Type: Package
Title: Real-Time PCR Data Sets by Batsch et al. (2008)
Version: 0.1.1
Description: Real-time quantitative polymerase chain reaction (qPCR) data sets by Batsch et al. (2008) <doi:10.1186/1471-2105-9-95>. This package provides five data sets, one for each PCR target: (i) rat SLC6A14, (ii) human SLC22A13, (iii) pig EMT, (iv) chicken ETT, and (v) human GAPDH. Each data set comprises a five-point, four-fold dilution series. For each concentration there are three replicates. Each amplification curve is 45 cycles long. Original raw data file: https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-95/MediaObjects/12859_2007_2080_MOESM5_ESM.xls.
License: CC BY 4.0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
Depends: R (≥ 2.10)
Imports: tibble
URL: https://github.com/ramiromagno/batsch, https://rmagno.eu/batsch/
BugReports: https://github.com/ramiromagno/batsch/issues
NeedsCompilation: no
Packaged: 2024-04-22 21:55:22 UTC; rmagno
Author: Ramiro Magno ORCID iD [aut, cre], Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-04-22 22:40:21 UTC

batsch: Real-Time PCR Data Sets by Batsch et al. (2008)

Description

Real-time quantitative polymerase chain reaction (qPCR) data sets by Batsch et al. (2008) doi:10.1186/1471-2105-9-95. This package provides five data sets, one for each PCR target: (i) rat SLC6A14, (ii) human SLC22A13, (iii) pig EMT, (iv) chicken ETT, and (v) human GAPDH. Each data set comprises a five-point, four-fold dilution series. For each concentration there are three replicates. Each amplification curve is 45 cycles long. Original raw data file: https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-95/MediaObjects/12859_2007_2080_MOESM5_ESM.xls.

Author(s)

Maintainer: Ramiro Magno rmagno@pattern.institute (ORCID)

Other contributors:

See Also

Useful links:

qPCR data sets by Batsch et al. (2008)

Description

Each data set comprises a five-point, four-fold dilution series. For each concentration there are three replicates. Each amplification curve is 45 cycles long.

A single reaction (total volume 10 µl) contained 1 µl master mix (LightCycler TaqMan Master; Roche 04735536001), 1 µmol/l each of forward and reverse primer, SYBR Green I at 1:30 dilution (Invitrogen S7563) or 50 nmol/l probe, and various amounts of cDNA or plasmid DNA. Contamination controls contained water instead of DNA. After enzyme activation (10 min, 95°C), thermocycling consisted of 45 cycles of 10 s at 95°C, 30 s at 55°C, and 1 s at 72°C; velocity of temperature change was 1.1°C/s. Please read the Methods section of Batsch et al. (2008) for more details.

Usage

SLC6A14r

SLC22A13h

EMTp

ETTch

GAPDHh

Format

Each data set is provided as a tibble with 675 rows and 9 variables:

plate

Plate identifier. Because one plate was used per target, the name of the plate is the same as the values in target.

well

Well identifier. Values are always NA (not available) for these data sets. This variable is kept nevertheless to be coherent with other data sets from other similar R data packages.

dye

Either SYBR Green I master mix (Roche) ("SYBR") or TaqMan probe ("TaqMan").

target

Target identifier: rat SLC6A14 ("SLC6A14r"), human SLC22A13 ("SLC22A13h"), pig EMT ("EMTp"), chicken ETT ("ETTch") or human GAPDH ("GAPDHh").

sample_type

Sample type (all curves are standards, i.e. "std").

replicate

Replicate identifier: 1 thru 3.

dilution

Dilution factor. Higher number means greater dilution.

cycle

PCR cycle.

fluor

Raw fluorescence values.

Source

doi:10.1186/1471-2105-9-95

Examples

SLC6A14r

SLC22A13h

EMTp

ETTch

GAPDHh