Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE163952
Status 2021/1/22
Title Neurodegeneration in herpes simplex virus 1 infected human brain organoids
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We describe the cellular response to HSV-1 infection in human iPSC-derived brain organoids
Samples
GSM ID Sample info Characteristics Description
GSM4991120 iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 1, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:3dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;gline_3dpi_rep1;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991121 iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 2, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:3dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;gline_3dpi_rep2;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991122 iPSC-2 line (Thermo Fisher A18945), 6dpi, replicate 1, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:6dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;gline_6dpi_rep1;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991123 iPSC-2 line (Thermo Fisher A18945), 6dpi, replicate 2, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:6dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;gline_6dpi_rep2;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991124 iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 1, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:NA; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;gline_ctrl_rep1;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991125 iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 2, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:NA; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;gline_ctrl_rep2;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991126 Xmoo1 line, 3dpi, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:3dpi; rna population:polyA+ RNA hg38HSV1GFPtc.Seurat.500.RDS.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NP2-60d-3dpi-Rep1;Dropseq including second strand synthesis
GSM4991127 Xmoo1 line, 3dpi, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:3dpi; rna population:polyA+ RNA hg38HSV1GFPtc.Seurat.500.RDS.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NP2-60d-3dpi-Rep2;Dropseq including second strand synthesis
GSM4991128 Xmoo1 line, 6dpi, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:6dpi; rna population:polyA+ RNA hg38HSV1GFPtc.Seurat.500.RDS.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NP2-60d-6dpi-Rep1;Dropseq including second strand synthesis
GSM4991129 Xmoo1 line, 6dpi, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:6dpi; rna population:polyA+ RNA hg38HSV1GFPtc.Seurat.500.RDS.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NP2-60d-6dpi-Rep2;Dropseq including second strand synthesis
GSM4991130 Xmoo1 line, ctrl, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:NA; rna population:polyA+ RNA hg38HSV1GFPtc.Seurat.500.RDS.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NP2-60d-Ctrl-Rep1;Dropseq including second strand synthesis
GSM4991131 Xmoo1 line, ctrl, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:NA; rna population:polyA+ RNA hg38HSV1GFPtc.Seurat.500.RDS.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NP2-60d-Ctrl-Rep2;Dropseq including second strand synthesis
GSM4991132 Xmoo1 line, ctrl, replicate 1, for FLAM-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:NA; rna population:polyA+ RNA NR_AR_ORG_HSV1_1_gene_polyA_length.csv.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NR_AR_ORG_HSV1_1;FLAMseq (Legnini et al. 2019)
GSM4991133 Xmoo1 line, ctrl, replicate 2, for FLAM-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:NA; rna population:polyA+ RNA NR_AR_ORG_HSV1_2_gene_polyA_length.csv.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NR_AR_ORG_HSV1_2;FLAMseq (Legnini et al. 2019)
GSM4991134 Xmoo1 line, ctrl, replicate 3, for FLAM-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:NA; rna population:polyA+ RNA NR_AR_ORG_HSV1_3_gene_polyA_length.csv.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NR_AR_ORG_HSV1_3;FLAMseq (Legnini et al. 2019)
GSM4991135 Xmoo1 line, 3dpi, replicate 1, for FLAM-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:3dpi; rna population:polyA+ RNA NR_AR_ORG_HSV1_4_gene_polyA_length.csv.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NR_AR_ORG_HSV1_4;FLAMseq (Legnini et al. 2019)
GSM4991136 Xmoo1 line, 3dpi, replicate 2, for FLAM-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:3dpi; rna population:polyA+ RNA NR_AR_ORG_HSV1_5_gene_polyA_length.csv.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NR_AR_ORG_HSV1_5;FLAMseq (Legnini et al. 2019)
GSM4991137 Xmoo1 line, 3dpi, replicate 3, for FLAM-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:3dpi; rna population:polyA+ RNA NR_AR_ORG_HSV1_6_gene_polyA_length.csv.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;NR_AR_ORG_HSV1_6;FLAMseq (Legnini et al. 2019)
GSM4991138 Xmoo1 line, 3dpi, replicate 1, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:3dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;xmoo1_3dpi_rep1;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991139 Xmoo1 line, 3dpi, replicate 2, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:3dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;xmoo1_3dpi_rep2;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991140 Xmoo1 line, 6dpi, replicate 1, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:6dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;xmoo1_6dpi_rep1;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991141 Xmoo1 line, 6dpi, replicate 2, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:yes; sampling timepoint:6dpi; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;xmoo1_6dpi_rep2;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991142 Xmoo1 line, ctrl, replicate 1, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:NA; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;xmoo1_ctrl_rep1;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM4991143 Xmoo1 line, ctrl, replicate 2, for bulk RNA-seq tissue:Brain organoid; hsv-1 infection status:no; sampling timepoint:NA; rna population:rRNA-depleted RNA merged_raw_read_counts.txt.gz;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;xmoo1_ctrl_rep2;TruSeq Stranded Total LT Sample Prep Kit (Illumina)
GSM6625471 Experiment 2, iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:no; treatment:NA; sampling timepoint:NA; rna population:polyA+ RNA CTRL.rds;all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625472 Experiment 2, iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:no; treatment:NA; sampling timepoint:NA; rna population:polyA+ RNA CTRL.rds;all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625473 Experiment 2, iPSC-2 line (Thermo Fisher A18945), 1dpi, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:1dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625474 Experiment 2, iPSC-2 line (Thermo Fisher A18945), 1dpi, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:1dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625475 Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625476 Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625477 Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi + ACV, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:ACV; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625478 Experiment 2, iPSC-2 line (Thermo Fisher A18945), 3dpi + ACV, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:ACV; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625479 Experiment 2, Xmoo1 line, ctrl, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:no; treatment:NA; sampling timepoint:NA; rna population:polyA+ RNA CTRL.rds;all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625480 Experiment 2, Xmoo1 line, ctrl, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:no; treatment:NA; sampling timepoint:NA; rna population:polyA+ RNA CTRL.rds;all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625481 Experiment 2, Xmoo1 line, 1dpi, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:1dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625482 Experiment 2, Xmoo1 line, 1dpi, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:1dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625483 Experiment 2, Xmoo1 line, 3dpi, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625484 Experiment 2, Xmoo1 line, 3dpi, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:NA; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.fa.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625485 Experiment 2, Xmoo1 line, 3dpi + ACV, replicate 1, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:ACV; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.gtf.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
GSM6625486 Experiment 2, Xmoo1 line, 3dpi + ACV, replicate 2, for single-cell RNA-seq tissue:Brain organoid; hsv-1 infection:yes; treatment:ACV; sampling timepoint:3dpi; rna population:polyA+ RNA all_timepoints.rds;HSV1GFPtrunc_corr.gtf.gz;HSV1GFPtrunc_corr.gtf.gz;Dropseq including second strand synthesis
Platform GPL18573  GPL20301  GPL26180  GPL26236  GPL29543  GPL29544  : Illumina NextSeq 500 (Homo sapiens);Illumina HiSeq 4000 (Homo sapiens);Sequel (Homo sapiens);Illumina NextSeq 500 (Homo sapiens; Human alphaherpesvirus 1);Illumina HiSeq 4000 (Homo sapiens; Human alphaherpesvirus 1);Sequel (Homo sapiens; Human alphaherpesvirus 1)
Literature 37349587  
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* p<0.05 ** p<0.01
scRNA-seq UMAP