Browse
Submit Data
Databases
API
Help

Dataset Information

65 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-sequencing of spike-specific CD4 and CD8 T cells after COVID-19 vaccination in healthy and XLA donors

ABSTRACT: Gao et al.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Curtis Cai

PROVIDER: E-MTAB-11845 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq data related to Booster mRNA vaccination post-SARS-CoV-2 infection enhances functional qualities of T cell immunity

Project description:We performed a study investigating donors previously infected with SARS-CoV-2 during the first wave of the COVID-19 pandemic to understand how vaccination may reshape T cell populations formed after infection. 10 donors were investigated using single-cell RNA-sequencing consisting of a) 3 mild non-hospitalised donors, b) 3 severe hospitalised donors, c) 1 mild recently vaccinated donor and d) 3 recently convalescent donors. For each of these groups we sampled at the following timepoints a) 6-9 months and 18 months after infection, b) 6-9 months and 18 months after infection, c) 13 months and 15 months after infection and d) 35 days after infection. All donors were unvaccinated at the first time point and vaccinated at the second time point. We stimulated PBMC with an overlapping peptide pool derived from the spike glycoprotein of the SARS-CoV-2 virus and sorted spike-specific CD4+ T cells (CD4+CD69+CD40L+) and spike-specific CD8+ T cells (CD8+CD69+4-1BB+) from every donor and time point using flow cytometry for 10X single-cell sequencing (5' protocol). Each time point from Dnr4868 was sequenced across two 10X reactions/libraries performed on the same day. Multiple samples were hashed and pooled together for sequencing using TotalSeq-C anti-human hashing antibodies from BioLegend. Individual library expression matrix files were generated using the CellRanger pipeline from 10X Genomics. The processed data file named immune.combined220929.rds is a Seurat Object containing all samples and generated using the Seurat package in R.

2023-06-30 | E-MTAB-12716 | biostudies-arrayexpress

Single cell sequencing for B cell repertoire of multi-year serial blood samples from two healthy donors.

Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from two healthy donors with an interval of 10 or 6 years.

2022-04-26 | E-MTAB-11174 | biostudies-arrayexpress

Single cell sequencing for B cell repertoire of multi-year serial blood samples from a healthy donors.

Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from a single healthy donor with an interval of 4 years.

2022-05-14 | E-MTAB-11697 | biostudies-arrayexpress

A high-resolution single-cell multiomic atlas of the human fetal lung - ATAC-seq

Project description:We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.

2022-01-27 | E-MTAB-11266 | biostudies-arrayexpress

Single cell ATAC-seq of human peripheral blood mononuclear cells under resting and stimulated conditions

Project description:Single cell ATAC-seq of PBMC - resting and stimulated. Used for comparison to asses the capabilies of the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication).

2021-04-13 | E-MTAB-10382 | biostudies-arrayexpress

Single cell five-prime end sequencing of PBMC - resting and stimulated

Project description:Single cell five-prime end sequencing of PBMC - resting and stimulated. Used to asses the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication)

2021-04-28 | E-MTAB-10378 | biostudies-arrayexpress

Single Cell data of B cells from patients with chronic Hepatitis C and sustained viral response

Project description:We dissect HCV imprinting of B cell repertoires in patients with chronic disease. The persistent character of the oncogenic B cell repertoire generated by HCV may point to a chronically elevated lymphoma risk in these patients even years after HCV cure.

2023-11-30 | E-MTAB-12502 | biostudies-arrayexpress

Single-cell RNA-seq data of cardiac cells derived from a human induced pluripotent stem cell control line

Project description:Characterization of cell-type diversity obtained after cardiac differentiation of hiPSC using single-cell RNA-Seq.

2022-12-05 | E-MTAB-11817 | biostudies-arrayexpress

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

Translational co-culture model reveals epithelial-mesenchymal mechanisms of lung fibrosis and identifies NF-κB as potential therapeutic target

Project description:The interaction of lung epithelial and lung mesenchymal cells was investigated in a novel co-culture model of human pulmonary fibrosis. Remarkably, co-culturing both cell types induced cell-type-specific responses, including fibroblast-to-myofibroblast differentiation and epithelial-to-mesenchymal transition (EMT), which were fully dependent on direct epithelial / fibroblast contact. We used single-cell RNA sequencing (scRNA-seq) to evaluate the transcriptional fate of the normal human lung fibroblasts (NHLF) and normal human bronchiolar epithelial cells (NHBE) during the course of co-cultivation, and compare the single cell profiles with their counterpart isolated from patients with idiopathic pulmonary fibrosis (IPF). NHLF and normal NHBE cells were grown as co-cultures, cell suspensions were collected at the time points t = 0h, 3h and 18h and analyzed by single-cell RNA-seq on a Chromium Platform. Eight samples were sequenced, resulting in a total of xx single cell transcription profiles.

2022-10-03 | E-MTAB-11847 | 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