title: GSM8209584: 20240402_KS235_ChIP_NCIH526_POU2F3_CST_CKX; Homo sapiens; ChIP-Seq
library_construction_protocol: For ChIP-Seq: Cells were fixed with 2mM disuccinimidyl glutarate 40min room temperature then 1.0% paraformaldehyde 10min room temperature, quenced with 375mM Tris HCL and then sonicated using Covaris E220 ultra-focused sonicator. 1-10ng of immunoprecipitated DNA was used for library prep.  For ATAC-Seq: 100K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 8 cycles of amplification  For RNA-Seq: All RNA was collected using the TRIzol extraction (Invitrogen) method and treated with DNAse using the DNA-free DNA Removal Kit (Invitrogen). 1ug of DNAse-treated RNA was used for the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for standard Illumina sequencing. ChIP-seq libraries were prepared with Illumina's NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.  ATAC-seq samples were sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.  RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on  Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.