| Title: | Real-Time PCR Data Sets by Lievens et al. (2012) |
| Version: | 0.0.1 |
| Description: | Real-time quantitative polymerase chain reaction (qPCR) data sets by Lievens et al. (2012) <doi:10.1093/nar/gkr775>. Provides one single tabular tidy data set in long format, encompassing three dilution series, targeted against the soybean Lectin endogene. Each dilution series was assayed in one of the following PCR-efficiency-modifying conditions: no PCR inhibition, inhibition by isopropanol and inhibition by tannic acid. The inhibitors were co-diluted along with the dilution series. The co-dilution series consists of a five-point, five-fold serial dilution. For each concentration there are 18 replicates. Each amplification curve is 60 cycles long. Original raw data file is available at the Supplementary Data section at Nucleic Acids Research Online <doi:10.1093/nar/gkr775>. |
| License: | CC BY 4.0 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.1 |
| Imports: | tibble |
| Depends: | R (≥ 2.10) |
| LazyData: | true |
| URL: | https://rmagno.eu/lievens/, https://github.com/ramiromagno/lievens |
| BugReports: | https://github.com/ramiromagno/lievens/issues |
| NeedsCompilation: | no |
| Packaged: | 2024-05-02 23:18:32 UTC; rmagno |
| Author: | Ramiro Magno 
[aut, cre],
Pattern Institute [cph, fnd] |
| Maintainer: | Ramiro Magno <rmagno@pattern.institute> |
| Repository: | CRAN |
| Date/Publication: | 2024-05-03 13:10:02 UTC |
lievens: Real-Time PCR Data Sets by Lievens et al. (2012)
Description
Real-time quantitative polymerase chain reaction (qPCR) data sets by Lievens et al. (2012) doi:10.1093/nar/gkr775. Provides one single tabular tidy data set in long format, encompassing three dilution series, targeted against the soybean Lectin endogene. Each dilution series was assayed in one of the following PCR-efficiency-modifying conditions: no PCR inhibition, inhibition by isopropanol and inhibition by tannic acid. The inhibitors were co-diluted along with the dilution series. The co-dilution series consists of a five-point, five-fold serial dilution. For each concentration there are 18 replicates. Each amplification curve is 60 cycles long. Original raw data file is available at the Supplementary Data section at Nucleic Acids Research Online doi:10.1093/nar/gkr775.
Author(s)
Maintainer: Ramiro Magno rmagno@pattern.institute (ORCID)
Other contributors:
Pattern Institute [copyright holder, funder]
See Also
Useful links:
Report bugs at https://github.com/ramiromagno/lievens/issues
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.
platePlate identifier. There is one identifier for each of the four data sets.
wellWell identifier, i.e. the position within a PCR plate. This information was not available from the original publication, thus all values are
NA.targetTarget identifier. In all data sets the target is an amplicon consisting of soybean Lectin endogene
"Le1".dyeType of fluorescence dye, in this data set it is always SYBR Green I master mix (Roche) (
"SYBR").inhibitorName of the molecule used as PCR inhibitor. In the case of the dilution series the value is
"none".inhibitor_concInhibitor concentration. Units are % (v/v) for isopropanol, and ug/mL for tannic acid.
sampleName of the biological sample. Samples have a simple consecutive identifier: S1, S2, ..., S5.
sample_typeSample type. All reactions are standard curves, i.e.
"std".replicateReplicate identifier.
copiesStandard copy number of the amplicon.
dilutionDilution factor. Higher number means greater dilution, e.g.
5means a 1:5 (five-fold) dilution relative to most concentrated standard.cyclePCR cycle.
fluorRaw fluorescence values.
Source
Examples
lievens