Single-cell BCR repertoire with paired heavy–light chains

---------------------------------Dataset summary

This dataset contains B cell receptor (BCR) repertoire data derived from single-cell V(D)J sequencing experiments from a patient  (donor D1). It includes V(D)J contig outputs generated using the Cell Ranger pipeline, processed repertoires generated with the Immcantation framework, and paired heavy–light chain BCR datasets used for downstream repertoire analyses.

The repository provides processed data and analysis-ready files. Raw sequencing data are available separately in the European Nucleotide Archive.

---------------------------------Dataset structuredataset/│├── cellranger_vdj_output/│   ├── Exp1/│   │   ├── NS1/│   │   └── SI1/│   ││   ├── Exp2/│   │   ├── NS2/│   │   └── SI2/│   ││   └── D1_concat/│└── files_for_repertoire_analysis/    ├── D1/    ├── H1/    └── H2/

cellranger_vdj_output contains V(D)J contig outputs generated by the Cell Ranger V(D)J pipeline.

files_for_repertoire_analysis contains processed BCR repertoire datasets used for downstream analyses.

---------------------------------Data processing workflow

Single-cell V(D)J sequencing data were processed using the Cell Ranger V(D)J pipeline to assemble contigs and generate V(D)J annotations.For donor D1, V(D)J contigs from the four samples were concatenated (four biological replicates: one IgLON5 specific -SI2- and three non specific).Subsequently, BCR repertoires were processed using the Change-O toolkit within the Immcantation framework. Paired heavy and light chain sequences were reconstructed using the script mergeHeavyLightForScRep.Rmd. This processing generated two files per donor:-airr_afterchangeo.csv – AIRR-formatted repertoire dataset after Change-O processing-BCR_paired.csv – table containing paired heavy and light chain BCR sequences

---------------------------------Downstream analysis

The processed datasets contained in files_for_repertoire_analysis were used for downstream BCR repertoire analyses.Analyses were performed using the script BCR_analysis_D1_PUB.Rmd, available in the associated GitHub repository:https://github.com/MathildeFogPerez/manuscript-XXXThe repository also contains the script mergeHeavyLightForScRep.Rmd, used to generate paired heavy–light chain repertoires.

---------------------------------Raw sequencing data

Raw sequencing data (FASTQ files) corresponding to the single-cell V(D)J sequencing experiments are available in the European Nucleotide Archive under accession:ENA accession: PRJEB109754

---------------------------------External datasets

Control donors H1 and H2 originate from the dataset published in: https://doi.org/10.1038/s41590-022-01230-1