DiB_fixed_WBC_scRNAseq

Code for manuscript: A Dataset Examining Technical Factors on Fixed White Blood Cell Single-Cell RNA-Seq

Abstract

This repository provides pre-processing scripts and basic analyses from the associated manuscript. The goal is to evaluate single-cell RNA sequencing (scRNA-seq) technology platforms on fragile immune cells, focusing on granulocytes. These cell types typically produce lower quality data compared to lymphocytes due to their high RNase content, fragility, and susceptibility to data loss during cryopreservation.

The associated dataset contains healthy RBC-depleted blood from humans processed with two technology platforms:

1. Honeycomb HIVE v1
2. 10x Genomics Flex v1

• The scripts/ directory contains pre-processing scripts that begin with FASTQ inputs and generate outputs compatible with popular packages such as Scanpy, Seurat, and the Bioconductor ecosystem.

• The metadata/ directory contains sample information and sample sheets required for the pre-processing scripts.

• The notebooks/ directory contains R code to load the outputs from the pre-processing scripts and generate a SingleCellExperiment object with associated metadata. It also includes notebooks for basic data visualization.

It is recommended to start with the SingleCellExperiment object. You can retrieve specific metadata and data using the following functions:

• Cell metadata: colData(sce)
• Gene metadata: rowData(sce)
• Cell-by-gene count matrix: counts(sce)

These functions also allow conversion into a Seurat object if preferred.

Data Availability

The dataset is available on GEO: GSE266615