.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 sequenc..., Illumina DNA sequencing pREF.
We first sequenced neat preparations of pREF. Four replicate libraries were prepared using the KAPA HyperPlus PCR-based kit (Illumina) according to the manufacturer’s instructions. Prepared libraries were quantified on a Qubit (Invitrogen) and verified on the Agilent 2100 Bioanalyzer with the Agilent High Sensitivity DNA Kit (Agilent Technologies). The libraries were then sequenced on a NovaSeq (Illumina). The sequencing was performed at the Kinghorn Centre for Clinical Genomics, Darlinghurst, New South Wales.
ONT DNA sequencing pREF.
pREF was linearised using restriction enzymes, and four replicate libraries were prepared for nanopore sequencing, with the LSK108 kit (1D ligation) according to the manufacturer’s instructions. The resulting libraries were sequenced on a PromethION instrument, at the Kinghorn Centre for Clinical Genomics, Darlinghurst, New South Wales. Base-calling was achieved using ONT Albacore Sequencing Pipeline Software (version 1.2.6).
..., , This README file was generated on 2024-01-25 by Helen Gunter

GENERAL INFORMATION

1\. Title of Dataset: bam alignment files of Illumina and ONT sequencing
of pREF plasmid

2\. Author information

A. Principle Investigator Contact Information Name: Timothy Mercer
Institution: Australian Institute for Bioengineering and Nanotechnology,
The University of Queensland Address: Brisbane, Qld, Australia Email:

B. Co-investigator Name: Helen Gunter Institution: Australian Institute
for Bioengineering and Nanotechnology, The University of Queensland
Address: Brisbane, Qld, Australia Email:

3\. Date of data collection: 2021

4\. Geographic location of data collection: Sydney, Australia

5\. Information about funding sources that supported the collection of
the data: NHMRC grants APP1108254, APP1114016, APP1136067, UNSW Tuition
Fee Scholarship and Cancer Institute NSW Early Career Fellowship
2018/ECF013.

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SHARING/ACCESS INFORMATION

1\. Licenses/restrictions placed on the data: CC0 1.0 U...