15. Supplementary Figure 9. Predicted gene module expression changes at 24hpi during HIV
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1 Supplementary Information Table of content 1. Supplementary Table 1. Summary of RNAseq data and mapping statistics 2. Supplementary Table 2. Biological functions enriched in 12 hpi DE genes, derived from IPA analysis. (MS Excel table submitted separately) 3. Supplementary Table 3. IPA predicted functions commonly enriched in DE genes induced by 1 infection and UV in activated virions. (MS Excel table submitted separately) 4. Supplementary Table 4. Top 2 drugs from connectivity map search 5. Supplementary Table 5. The enrichment of TF targets in genes with reversed expression changes. 6. Supplementary Table 6. The list of microarray datasets compiled from GEO. 7. Supplementary Figure 1. Summary of Total RNAseq enriched genes. 8. Supplementary Figure 2. Comparison of Total RNAseq measurements with qpcr and mrnaseq measurements. 9. Supplementary Figure 3. Heatmap of the full list of 1,933 DE genes at 12 hpi, similarly shown in Figure 2A. 1. Supplementary Figure 4. Radio plot showing the relative percentages of genes from the four subgroups in Figure 2, for each of 14 enriched functions. 11. Supplementary Figure 5. 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 1 infection. 12. Supplementary Figure 6. LncRNA function and TF inference. 13. Supplementary Figure 7. Regression coefficients of the predictive models learned from the compendium expression data. 14. Supplementary Figure 8. Predicted gene module expression changes at 12hpi during infection for all 9 gene modules. 15. Supplementary Figure 9. Predicted gene module expression changes at 24hpi during infection for all 9 gene modules. 16. Supplementary Figure 1. Supplementary Figure 1. Cell counts under lycorine treatment, without infection.
2 Supplementary Table 1. Summary of RNAseq data and mapping statistics NGS protocol mrnaseq TotalRNAseq Time point (hpi) Infection Mock Mock Mock UV Mock UV Replicate sample id rrna % % Human % Mock12hr1 34, ,558, Mock12hr2 35, ,447, Mock12hr3 242, ,4, hr7 322, ,989, ,916, hr8 369, ,313, ,68, hr9 215, ,564, ,227, Mock24hr1 386, ,686, Mock24hr2 24, ,958, Mock24hr3 241, ,75, hr7 178, ,276, ,253, hr8 224, ,924, ,848, hr9 2, ,98, ,182, ,427, ,925, ,342, ,7, ,147, ,456, ,116, ,429, ,248, ,659, ,16, ,632, ,798, , ,468, ,455, , ,865, ,74, , ,747, ,926, ,436, ,67, ,657, ,37, ,484, ,56, ,82, ,496, ,279, ,53, ,379, ,61, ,835, ,677, ,32, ,514, mrnaseq: 75nt single end reads. Total RNAseq: 2x9nt paired end reads. Mock: cells treated with conditioned medium, as control. : cells infected with intact 1 viruses. UV: cells treated with UV inactivated 1 virions. rrna: reads mapped to a collection of human ribosomal RNA sequences. : reads mapped to the reference 1 genome. Human: reads mapped to human reference genome.
3 Supplementary Table 4. Top 2 drugs from connectivity map search. Rank Compound name Mean of connectivity scores Number of instances Enrichment score Enrichment p value 1GW lycorine.699 (.629,.639,.672,.694,.86) trichostatin A camptothecin alsterpaullone irinotecan mitoxantrone azacitidine daunorubicin resveratrol ciclosporin vorinostat wortmannin methotrexate carbimazole SR Prestwick monensin diazoxide theobromine Notes: rows in blue are compounds with negative connectivity scores.inside parenthesis are the individual connectivity scores for lycorine.
4 Supplementary Table 5. The enrichment of TF targets in genes with reversed expression changes. Transcription Factor (TF) Enrichment p value TF DE at 12 hpi TF DE at 12 hpi and in subgroups a and b MYC TRUE TRUE ETS TRUE TRUE IRF TRUE TRUE ELK TRUE TRUE GTF2F TRUE FALSE TAF TRUE FALSE ELF TRUE FALSE REST TRUE FALSE BCLAF TRUE FALSE IRF TRUE FALSE ZBTB TRUE FALSE MAX.1178 FALSE FALSE ZNF FALSE FALSE E2F FALSE FALSE HEY FALSE FALSE TBP FALSE FALSE SP FALSE FALSE NRF FALSE FALSE NR3C FALSE FALSE E2F FALSE FALSE JUND FALSE FALSE GTF2B FALSE FALSE SRF FALSE FALSE TAF FALSE FALSE SETDB FALSE FALSE SP FALSE FALSE EP FALSE FALSE STAT FALSE FALSE STAT FALSE FALSE NFYA FALSE FALSE TCF FALSE FALSE STAT FALSE FALSE
