huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level.
Lize WuZiwei XueSiqian JinJinchun ZhangYixin GuoYadan BaiXuexiao JinChaochen WangLie WangZuozhu LiuJames Q WangLinrong LuWanlu LiuPublished in: Nucleic acids research (2021)
T-cell receptors (TCRs) and B-cell receptors (BCRs) are critical in recognizing antigens and activating the adaptive immune response. Stochastic V(D)J recombination generates massive TCR/BCR repertoire diversity. Single-cell immune profiling with transcriptome analysis allows the high-throughput study of individual TCR/BCR clonotypes and functions under both normal and pathological settings. However, a comprehensive database linking these data is not yet readily available. Here, we present the human Antigen Receptor database (huARdb), a large-scale human single-cell immune profiling database that contains 444 794 high confidence T or B cells (hcT/B cells) with full-length TCR/BCR sequence and transcriptomes from 215 datasets. All datasets were processed in a uniform workflow, including sequence alignment, cell subtype prediction, unsupervised cell clustering, and clonotype definition. We also developed a multi-functional and user-friendly web interface that provides interactive visualization modules for biologists to analyze the transcriptome and TCR/BCR features at the single-cell level. HuARdb is freely available at https://huarc.net/database with functions for data querying, browsing, downloading, and depositing. In conclusion, huARdb is a comprehensive and multi-perspective atlas for human antigen receptors.
Keyphrases
- single cell
- rna seq
- high throughput
- endothelial cells
- acute lymphoblastic leukemia
- induced pluripotent stem cells
- regulatory t cells
- tyrosine kinase
- immune response
- cell proliferation
- pluripotent stem cells
- emergency department
- electronic health record
- cell death
- artificial intelligence
- big data
- signaling pathway
- dna damage
- chronic myeloid leukemia
- data analysis
- bone marrow