Mar 04, 2025

Public workspaceSingle-cell RNA-sequencing data processing

DOI
dx.doi.org/10.17504/protocols.io.36wgqdxwxvk5/v1
  • 1Northwestern University
Luisa Cusick
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DOI: dx.doi.org/10.17504/protocols.io.36wgqdxwxvk5/v1
Protocol Citation: Alexander Misharin 2025. Single-cell RNA-sequencing data processing. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqdxwxvk5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 04, 2025
Last Modified: March 04, 2025
Protocol Integer ID: 123790
Abstract
This protocol describes the steps used for processing our single cell RNA-sequencing data set.
Single-cell RNA-sequencing data processing
Single-cell RNA-sequencing data processing
Align reads (.bcl files) to the mouse reference genome (mm10)
Analyze data using Seurat’s standard workflow
Include only cells containing between 200 and 5000 genes and less than 20% mitochondrial RNA
Using default parameters of Seurat, log normalize data across cells and identify the 1500 most highly variable genes
Identify cell types by clustering the data using the first 13 principal components and a clustering resolution of 0.3