library_construction_protocol: Primary B cells were isolated from adenoid samples of anonymous donors undergoing adenectomy. Adenoids were mechanically chopped and single cells were fractionated by Ficoll Hypaque gradient centrifugation. 20x10^6 primary human B cells were transfected with CD46-Cas9 complex targeting CD46 gene. 1hour after transfection, both CD46 RNP complex and mock electroporated cells were infected with wt EBV virus (6008_B95-8) with a multiplicity of infection of 0.1. 24 hours after transfection, newly transcribed RNAs were metabolically labeled with 4sU (Sigma Aldrich, T4506-25mg) by adding 4sU into culture medium to a final concentration of 100-200 uM and incubated at 37°C for 1 hour. The adenoid samples were rinsed with PBS on 100 µm cell strainer (FalconTm) several times, transferred to a sterile petri dish, and mechanically chopped by using two sterile scalpels adding PBS. The cell suspension was filtered through a 100 um strainer. This procedure was repeated several times to recover a maximum amount of cells. The volume of the collected cells was added up to 30 ml with PBS. The cell suspension was supplemented with 0.5 ml defibrinated sheep blood (Thermo Scientific Oxoid, catalog no. SR0051D) for T cells rosetting and 15 ml of Ficoll Hypaque was added underneath the cell suspension. The samples were centrifuged at 500 g for 30 min and the cells were carefully collected from the interphase and transferred to a new 50 ml tube. The cell suspension was washed with PBS to 50 ml and centrifuged with decreasing centrifugation parameters; 450, 400 and 300 g for 10 min each run. - EBV infected primary B cells were cultivated in RPMI-1640 medium supplemented with 8 % FCS, 100 µg/ml streptomycin, 100 U/ml penicillin, 1 mM sodium pyruvate, 100 nM sodium selenite, and 0.43 % α-thioglycerols at 37 °C and 5 % CO2.  - 2x10^6 primary B cells were freshly isolated, washed once with PBS, and resuspended in 20 µl Nucleofector solution with Supplement buffer, prepared following to the manufacturer's instructions (Lonza). Cells were mixed with 5 µl RNP mix gently by pipetting and transferred into nucleofection cuvettes. Primary human B cells were nucleofected using Program EH100 (Lonza) according to the manufacturer's protocol. Cells were immediately supplemented with prewarmed 100 µl of RPMI medium without any supplement and incubated for 15 min at 37 °C. The cells were transferred into a 24 well plate and supplemented with 20 % FCS medium for their fast recovery from the treatment and incubated at 37 °C, 5 % CO2 for 1 h before they were infected with EBV.  Total RNA from 4sU labeled cells were prepared using chloroform extraction and ethanol precipitation. Newly transcribed 4sU labeled RNAs were thiol-specifically biotinylated and ethanol precipitated. Biotinylated RNAs were separated from unlabeled RNA by streptavidin mediated enrichment by using µMACs Streptavidin Microbeads (Miltenyi) and columns. Ethanol based precipitation was repeated and total RNA concentration with their quality scores were determined using bioanalyzer prior to sequencing. After isolation of total RNA the RNA integrity was analyzed with the RNA 6000 Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). Prior to library generation, RNA was subjected to DNAse I digestion (Thermo Fisher Scientific) followed by RNeasy MinElute column clean up (Qiagen). RNA-Seq libraries were generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories) as per the manufacturer´s recommendations. From cDNA final libraries were generated utilizing the Nextera XT DNA Library Preparation Kit (Illumina).