Article: Derks et al, 2024

• Code available at: github.com/SlavovLab/Single-nucleus-proteomics

Demonstrated aim:

This work demonstrated an approach to infer novel functional regulators from (sub-)single-cell proteomics data. Specifically, the natural proteomic and functional variability of THP-1 macrophage-like cells was used to identify regulators of LPS-induced nucleocytoplasmic protein transport. Cells were treated with LPS for short durations (10, 30, or 60 minutes) or left not-treated.

Methods:

Bulk proteomics method: plexDIA

Sample preparation method: mPOP

Single-cell proteomics methods: plexDIA, SCoPE-DIA

Sample preparation method: nPOP

Data organized by experiments

All processed data from the article are organized in this directory.

• Single-nucleus data

• Bulk data

• Knockdown data

Meta data for mapping single-nuclei and bulk data are here

Raw data and search results from DIA-NN

The repository below contains raw mass-spectrometry data files generated by a timsTOF SCP as well as the search results from analyzing the raw files by DIA-NN (v.1.8.1).

• MassIVE Repository:
  • http: MSV000094829

Repeating the computational analyses:

The {targets} R package was used to ensure repeatability of our analyses. R scripts corresponding to bulk, single nucleus, and knock down data can be found in the “Code” folder of our Github. The DIA-NN outputs can be found in our MassIVE repository; meta data, and other misc files required to run the code can be found in our directory