bulk RNA-seq of ND224 PRDM1 KO CAR-T
On days 0 and 20 of the restimulation assay, dead cells were eliminated using the Dead Cell Removal Kit (Miltenyi Biotec) and CD8+ CAR T-cells were isolated using CD8 microbeads (Miltenyi Biotec). 100,000 cells per sample were cryopreserved. Nuclei were isolated from CD8+ T-cells for each replicate, followed by the transposition reaction in the presence of Tn5 transposase (Illumina, Inc.) for 45 minutes at 37C. Purification of transposed DNA was then completed with the MinElute Kit (Qiagen) and fragments were barcoded with dual indexes (Illumina Nextra). Library preparation and sequencing were performed by Novogene using NovaSeq 6000 (paired-end 150bp reads) at a depth of 30 x 10^6 reads per sample.