GSE189581 HCMV-infected BAL immune-cells: microbe scRNAseq panel
2025-1-21
GSE189581-The molecular principles governing HCMV infection outcome. samples: Bronchoalveolar lavage (BAL) cells, infected with TB40/E-GFP strain of HCMV at 20 and 70 hours post infectionpools.
Public on Jan 05, 2023
Infection with Human cytomegalovirus (HCMV) can result in either productive or non-productive infection, the latter potentially leading to establishment of latency, but the molecular factors that dictate these different infection outcomes are elusive. Macrophages are known targets of HCMV and considered to be permissive for productive infection, while monocytes, their precursors, are thought to support latent infection. Here we reveal that infection of macrophages is more complex than previously appreciated and can result in either productive or non-productive infection. By analyzing the progression of HCMV infection in c and macrophages using single cell transcriptomics, we uncover that the key characteristics that define productive and non-productive cells are the onset of viral gene expression, and activation of Interferon-stimulated genes (ISGs), respectively. We show that the level of viral gene expression, and specifically the expression of the major immediate early factor, IE1, is the principle barrier for establishing productive infection. On the cellular side, induction of ISGs in response to infection surprisingly does not dictate infection outcome, but we find that the cell intrinsic ISG levels is a main determinant of infection outcome. Indeed, intrinsic ISG level is downregulated with monocyte differentiation. We further show that, compared to monocytes, non-productive macrophages maintain slightly higher levels of viral transcripts and are able to reactivate, raising the possibility that they can serve as latency reservoirs in tissues. Moreover, we find that productive infection perturbs macrophage identity and function, likely affecting their immunological role during active infection. Overall, by harnessing the tractable system of monocyte differentiation we decipher the underlying principles that control HCMV infection outcome, and propose macrophages as a new potential HCMV reservoir in tissues.
10X Genomics Chromium Single Cell 3’
Weizmann Institute
Schwartz, M., Shnayder, M., Nachshon, A. et al. Molecular characterization of human cytomegalovirus infection with single-cell transcriptomics. Nat Microbiol 8, 455–468 (2023). https://doi.org/10.1038/s41564-023-01325-x
Illumina NovaSeq 6000 (Homo sapiens)
All raw fastq files were downloaded from NCBI and aligned in cellranger with assembly: hg38 + multiple bacterial sequences
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## CD8+ T-cells Macrophages CD4+ T-cells B-cells
## 9391 11110 2669 149
## DC NK cells Erythrocytes Monocytes
## 2321 924 4 217
## Epithelial cells HSC Neutrophils
## 17 6 1## Warning: The following requested variables were not found (10 out of 40445
## shown): NZ-BLCO01000004.1-bacteria, NZ-BLCO01000005.1-bacteria,
## NZ-BLCO01000006.1-bacteria, NZ-BLCO01000007.1-bacteria,
## NZ-BLCO01000008.1-bacteria, NZ-BLCO01000009.1-bacteria,
## NZ-BLCO01000010.1-bacteria, NZ-BLCO01000011.1-bacteria,
## NZ-BLCO01000012.1-bacteria, NZ-BLCO01000013.1-bacteria## All bacterial