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Table 2 Overview of processing of cells and RNA for RNA-seq data sets analyzed in this study

From: A map of gene expression in neutrophil-like cell lines

Data set Neutrophil isolation RNA enrichment Sequencing method Read mapping and analysis
this study N/A polyA enrichment Illimuna HiSeq, 1 × 75 bp All data sets were reanalyzed in this study with uniform read mapping and analysis methods. See Methods for details
Cusanovich et al N/A polyA enrichment Illumina NextSeq, 1 × 75 bp
Jiang et al density gradient sedimentation (Polymorphprep) polyA enrichment Illumina HiSeq, 2 × 75 bp paired end
Thomas et al. (samples 1 and 3) negative selection polyA enrichment Illimuna HiSeq, 1 × 50 bp
Thomas et al. (samples 2 and 4) density gradient sedimentation (Polymorphprep) polyA enrichment Illimuna HiSeq, 1 × 50 bp
Wright et al density gradient sedimentation (Polymorphprep) polyA enrichment Illimuna HiSeq, 1 × 50 bp
Taylor et al density gradient sedimentation (Percoll) polyA enrichment Illimuna HiSeq, 1 × 50 bp
Coffelt et al positive selection (Ly6G+) polyA enrichment Illimuna HiSeq, 1 × 50 bp
  1. The methods of neutrophil isolation (for studies involving primary neutrophils), mRNA enrichment, and sequencing are indicated in the table. All data sets were re-analyzed with a uniform computational pipeline (see Methods for details) to avoid potential systematic differences due to analysis methods