sisti dataset

qPCR data sets by Sisti et al. (2010)

One single tabular tidy data set in long format, encompassing four data sets of amplification curves: (i) six-point, ten-fold dilution series, (ii) tannic acid inhibition, (iii) IgG inhibition and (iv) quercitin inhibition. The target amplicon consisted of a 104 bp fragment of the mitochondrial gene NADH dehydrogenase 1 (MT-ND1). Please read the Methods section of Sisti et al. (2010) for more experimental details.

Dilution series

A six-point, ten-fold dilution series spanning an amplicon copy number range $3.14 \times 10^7$ thru $3.14 \times 10^2$. Each concentration is replicated twelve times. Each reaction has been amplified through 50 cycles.

dplyr::filter(sisti, plate == "calibration")
#> # A tibble: 3,600 x 13
#>    plate       well  target dye   sample sample_type inhibitor inhibitor_conc
#>    <fct>       <fct> <fct>  <fct> <fct>  <fct>       <fct>              <dbl>
#>  1 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  2 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  3 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  4 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  5 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  6 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  7 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  8 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#>  9 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#> 10 calibration <NA>  MT-ND1 SYBR  pGEM-T std         none                   0
#> # i 3,590 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: 0.000391, 0.000781, 0.00156, 0.00312, 0.00625, 0.0125, 0.025, 0.05 and 0.1 mg/mL. Each tannic acid concentration sample is replicated six times. Each reaction has been amplified through 40 cycles.

dplyr::filter(sisti, plate == "tannic acid")
#> # A tibble: 2,160 x 13
#>    plate       well  target dye   sample sample_type inhibitor   inhibitor_conc
#>    <fct>       <fct> <fct>  <fct> <fct>  <fct>       <fct>                <dbl>
#>  1 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  2 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  3 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  4 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  5 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  6 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  7 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  8 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#>  9 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#> 10 tannic acid <NA>  MT-ND1 SYBR  pGEM-T std         tannic acid            0.1
#> # i 2,150 more rows
#> # i 5 more variables: replicate <fct>, copies <int>, dilution <int>,
#> #   cycle <int>, fluor <dbl>

Immunoglobulin G (IgG) inhibition

A series of reactions subjected to inhibition by IgG with concentrations: 0.00781, 0.0156, 0.0312, 0.0625, 0.125, 0.25, 0.5, 1 and 2 mg/mL. Each IgG concentration sample is replicated six times. Each reaction has been amplified through 40 cycles.

dplyr::filter(sisti, plate == "IgG")
#> # A tibble: 2,160 x 13
#>    plate well  target dye   sample sample_type inhibitor inhibitor_conc
#>    <fct> <fct> <fct>  <fct> <fct>  <fct>       <fct>              <dbl>
#>  1 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  2 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  3 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  4 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  5 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  6 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  7 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  8 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#>  9 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#> 10 IgG   <NA>  MT-ND1 SYBR  pGEM-T std         IgG                    2
#> # i 2,150 more rows
#> # i 5 more variables: replicate <fct>, copies <int>, dilution <int>,
#> #   cycle <int>, fluor <dbl>

Quercitin inhibition

A series of reactions subjected to inhibition by quercitin with concentrations: 0.000312, 0.000625, 0.00125, 0.0025, 0.005, 0.01, 0.02, and 0.04 mg/mL. Each quercitin concentration sample is replicated six times. Each reaction has been amplified through 40 cycles.

dplyr::filter(sisti, plate == "quercitin")
#> # A tibble: 1,920 x 13
#>    plate     well  target dye   sample sample_type inhibitor inhibitor_conc
#>    <fct>     <fct> <fct>  <fct> <fct>  <fct>       <fct>              <dbl>
#>  1 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  2 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  3 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  4 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  5 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  6 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  7 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  8 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#>  9 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#> 10 quercitin <NA>  MT-ND1 SYBR  pGEM-T std         quercitin           0.04
#> # i 1,910 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 a 104 bp fragment of the mitochondrial gene NADH dehydrogenase 1 (MT-ND1), thus the values are all "MT-ND1".
• dye: Type of fluorescence dye, in this data set it is always SYBR Green I master mix (Roche) ("SYBR").
• sample: Name of the biological sample. All samples are based on a pGEM-T Promega plasmid, so all values are "pGEM-T".
• sample_type: Sample type. All reactions are standard curves, i.e. "std".
• inhibitor: Name of the molecule used as PCR inhibitor. In the case of the dilution series the value is "none".
• inhibitor_conc: Inhibitor concentration in mg/mL.
• replicate: Replicate identifier.
• copies: Standard copy number of the amplicon.
• dilution: Dilution factor. Higher number means greater dilution, e.g. 10 means a 1:10 (ten-fold) dilution.
• cycle: PCR cycle.
• fluor: Raw fluorescence values.

Source

tools:::Rd_expr_doi("10.1186/1471-2105-11-186")

Examples

sisti