Supplementary datasets: sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data (Ng et al.)

This repository contains data files from the manuscript Ng et al. "sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data".

Directories

Please untar the sciCSR-data-files.tar.gz archive.

Folder "Simulated_data"

• 'simulated_IGHC_reads' folder: containing list of simulated data (FASTQ sequence files and aligned BAM files) to test the accuracy of commonly used RNA-seq aligners (STAR, HISAT2) to distinguish sterile and productive heavy-chain transcripts. The code to generate these data is in the repository https://github.com/Fraternalilab/sciCSR-analysis.
• 'simulated_transitions.RData': .RData file containing list of Seurat objects of simulated datasets of different number of cells, to test the robustness of sciCSR-inferred transitions across different dataset sizes.

Folder "Seurat_objects"

• 'human_Bcells_atlas_IGHC_NMF_rank.rds': Nonnegative matrix factorization (NMF) results to derive isotype signatures from the human B cell atlas (see below).
• 'mouse_Bcells_atlas_IGHC_NMF_rank.rds': NMF results to derive isotype signatures from the mouse B cell atlas (see below)
• 'Human_Bcells_atlas_IGHC.rds': Seurat object containing cells forming the 'human B cell atlas' (i.e. merging data from Stewart et al (https://doi.org/10.3389/fimmu.2021.602539) and King et al (https://doi.org/10.1101/2020.04.28.054775))
• 'mouse_Bcells_atlas_IGHC.rds': Seurat object containing cells forming the 'mouse B cell atlas' (i.e. merging data from Mathew et al (https://doi.org/10.1016/j.celrep.2021.109286) and Luo et al (https://doi.org/10.1186/s13578-022-00795-6))
• 'Stewart_HumanPeripheral_Bcells_IGHC.rds': Seurat object containing cells from the Stewart et al (https://doi.org/10.3389/fimmu.2021.602539) peripheral blood B cell atlas.
• * 'King_HumanTonsil_Bcells_IGHC.rds': Seurat object containing cells from the King et al. (https://doi.org/10.1101/2020.04.28.054775) human tonsilar B cell atlas.
• 'Kim_Covid_Bcells_IGHC.rds': Seurat object containing cells from the Kim et al. (https://doi.org/10.1038/s41586-022-04527-1) time-course scRNA-seq data on human B cell response to SARS-CoV-2 vaccine.
• 'Gomez_AID_VDJ_IGHC.rds': Seurat object containing cells from the Gómez-Escolar et al. (https://doi.org/10.15252/embr.202255000) Aicda mouse knockout scRNA-seq data.
• 'Hong_IL23_Bcells_IGHC.rds': Seurat object containing cells from the Hong et al. (https://doi.org/10.4049/jimmunol.2000280) Il23 p19 mouse knockout scRNA-seq data.
• 'scIFNg.rds': Seurat object containing scRNA-seq data of time-course in vitro culture of B cells stimulated with interferon gamma generated in this work.