Puetz at 14:51, 25 March 2011

2011-03-25T14:51:36Z

127.0.0.1: making into a CategoryPage

2011-03-23T01:38:12Z

making into a CategoryPage

New page

==Phenotypes==
*Gene essentiality
*Multiple drug resistance
*Conditionally essential genes<ref name='PMID:21185072'/>

==Ontology Terms==
* table form
* OMPxxxxxxxx: increased tolerance to antibiotic
* GOxxxxxxx: persistance
* MOOxxxxxxx: small colonies

==Material and Methods==
===Strain Details===
Libraries obtained elsewhere.

===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<ref>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.</ref>
**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==
*[[PMID:21185072]]

==References==
<references/>

[[Category:Methods]][[Category:High-throughput Method]]

@@ Line 2: / Line 2: @@
 *Gene essentiality
 *Multiple drug resistance
 *Conditionally essential genes<ref name='PMID:21185072'/>
@@ Line 12: / Line 13: @@
 ==Material and Methods==
 ===Strain Details===
-Libraries obtained elsewhere.
+Keio single- gene deletion library<ref name='PMID: 16738554'/>
 ===Equipment and Reagents===

Category:Phenomic Profiling - Revision history

Puetz at 14:51, 25 March 2011

127.0.0.1: making into a CategoryPage