sequences detected## [1] "NZ-BLCD01000212.1-bacteria" "NZ-BTIO01000647.1-bacteria"
## [3] "NZ-BLDF01000324.1-bacteria" "NZ-JACHAQ010000041.1-bacteria"
## [5] "NZ-JACHAQ010000044.1-bacteria" "NZ-JACHAQ010000046.1-bacteria"
## [7] "NZ-JACHAQ010000054.1-bacteria" "NZ-JACHAQ010000064.1-bacteria"
## [9] "NZ-JACHAQ010000066.1-bacteria" "NZ-JACGZY010000075.1-bacteria"
## [11] "NZ-JACGZY010000076.1-bacteria" "NZ-JACGZY010000077.1-bacteria"
## [13] "NZ-JACGZY010000080.1-bacteria" "NZ-JACGZY010000083.1-bacteria"
## [15] "NZ-JACGZY010000102.1-bacteria" "NZ-JACGZY010000105.1-bacteria"
## [17] "NZ-JACGZY010000132.1-bacteria" "NZ-JACGZY010000138.1-bacteria"
## [19] "NZ-JACGZY010000143.1-bacteria" "NZ-JACGZY010000146.1-bacteria"
## [21] "NZ-JACGZY010000148.1-bacteria" "NZ-JACGZY010000157.1-bacteria"
## [23] "NZ-JACGZY010000170.1-bacteria" "NZ-JACGZY010000174.1-bacteria"
## [25] "NZ-JACGZY010000198.1-bacteria" "NZ-JACGZY010000206.1-bacteria"
## [27] "NZ-JACGZY010000211.1-bacteria" "NZ-JACGZY010000222.1-bacteria"
## [29] "NZ-JACGZY010000230.1-bacteria" "NZ-JAJUKN010000041.1-bacteria"
## [31] "NZ-JAJUKQ010000041.1-bacteria" "NZ-JAJUKQ010000044.1-bacteria"
## [33] "NZ-JAJUKQ010000047.1-bacteria" "NZ-JAJUKQ010000053.1-bacteria"
## [35] "NZ-JAJUKQ010000073.1-bacteria" "NZ-JAIZHC010000001.1-bacteria"
## [37] "NZ-JAIZHC010000020.1-bacteria" "NZ-JAKNPB010000065.1-bacteria"
## [39] "NZ-JAKNPB010000089.1-bacteria" "NZ-JAKNPB010000110.1-bacteria"
## [41] "NZ-JAKNPB010000113.1-bacteria" "NZ-JAKNPB010000114.1-bacteria"
## [43] "NZ-JAKNOW010000085.1-bacteria" "NZ-JAKNOW010000101.1-bacteria"
## [45] "NZ-JAKNOW010000126.1-bacteria" "NZ-JAKNPC010000007.1-bacteria"
## [47] "NZ-JACGEM010000043.1-bacteria" "NZ-JACGEM010000073.1-bacteria"
## [49] "NZ-JACGEM010000105.1-bacteria" "NZ-JACGEM010000123.1-bacteria"
## [51] "NZ-JAKNOU010000091.1-bacteria" "NZ-JAKNOU010000097.1-bacteria"
## [53] "NZ-JAKNOS010000002.1-bacteria" "NZ-JAKNOS010000005.1-bacteria"
## [55] "NZ-JAKNOS010000007.1-bacteria" "NZ-JAKNOS010000009.1-bacteria"
## [57] "NZ-JAKNOS010000010.1-bacteria" "NZ-JAKNOS010000011.1-bacteria"
## [59] "NZ-JAKNOS010000013.1-bacteria" "NZ-JAKNOS010000021.1-bacteria"
## [61] "NZ-JAKNOS010000022.1-bacteria" "NZ-JAKNOS010000171.1-bacteria"
## [63] "NZ-JAKNOS010000284.1-bacteria" "NZ-JAKNOS010000290.1-bacteria"
## [65] "NZ-JAKNOS010000293.1-bacteria" "NZ-JAKNOS010000295.1-bacteria"
## [67] "NZ-JAKNOS010000296.1-bacteria" "NZ-JAKNOS010000307.1-bacteria"
## [69] "NZ-JAKNOS010000312.1-bacteria" "NZ-JAKNQD010000014.1-bacteria"
## [71] "NZ-JAKNQD010000082.1-bacteria" "NZ-JAKNQD010000115.1-bacteria"
## [73] "NZ-JAKNOT010000091.1-bacteria" "NZ-JAKNOV010000037.1-bacteria"
## [75] "NZ-JAFJAF010000008.1-bacteria" "NZ-JAFIYX010000016.1-bacteria"
## [77] "NZ-JACGEO010000057.1-bacteria" "NZ-JACGEO010000060.1-bacteria"
## [79] "NZ-JACGEO010000064.1-bacteria" "NZ-JACHAD010000064.1-bacteria"
## [81] "NZ-JACHAD010000074.1-bacteria" "NZ-JACGFA010000057.1-bacteria"
## [83] "NZ-JACGEY010000061.1-bacteria" "NZ-JACGEY010000064.1-bacteria"
## [85] "NZ-JACGEY010000067.1-bacteria" "NZ-JACGEY010000068.1-bacteria"
## [87] "NZ-JACGEY010000076.1-bacteria" "NZ-JACGEY010000077.1-bacteria"
## [89] "NZ-JACHAN010000022.1-bacteria" "NZ-JACHAN010000027.1-bacteria"
## [91] "NZ-JACHAN010000028.1-bacteria" "NZ-JACHAN010000031.1-bacteria"
