KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti CD27-APC | BioLegend (mouse anti-Human CD27, clone M-T271) | Cat. #356410; RRID: AB_2561957 |
| Anti CD274-PE | BioLegend (mouse anti-Human CD274, clone 29E-2A3) | Cat. #329706; RRID: AB_940368 |
| Anti CD46-APC | BioLegend (mouse anti-Human CD46, clone TRA-2-10) | Cat. #352405; RRID: AB_2564356 |
| Anti CD46-PE | BioLegend (mouse anti-Human CD46, clone TRA-2-10) | Cat. #352402; RRID: AB_10895756 |
| Anti ICAM1-Pacific Blue | BioLegend (mouse anti-Human ICAM1, clone HCD54) | Cat. #322716; RRID: AB_893384 |
| Anti NRF2 | Invitrogen (rabbit anti-Human NRF2, polyclonal) | Cat. #PA5-27882; RRID: AB_2545358 |
| Anti IgG | Sigma Aldrich (goat anti-Rabbit IgG, polyclonal) | Cat. #12-348 |
| Bacterial and virus strains | ||
| Epstein-Barr virus (EBV), B95-8 strain | Luftig Lab (Original publication: Johannsen et al., 2004).31 | https://doi.org/10.1073/pnas.0407320101 |
| Biological samples | ||
| Whole blood samples | Gulf Coast Regional Blood Center (Houston, TX) | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| TrueCut™ Cas9 Protein v2 | ThermoFisher Scientific | Cat. #A36499 |
| Histopaque®-1077 | Sigma-Aldrich (Raleigh, NC) | Cat. #H8889 |
| Critical Commercial Assays | ||
| BD iMag B cell Negative Selection Kit | BD Biosciences (Franklin Lakes, NJ) | Cat. #558007 |
| 10x Chromium Next GEM Single | 10x Genomics (Pleasanton, CA) | Prod. #1000285 |
| Cell Multiome ATAC + Gene Expression Kit (2x) | ||
| Dual Index Kit TT Set A | 10x Genomics (Pleasanton, CA) | Prod. #1000215 |
| Single Index Kit N Set A | 10x Genomics (Pleasanton, CA) | Prod. #1000212 |
| 10x Chromium Chip J | 10x Genomics (Pleasanton, CA) | Prod. #1000230 |
| NovaSeq S2 Reagent Kit v1.5 | Illumina (San Diego, CA) | Cat. #20028314 |
| NuPage 4–12% Bis-Tris Gel | ThermoFisher Scientific (Invitrogen) | Cat. #NP0322 |
| PageRuler Pre-stained Protein Ladder, 10–250 kDa | ThermoFisher Scientific | Cat. #26619 |
| Revert 700 Total Protein Stain | Li-COR (Lincoln, NE) | Cat. #926-11011 |
| SuperSignal West Femto | ThermoFisher Scientific | Cat. #34096 |
| Gene Knockout Kit v2 (See Table S3) | Synthego (Redwood, CA) | N/A |
| Synthetic sgRNA Kit (See Table S3) | Synthego (Redwood, CA) | N/A |
| Neon™ Transfection System 10uL Kit | ThermoFisher Scientific | Cat. #MPK1096 |
| Deposited data | ||
| Donor 1 uninfected B cell scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695143; SRX13167303 |
| Donor 2 uninfected B cell scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695151; SRX13167311 |
| Donor 1 B cells day 2 post-EBV scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695145; SRX13167305 |
| Donor 2 B cells day 2 post-EBV scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695153; SRX13167313 |
| Donor 1 B cells day 5 post-EBV scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695147; SRX13167307 |
| Donor 2 B cells day 5 post-EBV scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695155; SRX13167315 |
| Donor 1 B cells day 8 post-EBV scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695149; SRX13167309 |
