Project description:A cryovial that contains frozen PBMCs (10^6 cells/vial) from each of 11 COVID-19 patients was thawed in 37oC water bath. Immediately after, thawed cells were transferred to 15-mL Falcon tube that contained 10 mL of cold culture medium. After centrifugation at 150g for 5 min, the cell pellets were resuspended in complete RPMI + 10% heat-inactivated FCS medium and plated onto 12-well plate at a concentration of 5 x 10^6 cells/3 mL/well. Then a peptide cocktail was added at a concentration of 5 μg/mL for 16hr in 5% CO2 37oC incubator. After 16-hour incubation, cells were washed 3 times and incubated for 10 minutes with Fc receptor block, following each sample was stained with a total of 6 HLA-A2+/peptide fluorescent tetramer (Tet) and pentamer (Pent) for 10 min. After cell washing at twice, each sample was stained with cell hashing antibodies for 20 min, respectively and then washed at three times and finally pooled. The combined cells were stained with CITE-seq and anti-human CD8 FACS antibody for 30 minutes. After cell washing at twice, viable HLA-A2+/peptide Tet/Pent positive CD8+ T cells were sorted by FACS Aria II. The scRNA-Seq libraries including GEX and CITE-seq libraries were prepared using the 10x Chromium single-cell 3’ reagent kits (v3.1 Chemistry), per manufacturer’s instructions. As a result, we have 2 separate groups of the single cell datasets. MKH datasets (MKH_GEX_... and MKH_FB...) contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 5 COVID-19 patients. MKK datasets contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 6 COVID-19 patients. Cell hashing and CITE-seq antibody information is available in the csv files.

2025-12-01 | E-MTAB-14727 | biostudies-arrayexpress

Shedding of infectious SARS-CoV-2 by hospitalized COVID-19 patients in relation to serum antibody responses.

Project description: Not available

| S-EPMC8159068 | biostudies-literature

Shedding Light on SARS-CoV-2, COVID-19, COVID-19 Vaccination, and Auditory Symptoms: Causality or Spurious Conjunction?

Project description: Not available

| S-EPMC8919951 | biostudies-literature

SARS-CoV-2 produces a microRNA, CoV2-miR-O8, in patients with COVID-19 infection

Project description: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. CoV2-miR-O8 is predicted to target specific human genes and can be detected by RTPCR assays in patients.

2023-12-11 | GSE230080 | GEO

Transcriptional response to the SARS-CoV-2 Delta variant in patients with severe COVID-19

Project description:For a more precise understanding of the course of the pathological process in patients with severe COVID-19, it is necessary to continue the search for factors that affect the course of the pathological process and the possibility of a favorable outcome in critically ill patients. Comparative analysis of the transcriptome of peripheral blood mononuclear cell (PBMCs) in patients with a severe clinical course of COVID-19 caused by the SARS-CoV2 Delta strain revealed a number of differentially expressed genes that distinguish patients with different clinical outcomes (survivors vs. nonsurvivors) in the period of 30 days after admission to the hospital. resuscitation. Most of them are associated with the "negative regulation of viral process" and "negative regulation of immune response" clusters. Moreover, in surviving patients, there is increased expression of the key genes C1QB, C1QA, ISG15, SERPING1, VSIG4, KLRD1, TRPM4, and HFE incorporated in these clusters. Among these key genes, the ISG15 gene, which links several clusters of GO enrichments and encodes an interferon-induced ubiquitin-like protein, deserves special attention. An increase in the level of expression of the ISG15 protein may play a role in response to the expression of the viral protease PLpro, but the exact role of this protein in the prevention of negative disease outcomes is not yet clear.

2025-05-15 | GSE272392 | GEO

Clinical symptoms and faecal shedding of SARS-CoV-2 RNA among hospitalized COVID-19 patients: Implication for transmission.

Project description: Not available

| S-EPMC11357088 | biostudies-literature

Prolonged viral shedding of SARS-CoV-2 and related factors in symptomatic COVID-19 patients: a prospective study.

Project description: Not available

| S-EPMC8711078 | biostudies-literature

SARS-CoV-2 Antibody Point-of-Care Testing in Dialysis and Kidney Transplant Patients With COVID-19.

Project description: Not available

| S-EPMC7834810 | biostudies-literature