title: GSM6119048: ChIP-seq SW480 RNAPII Rep 2; Homo sapiens; ChIP-Seq
library_construction_protocol: Cell resuspensions were next dounced ten times in a prechilled glass homogenizer. Nuclei were collected and resuspended in shearing buffer (0.1% SDS, 0.5% N-lauroylsarcosine, 1% Triton X-100, 10 mM Tris-HCl pH 8.1, 100 mM NaCl, 1 mM EDTA, 1 mM PMSF, PICs) and incubated on ice for 30 min. Chromatin was fragmented using an E220 Focused-Ultrasonicator (Covaris) to an average size of 200-600 bp. ChIP-seq libraries for all samples were generated and sequenced by Admera Health. Briefly, immunoprecipitated DNA was quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA) and quality assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep (Roche, Basel, Switzerland) following the manufacturers recommendations. All samples were subjected to end-repair, adaptor ligation followed by indexed PCR using Illumina® 8-nt dual-indices. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay and Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA). Final libraries were quantified using QuantStudio ® 5 System (Applied Biosystems, California, USA) prior to equimolar pooling based on qPCR QC values. Sequencing was performed on an Illumina NovaSeq (Illumina, CA, USA) with aread length configuration of 150 PE for 40 M PE reads 20 M in eachdirection) per sample. For TOP1cc-seq and RNA PolII CHIP-seq, the read length configuration was 75 SE.