GEO DataSets

(Submitter supplied) Defining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immuno-capture coupled to mass spectrometry. We apply this workflow to a cell-wide collection of membranous and membrane-less compartments. A graph-based analysis reveals the subcellular localization of over 7,600 proteins, defines spatial networks, and uncovers interconnections between cellular compartments. more...

Organism:

Human coronavirus OC43; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34943

2 Samples

Download data: CSV, FASTA, GTF, MTX, TSV

(Submitter supplied) The design of RNA-targeting antivirals offers a potent means in controlling viral infections. An essential prerequisite to this design depends on identifying functional RNA structures in the viral genome, as well as those that are readily accessible to drugs in cells. Techniques that probe RNA structures in situ have been developed recently including SHAPE-MaP. In this study, we report on the application of SHAPE-MaP to the Porcine Epidemic Diarrhea Virus (PEDV) RNA genome to categorize RNAs that are well folded, dynamic, or in the single strands by the combination of two parameters, SHAPE reactivity and Shannon entropy. more...

Organism:

Porcine epidemic diarrhea virus

Type:

Other

Platform:

GPL34659

3 Samples

Download data: CT, XML

(Submitter supplied) We demonstrate that the pseudoknot binder MTDB selectively degrades coronaviral pseudoknots in vitro, in cells and in a SARS-CoV-2 infection mouse model, which means it has great potential to be used as an anti-SARS-CoV-2 therapeutic.

Organism:

Severe acute respiratory syndrome coronavirus 2

Type:

Other

Platform:

GPL30554

3 Samples

Download data: BW

(Submitter supplied) Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). more...

Organism:

synthetic construct; Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28867 GPL19424

2060 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; synthetic construct; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing; Other

6 related Platforms

4153 Samples

Download data

(Submitter supplied) Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). more...

Organism:

Severe acute respiratory syndrome coronavirus 2; synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28867 GPL19424

2054 Samples

Download data: TXT

(Submitter supplied) Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2; synthetic construct

Type:

Other

6 related Platforms

39 Samples

Download data: TXT

(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) Porcine epidemic diarrhea virus (PEDV) is a deadly coronavirus for neonatal piglets and no effective vaccines are available. Transcriptional regulatory sequences (TRSs) are critical in regulating coronavirus discontinuous transcription. Also, TRSs contribute to a high recombination rate of coronaviruses, leading to difficulty in developing safe live vaccines. We hypothesize that recoding the TRS core sequences (TRS-CS) of PEDV can make the recombination impossible between the engineered vaccine virus and field strains or wildtype viruses. more...

Organism:

Porcine epidemic diarrhea virus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28571

2 Samples

Download data: TXT, XLSX

(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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Murine hepatitis virus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24973 GPL32147

28 Samples

Download data

(Submitter supplied) The mouse hepatitis virus (MHV) genomic RNA has a poly(A) tail required for replication. Here we investigated the presence of terminal poly(A) tail uridylation and guanylation in the virion RNA. After isolating the viral RNA followed by sequencing, we found a mean poly(A) tail of 66 nucleotides long with a peak of terminal uridylation on tails 55 to 66 nucleotides long.

Organism:

Murine hepatitis virus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32147

2 Samples

Download data: TSV

(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:

Severe acute respiratory syndrome coronavirus 2; Homo sapiens

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:

GPL29320 GPL26526

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

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

Type:

Protein profiling by protein array

Platform:

GPL32091

1373 Samples

Download data: CSV, XLS