Single-nucleus RNA sequencing data of macaque raphe nuclei

This dataset contains single-nucleus RNA sequencing (snRNA-seq) data and downstream analysis objects from macaque (*Macaca mulatta*) raphe nuclei. All libraries were sequenced on the **BGI DNBSEQ** platform. **Analysis pipeline** | Step | File prefix | Description ||------|-------------|-------------|| **step_1** | `step_1-DR-matrix1-concat` | Concatenation of individual sample matrices into a unified gene-expression matrix (`.h5ad`). || **step_2** | `step_2-macaque_DR_1_batch1` | Construction of Seurat objects per batch; ambient RNA removal with **SoupX**; initial QC and filtering. || **step_3** | `step_3-*harmony*` / `step_3-*batch_merge*` | **SCTransform** normalization followed by **Harmony** integration (across donor and batch); preliminary clustering and subclass identification. || **step_4** | `step_4-*forest*` / `step_4-*anno*` | **Random Forest (RF)** supervised classification for cell-type annotation; marker selection from downsampled training sets (`downsample3000`); donor-level cross-validation and annotation output (`.csv`/`.tsv`). || **step_5** | `step_5-classFiltSeurat*` / `step_5-41cl_*` | Iterative filtering of low-quality clusters; removal of `5-HT_9`; merging of 5-HT subtypes; exclusion of small clusters / non-neuronal filtering. | **Final annotated object (recommended for most users)**- **`step_5-最终保存classFiltSeurat.rds`** — The final curated Seurat object containing all 49 annotated subclasses. **Cell-type annotation**The final atlas comprises **49 subclasses** annotated in the `renew_type` metadata column:- Glut_1–5- GABA_1–19- Glut-GABA_1–3- 5-HT_1–8- DA_1- Microglia_1- Endothelial_1- Oligo_1–3- Astrocytes_1–4- OPC_1–4 **Supercluster resolution object****File format notes**- `.rds` files are **Seurat v5** objects; load in R with `readRDS()`.- `.h5ad` is the initial concatenated matrix; readable via `scanpy.read_h5ad()` or `SeuratDisk`.- Final **49-subclass** labels are stored in the `renew_type` metadata slot of the final Seurat object.