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.
Format
Each data set is provided as a tibble with 675 rows and 9 variables:
platePlate identifier. Because one plate was used per target, the name of the plate is the same as the values in
target.wellWell 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.dyeEither SYBR Green I master mix (Roche) (
"SYBR") or TaqMan probe ("TaqMan").targetTarget identifier: rat SLC6A14 (
"SLC6A14r"), human SLC22A13 ("SLC22A13h"), pig EMT ("EMTp"), chicken ETT ("ETTch") or human GAPDH ("GAPDHh").sample_typeSample type (all curves are standards, i.e.
"std").replicateReplicate identifier: 1 thru 3.
dilutionDilution factor. Higher number means greater dilution.
cyclePCR cycle.
fluorRaw fluorescence values.
Examples
SLC6A14r
#> # A tibble: 675 × 9
#> plate well dye target sample_type replicate dilution cycle fluor
#> <fct> <fct> <fct> <fct> <fct> <int> <int> <dbl> <dbl>
#> 1 SLC6A14r NA TaqMan SLC6A14r std 1 1 1 3.00
#> 2 SLC6A14r NA TaqMan SLC6A14r std 1 1 2 2.99
#> 3 SLC6A14r NA TaqMan SLC6A14r std 1 1 3 3.00
#> 4 SLC6A14r NA TaqMan SLC6A14r std 1 1 4 3.00
#> 5 SLC6A14r NA TaqMan SLC6A14r std 1 1 5 2.98
#> 6 SLC6A14r NA TaqMan SLC6A14r std 1 1 6 2.98
#> 7 SLC6A14r NA TaqMan SLC6A14r std 1 1 7 3.01
#> 8 SLC6A14r NA TaqMan SLC6A14r std 1 1 8 2.98
#> 9 SLC6A14r NA TaqMan SLC6A14r std 1 1 9 2.98
#> 10 SLC6A14r NA TaqMan SLC6A14r std 1 1 10 2.99
#> # ℹ 665 more rows
SLC22A13h
#> # A tibble: 675 × 9
#> plate well dye target sample_type replicate dilution cycle fluor
#> <fct> <fct> <fct> <fct> <fct> <int> <int> <dbl> <dbl>
#> 1 SLC22A13h NA TaqMan SLC22A13h std 1 1 1 5.61
#> 2 SLC22A13h NA TaqMan SLC22A13h std 1 1 2 5.63
#> 3 SLC22A13h NA TaqMan SLC22A13h std 1 1 3 5.64
#> 4 SLC22A13h NA TaqMan SLC22A13h std 1 1 4 5.68
#> 5 SLC22A13h NA TaqMan SLC22A13h std 1 1 5 5.68
#> 6 SLC22A13h NA TaqMan SLC22A13h std 1 1 6 5.68
#> 7 SLC22A13h NA TaqMan SLC22A13h std 1 1 7 5.69
#> 8 SLC22A13h NA TaqMan SLC22A13h std 1 1 8 5.68
#> 9 SLC22A13h NA TaqMan SLC22A13h std 1 1 9 5.70
#> 10 SLC22A13h NA TaqMan SLC22A13h std 1 1 10 5.67
#> # ℹ 665 more rows
EMTp
#> # A tibble: 675 × 9
#> plate well dye target sample_type replicate dilution cycle fluor
#> <fct> <fct> <fct> <fct> <fct> <int> <int> <dbl> <dbl>
#> 1 EMTp NA TaqMan EMTp std 1 1 1 1.96
#> 2 EMTp NA TaqMan EMTp std 1 1 2 1.97
#> 3 EMTp NA TaqMan EMTp std 1 1 3 1.97
#> 4 EMTp NA TaqMan EMTp std 1 1 4 1.98
#> 5 EMTp NA TaqMan EMTp std 1 1 5 1.99
#> 6 EMTp NA TaqMan EMTp std 1 1 6 2.00
#> 7 EMTp NA TaqMan EMTp std 1 1 7 1.99
#> 8 EMTp NA TaqMan EMTp std 1 1 8 2.01
#> 9 EMTp NA TaqMan EMTp std 1 1 9 2.02
#> 10 EMTp NA TaqMan EMTp std 1 1 10 2.04
#> # ℹ 665 more rows
ETTch
#> # A tibble: 675 × 9
#> plate well dye target sample_type replicate dilution cycle fluor
#> <fct> <fct> <fct> <fct> <fct> <int> <int> <dbl> <dbl>
#> 1 ETTch NA SYBR ETTch std 1 1 1 1.21
#> 2 ETTch NA SYBR ETTch std 1 1 2 1.20
#> 3 ETTch NA SYBR ETTch std 1 1 3 1.19
#> 4 ETTch NA SYBR ETTch std 1 1 4 1.21
#> 5 ETTch NA SYBR ETTch std 1 1 5 1.20
#> 6 ETTch NA SYBR ETTch std 1 1 6 1.19
#> 7 ETTch NA SYBR ETTch std 1 1 7 1.21
#> 8 ETTch NA SYBR ETTch std 1 1 8 1.21
#> 9 ETTch NA SYBR ETTch std 1 1 9 1.23
#> 10 ETTch NA SYBR ETTch std 1 1 10 1.25
#> # ℹ 665 more rows
GAPDHh
#> # A tibble: 675 × 9
#> plate well dye target sample_type replicate dilution cycle fluor
#> <fct> <fct> <fct> <fct> <fct> <int> <int> <dbl> <dbl>
#> 1 GAPDHh NA SYBR GAPDHh std 1 1 1 0.917
#> 2 GAPDHh NA SYBR GAPDHh std 1 1 2 1.51
#> 3 GAPDHh NA SYBR GAPDHh std 1 1 3 1.63
#> 4 GAPDHh NA SYBR GAPDHh std 1 1 4 1.67
#> 5 GAPDHh NA SYBR GAPDHh std 1 1 5 1.66
#> 6 GAPDHh NA SYBR GAPDHh std 1 1 6 1.67
#> 7 GAPDHh NA SYBR GAPDHh std 1 1 7 1.68
#> 8 GAPDHh NA SYBR GAPDHh std 1 1 8 1.69
#> 9 GAPDHh NA SYBR GAPDHh std 1 1 9 1.68
#> 10 GAPDHh NA SYBR GAPDHh std 1 1 10 1.69
#> # ℹ 665 more rows