lievens {lievens}

qPCR data sets by Lievens et al. (2012)

Description

One single tabular tidy data set in long format, encompassing three data sets of five-point, five-fold dilution series: (i) without any inhibitor, (ii) with isopropanol inhibition and (iii) with tannic acid inhibition. The target amplicon consisted of a sequence within the soybean Lectin endogene. Please read the Methods section of Lievens et al. (2012) for more experimental details.

Each data set consists of a five-point, five-fold dilution series spanning an amplicon copy number range from 100,000 down to 160. Each concentration is replicated 18 times. Each reaction has been amplified through 60 cycles.

Dilution series

dplyr::filter(lievens, inhibitor == "none")
#> # A tibble: 5,400 x 13
#>    plate well  target dye   inhibitor inhibitor_conc sample sample_type
#>    <fct> <fct> <fct>  <fct> <fct>              <dbl> <fct>  <fct>      
#>  1 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  2 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  3 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  4 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  5 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  6 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  7 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  8 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#>  9 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#> 10 soy   <NA>  Le1    SYBR  none                   0 S1     std        
#> # i 5,390 more rows
#> # i 5 more variables: replicate <fct>, copies <int>, dilution <int>,
#> #   cycle <int>, fluor <dbl>

Isopropanol inhibition

A series of reactions subjected to inhibition by isopropanol with concentrations: 2.5, 0.5, 0.1, 0.02, and 0.004 % (v/v). Because samples have been co-diluted, the initial copy numbers of the target amplicon also follow the same five-fold progression in tandem: 100,000, 20,000, 4,000, 800 and 160 copies.

dplyr::filter(lievens, inhibitor == "isopropanol")
#> # A tibble: 5,400 x 13
#>    plate          well  target dye   inhibitor inhibitor_conc sample sample_type
#>    <fct>          <fct> <fct>  <fct> <fct>              <dbl> <fct>  <fct>      
#>  1 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  2 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  3 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  4 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  5 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  6 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  7 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  8 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#>  9 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#> 10 soy+isopropan~ <NA>  Le1    SYBR  isopropa~            2.5 S1     std        
#> # i 5,390 more rows
#> # i 5 more variables: replicate <fct>, copies <int>, dilution <int>,
#> #   cycle <int>, fluor <dbl>

Tannic acid inhibition

A series of reactions subjected to inhibition by tannic acid with concentrations: 0.2, 0.04, 0.008, 0.0016 and 0.0032 ul/mL. Because samples have been co-diluted, the initial copy numbers of the target amplicon also follow the same five-fold progression in tandem: 100,000, 20,000, 4,000, 800 and 160.

dplyr::filter(lievens, inhibitor == "tannic acid")
#> # A tibble: 5,400 x 13
#>    plate          well  target dye   inhibitor inhibitor_conc sample sample_type
#>    <fct>          <fct> <fct>  <fct> <fct>              <dbl> <fct>  <fct>      
#>  1 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  2 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  3 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  4 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  5 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  6 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  7 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  8 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#>  9 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#> 10 soy+tannic ac~ <NA>  Le1    SYBR  tannic a~            0.2 S1     std        
#> # i 5,390 more rows
#> # i 5 more variables: replicate <fct>, copies <int>, dilution <int>,
#> #   cycle <int>, fluor <dbl>

Format

A tibble providing amplification curve data in long format. Each row is for an amplification curve point.

plate

Plate identifier. There is one identifier for each of the four data sets.

well

Well identifier, i.e. the position within a PCR plate. This information was not available from the original publication, thus all values are NA.

target

Target identifier. In all data sets the target is an amplicon consisting of soybean Lectin endogene "Le1".

dye

Type of fluorescence dye, in this data set it is always SYBR Green I master mix (Roche) ("SYBR").

inhibitor

Name of the molecule used as PCR inhibitor. In the case of the dilution series the value is "none".

inhibitor_conc

Inhibitor concentration. Units are % (v/v) for isopropanol, and ug/mL for tannic acid.

sample

Name of the biological sample. Samples have a simple consecutive identifier: S1, S2, ..., S5.

sample_type

Sample type. All reactions are standard curves, i.e. "std".

replicate

Replicate identifier.

copies

Standard copy number of the amplicon.

dilution

Dilution factor. Higher number means greater dilution, e.g. 5 means a 1:5 (five-fold) dilution relative to most concentrated standard.

cycle

PCR cycle.

fluor

Raw fluorescence values.

Source

doi:10.1093/nar/gkr775

Examples

lievens