilent 2100 Bioanalyzer. Finally, DNA libraries were sequenced using an Illumina NovaSeq 6000 instrument according to manufacturers instructions.