GSE220461 Processing Pipeline

Publication

Neuron (2024) — PMID 38697111

Dataset

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (scRNA-seq)

1. 1

   Cell Ranger (version 5.0.1, reference genome: mm10-2020-A<based on Gencode vM23, and filtering out pseudogenes, TEC, miRNA etc. a total of 32285 genes) was used to perform alignment, filtering, barcode counting, and UMI counting for single cell RNA-Seq.

   Cell Ranger v5.0.1

   $ Bash example

   # Install Cell Ranger (example, actual installation might vary)
   # Download Cell Ranger 5.0.1 from 10x Genomics website
   # wget https://cf.10xgenomics.com/releases/cell-ranger/cellranger-5.0.1.tar.gz
   # tar -xzf cellranger-5.0.1.tar.gz
   # export PATH=/path/to/cellranger-5.0.1:$PATH
   
   # Define paths for custom reference and input FASTQ files
   # The description specifies a custom reference:
   # "mm10-2020-A<based on Gencode vM23, and filtering out pseudogenes, TEC, miRNA etc. a total of 32285 genes)"
   # This would be a directory created by 'cellranger mkref' prior to running 'count'.
   CUSTOM_TRANSCRIPTOME_PATH="/path/to/your/mm10-2020-A_custom_transcriptome_ref"
   
   # Placeholder for the directory containing FASTQ files
   # FASTQ files should be named according to 10x Genomics conventions (e.g., SampleName_S1_L001_R1_001.fastq.gz)
   FASTQ_INPUT_DIR="/path/to/your/fastq_files"
   
   # Placeholder for the sample identifier
   SAMPLE_ID="your_single_cell_sample"
   
   # Execute Cell Ranger count for alignment, filtering, barcode counting, and UMI counting
   cellranger count \
       --id="${SAMPLE_ID}_cellranger_output" \
       --transcriptome="${CUSTOM_TRANSCRIPTOME_PATH}" \
       --fastqs="${FASTQ_INPUT_DIR}" \
       --sample="${SAMPLE_ID}" \
       --expect-cells=3000 # Common parameter, adjust based on expected cell recovery

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