Example data set from Wittmann et al. (2014)

Description

This OPMS object contains the measurements used in the study by Wittmann et al. (2014). Metadata have been added to fully describe the conducted OmniLog(R) phenotype microarray (PM) experiments. The plate type is ‘Generation III’, but the running mode was as for the usual PM plates.

Format

OPMS object with the dimensions 41 x 382 x 96, i.e. 41 plates with about 382 time points and 96 wells per plate. (38 plates have 384 time points; three plates have 382 time points).

Details

All plates also contain aggregated values generated via do_aggr using the "opm-fast" method without bootstrapping.

For 62 strains of the opportunistic pathogenic bacterium Achromobacter xylosoxidans PM experiments were conducted with Generation-III plates using inoculation fluid IF-A. All plates were incubated in the left plate sliding carriage of the OmniLog(R) reader.

In addition to ‘genus’, ‘species’ and ‘strain’, the following metadata entries are contained in the wittmann_et_al OPMS object:

country

Lists the geographical origin.

city

Lists the city where the strain was isolated.

year

Lists the year in which the strain was isolated.

isolated_from

Lists the scientist who isolated the strain.

source

Distinguishes between environmental or clinical origin, if known.

habitat

Lists details on the habitat, if known.

replicate

Lists the number of experimental plate replicates per strain. 2-3 replicates per strain were performed.

MLSTcluster

Name of phylogenetic cluster to which a strain is affiliated. See reference Wittmann et al (2014).

References

Bochner, B.R., Savageau, M.A. 1977. Generalized indicator plate for genetic, metabolic, and taxonomic studies with microorganisms. Applied and Environmental Microbiology 33, 434–444.

Wittmann, J., Dreiseikelmann, B., Rohde, C., Rohde, M., Sikorski, J. 2014 Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitious and opportunistic pathogen Achromobacter xylosoxidans. PLoS ONE 9, e86935.

Examples

data(wittmann_et_al)
plate_type(wittmann_et_al) # should indicate generation-III plates

## [1] "Gen III"

(d <- dim(wittmann_et_al))

## [1]  41 382  96

(ha <- has_aggr(wittmann_et_al))

##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [29] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

stopifnot(d == c(41, 382, 96), ha)

## Brief overview of the metadata
head(to_metadata(wittmann_et_al))

##       strain
## 1 CCUG 41513
## 2 CCUG 45179
## 3 CCUG 41513
## 4 CCUG 45179
## 5 CCUG 47074
## 6 CCUG 59527
##                                                                                   File
## 1                          ./41513_41513_41513_41513_1_28_PMX_357_6#8#2012_B_19A_2.csv
## 2                          ./45179_45179_45179_45179_1_28_PMX_357_6#8#2012_B_20A_3.csv
## 3 ./41513second_41513second_41513second_41513second_1_28_PMX_357_6#12#2012_A_19A_2.csv
## 4 ./45179second_45179second_45179second_45179second_1_28_PMX_357_6#12#2012_A_18A_1.csv
## 5                       ./Johannes_47074_24.8.2012__1_28_PMX_357_8#24#2012_D_11A_9.csv
## 6                       ./Johannes_59527_24.8.2012__1_28_PMX_357_8#24#2012_D_ 3A_1.csv
##        city country         genus habitat   isolated_from replicate
## 1      Wien Austria Achromobacter  sputum       H. Masoud         1
## 2      Wien Austria Achromobacter  sputum A. Makristathis         1
## 3      Wien Austria Achromobacter  sputum       H. Masoud         2
## 4      Wien Austria Achromobacter  sputum A. Makristathis         2
## 5 Goeteborg  Sweden Achromobacter  sputum         unknown         2
## 6 Goeteborg  Sweden Achromobacter  sputum         unknown         2
##        species  source year Parameter MLSTcluster
## 1 xylosoxidans medical 1998       AUC         Ax1
## 2 xylosoxidans medical 2001       AUC         Ax1
## 3 xylosoxidans medical 1998       AUC         Ax1
## 4 xylosoxidans medical 2001       AUC         Ax1
## 5 xylosoxidans medical 2002       AUC         Ax2
## 6 xylosoxidans medical 2010       AUC         Ax2