Seec_wastewater_2023
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB67638 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The goal of this study was to determine changes in the expression of genes in monoctic myleoid derived suppressor cells (M-MDSC) as a result of SARS CoV2 infection. The study aimed to investigate if M-MDSC are functionally active and inhibit T cell function in response to SARS CoV2 antigens 5 months after first detection of the virus. Methods: Peripheral blood mononuclear cells (PBMC) were collected from CoV2 (-) and CoV2 (+) donors (N=5 each group). M-MDSC were isolated by flow cytometry, and RNA extracted for RNA-seq studies. Filtering low quality reads and removal of the 3’ adapter sequences were performed using the Trim Galore tool. Reads were mapped to the latest version of the human genome (build hg38) using HISAT2. Mapped reads were counted against the human GENCODE annotation (v37) using HT-Seq. The EdgeR library in the R computing environment was used for quality control of the RNA-Seq data, and ComBat-seq method for correction of batch effects. Differential gene expression analysis was conducted using EdgeR. Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8. Results: An average of 34 million reads per sample were acquired and mapped to the human genome (build hg38). After applying filtering criteria, 9,217 human genes were identified with the HISAT2 and HTSeq workflow. Differential expression analysis was performed between CoV2 (+) and CoV2 (-) samples using EdgeR. A total of 188 differentially expressed genes (DEGs) were identified with nominal p-value <0.05; of which 63 were up- and 125 downregulated in CoV2 (+) samples. A total of 12 DEGs were identified with false discovery rate corrected p-value <0.05, of which 2 were up- and 10 downregulated. Pathway enrichment analysis identified pathways involved in immune response and innate immune signaling. Conclusion: The study demonstrated that CoV2 infection modulated the expression of genes involved in immune response and innate immune signaling. Most of the genes remained downregulated even after 5 months of first detection of SARS CoV2.
2022-06-03 | GSE199286 | GEO
Project description:On March 12, 2020, the World Health Organization (WHO) declared COVID-19 as a global pandemic. COVID-19 is produced by a novel β-coronavirus known as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) [1]. Several studies have detected SARS-CoV-2 RNA in urine, feces, and other biofluids from both symptomatic and asymptomatic people with COVID-19 [2], suggesting that SARS-CoV-2 RNA could be detected in human wastewater [3]. Thus, wastewater-based epidemiology (WBE) is now used as an approach to monitor COVID-19 prevalence in many different places around the world [4-10] . Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the most common SARS-CoV-2 detection method in WBE, but there are other methods for viral biomolecule detection that could work as well. The aim of this study was to evaluate the presence of SARS-CoV-2 proteins in untreated wastewater (WW) influents collected from six wastewater treatment plants (WWTPs), from Durham Region, Ontario, Canada, using a LC-MS/MS-based proteomics approach. We identified many SARS-CoV-2 proteins in these wastewater samples, with peptides from pp1ab being the most consistently detected and with consistent abundance.
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2022-02-10 | GSE193264 | GEO
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Project description:This dataset looks at the transcriptome of in vitro-differentiated primary lung cells infected with SARS-CoV2. Some cells have been treated with the drug Enzalutamide.
2022-05-04 | E-MTAB-10687 | biostudies-arrayexpress
Project description:New onsets of chronic urticaria (CU) have been reported after repeated immunizations, mainly with the Moderna mRNA-1273 vaccine (Spikevax). This study aims to evaluate patients with CU after COVID-19 mRNA vaccination. The contribution of SARS-Cov2 infection, atopy and IgE against the vaccine was analyzed. We monitored the features of patients who developed CU after vaccination in the Canton of Vaud through two surveys conducted in 2022 and 2023. Fifty individuals with CU underwent blood tests, and their results were compared with individuals without a history of urticaria (N=135). The presence of anti-vaccine IgE was detected with basophil activation tests (BAT). We assessed anti-SARS-Cov2 humoral response, and the presence of IgEs against common respiratory allergens (Phadiatop) as a surrogate for atopy. Post-vaccination CU occurred after a median interval of 10 days and significantly more after the Spikevax booster, affecting middle-aged individuals (median 41, 66% females). In 2023, CU was still active in 53% of the cases. Inducible forms of CU, primarily dermographism, were reported in 54% (2022) and 61% (2023) of the cases. BAT positivity was not specific to CU, anti-nucleocapsid positivity, or atopy but was significantly associated with higher anti-spike neutralizing activities and younger age. Four CU patients tolerated an additional dose of mRNA vaccine with no disease exacerbation/recurrence. The spikevax booster induced anti-vaccine IgE independently of CU, the latter being not directly associated with COVID-19 infection nor atopy. The tolerance to a new booster in 4/4 patients suggests that the Spikevax vaccine indirectly triggered CU in predisposed individuals.
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Project description:RNA-Seq was carried out in order to obtain the time dependent expression dynamics of SARS-CoV2 (Trondheim strain)-induced transcriptome changes in human lung epithelial Calu-3 cells.
2022-10-25 | E-MTAB-12134 | biostudies-arrayexpress