5 Supplementary Table 6. The list of microarray datasets compiled from GEO. Description GSE accession Publication Treated Jurkat cells GSE4699 PMID: Treated Jurkat cells GSE1737,GSE1232 PMID: Treated MM6 cells GSE1739,GSE1738,GSE 1233,GSE1234 PMID: Regulatory T cell time couse GSE11292 PMID: T effector cell time course GSE11292 PMID: T effector cell expressing GFP GSE11292 PMID: T effector cell over expressing GARP GSE11292 PMID: CD4+ T cells infected with 1 viruses that lack different viral proteins GSE12963 PMID: CD4+ T cells from positive or negative individuals GSE9927 PMID: Lymph nodes from positive or negative individuals GSE16363 PMID: Pathogen specific CD4+ T cell subpopulations from the same PBMC GSE42853 PMID: CD4+ T cells from both resistant and low risk negative individuals GSE14278 PMID: Th1 and Th1Th17 CD4+ T cells GSE5175 PMID:
6 RMRP TERC Total RNAseq mrnaseq mock mock mock mock ~4 bp ~68 bp A B % 2% 4% 6% 8% 1% Enriched Not coding lncrna sncrna intergenic pseudogene other
7 A B Infection/mock ΔΔCt by qpcr r=.898 r= hpi 24 hpi Total RNAseq Infection/mock log2 ratio Total RNAseq infection/mock log2 ratio hpi 8339 (182) r= mrnaseq infection/mock log2 ratio
8 Exon Intron Exon Total UV mrna Intron 24 hpi mrna a (22) b (416) c (24) d (157) 1.5 1
9 CTLA4 Signaling in Cytotoxic T Lymphocytes Mitochondrial Dysfunction differentiation of lymphocytes malignant lymphocytic neoplasm apoptosis of T lymphocytes Protein Ubiquitination Pathway Mitotic Roles of Polo Like Kinase.2.1 quantity of T lymphocytes Glucocorticoid Receptor and T Cell Receptor Signalings a.mrna b.rawp c.enriched d.total.de EIF2 Signaling IGF1 Signaling Pyridoxal 5'phosphate Rac and CXCR4 and Pyrimidine Signalings Ribonucleotides Salvage transcription of RNA Pathways
10 PBX3 RFX5 SP2 NFYA SP1 IRF3 USF1 BHLHE4 ATF3 MAX TCF4 NRF1 SETDB1 E2F1 E2F4 MXI1 E2F6 ELF1 HDAC8 ZBTB7A CTCFL TCF12 HMGN3 CCNT2 EGR1 BCLAF1 SRF POU2F2 YY1 MEF2C ZNF143 SIX5 MYC GABPB1 ELK4 ETS1 SIN3A THAP1 BRCA1 CHD2 ZBTB33 STAT3 STAT1 IRF1 STAT2 REST NFKB1 GTF2F1 TBP NELFE TAF7 TAF1 HEY1 GTF2B NR3C1 EP3 JUND
11 A 14 Functions enriched in 12 hpi DE genes & 9 gene modules 64 lncrnas (12 hpi DE) gene module D3 gene module D2 transcription of RNA gene module D5 gene module D1 gene module D6 Mitochondrial Dysfunction Protein Ubiquitination Pathway gene module D4 gene module U1 gene module U2 differentiation of lymphocytes Rac and CXCR4 Signalings quantity of T lymphocytes apoptosis of T lymphocytes malignant lymphocytic neoplasm log1(ernich pvalue) X direction of correlation negatively correlated Glucocorticoid Receptor and T Cell Receptor Signalings CTLA4 Signaling in Cytotoxic T Lymphocytes EIF2 Signaling IGF1 Signaling gene module U3 Pyridoxal 5'phosphate and Pyrimidine Ribonucleotides Salvage Pathways Mitotic Roles of PoloLike Kinase postiviely correlated B log2 fold change Enrichment log1 pvalue Coassociation MEF2C MEF2A RXRA BCL11A ESR1 HNF4A EP3 MAFF SUZ12 JUN L1 MEF2C MEF2A 62 + RXRA 61 + BCL11A 26 + ESR HNF4A 5 + EP MAFF 2 + SUZ JUN b L1 21 +
12 A B YY1 NFKB1 ETS1 IRF1 EGR1 MYC ELK4 E2F6 SIN3A D1 IRF1 E2F6 YY1 EGR1 SIN3A NFKB1 MYC ETS1 ELK D2 NFKB1 IRF1 E2F6 ETS1 MYC EGR1 YY1 SIN3A ELK D3 NFKB1 EGR1 MYC E2F6 IRF1 SIN3A YY D4 NFKB1 MYC EGR1 E2F6 ELK4 IRF1 ETS1 SIN3A YY D5 ELK4 IRF1 EGR1 NFKB1 MYC SIN3A E2F6 ETS1 YY D6 >> MYC GTF2F1 >> NFKB1 IRF3 RFXANK PA2G4 SCAND1 MAZ U1
13 D1, 12hpi D2, 12hpi D3, 12hpi D4, 12hpi e 14, 7.8e e 8, 2.4e e 9, 1.9e e 11, 4.4e D5, 12hpi D6, 12hpi U1, 12hpi U2, 12hpi e 12, 6.8e e 15, 1.1e , 2.6e , 1.5e 6 U3, 12hpi 1 predicted TFs as candidates TFs and lncrnas as candidates , 1
14 ..4.8 D1, 24hpi D2, 24hpi..4.8 D3, 24hpi..4 D4, 24hpi e 13, 9.1e e 8, 1.5e e 9, 3.2e e 11, 1e 14 D5, 24hpi D6, 24hpi U1, 24hpi U2, 24hpi e 13, 8.8e e 15, 5.2e , 2.7e , U3, 24hpi 1 predicted TFs as candidates 115 TFs and lncrnas as candidates ,.99
15 A B Percentage of viable cells um 3.3 um 1 um x1 3 cells/ml hr DMSO 1 um 3.3 um 1 um viable dead
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