Description
Human Host Cellular Response to HCoV-229E Infection Proteomics (ACS-JM-DP2)
The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected immortalized human lung epithelial cells (A549) (MOI 5) nuclear extracts, immortalized human lung fibroblasts cells (MRC5) (MOI5) nuclear extracts, and primary human airway epithelial (HAE) (MOI 3) cells from lung tissue and processed for proteome analysis.
Dataset Description
Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files and supporting metadata materials. Experimental proteomics samples were prepared using Limited Proteolysis (LiP) methods for Label-free quantification (LFQ) and global proteomic evaluation. Sample data was acquired using a Q-Exactive HF-X mass spectrometer and 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. See corresponding primary data accessions below and Viral Experiment LiP Analysis source code supporting data transparency and reuse. Experimental transcriptomics samples were collected in parallel and processed for RNA sequencing (RNA-Seq) as summarized under ACS-DP1 (https://data.pnnl.gov/group/nodes/dataset/34069).
Data Download Reference Citations
- Anderson, Lindsey N, Sarkar, Snigdha, Mitchell, Hugh D, Feng, Song, Sims, Amy C, Melchior, John T, & Waters, Katrina M (2024). Human Host Cellular Response to HCoV-229E Infection Multi-Omics (ACS-JM-DP2). https://doi.org/10.25584/PPI/2475744
Accessible Digital Data Downloads
The repository contains the following folders and files:
- Experimental_Metadata: Folder with additional information to understand the experimental data
- Raw Counts: Folder with files containing the sequence counts across all samples
- Processed Data: Folder with files containing normalized sequence counts and differential expression statistics
- Legal: Additional files with legal information
Total Download Size: 8.1 MB, zipped
Linked Publications
Sarkar S, S Feng, HD Mitchell, MR Berger, T Zhang, IK Attah, CM Hutchinson-Bunch, VN Prozapas, K Engbrecht, S King, AC Sims and JT Melchior. 2025. "Human coronavirus-229E hijacks key host-cell RNA processing complexes for replication." Journal of Proteome Research, 24(10), 5026-5045. https://doi.org/10.1021/acs.jproteome.5c00400
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 MSV000096303. This is an updated version of the MSV000096268.
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
Creative Commons Attribution 4.0 International (CC BY 4.0)
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