2024-Bulk_SC BCR Sequencing Data
Description
Data uploaded provides BCR repertoire sequencing data present for the Thomas et al., publication (2024). Transgenic mice containing immunoglobulin loci were immunised with the HIV Env gp120 (MGRM8 strain) with or without escalating affinity mAb infusion that targeted the CD4bs. Bulk VH sequencing was performed on IgG plasma cells enriched from bone marrow tissue at the end of the immunisation regimen (*_Bulk_Upload.csv). Single cell VH sequencing was also performed on IgG B cells sorted from immunised spleen and lymph node tissues. (*_Sanger_Upload.csv). Clonal assignments are contained in the CLONE column in all data frames, and are consistent across the relevant datasets (i.e., bulk VH sequences were clustered together with Sanger sequencing VH sequences and are therefore consistent between these data sets). Three items are uploaded. All contain the following columns: - SEQUENCE_ID (unique sequence identifier) - SAMPLE_ID (Identifier for the immunisation regimen). - FUNCTIONAL (Boolean value of if the mAb possessed stop codons) - SEQUENCE_IMGT (IMGT-aligned V(D)J sequence, containing IMGT defined gap positions) - GERMLINE_V_CALL (the germline V gene assigned by IgBLAST (using IMGT definitions)). - GERMLINE_J_CALL (the germline J gene assigned by IgBLAST (using IMGT definitions)). - JUNCTION_LENGTH (the length in nucleotides of the junction region (CDR3 + 5' Cysteine + 3' Tryptophan)) - CDR3_IMGT (the CDR3 sequence in nucleotides). - File 1: Antigen specific VH sequences, associated with experimentally calculated affinity and epitope assignment. Additional columns are: - GERMLINE_D_CALL (the germline D gene assigned by IgBLAST (using IMGT definitions)). - SENSORGRAM_ACCEPTED (whether or not the sensorgram was accepted for affinity analysis, i.e., if the sensorgram faithfully represented experimental data). - EPITOPE (the assigned epitope, regardless of if the sensorgram was reliable for affinity calculation). - KD (the SPR calculated affinity). - File 2: Antigen specific VK sequences, associated with experimentally calculated affinity and epitope assignment - File 3: Bulk IgG Plasma Cell VH sequences, no experimental data. Additional columns are: - CONSCOUNT (Number of reads contributing to the UMI consensus sequence from bulk NGS) - DUPCOUNT (Copy number of the sequence from bulk NGS)