Category:Phenomic Profiling
From OMPwiki
Contents
Phenotypes
- Gene essentiality
- Multiple drug resistance
- Growth defect
- Conditionally essential genes[1]
Ontology Terms
- table form
- OMPxxxxxxxx: increased tolerance to antibiotic
- GOxxxxxxx: persistance
- MOOxxxxxxx: small colonies
Material and Methods
Strain Details
Keio single- gene deletion library[2]
Equipment and Reagents
- Singer Rotor robot
- Canon G10 digital camera
- High density LB agar plates (1536 colonies/plate)
Growth conditions
- Wild-type and mutant strains were grown overnight to stationary phase in LB Lennox broth
- Diluted into fresh drug-containing LB broth (0.1μg/ml TMP and/or 50 μg/ml Sulfamethizole) at 1:1000 v/v.
- Cultures were then grown aerobically in 150 ml flasks at 37°C for 24 hours
Screen Conditions
- Chemical/stress was mixed into LB agar (except where indicated)
- Plates were allowed to dry for two days, and then pinned with the collection.
- For the majority of conditions, plates were removed from the incubator following 14-16 hrs growth at 37°C.
- Plates were imaged and colony size data was recorded
Data Analysis
- Condition-Gene score- generated using colony size data
- Quality control measures
- the interquartile range (IQR) of the distribution of normalized colony sizes for each screen
- the correlation between replicates of the same screen.
Phenotype Analysis
- estimate the mean and IQR of Condition-Gene scores and re-scaled the data to a standard normal distribution (IQR=1.35).
- a fraction of scores, p, will be less than the pth quantile of the normal distribution. If a fraction of scores, x (x>p), is found to be less than the pth quantile, then the false discovery rate (FDR) associated with the pth quantile would be p/x[3]
- classify all scores with FDR 5% or less as phenotypes
- Responsive genes were defined as strains for which at least one phenotype was identified.
- Conditionally-essential genes were identified using a combination of the probability scores and raw colony sizes.
- defined as those in which the probability score was 1 (definite outlier), and raw colony size was less than 60 pixels.
Links
References
- ↑ Nichols, RJ et al. (2011) Phenotypic landscape of a bacterial cell. Cell 144 143-56 PubMed OMPwiki page
- ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed OMPwiki page
- ↑ Efron, B., Tibshirani, R., Storey, J.D., and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment. J. Am. Stat. Assoc. 96, 1151–1160.
Pages in category "Phenomic Profiling"
This category contains only the following page.
