Monocyte gene expression data

Untreated primary monocytes were prepared from 174 healthy individuals of Northern European (British) ancestry recruited via the Oxford biobank. Poly-A RNA was paired-end 100bp sequenced in the Oxford Genome Centre using Illumina Hiseq-4000 machines (median = 47,735,438 reads per sample). Reads were aligned to CRGh38/hg38 using HISAT2 with default parameters. High mapping quality reads were selected based on MAPQ score using bamtools. Duplicate reads were marked and removed using picard (v 1.105). samtools was used to pass through the mapped reads and calculate statistics. Sample contamination and swaps were detected by comparing the imputed SNP-array genotypes with genotypes called from RNA-seq using verifyBamID. Genotyping was performed with Illumina HumanOmniExpress with coverage of 733,202 separate markers. Genotypes were pre-phased with SHAPEIT2, and missing genotypes were imputed with PBWT. Poly-A RNA was paired-end sequenced in the Oxford Genome Centre using Illumina Hiseq-4000 machines. The data consists of gene level count data from mapped transcriptomes prepared with HT-seq.