Long Read RNA Sequencing in Primary Lung Cell Types Reveals Principles of Nonsense-Mediated Decay
- 1. Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- 2. Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- 3. Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
- 4. The Institute for Experiential AI, Northeastern University, Boston, MA, USA
- 5. Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- 6. Division of Surgical Sciences, Department of Surgery, Duke University, Durham, NC, USA
- 7. Departments of Cell Biology and Medicine, Duke University, Durham, NC, USA
Description
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.
Files
annotation.zip
Files
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