GSM9588013: Raji RNA-seq RGS-SE knockout replicate 2; Homo sapiens; RNA-Seq
For RNA-seq: Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) per the manufacturer's protocol, treated with DNase I (Nippon Gene), and purified using TRIzol Reagent (Thermo Fisher Scientific). Poly(A)+ RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). For ATAC-seq: Approximately 50,000 Raji cells were lysed and transposition was performed using Tn5 transposase (Illumina, #FC121-1030) for 30 min at 37 degrees C. The reaction was purified using the MinElute PCR Purification Kit (Qiagen). For RNA-seq: Libraries were prepared with the SMARTer Stranded RNA-Seq Kit v2 (Takara Bio). Sequencing was performed on a DNBSEQ-G400 with paired-end reads. For ATAC-seq: Five PCR cycles were performed using custom Nextera primers with NEBNext Q5 Hot Start HiFi PCR Master Mix (New England BioLabs). Additional cycles were determined by qPCR of partially amplified products. Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881) with double size selection (left 1.4, right 0.5). Sequencing was performed on a DNBSEQ-G400.