Table 2.
Reagents and tools.
| Reagent/Resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Experimental models | ||
| Vero cells (C. aethiops) | ATCC | CCL-81 |
| MRC-5 cells (H. sapiens) | ATCC | CCL-171 |
| A20 HE-RIT (M. musculus) | Santana et al, 2017Pathogens | N/A |
| iSLK-BAC16 cells (H. sapiens) |
Brulois et al, 2012 Journal of Virology |
N/A |
| 293T cells (H. sapiens) | ATCC | CRL-3216 |
|
Akata, EBV-negative (-) cells (H. sapiens) |
Komano et al, 1998 Journal of Virology |
N/A |
| Daudi cells (H. sapiens) | ATCC | CCL-213 |
| BJAB cells (H. sapiens) | DSMZ | ACC757 |
| HDLEC cells (H. sapiens) | PromoCell | C-12216 |
| BALB/cAnNTac (M. musculus) | Taconic Biosciences | N/A |
| Recombinant DNA | ||
| pCMV-Thy1.1-F2A-dsGFP | Rodriguez et al, 2019Journal of Virology | N/A |
| pCMV-Thy1.1-F2A-vhs | Rodriguez et al, 2019Journal of Virology | N/A |
| pCMV-Thy1.1-F2A-BGLF5 | Rodriguez et al, 2019Journal of Virology | N/A |
| pCMV-Thy1.1-F2A-SOX | Rodriguez et al, 2019Journal of Virology | N/A |
| pCMV-Thy1.1-F2A-muSOX | Rodriguez et al, 2019Journal of Virology | N/A |
| Antibodies | ||
| Mouse monoclonal anti-Thy1.1, Alexa Fluor 647 conjugated | BioLegend, clone OX-7 | 202526 |
| Oligonucleotides and other sequence-based reagents | ||
| GAPDH_F | IDT | CAGAACATCATCCCTGCCTCTACT |
| GAPDH_R | IDT | GCCGAGCTTCCCGTTCA |
| UL23 (tk)_F | IDT | ACCCGCTTAACAGCGTCAACA |
| UL23 (tk)_R | IDT | CCAAAGAGGTGCGGGAGTTT |
| US1 (ICP22)_F | IDT | TTTGGGGAGTTTGACTGGAC |
| US1 (ICP22)_R | IDT | CAGACACTTGCGGTCTTCTG |
| UL44 (gC)_F | IDT | GTGACGTTTGCCTGGTTCCTGG |
| UL44 (gC)_R | IDT | GCACGACTCCTGGGCCGTAACG |
| GFP_F | IDT | GAAGCAGCACGACTTCTTCAA |
| GFP_R | IDT | AGTCGATGCCCTTCAGCTC |
| vhs_F | IDT | ATCCAACACAATATCACAGCCCATCAACAG |
| vhs_R | IDT | CGCCAACCTCTATCACACCAACACG |
| BGLF5_F | IDT | GACCTCTTGCATGGCCTCTT |
| BGLF5_R | IDT | GTGCCGCTTCAAGTACCTCT |
| SOX_F | IDT | TGGGCGAGTTTATTGGTAGTGAGG |
| SOX_R | IDT | CTCCACTAGACAGCAGATGTGG |
| muSOX_F | IDT | CCCTGGACACTGCTTTCAAT |
| muSOX_R | IDT | GCCTCACAGGGGTTTTTGTA |
| 18S rRNA_F | IDT | GTAACCCGTTGAACCCCATT |
| 18S rRNA_R | IDT | CCATCCAATCGGTAGTAGCG |
| ISG15_F | IDT | GAGAGGCAGCGAACTCATCT |
| ISG15_R | IDT | CTTCAGCTCTGACACCGACA |
| U6_F | IDT | GGAATCTAGAACATATACTAAAATTGGAAC |
| U6_R | IDT | GGAACTCGAGTTTGCGTGTCATCCTTGCGC |
| 7SL_F | IDT | CAAAACTCCCGTGCTGATCA |
| 7SL_R | IDT | GGCTGGAGTGCAGTGGCTAT |
| MALAT1_F | IDT | GTCATAACCAGCCTGGCAGT |
| MALAT1_R | IDT | GCTTATTCCCCAATGGAGGT |
| SHFL_F | IDT | GGCTCTGATGAGGAAATTCGGC |
| SHFL_R | IDT | TCCTGGGCATCCAGATCGTTAC |
| matGAPDH_F | IDT | AGCCTCAAGATCATCAGCAATG |
| matGAPDH_R | IDT | ATGGACTGTGGTCATGAGTCCTT |
| RPS13_F | IDT | TCGGCTTTACCCTATCGACGCAG |
| RPS13_R | IDT | ACGTACTTGTGCAACACCATGTGA |
