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Items: 1 to 20 of 957

1.

Single cell analysis reveals differential impact of Zika virus on the host antiviral landscape

(Submitter supplied) Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10x Genomics Chromium single cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human moDCs infected with ZIKV at the single cell level. more...
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL29682
12 Samples
Download data: MTX, TSV
Series
Accession:
GSE230571
ID:
200230571
2.

Herpesvirus remodel organization and function of mitochondria as infection proceeds

(Submitter supplied) During the infection, viruses target mitochondria to promote viral replication. Infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteractions of viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Our multimodal integration of advanced imaging, genomics, and metabolomics draws a comprehensive picture of time-dependent changes in mitochondria as HSV-1 infection proceeds from early to late infection.
Organism:
Chlorocebus aethiops
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL24584
6 Samples
Download data: TXT
Series
Accession:
GSE243613
ID:
200243613
3.

Immunization with the adenovirus-induced T cell response and apoptosis – prophylactic vaccine design against SARS-CoV-2

(Submitter supplied) New universal prophylactic vaccine platforms are needed to prevent or reduce the impact of future respiratory viral infections. While the attribute of T memory cells is particularly attractive in the context of vaccine design for viral infection, the efficiency of T and B memory cell-mediated protection generated under the adenoviral vector was tested. We studied the mechanism using the platform/ immunological factor combination (AdV1+rRBD): adenovirus AdV1 (adjuvant) armed with inducible co-stimulator ICOS and CD40 ligand in combination with recombinant spike protein rRBD (antigen) to promote the differentiation of memory T and B cells. more...
Organism:
Chlorocebus aethiops
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29682
6 Samples
Download data: CSV
Series
Accession:
GSE245876
ID:
200245876
4.

In-Depth Characterization of Cell Subculture Process based on Multi-Omics

(Submitter supplied) To investegate the mechanism of physiological changes during cell digestion, we analyzed the levels of RNAs in cells treated with animal-based enzymes and animal origin-free enzymes.
Organism:
Chlorocebus aethiops
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29682
30 Samples
Download data: XLS
Series
Accession:
GSE215840
ID:
200215840
5.

Effect of peroxisomal proteotoxic stress on gene expression in mammalian cells

(Submitter supplied) To establish the overall cell responses to peroxisomal proteotoxic stress, we analysed transcriptomes of NT- and LONP2-silenced cells using RNA sequencing in COS-7 and U2OS cells.
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL22096 GPL18573
12 Samples
Download data: XLSX
Series
Accession:
GSE224992
ID:
200224992
6.

Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the ongoing pandemic of coronavirus disease 2019 (COVID-19). Single cell RNA sequencing (scRNAseq) studies have been valuable for studying SARS-CoV-2 pathogenesis, but the performance of these methods to detect and quantify viral RNAs has not been evaluated. Here we develop an analysis pipeline, single cell coronavirus sequencing (scCoVseq), to quantify unambiguous reads derived from coronavirus genomic (gRNA) and subgenomic mRNAs (sgmRNAs). more...
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL18573 GPL22096
11 Samples
Download data: CSV, H5, RDS
Series
Accession:
GSE189900
ID:
200189900
7.

Identification of an outer membrane protease of Rickettsia rickettsii responsible for maturation of surface exposed autotransporters

(Submitter supplied) Members of the spotted fever group rickettsia express four large, surface-exposed autotransporters, at least one of which is a known virulence determinant. Autotransporter translocation to the bacterial outer surface, also known as type V secretion, involves formation of a b-barrel autotransporter domain in the periplasm that inserts into the outer membrane to form a pore through which the N-terminal passenger domain is passed and exposed on the outer surface. more...
Organism:
Rickettsia rickettsii; Chlorocebus aethiops
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL33220 GPL33219
24 Samples
Download data: TSV
Series
Accession:
GSE226832
ID:
200226832
8.