| Donor 2 B cells day 8 post-EBV scATAC-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695157; SRX13167317 |
| Donor 1 uninfected B cell scRNA-seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695144; SRX13167304 |
| Donor 2 uninfected B cell scRNA -seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695152; SRX13167312 |
| Donor 1 B cells day 2 post-EBV scRNA -seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695146; SRX13167306 |
| Donor 2 B cells day 2 post-EBV scRNA -seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695154; SRX13167314 |
| Donor 1 B cells day 5 post-EBV scRNA -seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695148; SRX13167308 |
| Donor 2 B cells day 5 post-EBV scRNA -seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695156; SRX13167316 |
| Donor 1 B cells day 8 post-EBV scRNA -seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695150; SRX13167310 |
| Donor 2 B cells day 8 post-EBV scRNA -seq | This study (GEO accession GSE189141; SRA accession SRP346796) | GSM5695158; SRX13167318 |
| GM12878 ATAC-seq | Buenrostro et al., 2013126 (GSE47753) | GSM1155957 |
| GM12878 EBNA1 ChIP-seq | Tempera et al., 201679 (GSE73887) | GSM1905009 |
| GM12878 EBNALP ChIP-seq | Portal et al., 201380 (GSE49338) | GSM1197603 |
| Mutu III EBNA2 ChIP-seq | McLellan et al., 201344 (GSE47629) | GSM1153765 |
| Mutu III EBNA3C ChIP-seq | McLellan et al., 201344 (GSE47629) | GSM1153766 |
| GM12878 IgG control ChIP-seq | Gunnell et al., 2016127 (GSE76869) | GSM2039169 |
| GM12878 RelA ChIP-seq | Zhao et al., 201482; Iannetti et al., 2014 81 (GSE55105) | GSM2628088 |
| GM12878 RelB ChIP-seq | Zhao et al., 201482; Iannetti et al., 201481 (GSE55105) | GSM2628090 |
| GM12878 cRel ChIP-seq | Zhao et al., 201482; Iannetti et al., 201481 (GSE55105) | GSM2628092 |
| GM12878 CTCF ChIP-seq | Lee et al., 2012128 (GSE32883) | GSM489290 |
| GM12878 RNA Pol II ChIP-seq | Raha et al., 201085 (GSE19550) | GSM487431 |
| GM12878 H2AZ ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733767 |
| GM12878 H3K4me1 ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733772 |
| GM12878 H3K4me3 ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733708 |
| GM12878 H3K9ac ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733667 |
| GM12878 H3K9me3 ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733664 |
| GM12878 H3K27ac ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733771 |
| GM12878 H3K27me3 ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733758 |
| GM12878 H3K36me3 ChIP-seq | ENCODE Project Consortium 201283 (GSE29611) | GSM733679 |
| GM12878 Hi-C | Rao et al., 2014129 (GSE63525) | GSE63525_GM12878_dilution_combined_30.hic |
| Oligonucleotides | ||
| GAGAAACAUGUCCAUAUAUA | Synthego sgRNA | sgRNA_CD46_1 |
| AACUCGUAAGUCCCAUUUGC | Synthego sgRNA | sgRNA_CD46_2 |
| UUGCUCCUUAGAGGAAAUAA | Synthego sgRNA | sgRNA_CD46_3 |
| GGCCAAGCACGAGAACACUC | Synthego sgRNA | sgRNA_BHLHE40_1 |
| CGAGACCACCCGGUGGAGGU | Synthego sgRNA | sgRNA_BHLHE40_2 |
| CAGCUCUCCGGCCAAAGGUU | Synthego sgRNA | sgRNA_BHLHE40_3 |
| GGAGGUCGAUGUGUUACACC | Synthego sgRNA | sgRNA_MEF2C_1 |
