Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE123782
Status 2019/3/4
Title Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We describe the viral gene expression cascade at the single-cell level, showing bifurcations and bottleneck states. Host gene expression changes are related to viral transcription. The role of cellular signaling pathways in infection is studied using trajectory analysis and the importance of the Nrf2 transcription factor studied in follow-up experiments.
Samples
GSM ID Sample info Characteristics Description
GSM3511315 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, 3hpi hsv-1 infection:Mock-infected 3h before harvesting; infection protocol:mock, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511316 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, 5hpi hsv-1 infection:Mock-infected 5h before harvesting; infection protocol:mock, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511317 NHDF cells, single-cell RNA-seq, synchronous 4C infection, uninfected, pilot replicate 1 hsv-1 infection:Uninfected; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep1_morethan2000genes_normcounts.txt.gz
GSM3511318 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 3hpi, pilot replicate 1 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep1_morethan2000genes_normcounts.txt.gz
GSM3511319 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 5hpi, pilot replicate 1 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep1_morethan2000genes_normcounts.txt.gz
GSM3511320 NHDF cells, single-cell RNA-seq, synchronous 4C infection, uninfected, Replicate 2 hsv-1 infection:Uninfected; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511321 NHDF cells, single-cell RNA-seq, synchronous 4C infection, uninfected, Replicate 3 hsv-1 infection:Uninfected; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511322 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 1hpi, Replicate 2 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511323 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 1hpi, Replicate 3 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511324 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 3hpi, Replicate 2 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511325 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 3hpi, Replicate 3 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511326 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 5hpi, Replicate 2 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511327 NHDF cells, single-cell RNA-seq, synchronous 4C infection, 5hpi, Replicate 3 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep23_morethan2000genes_normcounts.txt.gz
GSM3511328 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, uninfected, Replicate 4 hsv-1 infection:Uninfected; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511329 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, uninfected, Replicate 5 hsv-1 infection:Uninfected; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511330 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 4 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511331 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 5 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511297 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, uninfected, Replicate 2 hsv-1 infection:Uninfected; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511298 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, uninfected, Replicate 3 hsv-1 infection:Uninfected; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511299 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 1hpi, Replicate 2 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511300 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 1hpi, Replicate 3 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511301 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 3hpi, Replicate 2 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511302 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 3hpi, Replicate 3 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511303 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 5hpi, Replicate 2 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511304 NHDF cells, stranded polyA RNA-seq, synchronous 4C infection, 5hpi, Replicate 3 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 1h 4 degree, new medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511305 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, uninfected, Replicate 4 hsv-1 infection:Uninfected; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511306 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, uninfected, Replicate 5 hsv-1 infection:Uninfected; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511307 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 4 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511308 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 1hpi, Replicate 5 hsv-1 infection:Infected 1h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511332 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 4 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511333 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 5 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511334 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 4 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511335 NHDF cells, single-cell RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 5 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:single-cell RNA scRNA-seq;HSV1scRNA_rawcounts_allcells.txt.gz;scRNAseq_Rep45_morethan2000genes_normcounts.txt
GSM3511309 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 4 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511310 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 3hpi, Replicate 5 hsv-1 infection:Infected 3h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511311 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 4 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511312 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C infection, 5hpi, Replicate 5 hsv-1 infection:Infected 5h before harvesting; infection protocol:MOI 10, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511313 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, uninfected hsv-1 infection:Uninfected; infection protocol:mock, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
GSM3511314 NHDF cells, stranded polyA RNA-seq, non-synchronous 37C mock infection, 1hpi hsv-1 infection:Mock-infected 1h before harvesting; infection protocol:mock, 30min 37 degree, conditioned medium; rna isolation:total RNA; adapter sequence:GATCGGAAGAGCACACGT Stranded RNA-seq;bulk_RNA-seq_readcounts.txt
Platform GPL18573  GPL20301  : Illumina NextSeq 500 (Homo sapiens);Illumina HiSeq 4000 (Homo sapiens)
Literature 31653857  
Download Download xCell Data  Download Expression Analysis Data  
xCell Plot
* p<0.05 ** p<0.01