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Items: 1 to 20 of 588

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1.

Spatial transcriptomics of in vivo invasive trancheobronchitis biopsies obtained from patients with influenza-associated pulmonary aspergillosis or COVID-19-associated pulmonary aspergillosis

(Submitter supplied) To assess whether transcriptional differences exist in the epithelial tissue and the inflammatory infiltrate of invasive Aspergillus tracheobronchitis in patients with severe influenza or severe COVID-19, we performed GeoMx spatial transcriptomics on four biopsy samples in total: two of patients with influenza-associated pulmonary aspergillosis (IAPA) and two of patients with COVID-19-associated pulmonary aspergillosis (CAPA). more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Other
Platforms:
GPL29320 GPL24676
17 Samples
Download data: DCC, PKC, XLSX
Series
Accession:
GSE198096
ID:
200198096
2.

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

(Submitter supplied) Numerous host factors of SARS-CoV-2 have been identified by screening approaches, but delineating their molecular roles during infection and whether they can be targeted for antiviral intervention remains a challenge. Here we use Perturb-seq, a single-cell CRISPR screening approach, to investigate how CRISPR interference of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2; synthetic construct
Type:
Other
Platforms:
GPL29320 GPL26526
2 Samples
Download data
Series
Accession:
GSE208240
ID:
200208240
3.

Macrophages govern antiviral responses in human lung tissues protected from SARS-CoV-2 infection

(Submitter supplied) The majority of SARS-CoV-2 infections among healthy individuals result in asymptomatic to mild disease. However, the immunological mechanisms defining effective lung tissue protection from SARS-CoV-2 infection remain elusive. Unlike mice solely engrafted with human fetal lung xenograft (fLX), mice co-engrafted with fLX and a myeloid-enhanced human immune system (HNFL mice) are resistant to SARS-CoV-2 infection, severe inflammation, and histopathology. more...
Organism:
Homo sapiens; Mus musculus; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30391
12 Samples
Download data: CSV
Series
Accession:
GSE180063
ID:
200180063
4.

Profiling selective packaging of host RNA and viral RNA modification in the SARS-CoV-2 virion

(Submitter supplied) Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling on host RNA packaging were mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we apply both small RNA and large RNA sequencing of SARS-CoV-2 virions from six individual isolates in Vero cell cultures to profile packaging of host RNAs in a coronavirus and to explore SARS-CoV-2 genomic RNA modifications. more...
Organism:
Chlorocebus sabaeus; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL29240 GPL28895
42 Samples
Download data: TSV, XLSX
Series
Accession:
GSE182883
ID:
200182883
5.

SHAPE-guided RNA structure homology search and motif discovery

(Submitter supplied) The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. more...
Organism:
Severe acute respiratory syndrome coronavirus 2; Severe acute respiratory syndrome-related coronavirus
Type:
Other
Platforms:
GPL28588 GPL30986
4 Samples
Download data: WIG
Series
Accession:
GSE189259
ID:
200189259
6.

Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 Infection

(Submitter supplied) The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing worldwide has led to major issues in scaling the efforts of diagnostic labs and even in securing basic supplies for collection and processing of samples. This has in turn led to worldwide efforts by the scientific community to establish improved protocols that are cheaper, more scalable, and not as resource intensive. One such effort resulted in an assay called “Swab-Seq”, which was so named because it was originally developed to work with dry nasal swab samples, but is actually flexible in terms of the sample type it can accommodate for testing. more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL30234 GPL29228
10 Samples
Download data: TXT
Series
Accession:
GSE176224
ID:
200176224
7.

Preparation of chimeric recombinant SARS-CoV-2

(Submitter supplied) To investigate the virological properties of a SARS-CoV-2 variant, Omicron BA.2, we generated chimeric recombinant viruses that express GFP and encodes the S gene of B.1.1 (ancestral D614G-bearing virus), Delta, BA.1 and BA.2. To verify the genome sequence of the working viruses, we performed viral RNA-sequencing of the viral stock.
Organism:
Severe acute respiratory syndrome coronavirus 2
Type:
Other
Platform:
GPL28866
4 Samples
Download data: TXT
Series
Accession:
GSE196649
ID:
200196649
8.

Preparation of the working viruses of B.1.1, Delta and Omicron SARS-CoV-2

(Submitter supplied) To investigate the virological properties of SARS-CoV-2 variants, we amplified the clinical isolates of an early pandemic D614G-bearing isolate (B.1.1 lineage, strain TKYE610670; GISAID ID: EPI_ISL_479681), a Delta isolate (B.1.617.2 lineage, strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and an Omicron isolate (BA.1 lineage, strain TY38-873; GISAID ID: EPI_ISL_7418017) and prepared the working viruses.
Organism:
Severe acute respiratory syndrome coronavirus 2
Type:
Genome variation profiling by high throughput sequencing
Platform:
GPL28866
3 Samples
Download data: TXT
Series
Accession:
GSE192472
ID:
200192472
9.

SARS-CoV-2 infects and replicates in photoreceptor and retinal ganglion cells of human retinal organoids

(Submitter supplied) Recent data suggests that COVID-19 is a systemic disease affecting multiple organs including the central nervous system. Retinal involvement in COVID-19 has been indicated by several studies, yet many questions remain regarding the ability of SARS-CoV-2 to infect and replicate retinal cells and its effect on the retina. Here we have used human stem cell derived retinal organoids to study retinal infection by SARS-CoV-2. more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL30181 GPL30173
12 Samples
Download data: CSV
Series
Accession:
GSE174843
ID:
200174843
10.

Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb

(Submitter supplied) Anosmia, the loss of smell, is a common and often the sole symptom of COVID-19. The onset of the sequence of pathobiological events leading to olfactory dysfunction remains obscure. Here, we have developed a postmortem bedside surgical procedure to harvest endoscopically samples of respiratory and olfactory mucosae and whole olfactory bulbs. Our cohort of 85 cases included COVID-19 patients who died a few days after infection with SARS-CoV-2, enabling us to catch the virus while it was still replicating. more...
Organism:
Severe acute respiratory syndrome coronavirus 2; Homo sapiens
Type:
Other; Expression profiling by high throughput sequencing
Platform:
GPL29320
17 Samples
Download data: DCC, PKC, TXT
Series
Accession:
GSE176080
ID:
200176080
11.

SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances viral fusogenicity and pathogenicity

(Submitter supplied) During the current SARS-CoV-2 pandemic, a variety of mutations have been accumulated in the viral genome, and currently, four variants of concerns (VOCs) are considered as the hazardous SARS-CoV-2 variants to the human society. The newly emerging VOC, the B.1.617.2/Delta variant, closely associates with a huge COVID-19 surge in India in Spring 2021. However, its virological property remains unclear. more...
Organism:
Severe acute respiratory syndrome coronavirus 2
Type:
Genome variation profiling by high throughput sequencing
Platform:
GPL28866
6 Samples
Download data: TXT
Series
Accession:
GSE182738
ID:
200182738
12.

Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

(Submitter supplied) Programmed ribosomal frameshifting is the key event during translation of the SARS-CoV-2 RNA genome allowing synthesis of the viral RNA-dependent RNA polymerase and downstream viral proteins. Here we present the cryo-EM structure of the mammalian ribosome in the process of translating viral RNA paused in a conformation primed for frameshifting. We observe that the viral RNA adopts a pseudoknot structure lodged at the mRNA entry channel of the ribosome to generate tension in the mRNA that leads to frameshifting. more...
Organism:
Severe acute respiratory syndrome coronavirus 2
Type:
Other
Platform:
GPL29767
4 Samples
Download data: WIG
13.

SARS-CoV-2 utilizes a multipronged strategy to suppress host protein synthesis

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. Here, we use RNA-sequencing and ribosome profiling along SARS-CoV-2 infection and comprehensively define the mechanisms that are utilized by SARS-CoV-2 to shutoff cellular protein synthesis. more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL24676 GPL29320
42 Samples
Download data: TXT
Series
Accession:
GSE162323
ID:
200162323
14.

Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters

(Submitter supplied) COVID-19 is the third outbreak of zoonotic coronavirus (CoV) of the century after the epidemic Severe acute respiratory syndrome CoV (SARS-CoV) in 2003 and Middle East respiratory syndrome CoV (MERS-CoV) in 2012. Treatment options for CoVs are largely lacking. Here, we show that clofazimine, an anti-leprosy drug with favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2; Mesocricetus auratus
Type:
Expression profiling by high throughput sequencing
4 related Platforms
39 Samples
Download data: CSV
Series
Accession:
GSE162899
ID:
200162899
15.

Complete in vivo SHAPE-MaP structure of the SARS-CoV-2 genome

(Submitter supplied) SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero 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 minue 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:
Severe acute respiratory syndrome coronavirus 2
Type:
Other
Platform:
GPL28588
4 Samples
Download data: TXT
16.

Genome-scale deconvolution of RNA structure ensembles

(Submitter supplied) RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually exclusive conformations, including a conserved structural switch in the 3′ untranslated region. more...
Organism:
Severe acute respiratory syndrome coronavirus 2
Type:
Other
Platform:
GPL28588
2 Samples
Download data: JSON, TAR, WIG
Series
Accession:
GSE158052
ID:
200158052
17.

Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid

(Submitter supplied) We report that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with viral RNA. N-protein condenses with specific RNA genomic elements under physiological buffer conditions and condensation is enhanced at human body temperatures (33°C and 37°C) and reduced at room temperature (22°C). RNA sequence and structure in specific genomic regions regulate N-protein condensation while other genomic regions promote condensate dissolution, potentially preventing aggregation of the large genome. more...
Organism:
Severe acute respiratory syndrome coronavirus 2
Type:
Other
Platform:
GPL28866
27 Samples
Download data: CT, FASTA, TXT
18.

A novel cell culture system modeling the SARS-CoV-2 life cycle

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the global pandemic of COVID-19, and no effective antiviral agents and vaccines are available. SARS-CoV-2 is classified as a biosafety level-3 (BLS-3) agent, impeding the basic research into its biology and the development of effective antivirals. Here, we described a safe cell culture system for production of transcription and replication-competent, biologically contained SARS-CoV-2 virus like particles (trVLP) that express a reporter gene (GFP) replacing viral nucleocapsid gene, which is required for viral genome packaging and virion assembly (SARS-CoV-2-GFP/N trVLP). more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29320
2 Samples
Download data: TXT
Series
Accession:
GSE162629
ID:
200162629
19.

SARS-CoV-2 stock sequencing for infection of nonhuman primates

(Submitter supplied) SARS-CoV-2 USA/WA1 strain stock was sequenced to determine whether the furin cleavage site was intact.
Organism:
Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28866
1 Sample
Download data: XLSX
Series
Accession:
GSE162247
ID:
200162247
20.

bulk RNAseq of SARS-COV2 infected human lung organoid

(Submitter supplied) Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial 5 infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL29320 GPL24676
10 Samples
Download data: CSV
Series
Accession:
GSE160435
ID:
200160435
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