Summary of the genome and transcriptome structures of E. coli BL21(DE3)

Range Table - link
Organism Bacteria Escherichia coli
Reference Kim S et al., Genomic and transcriptomic landscape of Escherichia coli BL21(DE3). Nucleic Acids Res. 2017 May 19 45(9):5285-5293. doi: 10.1093/nar/gkx228 p.5288 table 1PubMed ID28379538
Method Abstract: "Here [investigators] present the most current genome annotation of E. coli BL21(DE3) based on the transcriptome structure of the strain that was determined for the first time. The genome was annotated using multiple automated pipelines and compared to the current genome annotation of the closely related strain, E. coli K-12. High-resolution tiling array data of E. coli BL21(DE3) from several different stages of cell growth in rich and minimal media were analyzed to characterize the transcriptome structure and to provide supporting evidence for open reading frames."
Comments P.5286 left column bottom paragraph: "The MR medium (pH 7.0) contained 10 g/l glucose, 4 g/l (NH4)2HPO4, 6.67 g/l KH2 PO4, 0.8 g/l citric acid, 0.8 g/l MgSO4·7H2O and 5 ml/l trace metal solution (ref 19)." P.5288 left column 3rd paragraph: "Determination of the transcriptome structure-Using statistical analysis of the expression of probes complementary to genomic sites, the TUs [transcription units] for the majority of genes and ncRNAs in E. coli BL21(DE3) were determined (Table 1). For the analysis, five samples were taken from batch fermentations in complex LB medium (two exponential phases and one stationary phase) and minimal MR medium (one exponential phase and one stationary phase) (Supplementary Figure S2). Samples representing the key phases of the E. coli growth curve were selected. For example, the two samples taken during the exponential phase in LB medium (cell densities of 0.24 and 1.54 in OD600) are distinct in terms of their carbon source usage (ref 26)." TIS=translation initiation sites
Entered by Uri M
ID 114111