GSE276986 Processing Pipeline

Publication

Nature neuroscience (2025) — PMID 40456907

Dataset

Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNA-seq]

1. 1

   RNA-Seq data was processed using the NF-Core architecture, which compiles several RNA-seq processing steps into a single executable command

   Nextflow vLatest stable version (Inferred with models/gemini-2.5-flash) GitHub

   $ Bash example

   # Install Nextflow (if not already installed)
   # For example, using Conda:
   # conda install -c bioconda -c conda-forge nextflow
   # Or via curl:
   # curl -s https://get.nextflow.io | bash
   # mv nextflow /usr/local/bin/
   
   # Install nf-core (if not already installed)
   # pip install nf-core
   
   # Create a dummy samplesheet.csv (replace with your actual data)
   # This is a minimal example. Refer to nf-core/rnaseq documentation for full samplesheet format.
   cat <<EOF > samplesheet.csv
   sample,fastq_1,fastq_2,group,replicate
   control_rep1,data/control_rep1_R1.fastq.gz,data/control_rep1_R2.fastq.gz,control,1
   treated_rep1,data/treated_rep1_R1.fastq.gz,data/treated_rep1_R2.fastq.gz,treated,1
   EOF
   
   # Ensure you have a Nextflow compatible container engine (e.g., Docker, Singularity) installed and running.
   # For a full list of available genomes, check: https://nf-co.re/rnaseq/usage#--genome
   # For custom genomes, provide --fasta and --gtf files.
   # Using a recent stable release (e.g., 3.14.0) as an example for the pipeline version.
   nextflow run nf-core/rnaseq \
       -profile docker \
       --input samplesheet.csv \
       --genome GRCh38 \
       --outdir results \
       -r 3.14.0

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