Simulated mouse long RNA-seq data used for benchmarking isoform identification and quantification as part of the paper: "Accurate strand-specific de novo long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution" by Yu et al. 2026 Genome resources are as follows: Reference GTF annotations: gencode.vM32.annotation.gtf : full gene set gencode.vM32.annotation_1isoformPerGene_reduced.gtf : single isoform retained per gene for use with ref-guided isoform ID experiments. gencode.vM32.annotation_expressed.gtf : expressed subset gencode.vM32.annotation_1isoformPerGene_expressed_kept.gtf : the single isoform retained among the expressed isoform subset. Quantification Truth set: Mouse_isoseqsim_ground_truth_transcript_id_count.tsv IsoSeqSim simulated reads aligned to the reference genome: Mouse_isoseqsim_simulated_reads_gpd_start_e0000_modified_sorted_filtered.bam : sequence error-free Mouse_isoseqsim_simulated_reads_gpd_start_e0016_modified_sorted_filtered.bam : 1.6% seq error Mouse_isoseqsim_simulated_reads_gpd_start_e0050_modified_sorted_filtered.bam : 5% seq error Mouse_isoseqsim_simulated_reads_gpd_start_e0085_modified_sorted_filtered.bam : 8.5% seq error