Table 3.
RNA-Seq data analyzed in this study.
| Model | Metadata | Accession | ||
|---|---|---|---|---|
| HSV-1 | Lytic infection | MRC-5 cells infected with HSV-1 strain KOS (MOI 10 PFU/cell) for 12 or 24 h. PMID: 36724259 |
n = 2–4 Illumina 150 PE |
SRR19779319, SRR19779318, SRR19787559 |
| Latent infection | Female 8-week-old BALB/cAnTAC mice infected with HSV-1 strain 17 (105 PFU) via the ocular route. Latently infected trigeminal ganglion (TG) were harvested 4 weeks after primary infection. |
n = 4 Illumina 150 PE |
SRR19792335, SRR19792334 | |
| Lytic reactivation | Female 8-week-old BALB/cAnTAC mice infected with HSV-1 strain 17 (105 PFU) via the ocular route. Trigeminal ganglia were explanted (TG explant) ~4 weeks after primary infection in the presence of vehicle or 2 µM JQ1 for 12 h. |
n = 2–3 Illumina 150 PE |
SRR25824398, SRR25824397, SRR25824394, SRR25824396 | |
| HCMV-Lytic infection | MRC-5 cells infected with HCMV strain TB40/E (MOI 3 PFU/cell) for 24 or 72 h. PMID: 28874566 |
n = 2 Illumina 100 PE |
SRR5629593, SRR5629594, SRR5629591, SRR5629592, SRR5629589, SRR5629590, SRR5629587, SRR5629588, SRR5629577, SRR5629578, SRR5629575, SRR5629576, SRR5629573, SRR5629574, SRR5629571, SRR5629572 | |
| KSHV | Lytic infection | LEC infected with KSHV strain BAC16 (MOI 1 PFU/cell) for 24 or 72 h. PMID: 36724259 |
n = 2 Illumina 150 PE |
SRR20020769, SRR25816558, SRR20020770 |
| Lytic reactivation | iSLK-BAC16 induced with 1 µg/mL Doxycycline 1 mM Sodium Butyrate for 24 or 72 h. PMID: 36724259 |
n = 4 Illumina 150 PE |
SRR25816557, SRR20020761, SRR25816556, SRR20020757, SRR20020758 | |
| MHV68 | Lytic infection | NIH 3T3 cells infected with MHV68 strain H2B-YFP (MOI 5 PFU/cell) for 6 or 18 h. |
n = 2 Illumina 150 PE |
SRR19792326, SRR25823339, SRR19792325 |
| Lytic reactivation | A20 HE-RIT cells induced with 5 µg/ml Dox and 20 ng/ml TPA for 6 or 24 h. |
n = 2 Illumina 150 PE |
SRR19792324, SRR25823338, SRR19792321 | |
| Interferon treatment | MRC-5, LEC, or Akata- cells treated with IFN-β or -γ or- for 48 h. |
n = 3 Illumina 150 PE |
SRR25905055, SRR25905049, SRR25905048, SRR25905050, SRR25905054, SRR25905051, SRR25905053, SRR25905052 | |
| EBV-Latent infection |
Akata+ (EBV positive) or Akata- (EBV negative) cells. 074301 Arraystar Human CircRNA microarray V2. PMID: 36724259 |
n = 3 Microarray |
GSE206824 | |
Overview of bulk RNA-Seq data analyzed in this study. If data from any of the sample sets was previously published we have included PubMed reference numbers.