Table 2 Genomic data available for comparison to HIV integration sites
From: HIV latency and integration site placement in five cell-based models
Group | Type | Source | Number | Types |
|---|---|---|---|---|
T cell expression | RNA-Seq | Unpublished | 1 | RNA |
Jurkat expression | RNA-Seq | Encode [31] | 1 | wgEncodeHudsonalphaRnaSeq |
Integration sites | Locations | Unpublished | 1 | Sites |
DNase sensitivity | DNA-Seq/peaks | Encode [31] | 1 | wgEncodeOpenChromDnase |
Methylation | DNA-Seq | [32] | 1 | Methyl |
CpG | Locations | UCSC [33] | 1 | cpgIslandExt |
Sequence-based | Continuous | — | 4 | % GC, HIV PWM score, distance to centrosome, chromosomal position |
Repeats | Locations | UCSC [33] | 16 | DNA, LINE, Low_complexity, LTR, Other, RC, RNA, rRNA, Satellite, scRNA, Simple_repeat, SINE, snRNA, srpRNA, tRNA, alphoid |
Histone acetylation | ChIP-Seq/Peaks | [34] | 18 | H2AK5ac, H2AK9ac, H2BK120ac, H2BK12ac, H2BK20ac, H2BK5ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, H3K36ac, H3K4ac, H3K9ac, H4K12ac, H4K16ac, H4K5ac, H4K8ac, H4K91ac |
Histone methylation and other proteins | ChIP-Seq/Peaks | [35] | 23 | CTCF, H2AZ, H2BK5me1, H3K27me1, H3K27me2, H3K27me3, H3K36me1, H3K36me3, H3K4me1, H3K4me2, H3K4me3, H3K79me1, H3K79me2, H3K79me3, H3K9me1, H3K9me2, H3K9me3, H3R2me1, H3R2me2, H4K20me1, H4K20me3, H4R3me2, PolII |
Chromatin state | Binary | [59] | 51 | State1,state2,…,state51 |
HATs and HDACs | ChIP-Seq | [36] | 11 | Resting-HDAC1, Resting-HDAC2, Resting-HDAC3, Resting-HDAC6, Resting-p300, Resting-CBP, Resting-MOF, Resting-PCAF, Resting-Tip60, Active-HDAC6, Active-Tip60 |
Nucleosome | ChIP-Seq | [37] | 2 | Resting-Nucleosomes, Active-Nucleosomes |
UCSC genes | Locations | [38] | 4 | In gene, in gene (same strand), gene count, distance to nearest gene, in exon, in intron |