The ADP1 single-gene deletion collection is a published complete collection of single-gene deletion mutants of acinetobacter-baylyi-adp1, described in de Berardinis V et al. (2008), “A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1,” Molecular Systems Biology 4:174 (PMID: 18319726). 1
Known aliases: “de Berardinis et al. (2008) deletion collection”, “ADP1 deletion mutant collection”, “ADP1 knockout collection”. External identifier: PMID 18319726. 1
Contents and measurements
As used in the deletion-phenotype project, the complete growth matrix covers 2,034 genes with growth ratio measurements on all 8 carbon sources. Growth ratios are mutant/wild-type: values < 1.0 indicate growth defects, while values > 1.0 indicate no defect or a slight apparent growth advantage that the source attributes to experimental normalization rather than necessarily a true advantage. Conditions span a 3.3-fold range in mean growth ratio, from 0.41 for urea to 1.36 for quinate. 1
The triple-essentiality project’s original analysis used the collection’s deletion-mutant growth rates on 8 carbon sources, listed there as glucose, acetate, asparagine, butanediol, glucarate, lactate, pyruvate and succinate, taken from de Berardinis et al. (2008). 2
Tensions
The two projects both describe the collection’s growth data as covering 8 carbon sources, but the condition lists they report differ: the deletion-phenotype project names urea and quinate as conditions in its matrix, while the triple-essentiality project’s enumerated list of 8 does not include either. The supplied evidence does not establish whether the projects used different subsets of the published conditions or different condition labels; this is recorded here without resolution. 1,2
Related pages
- ADP1 Deletion Collection Phenotype Analysis — condition-level analysis of the deletion growth matrix 1
- Triple Essentiality Concordance Analysis for *Acinetobacter baylyi* ADP1 — uses the deletion growth rates as one line of essentiality evidence 2
- gene-essentiality — broader context for deletion-based essentiality and growth-defect calls 2