GSM9098418: Jurkat_8B10_VAV1_CRISPRi_geneTargeting_rep_3; Homo sapiens; RNA-Seq
Approximately 200,000 cells from each Jurkat T cell clone underwent Ficoll density  gradient centrifugation for dead cell removal (Ficoll-Paque PLUS Medium, VWR #95038-168). Approximately 50,000 cells per aliquot (3 replicates per Jurkat T cell clone) were used for ATAC-seq and 50,000 cells per aliquot for RNA-seq. Triplicates of 50,000 cells were resuspended in TRIzol-reagent (Thermo Fisher Scientific, #15596026) for RNA extraction (Direct-zol-96 RNA, Zymo Research #R2056). To identify sense versus anti-sense host gene and HIV-1 RNA transcription, we used NEBNext Ultra II Orientational RNA Library Prep Kit for Illumina for RNA-sequencing (NEB #E7760) for library prep with NEBNext rRNA Depletion Kit v2 (NEB #E7400). cDNA libraries were sequenced on NovaSeq 6000.