GSE301408 eCLIP Data Processing

eCLIP geo_data_processing 3 steps

Publication

RNA triggers chronic stress during neuronal aging.

bioRxiv : the preprint server for biology (2025) — PMID 40799579

Dataset

GSE301408

Mitochondrial double-stranded RNA triggers chronic stress in aged neurons

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

    For RNA-seq and dsRNA-seq experiments, the fastq files were analyzed using NF-Core.

    Nextflow
  2. 2

    For eCLIP-seq experiments, Skipper was used to analyze the sequencing files.

    Skipper
  3. 3

    For Riboseq, the xtail package was used to determine footprinting reads and calculate translation efficiency.

Raw Source Text 
For RNA-seq and dsRNA-seq experiments, the fastq files were analyzed using NF-Core. For eCLIP-seq experiments, Skipper was used to analyze the sequencing files. For Riboseq, the xtail package was used to determine footprinting reads and calculate translation efficiency.
Assembly: hg38
Supplementary files format and content: For RNA-seq and dsRNA-seq experiments, the .tsv or .csv file contains the gene counts for each sample as analyzed by NF-Core. For eCLIP-seq, the .tsv file contains the reproducible enriched windows identified by Skipper.
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