Virus Dataset Detail

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Dataset Information
Accession GSE164485
Status 2021/6/16
Title The landscape of human brain immune response in patients with severe COVID-19
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We sought to further our understanding of the relationship between brain tropism, neuro-inflammation and host immune response in acute COVID-19 cases. 3 brain regions (dorsolateral prefrontal cortex, medulla oblongata and choroid plexus) from 5 patients with severe COVID-19 and 4 controls were examined. The presence of virus was assessed by western blot against viral spike protein, as well as viral transcriptome analysis covering >99% of SARS-CoV-2 genome and all potential serotypes. Droplet-based single-nucleus RNA sequencing (snRNA-seq) was performed in the same samples to examine the impact of COVID-19 on transcription in individual cells of the brain. Quantification of viral spike S1 protein and viral transcripts did not detect SARS-CoV-2 in the postmortem brain tissue. However, analysis of 68,557 single-nucleus transcriptomes from three distinct regions of the brain identified an increased proportion of stromal cells, monocytes and macrophages in the choroid plexus of COVID-19 patients. Furthermore, differential gene expression, pseudo-temporal trajectory and gene regulatory network analyses revealed transcriptional changes in cortical microglia associated with a range of biological processes, including cellular activation, mobility and phagocytosis. Despite the absence of detectable SARS-CoV-2 in the brain at time of death, the findings suggest significant and persistent neuroinflammation in patients with acute COVID-19.
Samples
GSM ID Sample info Characteristics Description
GSM5012032 Control 1-cDNA set2-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012033 Control 2-HTO set3-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012034 Control 2-cDNA set3-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012035 Control 2-HTO set3-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012036 Control 2-cDNA set3-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012037 Control 3-HTO set4-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012025 Control 4-HTO set1-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012026 Control 4-cDNA set1-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012027 Control 4-HTO set1-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012028 Control 4-cDNA set1-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012029 Control 1-HTO set2-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012030 Control 1-cDNA set2-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012031 Control 1-HTO set2-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012038 Control 3-cDNA set4-A diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012039 Control 3-HTO set4-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012040 Control 3-cDNA set4-B diagnosis:control; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012041 Case 2-HTO set5-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012042 Case 2-cDNA set5-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012043 Case 2-HTO set5-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012044 Case 2-cDNA set5-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012045 Case 4-HTO set6-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012046 Case 4-cDNA set6-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012047 Case 4-HTO set6-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012048 Case 4-cDNA set6-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012049 Case 5-HTO set7-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012050 Case 5-cDNA set7-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012051 Case 5-HTO set7-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012052 Case 5-cDNA set7-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012053 Case 3-HTO set8-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012054 Case 3-cDNA set8-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012055 Case 3-HTO set8-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012056 Case 3-cDNA set8-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012057 Case 1-HTO set9-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012058 Case 1-cDNA set9-A diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
GSM5012059 Case 1-HTO set9-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:HTO single nuclear RNAseq
GSM5012060 Case 1-cDNA set9-B diagnosis:COVID-19; tissue type:frozen brain/Prefrontal cortex/Medulla/Choroid plexus; cell type:nuclei; library type:cDNA single nuclear RNAseq
Platform GPL16791  : Illumina HiSeq 2500 (Homo sapiens)
Literature 34281603  
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scRNA-seq UMAP