.bam alignment files of Illumina and ONT sequencing of pREF plasmid

The expression of genes encompasses their transcription into mRNA followed
by translation into protein. In recent years, next-generation sequencing
and mass spectrometry methods have profiled DNA, RNA and protein abundance
in cells. However, there are currently no reference standards that are
compatible across these genomic, transcriptomic and proteomic methods, and
provide an integrated measure of gene expression. Here, we use synthetic
biology principles to engineer a multi-omics control, termed pREF, that
can act as a universal molecular standard for next-generation sequencing
and mass spectrometry methods. The pREF sequence encodes 21 synthetic
genes that can be in vitro transcribed into spike-in mRNA controls, and in
vitro translated to generate matched protein controls. The synthetic genes
provide qualitative controls that can measure sensitivity and quantitative
accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF
in metagenome DNA sequencing and RNA sequencing experiments and evaluate
the quantification of proteins using mass spectrometry. Unlike previous
spike-in controls, pREF can be independently propagated and the synthetic
mRNA and protein controls can be sustainably prepared by recipient
laboratories using common molecular biology techniques. Together, this
provides the first universal synthetic standard able to integrate genomic,
transcriptomic and proteomic methods.