Data directory for "Molecularly-guided spatial proteomics captures single-cell identity of the healthy and diseased nervous system"

This directory holds the processed input data required to run the analysis notebooks in the accompanying code repository (). # Molecularly-guided spatial proteomics captures single-cell identity of the healthy and diseased nervous system *DOI: [10.1101/2025.02.10.637505](https://www.biorxiv.org/content/10.1101/2025.02.10.637505v2)* Authors: Sayan Dutta#, Marion Pang#, Gerard M. Coughlin, Sirisha Gudavalli, Michael L. Roukes, Tsui-Fen Chou, Viviana Gradinaru* # Equal contribution * Corresponding author ## How to obtain these files The processed reports total ~4.3 GB and include individual files larger than GitHub’s 100 MB limit, so they are deposited on Zenodo rather than in the GitHub repository. 1. Download the archive from **Zenodo:** *10.5281/zenodo.23702709* 2. Unpack it so the folders below sit inside `data/` in a clone of this repository (keep this `data_README.md` in place). 3. Open the notebooks; they read paths of the form `data/<folder>/report.parquet` (or `report.tsv`). Raw mass spectrometry files are not required to reproduce the figures and can be downloaded from: - MassIVE: [MSV000100704](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=dd7f039446bd4db79a506b35a8dbb312) - ProteomeXchange: [PXD074008](https://proteomecentral.proteomexchange.org/ui?pxid=PXD074008) Transcriptomic reference data were obtained from the Allen Brain Atlas and Dropviz, as described in the manuscript. The pre-joined table used by the transcriptomics notebook is included in this data repository. ## Directory structure Each folder holds processed report files for one dataset. DIA-NN datasets were processed with DIA-NN; bulk datasets in `fixation-bulk/` were processed with Proteome Discoverer (PD). | Folder | Key input | Size | Figure(s) / notebook | Description | |---|---|---|---|---| | `2411_size` | `report.tsv` | 0.92 GB | Fig. 1; revision + preprint notebooks | Size series | | `2505_rna_prot_full` | `report.tsv` | 1.67 GB | Combined; Figs. 2, 4, 5 | Full multi-region dataset (`pdata_all_region_filtered`); also contains `prot_metadata.csv`, `file_metadata.xlsx` | | `file_annotation.csv` | (this file) | <1 MB | Figs. 2, 4, 5 | Sample annotation table used when cleaning `2505_rna_prot_full` | | `fixation-bulk` | PD `*_Proteins.txt` / `*_PeptideGroups.txt` | 48 MB | Fig. 1 | Bulk IF (`AbPBS`), HCR, and fixed-frozen PD exports | | `2512_Ab-HCR` | `report.parquet` | 86 MB | Fig. 1 | Single-cell IF and HCR | | `2511_ast-SWI-only` | `report.parquet` | 63 MB | Fig. 4 | Astrocyte SWI dataset | | `2511_Mus6moSnpcONLY` | `report.parquet` | 46 MB | Fig. 6 | 6-month mouse SNpc | | `2511_MusSNPC-1mo-3mo-6mo-combined` | `report.parquet` | 106 MB | Revision notebook (1/3/6-month mouse SNpc) | Combined mouse SNpc time course | | `2607_fixation` | `report.parquet` | 251 MB | `analysis_scSP_fixation.ipynb` | Fixation-method comparison (frozen, PFA, formalin, glutaraldehyde, glyoxal), including site-level UniMod reports | | `transcriptomics` | `joined_all_triple.parquet` | 1.17 GB | `analysis_scSPmanuscript_transcriptomics.ipynb` | Pre-joined Allen Brain Atlas table plus Fig. 2/3 DE CSVs |