Code for manuscript: A Dataset Examining Technical Factors on Fixed White Blood Cell Single-Cell RNA-Seq
Single-cell RNA sequencing (scRNA-seq) is a powerful technology that enables the measurement of gene expression in individual cells. Such precision provides insights into cellular heterogeneity that bulk methods might overlook. Fragile cells, in particular neutrophils, have posed significant challenges for scRNA-Seq due to their ex vivo fragility, high RNase content and consequent loss during cryopreservation.
The introduction of fixed scRNA-Seq methodology offers a promising solution to these challenges. We evaluated the performance of two different commercial platforms on red blood cell-depleted whole blood cells: 10x Genomics Flex v1 and Honeycomb HIVE v1. These data are publicly available from the Gene Expression Omnibus database (accession number GSExxx).
Further insights could be gained by correcting batch and technical effects introduced by storage time after fixation and cell numbers fixed. These data may be used to examine how reflective the transcriptome of neutrophils are of the native environment.
The dataset is available at GEO: GSE266615