Files in this Data Supplement:
Table S1 (Summary of RNAseq data and mapping statistics.)
Table S2 (Biological functions enriched in 12-hpi DE genes, derived from IPA analysis.)
Table S3 (IPA-predicted functions commonly enriched in DE genes induced by HIV‐1 infection and UV inactivated virions.)
Table S4 (Top 20 drugs from connectivity map search.)
Table S5 (Enrichment of TF targets in genes with reversed expression changes.)
Table S6 (List of microarray datasets compiled from GEO.)
Fig. S1 (Summary of Total RNAseq-enriched genes.)
Fig. S2 (Comparison of total RNAseq measurements with qPCR and mRNAseq measurements.)
Fig. S3 (Heat map of the full list of 1,933 DE genes at 12 hpi, similarly shown in Fig. 2A.)
Fig. S4 (Radio plot showing the relative percentages of genes from the four subgroups in Fig. 2, for each of 14 enriched functions.)
Fig. S5 (Hierarchical clustering of 58 enriched TFs, based on their binding site co-occurrences in the promoters of similar sets of DE genes at 12 hpi during HIV‐1 infection.)
Fig. S6 (LncRNA function and TF inference.)
Fig. S7 (Regression coefficients of the predictive models learned from the compendium expression data.)
Fig. S8 (Predicted gene module expression changes at 12 hpi during HIV infection for all 9 gene modules.)
Fig. S9 (Predicted gene module expression changes at 24 hpi during HIV infection for all 9 gene modules.)
Fig. S10 (Cell counts under lycorine treatment, without HIV infection.)
PDF, 2.3M
Table S2 (Biological functions enriched in 12 hpi DE genes, derived from IPA analysis.)
XLSX, 28K
Table S3 (IPA-predicted functions commonly enriched in DE genes induced by HIV-1 infection and UV inactivated virions.)
XLSX, 35K