![[feed]](/style/images/feed-icon-14x14.png){kind=icon}
Tools
Tools
Preview |
PDF (Preprint)
- Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
1MB |
| Item Type: | Preprint |
|---|---|
| Title: | Generation of cirVDJseq libraries from 3’-barcoded cDNA v1 |
| Creators Name: | Plumbom, Izabela, Obermayer, Benedikt and Conrad, Thomas |
| Abstract: | This protocol describes circVDJ-seq, a method for simplified and cost-efficient TCR VDJ profiling from 3’-barcoded cDNA generated in single-cell or single-nucleus nucleus RNA-seq, RNA+ATAC multi-omics, or spatial transcriptomics workflows. 3’-barcoded cDNA is modified with Gibson assembly overhangs, circularized, depleted of remaining linear DNA, and subjected to nested PCR and 10x Genomics VDJ library construction to generate sequencing-ready TCR libraries. The expected outcome is a discrete, high-quality VDJ library peak on TapeStation High Sensitivity DNA assays with sufficient yield for Illumina sequencing using custom primers. When applied to human tissues, circVDJ-seq enables robust recovery of TCRα/β VDJ sequences and clonal repertoires, allowing characterization of T cell clonality and immune microenvironments across diverse clinical samples. |
| Keywords: | Circvdj-Seq, T Cell Receptor, TCR Sequencing, VDJ Profiling, Immune Repertoire, T Cell Clonality, 3ʼ-Barcoded dDNA, Single-Nucleus RNA-Seq, RNA+ATAC Multi-Omics, Spatial Transcriptomics, Circular DNA Library Preparation, Gibson Assembly, 10x Genomics, Human Tissue, Adaptive Immunity, Cancer Immunology, Infectious Diseases, COVID-19, 10x Genomics VDJ Library Construction, Robust Recovery Of TCRα, Generation of CirVDJseq Library, CirVDJseq Library, Efficient TCR VDJ Profiling, Ready TCR Library, Immune Microenvironments across Diverse Clinical Sample, Spatial Transcriptomics Workflow, Tapestation High Sensitivity DNA Assay, Nucleus Nucleus RNA, cDNA, TCRα, Diverse Clinical Sample, CircVDJ, Clonal Repertoire, Remaining Linear DNA, Linear DNA, Immune Microenvironment, Quality VDJ Library Peak |
| Source: | protocols.io |
| Publisher: | Springer Nature |
| Article Number: | protocols.io.q26g77zx1gwz/v1 |
| Date: | 17 December 2025 |
| Official Publication: | https://dx.doi.org/10.17504/protocols.io.q26g77zx1gwz/v1 |
Repository Staff Only: item control page
