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 |