GEO DataSets

(Submitter supplied) SARS-CoV-2 can generate viral microRNAs (v-miRNAs) that target host gene expression. This study used small RNAseq to identify the v-miRNAs present in COVID-19 patients' nasopharyngeal swabs. The study identified a specific conserved v-miRNA sequence (CoV2-miR-O8) unique to SARS-CoV-2 that is highly present in COVID-19 patients' samples, interacts with Argonaute, and has features consistent with Dicer and Drosha generation. more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL28867

9 Samples

Download data: BW

(Submitter supplied) Diverse placental functions are compartmentalized to separate maternal-fetal antigens and restrict vertical transmission of pathogens. We hypothesized a high-resolution map, with single-cell and spatial resolution, would identify previously undetectable microbe immune microenvironments. To test this hypothesis, we utilized Visium Spatial Transcriptomics paired with H&E staining to generate 17,927 spatial transcriptomes and integrated these data with 273,944 published placenta single-cell and single-nuclei transcriptomes to generate a term placenta atlas of the maternal decidua, fetal chorionic villi, and chorioamniotic membranes. more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL29320

16 Samples

Download data: H5, JPG, PNG

(Submitter supplied) Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies through changes of epitopes on the receptor binding domain of the viral spike glycoprotein (S). Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. more...

Organism:

Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28866

8 Samples

Download data: TSV, TXT

(Submitter supplied) The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 100 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS) remains poorly understood. more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL29228

373 Samples

Download data: DCC, PKC, XLSX

(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:

Severe acute respiratory syndrome coronavirus 2; Homo sapiens

Type:

Other

Platforms:

GPL29320 GPL24676

17 Samples

Download data: DCC, PKC, XLSX

(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:

GPL26526 GPL29320

2 Samples

Download data

(Submitter supplied) The effectiveness of virus culturing in 24 hours for the sequencing of SARS-CoV-2

Organism:

Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29240

9 Samples

Download data: SF, TSV, WIG

(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

(Submitter supplied) NSP1 is a major shutoff factor of the SARS-CoV-2 coronavirus, which is responsible for the COVID-19 pandemic. The functions of NSP1 and its contribution to SARS-CoV-2 propagation is not well understood. We tackled these questions utilizing methods such as RNA sequencing, ribosome profiling, and SLAMseq.

Organism:

Mesocricetus auratus; Chlorocebus sabaeus; Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

159 Samples

Download data: CSV

(Submitter supplied) Individualized antibody reacitivty levels for SARS-CoV-2 antigens were successfully quantified and reactivity classification (Reactive non reactive) was performed based on a logistic regression model. Individuals were tested at several time points including their reactivity before the mRNA vaccination (Pfizer and Moderna), soon after first and second doses and up to 6 months after immunization

Organism:

Influenza A virus; Severe acute respiratory syndrome-related coronavirus; Middle East respiratory syndrome-related coronavirus; Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Protein profiling by protein array

Platform:

GPL32091

1373 Samples

Download data: CSV, XLS

(Submitter supplied) The global spread of SARS-CoV-2 lead to the most challenging pandemic in this century, posing major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SARS-CoV-2 can provide insights into the virus pathogenesis, and facilitates the development of novel broad-spectrum host-directed therapeutics. Here, employing genome-scale CRISPR screens, we provide a comprehensive data-set of cellular factors that are exploited by WT-SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Other

Platforms:

GPL15520 GPL30234

9 Samples

Download data: TXT

(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

(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-related coronavirus; Severe acute respiratory syndrome coronavirus 2

Type:

Other

Platforms:

GPL28588 GPL30986

4 Samples

Download data: WIG

(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

(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

(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

(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

(Submitter supplied) Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. The kinetics and efficiency of sgRNAs production during viral replication in different cell types or sgRNA transcription by individual viral strains or variants are yet to be studied to shed light on fundamental mechanisms necessary for viral replication. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study a growing number of next-generation sequencing (NGS) data of SARS-CoV-2. more...

Organism:

Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28588

3 Samples

Download data: CSV

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2–infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL29105

51 Samples

Download data: BEDGRAPH, CSV, XLSX

(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