Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell Transcriptomic and Immune Receptor Profiling of PBMCs from Dengue-Infected Individuals with Varying Disease Severities

ABSTRACT: This dataset comprises single-cell RNA sequencing (scRNA-seq) and immune receptor (TCR/BCR) profiling of peripheral blood mononuclear cells (PBMCs) collected from individuals infected with dengue virus (DENV) exhibiting different clinical severities: asymptomatic dengue (AD), dengue fever (DF), and dengue hemorrhagic fever (DHF). PBMCs were collected during the acute phase and, in some cases, during convalescence. The data provide a resource for understanding protective versus pathogenic immune responses in dengue infection.

INSTRUMENT(S): NA, Illumina HiSeq X, 10x Chromium™ Controller

ORGANISM(S): Homo sapiens

SUBMITTER: Waradon Sungnak

PROVIDER: E-MTAB-15328 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-Seq of dengue seronegative and seropositive individuals

Project description:Single cell RNA-seq was conducted on peripheral blood mononuclear cells (PBMCs) collected from study participants that were dengue seronegative (n=3) or dengue seropositive (n=3). Baseline single cell gene expression profiling was conducted using 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index).

2025-09-08 | E-MTAB-13441 | biostudies-arrayexpress

Single-cell RNA-seq of human peripheral blood mononuclear cells (PBMCs) throughout the febrile, critical, and convalescence phases of dengue virus infection

Project description:We investigated the abundances and transcriptomic changes of immune cells at several time points over the course of dengue virus infection. The PBMC samples were obtained from one dengue fever (DF) and one dengue hemorrhagic fever (DHF) patients (8 samples in total). The samples were harvested at two and one days before defervescence (febrile phase), at defervescence (critical phase), and two-week convalescence. Single-cell RNA-seq libraries were prepared using the 10x genomic protocol and were sequenced using the Illumina Hiseq platform. One healthy control sample analysed by the same protocol was included.

2022-02-16 | E-MTAB-9467 | biostudies-arrayexpress

The effect of anti-HER2/CD3 TDB on transcription in human PBMCs (single-cell)

Project description:Single-cell RNA-seq libraries were generated from human PBMCs that were incubated with anti-HER2/CD3 TDB in the presence of KPL-4 cells. This dataset only contains the metadata and processed data. Raw data can be accessed via the EGA accession EGAS00001003734

2019-09-06 | E-MTAB-8212 | biostudies-arrayexpress

Single cell RNA, BCR and CITE-Seq of longitudinal COVID-19 patients

Project description:6 patients with severe COVID-19 were followed longitudinally during hospitalization and up to 1 year after infection, when they also received a vaccine. For each time point and patient, PBMCs were collected and split into 3 pools: 1/3 was sequenced straight; from 1/3 of the samples B cells were enriched (B cell enrichment kit from StemCell) and from 1/3 of the samples, antigen-specific cells were sorted using barcoded N, S and RBD probes. All samples were further stained using a cocktail of 181 barcoded Abs. For all samples we have sequences gene-expression, B cell receptor and Cell surface proteins.

2022-12-06 | E-MTAB-12392 | biostudies-arrayexpress

Single-Cell RNA-Seq of Memory B cells in Early Untreated Rheumatoid Arthritis Patients (Gene Expression Data)

Project description:In recent years, a circulating subset of B cells phenotypically negative for CD21 has been reported to be expanded in chronic infectious and autoimmune inflammatory diseases. While reports on the function of these cells differ by disease origin, their role in rheumatoid arthritis (RA) has remained elusive. Here, we combine clinical data with flow cytometric analyses for patients untreated for and newly diagnosed with RA. We show correlations between the frequency of CD21-Tbet+CD11c+ and destruction of both cartilage and bone in in the joints of patients at the time of diagnosis. Combining single-cell 5’ RNA sequencing with B-cell receptor (VDJ)-enriched sequencing, we are able to identify the Tbet+CD11c+ cells in the scRNA-seq data from untreated newly diagnosed RA patients. Further, we describe a characteristic gene expression pattern, with overrepresentation of upregulated genes involved in antigen processing and presenting processes. The same gene signature is near identically expressed by autoimmune-associated cells infiltrating synovial tissue of RA patients. Our findings suggest that Tbet+CD11c+ B cells may be poised for antigen presentation in the periphery, and could be capable of recirculating between the periphery and joint tissue, thereby promoting autoimmune responses. Overall, we demonstrate a potential pathogenic role of Tbet+CD11c+ B cells in RA, in which they contribute to joint destruction.

2025-12-31 | E-MTAB-11961 | biostudies-arrayexpress

Single-cell V(D)J-seq of CD3+ and CD19+ lymphocytes from PBMCs of COVID-19 patients

Project description:We selected COVID-19 positive individuals, their direct contacts, and unmatched controls. CD3+ and CD19+ cells were sorted from PBMCs and they were analyzed for surface expression, 5' gene expression, and TCR/BCR profiling at single-cell resolution. For each group, three samples were pooled using Biolegend hashtag antibodies (TotalSeq™-C C0251, TotalSeq™-C C0252, and TotalSeq™-C C0253 ) and multiple runs were performed per library. The raw data for each run will be provided upon request.

2025-12-03 | E-MTAB-10636 | biostudies-arrayexpress

Interference of B-Cell and T-Cell Receptor Genes in Single-Cell RNA Sequencing Data

Project description:B and T cells play central roles in immune responses and, as such, are integral in many diseases, such as autoimmunity. Characterizing these cells, their subsets, and exploring their transcriptomes to understand the underlying biology, can be achieved using single-cell RNA sequencing (scRNA-seq). While some studies report removing the transcripts encoding the variable regions of the B- and T-cell antigen receptors prior to downstream analyses, a systematic analysis of the effects of retaining versus removing these genes has been lacking. We investigated the effects these transcripts in B and T cells impose on supervised clustering and downstream analyses of scRNA-seq data.

2025-12-16 | E-MTAB-12346 | biostudies-arrayexpress

Single cell CITE-seq and VDJ sequencing of CD8+ central memory blood T cells (TCM) and their in-vivo matured tissue-resident memory-like T cells (TRM)

Project description:The aim of the experiment was to understand the clonal relationship between CD8+ central memory blood T cells (TCM) and the in-vivo matured TCM tissue-resident memory-like T cells (TRM) on day 14. TCM were FACS sorted from human PBMCs (n=5). Half of the cells were processed on day 1 and half of the cells of each donor were matured into TRM with anti-CD3, IL-15 and TGF beta for 14 days. Both day 1 TCM and matured day 14 TRM-like cells were further processed using the 5´10X genomics workflow.

2023-06-12 | E-MTAB-12840 | biostudies-arrayexpress

Single-cell RNAseq and scTCRseq of human CD8 T cells from blood and skin compartments in Dengue patients

Project description:Using a skin-blister induction model established for dengue, we investigated the transcriptional signatures and TCR repertoire of matched CD8 T cells in skin and blood samples

2026-04-14 | E-MTAB-16332 | biostudies-arrayexpress

Single-cell RNA-seq of PBMCs from HCC patients pre- and post-curative therapy

Project description:This dataset contains processed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) collected from six hepatocellular carcinoma (HCC) patients, before and after curative therapy. Samples were profiled using the 10x Genomics Chromium platform. The dataset includes gene expression matrices and associated metadata for 12 samples (6 pre-therapy, 6 post-therapy). These data support the analysis of peripheral immune cell dynamics in response to tumor removal

2026-01-13 | E-MTAB-16408 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data