GEO DataSets

(Submitter supplied) NSP12 as the key RNA transcription polymerase of SARS-CoV-2, we intend to know whether NSP12 regulate the mRNA transcription of host cell upon viral infection

Organism:

Chlorocebus aethiops; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL24584

8 Samples

Download data: XLSX

(Submitter supplied) SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero or C6/36 cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minuse reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. more...

Organism:

Chlorocebus aethiops; Aedes albopictus

Type:

Other

Platforms:

GPL22096 GPL22031

8 Samples

Download data: TXT

(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

(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

(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

(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

(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:

GPL18573 GPL22096

12 Samples

Download data: XLSX

(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

(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:

Chlorocebus aethiops; Rickettsia rickettsii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33219 GPL33220

24 Samples

Download data: TSV

(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

(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

(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

(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

(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:

Chlorocebus aethiops; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

23 Samples

Download data: CEL

(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:

GPL24676 GPL29682

21 Samples

Download data: XLSX

(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

(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

(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

(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

(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