Table 1 Gene Expression Fold Change* HIV∆2GFP HIV∆3GFP Gene Symbol Gene Title: a B C a B C

Table 1 Gene Expression Fold Change* HIV∆2GFP HIV∆3GFP Gene Symbol Gene Title: A B C A B C . Apoptosis and Cell Cycle BCAR3 breast cancer anti-estrogen resistance 3 3.9 2.0 2.3 4.8 1.6 3.0 BCL2A1 BCL2-related protein A1 4.1 5.1 3.5 3.4 3.5 2.0 CYP4V2 cytochrome P450, family 4, subfamily V, polypeptide 2 2.4 1.4 2.5 2.0 1.6 2.4 DDIT4 DNA-damage-inducible transcript 4 2.5 2.5 1.8 2.8 2.8 1.9 EGFL6 EGF-like-domain, multiple 6 2.1 3.0 4.0 1.9 1.8 2.3 F2R coagulation factor II (thrombin) receptor 3.6 2.3 3.4 1.7 1.2 2.1 FOXO3A Forkhead box O3A 1.7 4.3 2.3 1.1 3.7 2.2 GZMB granzyme B (cytotoxic T-lymphocyte-associated serine esterase 1) 3.7 2.7 1.4 4.2 2.7 1.4 GZMH granzyme H (cathepsin G-like 2, protein h-CCPX) 2.9 3.7 2.2 3.3 2.8 2.6 IER3 immediate early response 3 1.5 3.3 5.2 1.8 3.9 3.6 MDM2 Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) 1.6 2.2 2.4 2.1 1.7 1.9 NCKAP1 NCK-associated protein 1 3.1 2.4 1.6 1.7 1.8 1.0 PHLDA1 pleckstrin homology-like domain, family A, member 1 2.3 2.1 1.7 3.1 3.6 2.6 PMAIP1 phorbol-12-myristate-13-acetate-induced protein 1 2.1 1.8 3.4 2.0 2.1 3.2 PPAP2A phosphatidic acid phosphatase type 2A 3.3 1.7 2.7 2.7 2.1 2.5 RAP1A RAP1A, member of RAS oncogene family 4.9 6.5 4.5 4.2 4.7 4.5 RNF130 ring finger protein 130 10.4 3.4 2.5 7.0 2.4 2.7 SQSTM1 Sequestosome 1 1.0 3.5 1.9 1.3 2.7 2.2 TNFAIP3 tumor necrosis factor, alpha-induced protein 3 1.1 2.2 2.5 1.7 2.8 3.0 TNFSF10 tumor necrosis factor (ligand) superfamily, member 10 1.3 3.0 1.9 1.6 2.2 1.9 TNFRSF10A tumor necrosis factor receptor superfamily, member 10a 2.1 1.6 1.8 1.6 1.2 1.6 TNFRSF10B tumor necrosis factor receptor superfamily, member 10b 2.0 4.2 5.1 2.6 2.4 1.8 TNFRSF18 tumor necrosis factor receptor superfamily, member 18 2.0 2.8 2.2 2.7 2.0 1.9 TRAF4 TNF receptor-associated factor 4 2.2 1.8 1.9 2.5 2.3 1.9 Cell Adhesion BTBD9 BTB (POZ) domain containing 9 2.3 1.6 2.5 2.5 1.4 1.8 CALD1 caldesmon 1 3.5 3.9 3.2 3.6 8.7 4.6 CCL3 chemokine (C-C motif) ligand 3 1.2 4.6 2.4 7.1 14.6 4.2 CELSR2 cadherin, EGF LAG seven-pass G-type receptor 2 5.0 2.7 2.0 5.1 1.9 2.2 CMTM2 CKLF-like MARVEL transmembrane domain containing 2 1.5 1.7 3.9 2.0 2.5 4.1 INPP5A inositol polyphosphate-5-phosphatase, 40kDa 1.9 2.2 2.1 1.6 2.2 1.8 PECAM1 Platelet/endothelial