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Differential expression analysis of Lactiplantibacillus plantarum transcriptome during growth in EET-conducive conditions

Harvard Dataverse (Africa Rice Center, Bioversity International, CCAFS, CIAT, IFPRI, IRRI and WorldFish)

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Title Differential expression analysis of Lactiplantibacillus plantarum transcriptome during growth in EET-conducive conditions
 
Identifier https://doi.org/10.7910/DVN/SAQ5AT
 
Creator Stevens, Eric
 
Publisher Harvard Dataverse
 
Description DESeq2 analysis of L. plantarum transcriptome data using the Wald test in the R-studio shiny app DEBrowser (ver 1.14.2) was used to quantify differential gene expression based on culture conditions stimulating extracellular electron transfer (EET) (methods described here: https://doi.org/10.1101/2021.05.26.445846).

The significance cutoff for differential expression was set to a False-discovery-rate (FDR)-adjusted p-value < 0.05 and a Log2 (fold-change) > 0.5. Clusters of Orthologous Groups (COGs) were also assigned to genes based the eggNOG (ver. 5.0) database.

L. plantarum raw RNA-seq data are available in the NCBI Sequence Read Archive
(SRA) under BioProject accession no. PRJNA717240.
 
Subject Medicine, Health and Life Sciences
Extracellular electron transfer, lactic acid bacteria, quinones, ferric iron, oxidation-reduction, fermentation
 
Contributor Stevens, Eric