## [93] "NZ-JACHAN010000039.1-bacteria" "NZ-JACHAN010000040.1-bacteria"
## [95] "NZ-JACHAN010000047.1-bacteria" "NZ-JACHAN010000052.1-bacteria"
## [97] "NZ-JACHAN010000053.1-bacteria" "NZ-JACHAN010000059.1-bacteria"
## [99] "NZ-JACHAL010000051.1-bacteria" "NZ-JACHAL010000053.1-bacteria"
## [101] "NZ-JACHAL010000055.1-bacteria" "NZ-JACHAL010000060.1-bacteria"
## [103] "NZ-JACHAL010000062.1-bacteria" "NZ-JACHAL010000063.1-bacteria"
## [105] "NZ-JACHAL010000064.1-bacteria" "NZ-JACHAL010000067.1-bacteria"
## [107] "NZ-JACHAL010000068.1-bacteria" "NZ-JACGES010000047.1-bacteria"
## [109] "NZ-JACGES010000049.1-bacteria" "NZ-JACGES010000052.1-bacteria"
## [111] "NZ-JACGES010000053.1-bacteria" "NZ-JACGES010000054.1-bacteria"
## [113] "NZ-JACGES010000057.1-bacteria" "NZ-JACGES010000060.1-bacteria"
## [115] "NZ-JACGES010000066.1-bacteria" "NZ-JACGES010000068.1-bacteria"
## [117] "NZ-JACGES010000074.1-bacteria" "NZ-JACGEV010000058.1-bacteria"
## [119] "NZ-JACGEV010000059.1-bacteria" "NZ-JACGEV010000066.1-bacteria"
## [121] "NZ-JACGEV010000081.1-bacteria" "NZ-JACGEV010000090.1-bacteria"
## [123] "NZ-JACGEZ010000045.1-bacteria" "NZ-JACHAO010000054.1-bacteria"
## [125] "NZ-JACHAO010000082.1-bacteria" "NZ-JACHAO010000091.1-bacteria"
## [127] "NZ-JACHAO010000094.1-bacteria" "NZ-JACHAO010000101.1-bacteria"
## [129] "NZ-JACHAO010000107.1-bacteria" "NZ-JACHAO010000127.1-bacteria"
## [131] "NZ-JACHAO010000137.1-bacteria" "NZ-JACHAO010000142.1-bacteria"
## [133] "NZ-JACHAO010000165.1-bacteria" "NZ-JACHAO010000170.1-bacteria"
## [135] "NZ-JACHAE010000055.1-bacteria" "NZ-JACHAE010000056.1-bacteria"
## [137] "NZ-JACHAG010000081.1-bacteria" "NZ-JACHAG010000091.1-bacteria"
## [139] "NZ-JACHAG010000094.1-bacteria" "NZ-JACHAG010000112.1-bacteria"
## [141] "NZ-JACHAG010000114.1-bacteria" "NZ-JACHAG010000124.1-bacteria"
## [143] "NZ-JACHAG010000135.1-bacteria" "NZ-JACHAG010000172.1-bacteria"
## [145] "NZ-JACHAG010000187.1-bacteria" "NZ-JACHAG010000194.1-bacteria"
## [147] "NZ-JACHAG010000221.1-bacteria" "NZ-JACHAG010000227.1-bacteria"
## [149] "NZ-JACHAG010000240.1-bacteria" "NZ-JACGFB010000042.1-bacteria"
## [151] "NZ-JACHAK010000063.1-bacteria" "NZ-JACGEW010000030.1-bacteria"
## [153] "NZ-JACGEW010000035.1-bacteria" "NZ-JACGEW010000040.1-bacteria"
## [155] "NZ-JACHAB010000035.1-bacteria" "NZ-JACHAB010000044.1-bacteria"
## [157] "NZ-JACHAB010000060.1-bacteria" "NZ-JACHAB010000064.1-bacteria"
## [159] "NZ-JACHAB010000080.1-bacteria" "NZ-JACHAB010000084.1-bacteria"
## [161] "NZ-JACHAB010000097.1-bacteria" "NZ-BLDA01000367.1-bacteria"##
## BAL_hcmv_20hpi.BAC BAL_hcmv_70hpi.BAC
## 11928 11928
## Differentially expressed bacterial sequences detected## Warning in DoHeatmap(data_subset, features = c("PTPRC", "CD163", "S100A8", :
## The following features were omitted as they were not found in the scale.data
## slot for the RNA assay: NA
## p_val avg_log2FC pct.1 pct.2
## NZ-JACGES010000074.1-bacteria 7.805034e-181 0.36983021 0.372 0.189
## NZ-JAKNOW010000101.1-bacteria 1.261426e-108 0.38388456 0.296 0.165
## NZ-JACHAG010000124.1-bacteria 4.187072e-88 0.36142221 0.155 0.070
## NZ-JAKNPB010000113.1-bacteria 3.514603e-78 0.49687043 0.113 0.046
## NZ-JAKNOS010000013.1-bacteria 2.454165e-67 0.04428636 0.643 0.467
## NZ-JAKNOS010000009.1-bacteria 