Description
Last updated on 2024-10-01T21:34:23+00:00 by LN Anderson
Human Cell & Tissue Response to HCoV-229E Infection Proteomics (ACS-JM-DP2)
The purpose of this experiment was to evaluate the human host response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected (MOI 5) immortalized human lung epithelial cells (A549), immortalized human lung fibroblasts cells (MRC5), and primary human lung tissue and processed for proteome and transcriptome expression analysis.
Accessible Digital Data Downloads*
Processed datasets are openly accessible from the download button and contain secondary processed proteomic and transcriptomic results files and supporting metadata materials. Limited Proteolysis (LiP), Tandem Mass Tag 16-Plex (TMT16), and global proteomic data was acquired using a Q-Exactive HF-X mass spectrometer and data was processed and compiled using MaxQuant software (v.1.6.17.0). Processed proteomic data downloads include a sample naming key, processed MaxQuant results/parameters, and protein annotated relative abundance files. Processed RNA sequencing (RNA-Seq) results files and supporting metadata materials include a sample naming key, infection titer metadata, normalized counts, and relevant computational source code information. See corresponding primary data accessions below supporting data transparency and reuse.
*Corresponding primary publication pending.
Linked Primary Data
Primary liquid chromatography-mass spectrometry (LC-MS) raw measurement data are openly accessible for download at the Mass Spectrometry Interactive Virtual Environment (MassIVE) community repository under the accession MSV0000##### and can be formally cited using the MassIVE registered digital object identifier at https://doi.org/10.25345/XXXXXXXXX. Primary RNA-Seq raw measurement data are openly accessible for download at the Gene Expression Omnibus (GEO) community repository under the accession [GSE#####], corresponding to BioProject [PRJNA######], and have been linked to corresponding Multi-omics primary experimental datasets where applicable.
Funding Acknowledgments
The research data described here was funded in whole or in part by the Predictive Phenomics Initiative (PPI) at Pacific Northwest National Laboratory (PNNL). This work was conducted under the Laboratory Directed Research and Development Program at PNNL. A portion of this research was performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy (DOE) Office of Science located at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the DOE under Contract No. DE-AC05-76RL01830.
Citation Policy
In efforts to enable discovery, reproducibility, and reuse of PPI-funded project dataset citations in accordance with best practices (as outlined by the FORCE11 Data Citation Principles), we ask that all reuse of project data and metadata download materials acknowledge all primary and secondary dataset citations and corresponding journal articles where applicable.
Data Licensing
CC BY 4.0 (dataset DOI downloads), CC0 1.0 (PNNL DataHub policy default)
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