Berry-derived gold nanoparticles induce integrated oxidative stress-mediated apoptosis, immune modulation, and transcriptomic remodeling in 4T1 triple-negative cancer cells
Genomic DNA was extracted from 4T1 triple-negative breast cancer cells using QuickExtract DNA extraction solution. The cell lysate was heated in a Veriti thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA) at 65oC for 10 min followed by 98oC for 5 min. Genomic DNA was QCed, used to construct the NGS library (Illumina Phix control library), and was subjected to whole-genome next-generation sequencing (WG-NGS) on Illumina NextSeq 1000 (Illumina, Inc., San Diego, CA, USA; S/N: VL00482) at ACGT Inc. (ACGT DNA Sequencing Services, Wheeling, IL, USA, ACGT ID: 855012, Illumina NextSeq Run ID: 241030_VL00482_40_AACJNGWM5). The Illumina NextSeq 1000 was equipped with P1 reagents and XLEAP-SBS chemistry on a 600-cycle run (2 x 300 bp) to ensure an accurate quality score of 85% of bases higher than Q30.