3.853299e-61 0.32261432 0.118 0.056
## NZ-JAJUKN010000041.1-bacteria 7.659004e-61 0.25112385 0.117 0.055
## NZ-JAKNPB010000089.1-bacteria 6.574966e-57 0.22302617 0.147 0.079
## p_val_adj
## NZ-JACGES010000074.1-bacteria 1.143281e-176
## NZ-JAKNOW010000101.1-bacteria 1.847738e-104
## NZ-JACHAG010000124.1-bacteria 6.133222e-84
## NZ-JAKNPB010000113.1-bacteria 5.148191e-74
## NZ-JAKNOS010000013.1-bacteria 3.594861e-63
## NZ-JAKNOS010000009.1-bacteria 5.644312e-57
## NZ-JAJUKN010000041.1-bacteria 1.121891e-56
## NZ-JAKNPB010000089.1-bacteria 9.631010e-53## Pectobacterium brasiliense strain NAK:396 AAMGLDMF_74, whole genome shotgun sequence
## Vibrio fluvialis strain PV92 C247, whole genome shotgun sequence
## Comparisons between cell types## Warning in DoHeatmap(data_subset, features = c("PTPRC", "CD163", "S100A8", :
## The following features were omitted as they were not found in the scale.data
## slot for the RNA assay: NA
## p_val avg_log2FC pct.1 pct.2
## NZ-JACGES010000074.1-bacteria 3.251665e-222 -0.0006385509 0.428 0.156
## NZ-JACHAG010000124.1-bacteria 2.401511e-130 -0.0568428543 0.183 0.054
## NZ-JAKNOW010000101.1-bacteria 8.150829e-115 -0.2622864962 0.323 0.143
## NZ-JAJUKN010000041.1-bacteria 1.307584e-114 0.1578806205 0.143 0.038
## NZ-JAKNOS010000013.1-bacteria 1.529483e-112 -0.0543485923 0.743 0.395
## NZ-JAKNPB010000089.1-bacteria 2.832107e-94 -0.2007201749 0.173 0.063
## NZ-JAKNOS010000009.1-bacteria 5.522006e-86 -0.2572639198 0.137 0.045
## NZ-JAKNPB010000113.1-bacteria 2.132336e-77 -0.2205089747 0.126 0.043
## NZ-JAKNPC010000007.1-bacteria 7.604827e-58 -0.1847555752 0.100 0.036
## p_val_adj
## NZ-JACGES010000074.1-bacteria 4.763039e-218
## NZ-JACHAG010000124.1-bacteria 3.517734e-126
## NZ-JAKNOW010000101.1-bacteria 1.193933e-110
## NZ-JAJUKN010000041.1-bacteria 1.915349e-110
## NZ-JAKNOS010000013.1-bacteria 2.240387e-108
## NZ-JAKNPB010000089.1-bacteria 4.148471e-90
## NZ-JAKNOS010000009.1-bacteria 8.088634e-82
## NZ-JAKNPB010000113.1-bacteria 3.123446e-73
## NZ-JAKNPC010000007.1-bacteria 1.113955e-53## Pectobacterium brasiliense strain NAK:396 AAMGLDMF_74, whole genome shotgun sequence
## Campylobacter lari strain CLFY2011012 CLFY2011012_contig_51, whole genome shotgun sequence
## Pectobacterium brasiliense and Vibrio fluvialis strains are elevated at 70hpi when compared to 20hpi.##
## CD8+ T-cells Macrophages CD4+ T-cells B-cells
## 9378 11115 2667 148
## DC NK cells Erythrocytes Monocytes
## 2331 927 5 218
## Epithelial cells HSC Neutrophils
## 17 6 1## Warning in DoHeatmap(data, features = c(viral1_1.genes, hcmv), size = 2): The
## following features were omitted as they were not found in the scale.data slot
## for the RNA assay: US2-hcmv, UL148D-hcmv, UL148C-hcmv, UL148B-hcmv,
## UL148A-hcmv, UL134-hcmv, UL137-hcmv, UL139-hcmv, UL140-hcmv, trunc-UL141-hcmv,
## UL142-hcmv, UL144-hcmv, UL146-hcmv, UL147A-hcmv, UL131A-hcmv, UL130-hcmv,
## UL127-hcmv, UL121-hcmv, UL120-hcmv, UL117-hcmv, UL116-hcmv, UL104-hcmv,
## UL98-hcmv, UL97-hcmv, UL96-hcmv, UL93-hcmv, UL92-hcmv, UL91-hcmv, UL90-hcmv,
## UL89-hcmv, UL88-hcmv, UL87-hcmv, UL86-hcmv, UL85-hcmv, UL80-5-hcmv, UL80-hcmv,
## UL79-hcmv, UL78-hcmv, UL77-hcmv, UL76-hcmv, UL74, UL73-hcmv, UL71-hcmv,
## UL60-hcmv, UL53-hcmv, UL51-hcmv, UL50-hcmv, UL49-hcmv, UL47-hcmv, UL41A-hcmv,
