Human Liver Epithelium Response to HCoV-229E Infection Epigenomics (ACS-DP4)

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Created on 2024-10-15T19:55:00+00:00 by LN Anderson; Last updated 2024-11-13T15:01:44+00:00 and is pending public release.

Human Liver Epithelium Response to HCoV-229E Infection Epigenomics (ACS-DP4)

The purpose of this experiment was to evaluate how wild-type Human coronavirus strain 229E (HCoV-229E) infection alters chromatin accessibility in infected cells only. Sample data was obtained for mock and infected (active vs. UV-inactivated) immortalized human liver cells (HuH-7) and collected 24 hrs. post infection. Samples were processed using assay for transposase-accessible chromatin using high-throughput sequencing (ATAC-seq) methods for reported bar coded libraries. Sample data was acquired using a Illumina HiSeq 2500 sequencer system and further processed for ATAC-Seq expression analysis.

Accessible Digital Data Downloads*

Processed ATAC-Seq datasets are openly accessible from the download button and contain secondary processed RNA-seq results files and supporting metadata materials. Data download includes a sample naming key, infection titer metadata, normalized counts, and relevant computational source code information supporting data transparency and reuse.

*Corresponding primary publication pending.

Linked Primary Data

Primary RNA-Seq raw measurement data are openly accessible for download at the Gene Expression Omnibus (GEO) community repository under the accession GSE280627 and have been linked to corresponding 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. 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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Amy Sims, PhD is a Biomedical Scientist in the Chemical and Biological Signatures Division of the National Security Directorate at the Pacific Northwest National Laboratory (PNNL) in Richland, WA. She earned her Ph.D. from Vanderbilt University Medical Center and worked with Ralph Baric, PhD at the...

Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...