cell adhesion molecule (CD31 antigen) 3.1 2.3 3.7 2.2 1.1 2.0 Cell Growth and Development ATN1 Atrophin 1 1.8 1.6 1.8 2.3 2.9 1.8 CRIM1 cysteine rich transmembrane BMP regulator 1 (chordin-like) 2.3 2.0 1.5 1.8 1.7 1.3 CSF1 colony stimulating factor 1 (macrophage) 2.2 2.0 1.7 2.5 3.4 2.1 EPAS1 endothelial PAS domain protein 1 2.4 4.3 3.1 2.6 3.1 2.8 FMNL3 Formin-like 3 3.6 1.9 2.7 2.0 1.1 3.2 IL12RB2 Interleukin 12 receptor, beta 2 2.0 1.3 2.3 3.0 1.6 3.1 VAT1 vesicle amine transport protein 1 homolog (T californica) 3.4 1.7 2.0 2.8 1.7 0.8 Chromatin Remodeling CTAGE5 CTAGE family, member 5 2.4 1.2 2.0 2.4 1.6 2.0 RBM6 RNA binding motif protein 6 2.1 1.5 2.6 1.9 1.2 1.6 SATB1 Special AT-rich sequence binding protein 1 2.3 2.3 1.8 1.7 1.4 1.6 SIRT2 Sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae) 1.7 3.2 3.1 1.5 2.5 2.2 Immune Response ALOX5 arachidonate 5-lipoxygenase 4.5 1.7 4.7 1.6 0.8 3.2 BCL6 B-cell CLL/lymphoma 6 (zinc finger protein 51) 11.9 26.6 15.4 3.9 5.7 3.5 C3AR1 complement component 3a receptor 1 2.4 2.2 1.7 1.7 2.1 1.9 CCL5 chemokine (C-C motif) ligand 5 2.2 2.3 1.7 2.2 2.3 1.5 CCR1 chemokine (C-C motif) receptor 1 2.1 1.2 2.0 2.5 1.8 2.5 CD69 CD69 molecule 2.8 2.6 3.0 2.6 2.5 3.1 CD96 CD96 molecule 2.3 2.0 2.1 2.1 1.5 1.9 CYSLTR1 cysteinyl leukotriene receptor 1 6.1 3.5 3.2 2.5 1.4 2.3 IFI44L interferon-induced protein 44-like 2.4 4.9 7.4 1.4 2.0 1.7 IFIT2 interferon-induced protein with tetratricopeptide repeats 2 2.1 5.7 3.4 1.8 1.7 2.3 IL13 interleukin 13 1.4 1.9 1.6 5.6 2.6 3.2 IL17A interleukin 17A 2.6 9.2 2.5 3.7 14.2 3.3 IL18R1 interleukin 18 receptor 1 3.2 2.8 4.1 2.8 2.4 2.9 IL18RAP interleukin 18 receptor accessory protein 7.0 6.2 6.3 4.3 2.1 2.1 IL1RN interleukin 1 receptor antagonist 3.2 3.0 4.8 3.7 7.2 3.6 IRAK2 interleukin-1 receptor-associated kinase 2 1.7 3.6 2.9 1.6 2.5 2.2

*relative to eGFP control Table 1 Gene Expression Fold Change* HIV∆2GFP HIV∆3GFP Gene Symbol Gene Title: A B C A B C . OASL 2'-5'-oligoadenylate synthetase-like 1.8 2.8 2.2 2.1 3.1 2.2 PROCR Protein C receptor, endothelial (EPCR) 4.9 2.7 1.9 2.8 2.0 2.1 TNFSF4 tumor necrosis factor (ligand) superfamily, member 4 4.4 7.6 4.7 3.3 2.0 2.1 Metabolism CTH cystathionase (cystathionine gamma-lyase) 2.1 1.8 2.1 2.2 2.5 1.8 DHCR7 7-dehydrocholesterol reductase 2.1 2.0 1.7 1.4 1.9 1.6 DHRS3 dehydrogenase/reductase (SDR family) member 3 1.7 8.9 11.2 1.9 2.6 7.6 HBS1L HBS1-like (S. cerevisiae) 2.3 1.7 2.4 1.8 1.1 2.1 MAN1C1 mannosidase, alpha, class 1C, member 1 2.3 4.2 3.6 2.5 1.4 3.0 MOCOS molybdenum cofactor sulfurase 2.8 2.1 1.5 2.7 2.5 1.5 MTHFD1 Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 4.2 3.4 3.0 2.4 4.0 3.3 P4HA2 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase) 2.7 3.9 4.4 2.8 2.6 4.3 TMEM23 Transmembrane protein 23 10.4 2.9 2.4 8.9 1.8 2.1 TUBB2A tubulin, beta 2A 1.7 3.3 1.9 2.4 3.3 1.9 Protein Modification CDKL3 cyclin-dependent kinase-like 3 2.5 2.3 1.5 1.6 1.3 1.6 CPM Carboxypeptidase M 1.5 3.1 3.7 1.5 2.1 1.7 CTSL cathepsin L 2.8 3.6 1.9 2.1 2.1 1.2 DNAJB2 DnaJ (Hsp40) homolog, subfamily B, member 2 1.9 2.2 2.3 1.6 2.0 2.0 MGAT5 Mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase 6.2 14.0 1.4 3.0 8.7 2.2 PRKCE protein kinase C, epsilon 2.8 3.5 3.3 1.6 1.9 3.3 PTPN2 Protein tyrosine phosphatase, non-receptor type 2 1.4 2.3 2.2 1.4 1.6 1.8 RNF144 ring finger protein 144 2.7 2.6 3.6 1.2 1.7 3.7 YES1 V-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 2.0 2.8 3.3 1.8 1.4 2.3 Signal Transduction ANK3 ankyrin 3, node of Ranvier (ankyrin G) 2.0 4.0 3.4 1.4 2.2 1.9 DUSP8 dual specificity phosphatase 8 1.7 3.3 2.2 1.5 4.4 2.1 HBEGF heparin-binding EGF-like growth factor 2.7 2.6 2.0 2.0 2.7 2.0 ITPR1 Inositol 1,4,5-triphosphate receptor, type 1 6.6 1.5 2.0 4.8 1.7 1.9 NFKBIZ nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta 1.8 2.1 2.5 2.0 2.3 2.9 P2RY14 purinergic receptor P2Y, G-protein coupled, 14 2.6 9.4 4.4 2.6 4.7 3.9 PDE3B Phosphodiesterase 3B, cGMP-inhibited 2.1 2.3 2.6 2.2 1.8 3.1 PDE4A phosphodiesterase 4A, cAMP-specific 2.4 2.0 2.1 1.8 1.6 1.6 PDE4D Phosphodiesterase 4D, cAMP-specific 2.0 1.6 2.0 2.1 1.6 2.3 PIK3AP1 phosphoinositide-3-kinase adaptor protein 1 2.1 1.4 2.1 2.5 1.2 2.3 PMCH pro-melanin-concentrating hormone 2.2 5.1 8.4 2.5 3.3 3.2 PPAP2A phosphatidic acid phosphatase type 2A 3.3 1.7 2.7 2.7 2.1 2.5 RASGRF2 Ras protein-specific guanine nucleotide-releasing factor 2 4.5 2.9 2.1 2.2 2.5 2.8 SOS2 Son of sevenless homolog 2 (Drosophila) 1.7 3.0 2.9 1.4 1.8 1.9 SYTL3 synaptotagmin-like 3 1.5 3.5 2.7 1.4 2.7 2.0 TFG TRK-fused gene 3.2 0.4 1.6 2.8 1.5 2.7 TIAM1 T-cell lymphoma invasion and metastasis 1 3.6 2.2 2.0 2.1 1.4 1.6 Transcription ATF3 activating transcription factor 