## vMIA-hcmv, UL32-hcmv, UL29-hcmv, UL28-hcmv, UL25-hcmv, UL24-hcmv, UL19-hcmv,
## UL18-hcmv, UL17-hcmv, UL16-hcmv, UL14-hcmv, UL12-hcmv, UL11-hcmv, UL10-hcmv,
## UL9-hcmv, UL8-hcmv, UL7-hcmv, UL3-hcmv, UL2-hcmv, UL1-hcmv, RL11-hcmv,
## RL10-hcmv, RL1-hcmv, US34A-hcmv, US33-hcmv, US31-hcmv, US30-hcmv, US29-hcmv,
## US27-hcmv, US21-hcmv, US20-hcmv, US19-hcmv, US17-hcmv, US15-hcmv, US14-hcmv,
## US9-hcmv, NC-091965.1, NC-091964.1, NC-026314.1, NC-086348.1, NC-086347.1,
## NC-086346.1, NC-083851.1, NG-242639.1, NG-242638.1, NG-242637.1, NC-001803.1,
## NC-047837.1, NC-024625.1, NC-042134.1, NC-029642.1, NC-030692.1, NC-023861.2,
## NC-001798.2, NC-079184.1, NC-079185.1, NC-079175.1, NC-079186.1, NC-079180.1,
## NC-079183.1, NC-079174.1, NC-079176.1, NC-079187.1, NC-079188.1, NC-079177.1,
## NC-079178.1, NC-079179.1, NC-079181.1, NC-079182.1, NC-005859.1, NC-070779.1,
## NC-073071.1, NC-061437.1, NC-047856.1, NC-025440.1, NC-027399.1, NC-079143.1,
## NC-079146.1, NC-079140.1, NC-079142.1, NC-079145.1, NC-055052.1, NC-025824.1,
## NC-079141.1, NC-078858.1, NC-078857.1, NC-078856.1, NC-079144.1, NC-077680.1,
## NC-074657.1, NC-074656.1, NC-055055.1, NC-074765.1, NC-028944.1, NC-055053.1,
## NC-047731.1, NC-047732.1, NC-047730.1, NC-047729.1, NC-055054.1, NC-047872.1,
## NC-047871.1, NC-074762.1, NC-047744.1, NC-025417.1, NC-047721.1, NC-020877.1,
## NC-047724.1, NC-047727.1, NC-047726.1, NC-047725.1, NC-047723.1, NC-047722.1,
## NC-021781.2, NC-047745.1, NC-019548.1, NC-047735.1, NC-047736.1, NC-047720.1,
## NC-047853.1, NC-055051.1, NC-012757.1, NC-047728.1, NC-003311.2, NC-005949.1,
## NC-002363.1, NC-074763.1, NC-075033.1, NC-075032.1, NC-075031.1, NC-075030.1,
## NC-075029.1, NC-075028.1, NC-075027.1, NC-075026.1, NC-075025.1, NC-025823.1,
## NC-077770.1, NC-077769.1, NC-077930.1, NC-077929.1, NC-077928.1, NC-079139.1,
## NC-077948.1, NC-077947.1, NC-077946.1, NC-077942.1, NC-077941.1, NC-077940.1,
## NC-078322.1, NC-078321.1, NC-078320.1, NC-077936.1, NC-077935.1, NC-077934.1,
## NC-077927.1, NC-077926.1, NC-077925.1, NC-077918.1, NC-077917.1, NC-077916.1,
## NC-078145.1, NC-078144.1, NC-078143.1, NC-077915.1, NC-077914.1, NC-077913.1,
## NC-077984.1, NC-077983.1, NC-077982.1, NC-077981.1, NC-077980.1, NC-077979.1,
## NC-077975.1, NC-077974.1, NC-077973.1, NC-077972.1, NC-077971.1, NC-077970.1,
## NC-077900.1, NC-077899.1, NC-077898.1, NC-078005.1, NC-078004.1, NC-078003.1,
## NC-077987.1, NC-077986.1, NC-077985.1, NC-077807.1, NC-077806.1, NC-078015.1,
## NC-078014.1, NC-078013.1, NC-078012.1, NC-078011.1, NC-078010.1, NC-078009.1,
## NC-078008.1, NC-078007.1, NC-078006.1, NC-078646.1, NC-078645.1, NC-078644.1,
## NC-078643.1, NC-078642.1, NC-078641.1, NC-078640.1, NC-073936.1, NC-074467.1,
## NC-073908.1, NC-074611.1, NC-074252.1, NC-074492.1, NC-074489.1, NC-074449.1,
## NC-074591.1, NC-074517.1, NC-047778.1, NC-078314.1, NC-078313.1, NC-078312.1,
## NC-078866.1, NC-078865.1, NC-078864.1, NC-078869.1, NC-078868.1, NC-078867.1,
## NC-078872.1, NC-078871.1, NC-078870.1, NC-078875.1, NC-078874.1, NC-078873.1,
## NC-078431.1, NC-078430.1, NC-078429.1, NC-078428.1, NC-078419.1, NC-078418.1,
## NC-078417.1, NC-078416.1, NC-078415.1, NC-078414.1, NC-078413.1, NC-078412.1,
## NC-078411.1, NC-078648.1, NC-078647.1, NC-078662.1, NC-078661.1, NC-078660.1,