Coronavirus replication is controlled by both host and viral RNA m6A methylations

(Submitter supplied) N6–methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it plays an important role in RNA metabolism and function. Recent studies have revealed that viral RNA m6A modification can play an anti-viral or pro-viral role in virus life cycle. However, whether m6A methylation can modulate replication of coronaviruses, which contain the largest known RNA genomes, remains elusive. more...
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Other
Platforms:
GPL27829 GPL20795
16 Samples
Download data: BED
Series
Accession:
GSE141291
ID:
200141291
9.

High throughput sequencing of MARC145, A549, HEK293, and HRT18 cells infected with Shaan virus

(Submitter supplied) Purpose: The goals of this study are to monitor the evolution pattern of Shaan virus in depending host cells by viral transcriptome sequencing analysis of MARC145, A549, HEK293, and HRT18 cells infected with Shaan virus. Methods: The original isolate of Shaan virus (B16-40, Genbank accession no. MG230624.1) was passaged in MARC-145 cells. Low-passaged virus was obtained from the virus 4 times serially passaged in MARC-145 cells. more...
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL29682 GPL24676
24 Samples
Download data: XLSX
Series
Accession:
GSE201344
ID:
200201344
10.

SARS-CoV-2 produces a diverse small viral RNA landscape capable of targeting host transcripts

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, which may be lethal. In this study, we used a comparative transcriptomics approach to investigate the effects of SARS-CoV-2 infection on the host mRNA and sRNA expression programs in two primate cell lines. Upon infection, we observed global changes in host gene expression and differential expression of dozens of host miRNAs, many with known links to viral infection and immune response. more...
Organism:
Homo sapiens; Chlorocebus aethiops
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL24676 GPL20301 GPL22915
99 Samples
Download data: BED, CSV
Series
Accession:
GSE197521
ID:
200197521
11.

mRNA expression analysis of the hippocampus in a vervet monkey model of fetal alcohol spectrum disorder

(Submitter supplied) Alcohol preferring vervet dams were permitted to ingest alcohol 4 days/week during the second half of gestation (e90-e165) and paired with sucrose matched controls. Cases and controls were sacrificed with subsequent hippocampal extraction at 5 months and 2 years. RNA was extracted according to the manufacturer's protocol and hybridized to the Affymetrix Rhesus Genechip microarray. We sought to identify pathways and genes involved in the development of fetal alcohol spectrum disorder in a non-human primate in order to develop an understanding of how this disorder may develop in humans.
Organism:
Chlorocebus aethiops; Macaca mulatta
Type:
Expression profiling by array
Platform:
GPL3535
24 Samples
Download data: CEL
Series
Accession:
GSE173516
ID:
200173516
12.

miRNA expression analysis of the hippocampus in a vervet monkey model of fetal alcohol spectrum disorder

(Submitter supplied) Alcohol preferring vervet dams were permitted to ingest alcohol 4 days/week during the second half of gestation (e90-e165) and paired with sucrose matched controls. Cases and controls were sacrificed with subsequent hippocampal extraction at 5 months and 2 years. RNA was extracted according to the manufacturer's protocol and hybridized to the Affymetrix Rhesus Genechip microarray. We sought to identify whether global downregulation in mRNA dataset was related to miRNA expression in a non-human primate model of FASD in order to develop an understanding of how this disorder may develop in humans.
Organism:
synthetic construct; Chlorocebus aethiops
Type:
Non-coding RNA profiling by array
Platform:
GPL16384
23 Samples
Download data: CEL
Series
Accession:
GSE181456
ID:
200181456
13.