| ECE1_F | IDT | CGGAGCACGCGAGCTATGA |
| ECE1_R | IDT | CCGCCAGAAGTACCACCAAC |
| EPSTI1_F | IDT | GACAGAAGTGCCTGTCAAAGTG |
| EPSTI1_R | IDT | GCCGTTTCAGTTCCAGTAATTC |
| IPO7_F | IDT | TCAATTTTGGAGGCCCAGCA |
| IPO7_R | IDT | AGGTTGCATGATCAGGTCCC |
| MAN1A2_F | IDT | CACATGATGATGTACAGCAGAGC |
| MAN1A2_R | IDT | ATCGAACAGCAGGATTACCTGA |
| RELL1_F | IDT | GCAGTGGCACAGAGTAGCAG |
| RELL1_R | IDT | CAGTGCAGCCTTACCAGTTG |
| TNPO3_F | IDT | ACATTGCAGCTCGTGTACCA |
| TNPO3_R | IDT | AGCATGACTCCACATCCTGC |
| circECE1_F | IDT | ACCTCTGGGAACACAACCAA |
| circECE1_R | IDT | GCCGTTGGGGTATGCGTC |
| circEPSTI1_F | IDT | AAGCTGAAGAAGCTGAACTC |
| circEPSTI1_R | IDT | GTGTATGCACTTGTGTATTGC |
| circIPO7_F | IDT | GGGCCAGATGAAGAAGGTAGT |
| circIPO7_R | IDT | GAGCCTGCATTACAGGTCTGAT |
| circMAN1A2_F | IDT | TAGGACATATGGGTGGGGAC |
| circMAN1A2_R | IDT | TGCTTCTTCCAAGGCCTTCT |
| circRELL1_F | IDT | ATGTCTGTTAGTGGGGCTGA |
| circRELL1_R | IDT | TATCTGCTACCATCGCCTTT |
| circTNPO3_F | IDT | GCTAATCGGCGCACAGAAAT |
| circTNPO3_R | IDT | GGTCTGAGATCTCCCATGCA |
| CpG DNA | IDT, RNase Free HPLC Purification, * Phosphorothioate Bond | T*C*G*T*C*G*T*T*T*T*G*T*C*G*T*T*T*T*G*T*C*G*T*T |
| siCircRELL1 | Horizon Life Sciences | AGUAGCAGCGAAUGCUGAUGUUU |
| Chemicals, enzymes and other reagents | ||
| JQ1 | Cayman Chemical | CAS: 1268524-70-4 |
| Human IFN-β | Peprotech | 300-02BC |
| Human IFN-γ | Peprotech | 300-02 |
| Transporter 5 | Polysciences | 26008 |
| CD90.1 MicroBeads | Miltenyi | 130-121-273 |
| Direct-zol RNA miniprep kit | Zymo | R2053 |
| ReverTra Ace qPCR RT master mix | Toyobo | FSQ-101 |
| Thunderbird Next SYBR qPCR mix | Toyobo | QPX-201 |
| TruSeq Stranded Total RNA Ribo-Zero Gold | Illumina | RS-122-2303 |
| Stranded Total RNA Prep with Ribo-Zero Plus | Illumina | 20040525 |
| ERCC spike-in controls | ThermoFisher | 4456740 |
| Software | ||
| Cutadapt |
M. Martin 2011 EMBnet.journal |
N/A |
| STAR |
Dobin et al, 2012 Bioinformatics |
N/A |
| CIRCExplorer3 (CLEAR) |
Ma et al, 2019 Genomics Proteomics Bioinformatics |
N/A |
| RankProd R package |
Del Carratore et al, 2017 Bioinformatics |
N/A |
| FIMO version 5.5.4 |
Grant et al, 2011 Bioinformatics |
N/A |
| FlowJo v.10.9.0 | BD | N/A |
| miEAA v.2.0 | Kern et al, 2020Nucleic Acids Research | N/A |
| Cytoscape 3.10 | Shannon et al, 2003Genome Research | N/A |
| DIANA-TarBase v8.0 | Karagkouni et al, 2018Nucleic Acids Research | N/A |
| WebGestalt | Liao et al, 2019Nucleic Acids Research | N/A |
| Ingenuity Pathway Analysis v.1.22.01 | Qiagen | N/A |
| Other | ||
| Illumina NextSeq 550 | Illumina | N/A |
| Illumina NovaSeq SP | Illumina | N/A |
| CytoFlex S | Beckman Coulter | N/A |
| StepOnePlus real-time PCR system | ThermoFisher | N/A |