## NC-078659.1, NC-078657.1, NC-078473.1, NC-078472.1, NC-078471.1, NC-078470.1,
## NC-078637.1, NC-078636.1, NC-078635.1, NC-078325.1, NC-078324.1, NC-078323.1,
## NC-078612.1, NC-078611.1, NC-078610.1, NC-078609.1, NC-078608.1, NC-078607.1,
## NC-078606.1, NC-078605.1, NC-078626.1, NC-078625.1, NC-078631.1, NC-078630.1,
## NC-078629.1, NC-078578.1, NC-078577.1, NC-078576.1, NC-078575.1, NC-078574.1,
## NC-078573.1, NC-078572.1, NC-078571.1, NC-078570.1, NC-078569.1, NC-078568.1,
## NC-078624.1, NC-078623.1, NC-078622.1, NC-078634.1, NC-078633.1, NC-078632.1,
## NC-078850.1, NC-078849.1, NC-078848.1, NC-078847.1, NC-078846.1, NC-078615.1,
## NC-078614.1, NC-078613.1, NC-078601.1, NC-078600.1, NC-078599.1, NC-078598.1,
## NC-078597.1, NC-078596.1, NC-078271.1, NC-078270.1, NC-078269.1, NC-078604.1,
## NC-078603.1, NC-078602.1, NC-018667.1, NC-078878.1, NC-078877.1, NC-078876.1,
## NC-078581.1, NC-078580.1, NC-078579.1, NC-018617.1, NC-078467.1, NC-078466.1,
## NC-077801.1, NC-077800.1, NC-077671.1, NC-077670.1, NC-077669.1, NC-078036.1,
## NC-078035.1, NC-078034.1, NC-078033.1, NC-078032.1, NC-078773.1, NC-078772.1,
## NC-078771.1, NC-078770.1, NC-078769.1, NC-078768.1, NC-078465.1, NC-055942.1,
## NC-078469.1, NC-078468.1, NC-078654.1, NC-078653.1, NC-078652.1, NC-078651.1,
## NC-078650.1, NC-078649.1, NC-077820.1, NC-077819.1, NC-077818.1, NC-077817.1,
## NC-017918.2, NC-077696.1, NC-077695.1, NC-078049.1, NC-078048.1, NC-078047.1,
## NC-078462.1, NC-078461.1, NC-074761.1, NC-074760.1, NC-074759.1, NC-038702.1,
## NC-078881.1, NC-078880.1, NC-078879.1, NC-078734.1, NC-078733.1, NC-078732.1,
## NC-078731.1, NC-078730.1, NC-078729.1, NC-078728.1, NC-078247.1, NC-078246.1,
## NC-078245.1, NC-077675.1, NC-077674.1, NC-077216.1, NC-077836.1, NC-077835.1,
## NC-077834.1, NC-076961.1, NC-076960.1, NC-017829.1, NC-044935.1, NC-014955.1,
## NC-001472.1, NC-001612.1, NC-079072.1, NC-079071.1, NC-078940.1, NC-078939.1,
## NC-078938.1, NC-078973.1, NC-078972.1, NC-078971.1, NC-079038.1, NC-079037.1,
## NC-079033.1, NC-079032.1, NC-079054.1, NC-079053.1, NC-079115.1, NC-079114.1,
## NC-079113.1, NC-079102.1, NC-079101.1, NC-079106.1, NC-079105.1, NC-079104.1,
## NC-079103.1, NC-079068.1, NC-079067.1, NC-079028.1, NC-079027.1, NC-079026.1,
## NC-079025.1, NC-079024.1, NC-079023.1, NC-079046.1, NC-079045.1, NC-079056.1,
## NC-079055.1, NC-079061.1, NC-079060.1, NC-079059.1, NC-079058.1, NC-079057.1,
## NC-079077.1, NC-079076.1, NC-079075.1, NC-079074.1, NC-079073.1, NC-079066.1,
## NC-079065.1, NC-079064.1, NC-079063.1, NC-079062.1, NC-079112.1, NC-079111.1,
## NC-079110.1, NC-079109.1, NC-079128.1, NC-079127.1, NC-079031.1, NC-079030.1,
## NC-079029.1, NC-078227.1, NC-078226.1, NC-078225.1, NC-078282.1, NC-078281.1,
## NC-078280.1, NC-078127.1, NC-078126.1, NC-078125.1, NC-078124.1, NC-078052.1,
## NC-078051.1, NC-078050.1, NC-078293.1, NC-078292.1, NC-078316.1, NC-078315.1,
## NC-078106.1, NC-078105.1, NC-078698.1, NC-078697.1, NC-078696.1, NC-078695.1,
## NC-078184.1, NC-078183.1, NC-079018.1, NC-079017.1, NC-079044.1, NC-079043.1,
## NC-079013.1, NC-079012.1, NC-079011.1, NC-079133.1, NC-079132.1, NC-079131.1,
## NC-079100.1, NC-079099.1, NC-079098.1, NC-079052.1, NC-079051.1, NC-079022.1,
## NC-079021.1, NC-079020.1, NC-078656.1, NC-078655.1, NC-079016.1, NC-079015.1,
