Jκ5-Barcoded mm9 Mouse Reference Genomes (mm9_JK5DB3_1_T and mm9_JK5DB3_1_ATAA)

Jκ5-Barcoded mm9 Mouse Reference Genomes (mm9_JK5DB3_1_T and mm9_JK5DB3_1_ATAA) This record provides two custom mm9-based mouse reference genomes, mm9_JK5DB3_1_T and mm9_JK5DB3_1_ATAA, representing the two allele-specific Jκ5 barcode sequences used for HTGTS-V(D)J-seq analysis of Igκ recombination. Genome construction Both reference genomes were derived from the UCSC mm9 mouse genome assembly and modified at an allele-specific barcode site downstream of the Jκ5 coding segment. This site is located approximately 85 bp downstream of the Jκ5-RSS heptamer and approximately 40 bp upstream of the Jκ5 HTGTS-V(D)J-seq bait primer, as described in Zhang et al. (2024). In the mm9 reference genome, the barcode site spans approximately chr6:70,673,966-70,673,967 and contains the sequence AT. The two custom genomes carry different barcode variants at this site: mm9_JK5DB3_1_T contains T, corresponding to a 1-bp deletion relative to mm9. mm9_JK5DB3_1_ATAA contains ATAA, corresponding to a 2-bp insertion relative to mm9. Both custom genomes retain the complete Jκ1-Jκ5 region. They are therefore distinct from the subsequently generated single-Jκ5 allele system, in which Jκ1-Jκ4 were deleted. Apart from the barcode modification, the surrounding Jκ5-region sequence is preserved relative to mm9. Biological context and application These sequence variants represent the two Jκ5 barcode alleles of the Jκ5-barcoded v-Abl pro-B cell line described by Zhang et al. (Nature, 2024). In that system, allele-specific 1-4 bp indels were introduced downstream of the Jκ5 RSS and upstream of the Jκ5 HTGTS-V(D)J-seq bait primer, allowing sequencing reads derived from the two Igk alleles to be distinguished within the same sample. The two genome builds deposited here correspond to the barcode-specific custom reference genomes encompassed by the "indicated custom genomes" described in the sequencing analysis methods of that study. They were used to support allele-specific alignment and analysis of HTGTS-V(D)J-seq data from the Jκ5-barcoded system. Published application These reference genomes are associated with the Jκ5-barcoded experiments reported in: Zhang Y, Li X, Ba Z, et al. Molecular basis for differential Igk versus Igh V(D)J joining mechanisms. Nature. 2024;630:189-197.DOI: 10.1038/s41586-024-07477-y The associated sequencing datasets are available through GEO SuperSeries GSE263124, including HTGTS-V(D)J-seq datasets in GSE254039. Intended use These custom reference genomes are provided to facilitate reproducible alignment and allele-specific analysis of sequencing data generated from the Jκ5-barcoded Igk system. Files This Zenodo record provides the mm9_JK5DB3_1_T and mm9_JK5DB3_1_ATAA reference genome FASTA files, each split into compressed parts for reliable upload and download, together with checksum files for verification of file integrity. The included files are: mm9_JK5DB3_1_T.fa.gz.part01 to mm9_JK5DB3_1_T.fa.gz.part04 mm9_JK5DB3_1_T.parts.md5 mm9_JK5DB3_1_T.fa.gz.md5 mm9_JK5DB3_1_ATAA.fa.gz.part01 to mm9_JK5DB3_1_ATAA.fa.gz.part04 mm9_JK5DB3_1_ATAA.parts.md5 mm9_JK5DB3_1_ATAA.fa.gz.md5 Users should cite this Zenodo record when using the distributed reference genomes and should also cite the relevant original publication describing their experimental application. Download and reconstruction The compressed FASTA files have been split into multiple parts for reliable upload and download. All corresponding part files are required to reconstruct each original genome file. For mm9_JK5DB3_1_T, first verify that all downloaded parts are present and intact: md5sum -c mm9_JK5DB3_1_T.parts.md5 Then reconstruct the original compressed FASTA file: cat mm9_JK5DB3_1_T.fa.gz.part* > mm9_JK5DB3_1_T.fa.gz Verify the reconstructed file: md5sum -c mm9_JK5DB3_1_T.fa.gz.md5 For mm9_JK5DB3_1_ATAA, first verify the downloaded parts: md5sum -c mm9_JK5DB3_1_ATAA.parts.md5 Then reconstruct the original compressed FASTA file: cat mm9_JK5DB3_1_ATAA.fa.gz.part* > mm9_JK5DB3_1_ATAA.fa.gz Verify the reconstructed file: md5sum -c mm9_JK5DB3_1_ATAA.fa.gz.md5 To decompress the reconstructed genome FASTA files: gunzip mm9_JK5DB3_1_T.fa.gzgunzip mm9_JK5DB3_1_ATAA.fa.gz