GSE314059 scRNA-seq Data Processing

scRNA-seq geo_data_processing 4 steps

Publication

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

Nature (2026) — PMID 41708856

Dataset

GSE314059

Single-cell and isoform-specific translational profiling of the mouse brain with long-read sequencing [scRNA-Seq, longread]

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. 1

    Aligned with pbmm2 to mm10 + tdTomato reference

  2. 2

    CPM and log normalization for reads.

  3. 3

    Raw edits were normalized by Stamp expression via regression.

  4. 4

    EditsC = total Edited Cs in transcript / (total Cs in transcript annotation * total reads) and Cell assignments are based on short-read scRNA-seq from same samples which were filtered for doublets and low-quality cells.

    scRNA-seq

Tools Used

scRNA-seq
Raw Source Text 
Aligned with pbmm2 to mm10 + tdTomato reference
CPM and log normalization for reads. Raw edits were normalized by Stamp expression via regression. EditsC = total Edited Cs in transcript / (total Cs in transcript annotation * total reads) and Cell assignments are based on short-read scRNA-seq from same samples which were filtered for doublets and low-quality cells.
Assembly: mm10
Supplementary files format and content: Read count matrices: gene-level and transcript-level read counts in TSV format (longread_read_count_matrix_*_gene_id.tsv, longread_read_count_matrix_*_gene_name.tsv, longread_read_count_matrix_*_transcript_id.tsv)
Supplementary files format and content: Edit count matrices: gene-level and transcript-level edit counts in TSV format (longread_number_edits_matrix_*_gene_id.tsv, longread_number_edits_matrix_*_gene_name.tsv, longread_number_edits_matrix_*_transcript_id.tsv)
Supplementary files format and content: AnnData objects: normed and filtered counts by transcript (longread_normed_counts_transcript_adata_*.h5ad), filtered and STAMP-normalized edits by transcript (longread_normed_edits_adata_*.h5ad), and filtered edit-to-coverage ratio by transcript (longread_EditsC_transcript_adata_*.h5ad)
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