## NC-079014.1, NC-079126.1, NC-079125.1, NC-079097.1, NC-079096.1, NC-079095.1,
## NC-079094.1, NC-079093.1, NC-079130.1, NC-079129.1, NC-078999.1, NC-078998.1,
## NC-078997.1, NC-079008.1, NC-079007.1, NC-079006.1, NC-078674.1, NC-078673.1,
## NC-078583.1, NC-078582.1, NC-079092.1, NC-079091.1, NC-079090.1, NC-079089.1,
## NC-079088.1, NC-079002.1, NC-079001.1, NC-079000.1, NC-079124.1, NC-079123.1,
## NC-079122.1, NC-079121.1, NC-079120.1, NC-079119.1, NC-078363.1, NC-078362.1,
## NC-078361.1, NC-078639.1, NC-078638.1, NC-078680.1, NC-078679.1, NC-078678.1,
## NC-078677.1, NC-078676.1, NC-078675.1, NC-078993.1, NC-078992.1, NC-078991.1,
## NC-078357.1, NC-078356.1, NC-078355.1, NC-078354.1, NC-078353.1, NC-078352.1,
## NC-078348.1, NC-078347.1, NC-078346.1, NC-078351.1, NC-078350.1, NC-078349.1,
## NC-078360.1, NC-078359.1, NC-078358.1, NC-078448.1, NC-078447.1, NC-078446.1,
## NC-079108.1, NC-079107.1, NC-078916.1, NC-078915.1, NC-078914.1, NC-078896.1,
## NC-078895.1, NC-078894.1, NC-078902.1, NC-078901.1, NC-078900.1, NC-078913.1,
## NC-078912.1, NC-078911.1, NC-078964.1, NC-078963.1, NC-078962.1, NC-078893.1,
## NC-078892.1, NC-078891.1, NC-078905
## Warning: The following requested variables were not found (10 out of 18778
## shown): NC-029549.1, NC-029550.1, NC-029551.1, NC-029552.1, NC-029553.1,
## NC-029570.1, NC-029554.1, NC-029555.1, NC-029558.1, NC-029559.1## All viral sequences detected## [1] "NC-028250.1" "NC-029302.1" "NC-031338.1" "NC-024502.1"
## [5] "NC-021097.1" "NC-021099.1" "NC-022518.1" "NC-004812.1"
## [9] "NC-006273.2" "NC-001782.1" "NC-008580.1" "NC-009758.1"
## [13] "NC-001479.1" "NC-009127.1" "NC-006960.1" "NC-013221.1"
## [17] "NC-008310.2" "NC-038828.1" "NC-043054.1" "NC-043569.1"
## [21] "NC-040589.1" "NC-028095.1" "NC-055142.1" "NC-006553.1"
## [25] "NC-049922.1" "NC-031032.1" "NC-049835.1" "NC-041925.1"
## [29] "NC-076609.1" "US7-hcmv" "US8-hcmv" "US10-hcmv"
## [33] "US11-hcmv" "US12-hcmv" "US13-hcmv" "US16-hcmv"
## [37] "US18-hcmv" "US22-hcmv" "US23-hcmv" "US24-hcmv"
## [41] "US26-hcmv" "US28-hcmv" "US32-hcmv" "US34-hcmv"
## [45] "RL12-hcmv" "RL13-TRL14-hcmv" "UL4-hcmv" "UL5-hcmv"
## [49] "UL6-hcmv" "UL13-hcmv" "UL15A-hcmv" "UL20-hcmv"
## [53] "UL21A-hcmv" "UL22A-hcmv" "UL23-hcmv" "UL26-hcmv"
## [57] "UL27-hcmv" "UL30-hcmv" "UL31-hcmv" "UL33-hcmv"
## [61] "UL34-hcmv" "UL35-hcmv" "UL36-hcmv" "UL37-hcmv"
## [65] "UL38-hcmv" "UL40-hcmv" "UL42-hcmv" "UL43-hcmv"
## [69] "UL44-hcmv" "UL46-hcmv" "UL48-hcmv" "UL48A-hcmv"
## [73] "UL52-hcmv" "UL54-hcmv" "UL55-hcmv" "UL56-hcmv"
## [77] "UL57-hcmv" "UL59-hcmv" "UL69-hcmv" "UL70-hcmv"
## [81] "UL72-hcmv" "UL75-hcmv" "UL82-hcmv" "UL83-hcmv"
## [85] "UL84-hcmv" "UL94-hcmv" "UL95-hcmv" "UL99-hcmv"
## [89] "UL100-hcmv" "UL102-hcmv" "UL103-hcmv" "UL105-hcmv"
## [93] "UL112-hcmv" "UL114-hcmv" "UL115-hcmv" "UL119-hcmv"
## [97] "UL122-hcmv" "UL123-hcmv" "UL124-hcmv" "UL128-hcmv"
## [101] "UL132-hcmv" "UL148-hcmv" "UL147-hcmv" "UL145-hcmv"
## [105] "UL138-hcmv" "UL136-hcmv" "UL135-hcmv" "UL133-hcmv"
## [109] "UL149-hcmv" "UL150-hcmv"##
## BAL_hcmv_20hpi.VIR BAL_hcmv_70hpi.VIR
## 11928 11928
## Differentially expressed viral sequences detected## Warning in DoHeatmap(data_subset, features = c("PTPRC", "CD163", "S100A8", :
## The following