Ma2025

This is the public code and data repository for Ma et al. 2025.

Data

These are datasets in this repository.

1. all_RM_ApexGT6_processed_combined includes the processed 10X datasets with paired heavy and light chains. In addition to having all AIRR compliant fields, this dataset contains the following:

Field	Description
sequence_id	The barcode from the 10X GEM
week	Weeks post vaccination. 2, 4, 8, 12 or 10, 17
env	Immunogen-reactive population of this sequence [Pos, Neg]
nhp_id	The NHP animal ID
epitope_specific	Probe population of this sequence [Env-, Env+KO+, Env+KO-]
group	ApexGT6 immunogens delivered as protein or mRNA

1. Sequences and binding affinity data for RM Apex bnAb-like mAbs.xlsx is the document of all the rhesus macaque monoclonal antibodies after immunization, produced as IgG and tested. this dataset contains the following:

Field	Description
Monoclonal Antibody Name	Antibody identifier referenced in Figures 3E and 4G
Sequence_id	The barcode from the 10X GEM
Tissue	GC or MBC
Group	ApexGT6 immunogens delivered as protein or mRNA
HCDR3 aa length	22 aa, 23 aa, or ≥ 24 aa
Heavy_Chain_VDJ	Variable region sequence (V-D-J) of heavy chain
Light_Chain_VJ	Variable region sequence (V-J) of light chain
Affinity by SPR (M)	Dissociation constant (KD) of the antibody binding to Apex trimers, measured in molar units

Notebooks

We also are adding local notebooks and EMR notebooks that were used in this study.

Local Notebooks

GT6-NHP-GC.ipynb reads in 10X data of RM_post-priming_FNA_BCR_sequences.xlsx from all_RM_ApexGT6_processed_combined.

GT6-NHP-MBC-protein.ipynb reads in 10X data of RM_protein_post-priming_memory_BCR_sequences.xlsx from all_RM_ApexGT6_processed_combined.

GT6-NHP-MBC-mRNA.ipynb reads in 10X data of RM_mRNA_post-priming_memory_BCR_sequences.xlsx from all_RM_ApexGT6_processed_combined.

EMR Notebooks

Apex_human_precursor_2025.ipynb searched for human precursors and calculate their frequencies on NGS datasets of 1.1 billion human BCR heavy chain sequences from 14 human donors that were previously described (Briney et al., 2019; Steichen et al., 2019; Willis et al., 2022).

Apex_macaque_precursor_2025.ipynb searched for rhesus macaque BG18-like precursors and calculate their frequencies on 154 datasets of 95.4 million macaque BCR sequences from 60 macaques that were previously described (Steichen et al., 2014).