Category
Description
Created 2024-12-20T23:47:47+00:00 by LN Anderson; Last updated 2025-03-14T00:10:28+00:00
S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3)
The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Sample data was acquired using a Illumina HiSeq sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis. Transcriptomic differential expression analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism.
Accessible Digital Data Downloads
Processed RNA-Seq datasets are openly accessible from the download button and contain secondary processed RNA sequencing results files and supporting metadata materials. Data download includes experimental metadata, normalized counts, and relevant computational source code information supporting data transparency and reuse.
Data Download Reference Citations
- Anderson, Lindsey N, Johnson, Zachary D, Waters, Katrina M, & Bohutskyi, Pavlo (2024). PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3). United States. 2024. PNNL DataHub (Web). DOI: 10.25584/2510500
- Gilliam, A., Sadler, N. C., Li, X., Garcia, M., Johnson, Z., Veličković, M., Kim, Y. M., Feng, S., Qian, W. J., Cheung, M. S., & Bohutskyi, P. (2025). Cyanobacterial circadian regulation enhances bioproduction under subjective nighttime through rewiring of carbon partitioning dynamics, redox balance orchestration, and cell cycle modulation. Microbial cell factories, 24(1), 56. doi: 10.1186/s12934-025-02665-5
Linked Primary Data
Primary RNA-Seq raw measurement data are openly accessible for download at the Gene Expression Omnibus (GEO) community repository under the study accession GSE288532 and have been linked to corresponding primary metabolomics experimental datasets.
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)