features were omitted as they were not found in the scale.data
## slot for the RNA assay: NA
## p_val avg_log2FC pct.1 pct.2 p_val_adj
## NC-031032.1 9.888188e-288 0.60323316 0.504 0.257 1.443181e-283
## NC-001782.1 2.110640e-254 0.51144030 0.529 0.289 3.080479e-250
## NC-013221.1 9.730007e-144 0.44130647 0.237 0.106 1.420095e-139
## NC-043054.1 6.425787e-57 0.09279819 0.820 0.644 9.378437e-53
## NC-006273.2 2.509417e-20 1.24226525 0.155 0.110 3.662495e-16## Human herpesvirus 5 strain Merlin, complete genome
## Saccharomyces cerevisiae killer virus M1, complete genome
## Bacillus phage Stitch, complete genome
## Comparisons between cell types## Warning in DoHeatmap(data_subset, features = c("PTPRC", "CD163", "S100A8", :
## The following features were omitted as they were not found in the scale.data
## slot for the RNA assay: NA
## p_val avg_log2FC pct.1 pct.2 p_val_adj
## NC-031032.1 2.771628e-233 0.15249547 0.557 0.227 4.045191e-229
## NC-013221.1 4.603935e-173 0.02289590 0.270 0.087 6.719443e-169
## NC-001782.1 1.938233e-167 -0.04078704 0.580 0.267 2.828852e-163
## NC-038828.1 6.664537e-73 -0.03173920 0.101 0.031 9.726892e-69
## NC-006273.2 6.430412e-38 2.82113132 0.171 0.099 9.385186e-34
## NC-043054.1 1.511772e-11 -0.11278877 0.877 0.612 2.206431e-07## Human herpesvirus 5 strain Merlin, complete genome
## Saccharomyces cerevisiae killer virus M1, complete genome
## Bacillus phage Stitch, complete genome
## Human herpesvirus 5, Bacillus phage Stitch, and Saccharomyces cerevisiae killer virus M1 are elevated at 70hpi when compared to 20hpi.## Warning in DoHeatmap(data_subset, features = c("PTPRC", "CD274", "PDCD1LG2", :
## The following features were omitted as they were not found in the scale.data
## slot for the RNA assay: US2-hcmv, UL148D-hcmv, UL148C-hcmv, UL148B-hcmv,
## UL148A-hcmv, UL134-hcmv, UL137-hcmv, UL139-hcmv, UL140-hcmv, trunc-UL141-hcmv,
## UL142-hcmv, UL144-hcmv, UL146-hcmv, UL147A-hcmv, UL131A-hcmv, UL130-hcmv,
## UL127-hcmv, UL121-hcmv, UL120-hcmv, UL117-hcmv, UL116-hcmv, UL104-hcmv,
## UL98-hcmv, UL97-hcmv, UL96-hcmv, UL93-hcmv, UL92-hcmv, UL91-hcmv, UL90-hcmv,
## UL89-hcmv, UL88-hcmv, UL87-hcmv, UL86-hcmv, UL85-hcmv, UL80-5-hcmv, UL80-hcmv,
## UL79-hcmv, UL78-hcmv, UL77-hcmv, UL76-hcmv, UL74, UL73-hcmv, UL71-hcmv,
## UL60-hcmv, UL53-hcmv, UL51-hcmv, UL50-hcmv, UL49-hcmv, UL47-hcmv, UL41A-hcmv,
## vMIA-hcmv, UL32-hcmv, UL29-hcmv, UL28-hcmv, UL25-hcmv, UL24-hcmv, UL19-hcmv,
## UL18-hcmv, UL17-hcmv, UL16-hcmv, UL14-hcmv, UL12-hcmv, UL11-hcmv, UL10-hcmv,
## UL9-hcmv, UL8-hcmv, UL7-hcmv, UL3-hcmv, UL2-hcmv, UL1-hcmv, RL11-hcmv,
## RL10-hcmv, RL1-hcmv, US34A-hcmv, US33-hcmv, US31-hcmv, US30-hcmv, US29-hcmv,
## US27-hcmv, US21-hcmv, US20-hcmv, US19-hcmv, US17-hcmv, US15-hcmv, US14-hcmv,
## US9-hcmv
## PDL1 expression and HCMV viral transcripts increase after 20hpi and were found to be highly expressed in macrophages, a potential HCMV reservoir in tissues.R version 4.4.2 (2024-10-31) – “Pile of Leaves” Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu
RStudio 2024.09.1+394 “Cranberry Hibiscus” Release (a1fe401fc08c232d470278d1bc362d05d79753d9, 2024-11-03) for Ubuntu Jammy Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) rstudio/2024.09.1+394 Chrome/124.0.6367.243 Electron/30.4.0 Safari/537.36, Quarto 1.5.57