Novel insights into immune cell diversity and maturation in the pteropodid bat Eonycteris spelaea via single-cell transcriptome analysis

This Zenodo record provides the Eonycteris spelaea genome reference used for scRNA-seq analyses in this study: (i) the genome assembly (FASTA) and (ii) a Peaks2UTR-refined gene annotation (GTF) with improved 3′ UTR boundaries. Raw sequencing data supporting the assembly/annotation are available at NCBI under BioSample SAMN4835912 (and associated accessions therein). To improve 3′ transcript end annotation, we refined the baseline GTF using Peaks2UTR which leverages aggregated read coverage to infer and extend 3′ UTR boundaries. Briefly, all scRNA-seq libraries (bone marrow, blood, liver) were first aligned to the in-house reference (FASTA + baseline GTF) using Cell Ranger to produce coordinate-sorted BAM files. BAM files were then merged across libraries to increase coverage at transcript termini and provided as input to Peaks2UTR to identify 3′ end peaks and update transcript models accordingly. Peaks2UTR output annotations (GFF) were converted to GTF format and used, together with the unchanged genome FASTA, to build the final reference for remapping all scRNA-seq datasets in this study with Cell Ranger prior to downstream analyses.