High throughput sequencing of Vero, A549, CaCO2, and HRT18 cells infected with SARS-CoV2

(Submitter supplied) Purpose: The goals of this study are to monitor the evolution pattern of SARS-CoV2 in depending host cells by viral transcriptome sequencing analysis of Vero, A549, Caco2, and HRT18 cells infected with SARS-CoV2. Methods: SARS-CoV-2 isolate was passaged 4 time on Vero cells and used to extract RNA for the high-throughput sequencing. The 8×104 PFU of SARS-CoV2 stocks passaged on vero cells were inoculated to the monolayer of A549, CaCO2, and HRT-18 cell lines in 75T flask for 1hour at 37℃ in a 5% CO2 incubator with gentle shaking of 15 minutes interval. more...
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL29682 GPL24676
21 Samples
Download data: XLSX
Series
Accession:
GSE190350
ID:
200190350
14.

A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome

(Submitter supplied) COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. more...
Organism:
Chlorocebus aethiops; Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL29105 GPL29166
127 Samples
Download data: BW
Series
Accession:
GSE157490
ID:
200157490
15.

SARS-CoV-2 infected and uninfected VeroE6 and A549-ACE2: Bemcentinib and liposome treatments

(Submitter supplied) VeroE6 or A549-ACE2 cells were treated with inhibitors of phosphatidylserine receptors and infected with SARS-CoV-2.
Organism:
Chlorocebus aethiops; Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing
4 related Platforms
70 Samples
Download data: TXT, XLSX
Series
Accession:
GSE178942
ID:
200178942
16.

m6A modification in SARS-CoV-2 virus regulates host cell innate immune response

(Submitter supplied) It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlying molecular mechanism. RNA modification landscape of SARS-CoV-2 and its functional relevance to host cell innate immune response remain unknown. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. more...
Organism:
Chlorocebus aethiops; Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL29742 GPL29320
16 Samples
Download data: BEDGRAPH, BW, XLSX
Series
Accession:
GSE167075
ID:
200167075
17.

High-throughput splicing assays identify missense and silent splice-disruptive POU1F1 variants underlying pituitary hormone deficiency

(Submitter supplied) Using a high throughput splicing reporter assay, we tested 1,080 single nucleotide variants in POU1F1, a key transcription factor essential for pituitary development. Our saturation splicing effect map identifies 96 splice disruptive variants, including 14 synonymous variants, of which 8 were found in unrelated patients diagnosed with hypopituitarism.
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Other
Platforms:
GPL20301 GPL22915
18 Samples
Download data: FA, TSV, TXT
Series
Accession:
GSE172504
ID:
200172504
18.

Transcriptome analysis of HEK-293, A549 and HRT18 cells infected with shaan virus

(Submitter supplied) propose: The goals of this study are viral transcript of host cells infected with shaan virus and host cell responses in HEK293, A549 and HRT18 infected with shaan virus. Methods: We infected the virus at an MOI of 0.5 to human tissues-derived cell lines including HEK-293, A549 and HRT18. The infected cells were harvested at 24 hours post infection, and a total RNA was extracted from the harvested cells with Trizol LS reagent. more...
Organism:
Chlorocebus aethiops; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL29682
8 Samples
Download data: XLSX
Series
Accession:
GSE165900
ID:
200165900
19.

SARS-CoV-2 infection dynamics in lungs of African green monkeys

(Submitter supplied) Detailed knowledge about dynamics of SARS-CoV-2 infection in vivo is important for unraveling the viral and host response factors that contribute to COVID-19 pathogenesis. The unknown dose and exposure timing in human infections makes the needed well-controlled time course studies impossible and thus animal models of disease are essential to fill in the gaps in our understanding of disease progression. more...
Organism:
Chlorocebus aethiops
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29061
20 Samples
Download data: TAR
Series
Accession:
GSE156755
ID:
200156755
20.

Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2

(Submitter supplied) Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which is the cause of a present global pandemic, infects human lung alveolar type 2 (hAT2) cells. Characterizing pathogenesis is crucial for developing vaccines and therapeutics. However, the lack of models mirroring the cellular physiology and pathology of hAT2 cells limits the study. Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for hAT2 cells, and investigate infection response to SARS-CoV-2. more...
Organism:
Chlorocebus aethiops
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22096
6 Samples
Download data: TXT
Series
Accession:
GSE159316
ID:
200159316
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