| GAGCCAGUGGCAAUAGGUUG | Synthego sgRNA | sgRNA_MEF2C_2 |
| GAGACUGGCAUCUCGAAGUU | Synthego sgRNA | sgRNA_MEF2C_3 |
| UAGUUGUAACUGAGCGAAAA | Synthego sgRNA | sgRNA_NFE2L2_1 |
| GCGACGGAAAGAGUAUGAGC | Synthego sgRNA | sgRNA_NFE2L2_2 |
| AUUUGAUUGACAUACUUUGG | Synthego sgRNA | sgRNA_NFE2L2_3 |
| UGGGCAGAUCCCGGACCCUU | Synthego sgRNA | sgRNA_JDP2_1 |
| CCGAGCUGGGGAGCCCGGUC | Synthego sgRNA | sgRNA_JDP2_2 |
| CAAUCAUGGCCCCGAGGUUG | Synthego sgRNA | sgRNA_JDP2_3 |
| AAGUAAGUUGAUCUCACCUA | Synthego sgRNA | sgRNA_CD274_dss_1 |
| UCCACCAAUUAGAGCACGGC | Synthego sgRNA | sgRNA_CD274_dss_2 |
| ACUCAAUGAACCACGAGAGG | Synthego sgRNA | sgRNA_CD274_dss_3 |
| UGGGUCUCUGGAAUCACGAC | Synthego sgRNA | sgRNA_CD274_ctrl_1 |
| GCGGUGUUGCCCAUGAGAUA | Synthego sgRNA | sgRNA_CD274_ctrl_2 |
| TTCAGTGTAATTCTTCTCTGAGCA | IDT | BHLHE40 Forward Primer |
| AGGAACGGGGAGCTGATCA | IDT | BHLHE40 Reverse Primer |
| AGGGAGGACGAGCAGAAGTA | IDT | MEF2C Forward Primer |
| TGGAGTCTAATGAAATGGGGCT | IDT | MEF2C Reverse Primer |
| CAGGAGGCTGAGGTTGGAAA | IDT | NFE2L2 Forward Primer |
| AACCATTTGTGACTTTGCCCT | IDT | NFE2L2 Reverse Primer |
| TGCCTATGATTGGGTCAAGCA | IDT | JDP2 Forward Primer |
| GCCCAGTGCTTCTCAAGTGT | IDT | JDP2 Reverse Primer |
| Software and algorithms | ||
| CellRanger (cellranger-arc) | 10x Genomics (Pleasanton, CA); functions used: cellranger-arc mkref, cellranger-arc mkfastq, cellranger-arc count | v2.0 |
| R/R Studio | Open Source/RStudio, PBC (Boston, MA) | v4.0/v1.4.1106 |
| Seurat (R package) | Macosko et al., 2015108; Satija et al., 2015109; Stuart et al., 2019110 | v4.0 |
| Signac (R package) | Stuart et al.,202134 | v1.4.0 |
| Monocle3 (R package) | Qiu et al., 2017130 | v0.2.3 |
| Bioconductor (R package) | bioconductor.org; R libraries used include: GenomeInfoDB, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, motifmatcher, JASPAR2020, TFBSTools) | v3.14 |
| macs2/macs3 | Liu, 2014113 | v2.2.7/v3.0 |
| bedtools | Quinlan and Hall, 2010117; functions used: multiinter | |
| GREAT | McLean et al., 201033; http://great.stanford.edu/public/html/ | v4.0.4 |
| hicExplorer | Ramirez et al., 2018118; Wolff et al., 2018119; Wolff et al., 2020120 | v3.7.2 |
| IGV | Robinson et al., 2011121 | v2.9.2 |
| Juicebox | Durand et al.,2016122 | v1.5.1 |
| Cytoscape | Shannon et al., 2003123 | v3.8.2 |
| Other | ||
| RPMI 1640 | Sigma-Aldrich (Raleigh, NC) | Cat. #11875093 |
| FBS, heat inactivated | Corning (Durham, NC) | Cat. #35-010-CV |
| DMSO | Sigma-Aldrich (Raleigh, NC) | Cat. #D2660-100ML |
| 10x Chromium Controller | 10x Genomics (Pleasanton, CA) | Prod. #1000204 |
| NovaSeq 6000 | Illumina (San Diego, CA) | Cat. #20012850 |
| BD FACS Canto II | BD Biosciences (Franklin Lakes, NJ) | N/A |
| Sony SH800 Sorter | Sony Biotechnology | N/A |
| Neon™ Transfection System | ThermoFisher Scientific | Cat. #MPK5000 |
| Human (hg38) reference genome | Genome Reference Consortium | GRCh38.p13 |
| Type 1 EBV reference genome | de Jesus et al. 2003131; FASTA accessed via NCBI | NC_007605.1 |
| hg38+EBV reference genome | Generated via concatenation of the genomes listed above | N/A |