PXD035035

PXD035035 is an original dataset announced via ProteomeXchange.

Title	A synthetic control genome provides a universal molecular standard to measure DNA, mRNA and protein expression
Description	The phi X 174 bacteriophage was first sequenced in 1977, and has since become the most widely used standard in molecular biology and next-generation sequencing. However, with the advent of affordable DNA synthesis and de novo gene design, we considered whether we could engineer a synthetic genome, termed SynX, specifically tailored for use as a universal molecular standard. The SynX genome encodes 21 synthetic genes that can be in vitro transcribed to generate matched mRNA controls, and in vitro translated to generate matched protein controls. This enables the use of SynX as a matched control to compare across genomic, transcriptomic and proteomic experiments. The synthetic genes provide qualitative controls that measure sequencing accuracy across k-mers, GC-rich and repeat sequences, as well as act as quantitative controls that measure sensitivity and quantitative accuracy. We show how the SynX genome can measure DNA sequencing, evaluate gene expression in RNA sequencing experiments, or quantify proteins in mass spectrometry. Unlike previous spike-in controls, the SynX DNA, RNA and protein controls can be independently and sustainably prepared by recipient laboratories using common molecular biology techniques, and widely shared as a universal molecular standard.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:34:23.181.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Timothy McCubbin
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-30 07:23:54	ID requested
1	2024-03-21 20:14:59	announced
⏵ 2	2024-10-22 06:34:23	announced	2024-10-22: Updated project metadata.

10.1038/S41467-024-46456-9;

submitter keyword: synthetic peptide, protein control,DIA

Tim Mercer
contact affiliation	Australian Institute for Bioengineering and Nanotechnology, The University of Queensland
contact email	t.mercer@uq.edu.au
lab head
Timothy McCubbin
contact affiliation	University of Queensland
contact email	t.mccubbin@uq.edu.au
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/03/PXD035035

PRIDE project URI

• PRIDE
  1. PXD035035
     1. Label: PRIDE project
     2. Name: A synthetic control genome provides a universal molecular standard to measure DNA, mRNA and protein expression