Long Read RNA Sequencing in Primary Lung Cell Types Reveals Principles of Nonsense-Mediated Decay

Source data for Leshem et al., Long-read RNA sequencing in primary lung cell types reveals principles of nonsense-mediated decay. The starting data for every analysis in the paper — the processed quantification, annotation and model outputs that the analysis code reads and cannot produce for itself. Paired short-read and PacBio Iso-Seq sequencing of four primary human lung cell types (AT2, LAE, FB, MV) under SMG1 inhibition versus vehicle: 26 samples, 13 donor-matched pairs. Download the twelve data files, 695 MB — that is every input the code needs. The two files of about 8 GB each are the packaged software environment the analyses ran in, and are optional. README.md, included in this record, has the full instructions: how to arrange the files, what each one is, and what will trip you up. Analysis code: github.com/peter4244/nmd_lung_longread_reproduction (DOI 10.5281/zenodo.21897099). Raw sequencing reads are in NCBI GEO under GSE329233.