GSE314058 scRNA-seq Data Processing

scRNA-seq geo_data_processing 7 steps

Publication

Single-cell and isoform-specific translational profiling of the mouse brain.

Nature (2026) — PMID 41708856

Dataset

Single-cell and isoform-specific translational profiling of the mouse brain [scRNA-seq]

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook

1

Aligned with cellranger-3.0.0 to mm10 + tdTomato reference

Cell Ranger v3.0.0
2

Doublet removal with Scrublet
3

QC filtering: removed low-quality cells and genes, mitochondrial filtering, replicate-specific Gm42418 filtering
4

CPM and log normalization.
5

Raw edits were normalized by Stamp expression via regression.
6

EPR = normed edits / raw reads
7

BBKNN batch correction, cell type assignment with marker genes using Scanpy

Scanpy

Tools Used

Scanpy

Raw Source Text

Aligned with cellranger-3.0.0 to mm10 + tdTomato reference
Doublet removal with Scrublet
QC filtering: removed low-quality cells and genes, mitochondrial filtering, replicate-specific Gm42418 filtering
CPM and log normalization. Raw edits were normalized by Stamp expression via regression. EPR = normed edits / raw reads
BBKNN batch correction, cell type assignment with marker genes using Scanpy
Assembly: mm10
Supplementary files format and content: Barcodes: cell barcodes (barcodes.tsv.gz)
Supplementary files format and content: Features: gene IDs and names (features.tsv.gz). Matrix: gene expression counts in Matrix Market format (matrix.mtx.gz)
Supplementary files format and content: Adatas (.h5ad files): filtered and normalized counts (shortread_normed_counts_adata_*), filtered and Stamp normalized edits (shortread_normed_edits_adata_*), filtered EPR adata (shortread_epr_adata_*)
Supplementary files format and content: MARINE output of raw edits: raw_edits_per_cell_per_gene_*.tsv

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