3 2.5 3.5 2.9 2.5 1.9 2.4 BCL6 B-cell CLL/lymphoma 6 (zinc finger protein 51) 11.9 26.6 15.4 3.9 5.7 3.5 BCORL2 BCL6 co-repressor-like 2 2.5 1.9 2.1 2.1 0.6 2.7 CREM cAMP responsive element modulator 2.0 2.7 2.5 2.6 3.2 2.6 EGR1 early growth response 1 3.9 3.3 1.8 4.9 4.6 2.0 ETV6 Ets variant gene 6 (TEL oncogene) 2.0 2.3 3.1 1.4 1.6 2.9 FOSL2 FOS-like antigen 2 2.0 1.7 2.0 1.7 2.3 2.0 FOXP1 Forkhead box P1 4.3 2.3 3.2 2.8 1.2 2.7 HDAC4 histone deacetylase 4 1.9 2.1 2.4 1.2 1.6 1.9 HLF hepatic leukemia factor 0.8 2.7 1.9 3.3 4.7 3.0 IRF8 interferon regulatory factor 8 2.5 2.1 2.0 1.8 1.6 1.9 JUN v-jun sarcoma virus 17 oncogene homolog (avian) 2.5 2.3 2.7 1.9 2.1 1.9 MAML3 mastermind-like 3 (Drosophila) 1.7 1.8 5.6 2.1 3.6 4.3 NR3C1 Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) 2.2 1.6 2.0 2.2 1.3 3.0 RUNX1 runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) 1.3 2.9 2.6 1.7 2.4 2.4 SMAD1 SMAD, mothers against DPP homolog 1 (Drosophila) 1.0 6.8 2.8 0.9 1.8 1.6 STAT3 Signal transducer and activator of transcription 3 (acute-phase response factor) 1.5 1.8 2.5 1.7 2.2 2.1 TCERG1 Transcription elongation regulator 1 2.4 1.0 1.6 2.9 3.3 1.9 TWIST1 twist homolog 1 (acrocephalosyndactyly 3; Saethre-Chotzen syndrome) 4.6 2.4 2.2 5.6 1.6 1.7 ZBTB10 Zinc finger and BTB domain containing 10 2.2 3.6 2.4 1.5 1.6 1.6

*relative to eGFP control Table 1 Gene Expression Fold Change* HIV∆2GFP HIV∆3GFP Gene Symbol Gene Title: A B C A B C . ZBTB20 zinc finger and BTB domain containing 20 2.0 3.8 2.3 1.2 2.0 1.7 ZNF44 zinc finger protein 44 2.2 1.8 2.5 0.9 2.1 2.7 ZNF117 Zinc finger protein 117 (HPF9) 2.1 1.8 2.4 2.2 1.8 2.5 ZNF167 zinc finger protein 167 1.7 14.3 2.6 2.1 6.1 2.9 ZNF222 zinc finger protein 222 2.2 2.8 2.0 2.0 2.9 3.0 ZNF282 zinc finger protein 282 3.1 3.6 2.3 4.0 2.8 1.6 ZNF439 Zinc finger protein 439 4.4 2.0 4.9 2.5 1.4 3.3 ZNF483 Zinc finger protein 483 2.5 2.0 2.6 1.9 1.7 2.2 ZNF585A zinc finger protein 585A 2.6 3.2 2.1 2.7 1.7 3.0 ZNF606 zinc finger protein 606 2.1 1.9 2.6 1.8 1.4 1.9 ZNF677 Zinc finger protein 677 3.8 3.0 3.6 2.7 3.2 4.0 Transport BET1 BET1 homolog (S. cerevisiae) 2.4 3.4 1.5 2.1 1.7 1.9 MCOLN3 mucolipin 3 1.9 2.3 2.1 1.2 1.8 2.0 NPTX1 neuronal pentraxin I 1.9 1.8 1.8 2.9 1.7 2.4 SLC41A2 solute carrier family 41, member 2 0.6 2.4 2.7 2.1 2.2 1.9 STX4 Syntaxin 4 2.4 2.4 2.3 2.3 2.0 2.1 