Resource data for: Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome

Resource data for the publication: Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome.

The Resources.zip file contains all intermediate output data needed to reproduce the analyses in the manuscript. The respective code needed to run the analyses can be found in the GitHub repository (https://github.com/boehmv/2025_UPF1_NMDRHT). Please note that the codes require the Resources to be present in the following folder structure:

2025_UPF1_NMDRHT/
├── Resources/ // Contents from the Resources.zip from Zenodo│ ├── bakR/ // First resource folder
│ └── ... // Other resource folders
├── Plots/ // Output for analyses plots
│ ├── Figure1/ // Plots for Figure1
│   └── ...         // Other Plots folders
├── .../ // Other folders from GitHub, e.g. "Analyses" or "Tables"
├── UPF1_NMDRHT_Analysis.R         // Top-level R analysis script
└── ... // Other R analysis scripts

The RawData.zip file contains the raw image files from RT-PCR gels and Western blots used in the study. For RT-PCR images, TIF (.tif) and raw Bio-Rad Image Lab Image Document (.scn) files are provided. For Western blots, multi-page TIFs (pages: 1. overlay, 2. raw chemiluminescence, 3. marker image, 4. final) are provided.

Note: the unpacked Resources.zip is over 80 GB in size, please make sure you either have enough space or just extract the relevant data.