TABLE 1.
Gene biotypea | Annotation | No. of differentially expressed genes identified in cells infected with: |
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---|---|---|---|---|---|---|---|
Intact HIV |
UV-inactivated HIV |
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Total | 12 hpi | 24 hpi | Total | 12 hpi | 24 hpi | ||
Coding | 20,317 | 8,570 | 1,660 | 8,189 | 1,118 | 826 | 425 |
Intergenic | 359 | 248 | 64 | 234 | 51 | 44 | 17 |
lncRNA | 16,927 | 1,098 | 98 | 1,074 | 45 | 29 | 18 |
sncRNA | 8,527 | 29 | 4 | 26 | 6 | 0 | 6 |
Pseudogene | 14,138 | 1,144 | 107 | 1,115 | 96 | 27 | 74 |
Other | 841 | 5 | 0 | 5 | 1 | 1 | 0 |
Total | 61,109 | 11,094 | 1,933 | 10,643 | 1,317 | 927 | 540 |
Gene biotype was based on the GENCODE classification. For lncRNA, processed_transcript, lincRNA,3prime_overlapping_ncrna, antisense, sense_intronic, sense_overlapping. For sncRNA, snRNA, snoRNA, misc_RNA, miRNA. For pseudogene, polymorphic_pseudogene, pseudogene, IG_V_pseudogene, TR_V_pseudogene. For “other,” IG_V_gene, TR_C_gene, TR_J_gene, TR_V_gene, rRNA.