Bulk short- and long-read RNA-sequencing of iNeurons in Fragile-X and control cell-lines
This study benchmarks bulk and single-cell long-read RNA sequencing technologies in a human neuronal model of Fragile X syndrome. NGN2-induced neurons were generated from patient-derived iPSCs carrying a silenced FMR1 gene (FXS line E3) and an isogenic CRISPR-corrected rescue line (IsoB11) in which FMR1 expression is restored. These conditions provide a defined system to evaluate transcript detection and quantification across sequencing platforms.   Bulk and single-cell RNA-seq datasets were generated using Illumina short-read sequencing and long-read sequencing from Pacific Biosciences (PB) and Oxford Nanopore Technologies (ONT). Single-cell libraries were prepared using the 10x Genomics Chromium platform. ERCC and SIRV spike-in controls were added to bulk samples to enable benchmarking of transcript quantification accuracy.   Three biological replicates were sequenced for each condition. The dataset enables cross-platform comparisons of transcript detection, quantification methods, transcript length biases, and sequencing depth requirements for long-read transcriptomic analyses.