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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T cell expression RNA-Seq Unpublished 1 RNA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Integration sites Locations Unpublished 1 Sites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