Unknown ACTA2 actin, alpha 2, smooth muscle, aorta 2.0 4.4 2.2 2.2 2.6 1.8 ANKRD42 Ankyrin repeat domain 42 1.5 2.7 2.5 1.6 1.2 2.5 ATHL1 ATH1, acid trehalase-like 1 (yeast) 2.0 3.1 2.4 1.8 2.3 1.8 BZRAP1 benzodiazapine receptor (peripheral) associated protein 1 2.3 1.7 1.8 3.8 2.2 2.2 CLN5 ceroid-lipofuscinosis, neuronal 5 1.7 2.4 2.3 1.7 1.3 1.7 DCUN1D3 DCN1, defective in cullin neddylation 1, domain containing 3 (S. cerevisiae) 1.8 2.1 2.4 2.2 2.9 2.7 DDX42 DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 6.1 4.2 2.4 6.3 1.8 2.5 DFNA5 deafness, autosomal dominant 5 6.4 7.4 5.7 3.7 2.7 2.4 DMRTC1 DMRT-like family C1 1.6 2.7 2.8 2.5 2.2 1.7 FLJ38725 hypothetical protein FLJ38725 1.8 2.6 2.7 2.2 2.1 2.7 KLHDC1 kelch domain containing 1 2.1 2.3 2.7 1.6 1.1 2.3 LCMT2 leucine carboxyl methyltransferase 2 1.8 3.1 1.7 1.6 3.1 2.1 METRNL meteorin, glial cell differentiation regulator-like 3.0 2.5 2.5 2.2 2.4 1.9 MOBKL2B MOB1, Mps One Binder kinase activator-like 2B (yeast) 2.7 2.6 3.7 2.0 1.0 2.3 MPP7 membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7) 5.3 2.9 2.4 3.3 2.1 2.4 MYO1E Myosin IE 1.5 2.4 2.3 1.4 1.7 2.2 NTN4 netrin 4 2.4 2.8 2.7 2.3 2.5 2.6 PELI2 pellino homolog 2 (Drosophila) 1.9 3.6 2.1 1.7 1.7 1.5 PLAC8 placenta-specific 8 4.0 4.0 2.5 2.0 1.1 1.5 PSTPIP2 proline-serine-threonine phosphatase interacting protein 2 6.6 3.1 2.9 4.1 1.5 3.3 RSAD2 radical S-adenosyl methionine domain containing 2 4.0 6.5 5.6 2.4 3.5 4.0 SAMSN1 SAM domain, SH3 domain and nuclear localisation signals, 1 2.2 2.1 1.9 1.8 1.5 2.5 SAT Spermidine/spermine N1-acetyltransferase 1.5 3.0 2.1 1.4 1.6 1.9 SCARNA17 small Cajal body-specific RNA 17 2.4 3.2 2.0 1.9 2.9 1.7 SCML4 sex comb on midleg-like 4 (Drosophila) 2.5 5.8 4.0 0.5 3.2 2.0 SYNGR3 synaptogyrin 3 2.2 5.7 4.1 2.9 4.7 2.5 THAP2 THAP domain containing, apoptosis associated protein 2 3.1 2.4 1.5 1.6 2.0 1.1 TMEM149 transmembrane protein 149 1.6 2.9 2.4 1.7 1.7 1.5 TncRNA trophoblast-derived noncoding RNA 2.4 3.3 2.5 1.7 1.7 1.8 ZBED2 zinc finger, BED-type containing 2 2.3 4.9 7.9 1.6 3.1 4.6 ZC3H12C zinc finger CCCH-type containing 12C 0.5 2.0 2.8 2.5 1.8 2.1 ZFP3 zinc finger protein 3 homolog (mouse) 3.0 2.5 3.5 2.4 1.9 3.6 ZNF320 zinc finger protein 320 5.4 1.7 2.1 2.5 1.5 2.5

