{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jie Shu"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16268"],"description":["The precise role of Marginal Zone B (MZB) cells in shaping the adaptive immune response to virus-like particle (VLP) immunization remains incompletely defined. Here, we combined VLP immunization of wild-type and MZB-deficient mice with single-cell RNA sequencing (scRNA-seq) and paired TCR/BCR profiling of splenocytes. This integrated approach directly links the cellular transcriptome with its unique immune receptor at a single-cell resolution, allowing us to deconvolute the splenic immune landscape and precisely identify the molecular and clonal alterations resulting from the absence of MZB cells.Our analysis provides the first comprehensive insight into the gene expression programs and receptor repertoires that define the disrupted humoral immunity in MZB KO mice following vaccination. This strategy establishes a framework for definitively linking specific immune cell subsets to functional antibody responses and can be broadly applied to dissect the mechanisms of action of other vaccine platforms."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - According to the manufacturer's instructions, a single-cell RNA-seq library was constructed using the Chromium Next GEM Single-Cell 5' Kit (10x Genomics). Cell lysis and reverse transcription were performed within the GEM to generate barcoded cDNA. The GEM was then lysed, the cDNA was purified, and amplified by PCR to generate the final sequencing library.","Nucleic Acid Extraction - Single-cell suspensions were prepared from mouse spleens. Cell lysis and poly(A) RNA capture were performed simultaneously within the 10x Genomics GEMs, bypassing conventional RNA extraction.","Sample Collection - Wild-type mice were purchased from Shanghai SLAC Laboratory Animal Co. (Shanghai, China).All mice were housed in a Specific Pathogen Clearance (SPF) grade animal facility with a 12-hour light/dark cycle. Mice had free access to standard autoclaved feed and sterile water. All animal experimental procedures were conducted in accordance with the Guidelines for the Household and Use of Laboratory Animals and were approved by the Animal Ethics Committee.Following the stipulated immunization protocol, mice were humanely euthanized. Spleens were aseptically and surgically resected for subsequent single-cell suspension preparation and analysis.","Sequencing - The constructed libraries were quantified and quality-checked. Sequencing was performed on an Illumina NovaSeq platform using a 150 bp paired-end read configuration."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Single-cell RNA sequencing data were analyzed using the Seurat (v4.0.6) package in R. After quality control (nFeature_RNA > 200 and < 10000 and percent.mt < 10), the data were normalized using the LogNormalize method. Batch correction was performed using Harmony. Cell clustering was performed using the Louvain algorithm on the top 20 principal components. Differentially expressed genes (DEGs) were identified using the FindAllMarkers function (min.pct = 0.25, logfc.threshold = 0.25), with selection criteria of P < 0.01 and |log2FC| > 0.585."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Jie Shu"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell profiling (scRNA-seq with paired V(D)J) of the splenic response to VLP immunization in MZB KO versus wild-type mice","description":"The precise role of Marginal Zone B (MZB) cells in shaping the adaptive immune response to virus-like particle (VLP) immunization remains incompletely defined. Here, we combined VLP immunization of wild-type and MZB-deficient mice with single-cell RNA sequencing (scRNA-seq) and paired TCR/BCR profiling of splenocytes. This integrated approach directly links the cellular transcriptome with its unique immune receptor at a single-cell resolution, allowing us to deconvolute the splenic immune landscape and precisely identify the molecular and clonal alterations resulting from the absence of MZB cells.Our analysis provides the first comprehensive insight into the gene expression programs and receptor repertoires that define the disrupted humoral immunity in MZB KO mice following vaccination. This strategy establishes a framework for definitively linking specific immune cell subsets to functional antibody responses and can be broadly applied to dissect the mechanisms of action of other vaccine platforms.","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-05-27T14:58:27.084Z","creation":"2025-11-24T13:44:14.905Z"},"accession":"E-MTAB-16268","cross_references":{"ENA":["ERP185557"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}