Apoptosis and Cell Cycle CCNA2 cyclin A2 0.4 0.5 0.3 0.6 0.8 0.5 CCNE1 cyclin E1 0.3 0.5 0.4 0.5 0.7 0.4 E2F8 E2F transcription factor 8 0.5 0.4 0.6 0.5 0.6 0.6 MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast) 0.4 0.5 0.3 0.6 0.9 0.5 PAK1 p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) 0.4 0.7 0.3 0.4 0.9 0.4 RAD54L RAD54-like (S. cerevisiae) 0.4 0.6 0.4 0.5 0.7 0.4 RCC1 regulator of chromosome condensation 1 0.5 0.5 0.7 0.6 0.5 0.8 S100A6 S100 calcium binding protein A6 (calcyclin) 0.4 0.4 0.3 0.6 0.6 0.3 SGOL2 shugoshin-like 2 (S. pombe) 0.6 0.4 0.3 0.5 1.1 0.4 UHRF1 ubiquitin-like, containing PHD and RING finger domains, 1 0.5 0.4 0.5 0.5 0.7 0.6

*relative to eGFP control Table 1 Gene Expression Fold Change* HIV∆2GFP HIV∆3GFP Gene Symbol Gene Title: A B C A B C . ZAK sterile alpha motif and leucine zipper containing kinase AZK 0.1 0.4 0.5 1.0 0.5 0.5 Cell Adhesion OIP5 Opa interacting protein 5 0.5 0.4 0.5 0.6 0.6 0.6 Cell Growth and Development FSHPRH1 FSH primary response (LRPR1 homolog, rat) 1 0.5 0.7 0.5 0.5 0.6 0.4 Chromatin Remodeling GEMIN4 gem (nuclear organelle) associated protein 4 0.6 0.5 0.7 0.5 0.6 0.5 Immune Response HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 0.6 0.4 0.9 0.5 0.5 0.8 Metabolism GLUL glutamate-ammonia ligase (glutamine synthetase) 0.7 0.5 0.6 0.6 0.4 0.5 PFAS phosphoribosylformylglycinamidine synthase (FGAR amidotransferase) 0.5 0.6 0.4 0.6 0.7 0.6 Protein Modification DNAJC9 DnaJ (Hsp40) homolog, subfamily C, member 9 0.5 0.5 0.4 0.5 0.6 0.6 Signal Transduction CDC42SE2 CDC42 small effector 2 0.2 0.3 0.2 0.4 0.5 0.4 DEPDC1B DEP domain containing 1B 0.4 0.3 0.7 0.5 0.6 1.0 Transcription HDAC8 histone deacetylase 8 0.4 0.5 0.7 0.5 0.6 0.7 MYCBP c-myc binding protein 0.4 0.5 0.5 0.8 0.6 0.6 ZNF146 zinc finger protein 146 0.5 0.4 0.4 0.6 0.5 0.4 Transport SLC29A1 solute carrier family 29 (nucleoside transporters), member 1 0.4 0.6 0.5 0.6 1.0 0.6 Unknown ATAD2 ATPase family, AAA domain containing 2 0.5 0.5 0.4 0.4 0.6 0.6 DBF4 DBF4 homolog (S. cerevisiae) 0.7 0.4 0.4 0.7 0.5 0.5 DTL denticleless homolog (Drosophila) 0.5 0.7 0.5 0.5 0.7 0.5 GLOXD1 glyoxalase domain containing 1 0.2 0.7 0.5 0.4 0.4 0.6 MCPH1 microcephaly, primary autosomal recessive 1 0.4 0.4 0.8 0.5 0.6 1.2 NETO2 neuropilin (NRP) and tolloid (TLL)-like 2 0.4 0.6 0.5 0.6 1.0 0.6 SPBC25 spindle pole body component 25 homolog (S. cerevisiae) 0.5 0.4 0.7 0.5 0.6 0.7

*relative to eGFP control