pds_raw: Plasmid dilution series raw data

Description

These are the raw data from the pds_raw data set as measured by the BioRad QX100 Droplet Digital PCR System.

Arguments

format

The format is: List of 32 $ A01:'data.frame': 11964 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11964] 397 399 402 416 417 ... ..$ Assay2.Amplitude: num [1:11964] 3732 3808 4007 3778 3685 ... ..$ Cluster : int [1:11964] 4 4 4 4 4 4 4 4 4 4 ... $ A02:'data.frame': 11198 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11198] 310 429 433 445 445 ... ..$ Assay2.Amplitude: num [1:11198] 605 1092 994 1092 1140 ... ..$ Cluster : int [1:11198] 1 1 1 1 1 1 1 1 1 1 ... $ A03:'data.frame': 9672 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:9672] 413 469 477 480 489 ... ..$ Assay2.Amplitude: num [1:9672] 781 1160 1205 1117 1098 ... ..$ Cluster : int [1:9672] 1 1 1 1 1 1 1 1 1 1 ... $ A04:'data.frame': 11901 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11901] 442 459 468 469 470 ... ..$ Assay2.Amplitude: num [1:11901] 3169 1161 1098 1064 1107 ... ..$ Cluster : int [1:11901] 4 1 1 1 1 1 1 1 1 1 ... $ B01:'data.frame': 11592 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11592] 438 449 451 453 454 ... ..$ Assay2.Amplitude: num [1:11592] 3996 4237 3910 3648 3832 ... ..$ Cluster : int [1:11592] 4 4 4 4 4 4 4 4 4 4 ... $ B02:'data.frame': 11715 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11715] 341 404 411 417 465 ... ..$ Assay2.Amplitude: num [1:11715] 705 1013 892 936 996 ... ..$ Cluster : int [1:11715] 1 1 1 1 1 1 1 1 1 1 ... $ B03:'data.frame': 11194 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11194] 31.2 266.9 281.6 286.1 300.3 ... ..$ Assay2.Amplitude: num [1:11194] 668 555 508 585 571 ... ..$ Cluster : int [1:11194] 1 1 1 1 1 1 1 1 1 1 ... $ B04:'data.frame': 12813 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12813] 380 464 474 483 487 ... ..$ Assay2.Amplitude: num [1:12813] 830 913 1143 1157 1032 ... ..$ Cluster : int [1:12813] 1 1 1 1 1 1 1 1 1 1 ... $ C01:'data.frame': 10903 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:10903] 427 442 443 444 445 ... ..$ Assay2.Amplitude: num [1:10903] 3803 3832 3634 3899 3932 ... ..$ Cluster : int [1:10903] 4 4 4 4 4 4 4 4 4 4 ... $ C02:'data.frame': 9638 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:9638] 442 446 454 454 457 ... ..$ Assay2.Amplitude: num [1:9638] 1107 1131 3644 881 3460 ... ..$ Cluster : int [1:9638] 1 1 4 1 4 4 1 1 1 1 ... $ C03:'data.frame': 12194 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12194] 461 466 470 475 475 ... ..$ Assay2.Amplitude: num [1:12194] 842 1089 1156 1115 1194 ... ..$ Cluster : int [1:12194] 1 1 1 1 1 1 1 1 1 1 ... $ C04:'data.frame': 10889 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:10889] 343 448 456 466 474 ... ..$ Assay2.Amplitude: num [1:10889] 633 1149 1073 1161 1089 ... ..$ Cluster : int [1:10889] 1 1 1 1 1 1 1 1 1 1 ... $ D01:'data.frame': 11196 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11196] 110 413 417 435 444 ... ..$ Assay2.Amplitude: num [1:11196] 734 3752 3736 3885 3720 ... ..$ Cluster : int [1:11196] 1 4 4 4 4 4 4 4 4 4 ... $ D02:'data.frame': 12013 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12013] 453 457 459 463 462 ... ..$ Assay2.Amplitude: num [1:12013] 1113 1178 1054 1088 3108 ... ..$ Cluster : int [1:12013] 1 1 1 1 4 1 4 1 1 4 ... $ D03:'data.frame': 11126 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11126] 323 460 463 471 473 ... ..$ Assay2.Amplitude: num [1:11126] 661 1138 1103 1091 1138 ... ..$ Cluster : int [1:11126] 1 1 1 1 1 1 1 1 1 1 ... $ D04:'data.frame': 12793 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12793] 363 433 442 459 460 ... ..$ Assay2.Amplitude: num [1:12793] 703 1065 1071 1060 1119 ... ..$ Cluster : int [1:12793] 1 1 1 1 1 1 1 1 1 1 ... $ E01:'data.frame': 11823 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11823] 368 434 448 453 462 ... ..$ Assay2.Amplitude: num [1:11823] 778 3751 3585 1125 3797 ... ..$ Cluster : int [1:11823] 1 4 4 1 4 4 4 1 1 4 ... $ E02:'data.frame': 12046 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12046] 268 413 414 454 455 ... ..$ Assay2.Amplitude: num [1:12046] 582 3738 2412 1071 1076 ... ..$ Cluster : int [1:12046] 1 4 4 1 1 1 1 1 1 1 ... $ E03:'data.frame': 11026 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11026] 357 446 456 456 460 ... ..$ Assay2.Amplitude: num [1:11026] 675 1138 1095 1145 1138 ... ..$ Cluster : int [1:11026] 1 1 1 1 1 1 1 1 1 1 ... $ E04:'data.frame': 12838 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12838] 460 467 472 477 482 ... ..$ Assay2.Amplitude: num [1:12838] 1207 1238 1143 3754 1153 ... ..$ Cluster : int [1:12838] 1 1 1 4 1 1 1 4 4 1 ... $ F01:'data.frame': 12173 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12173] 354 389 457 456 466 ... ..$ Assay2.Amplitude: num [1:12173] 739 2714 3888 3775 3857 ... ..$ Cluster : int [1:12173] 1 4 4 4 4 4 4 1 1 4 ... $ F02:'data.frame': 13786 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:13786] 338 359 439 459 461 ... ..$ Assay2.Amplitude: num [1:13786] 525 638 674 3891 1046 ... ..$ Cluster : int [1:13786] 1 1 1 4 1 1 1 1 1 1 ... $ F03:'data.frame': 11249 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11249] 431 445 447 448 455 ... ..$ Assay2.Amplitude: num [1:11249] 1090 3330 1048 1187 1098 ... ..$ Cluster : int [1:11249] 1 4 1 1 1 1 1 1 1 1 ... $ F04:'data.frame': 12076 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12076] 407 424 436 446 447 ... ..$ Assay2.Amplitude: num [1:12076] 699 1047 3683 1085 1088 ... ..$ Cluster : int [1:12076] 1 1 4 1 1 1 1 1 1 1 ... $ G01:'data.frame': 10188 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:10188] 460 468 470 471 482 ... ..$ Assay2.Amplitude: num [1:10188] 3813 3213 3949 3658 2202 ... ..$ Cluster : int [1:10188] 4 4 4 4 4 4 4 1 4 4 ... $ G02:'data.frame': 11018 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:11018] 445 452 460 460 461 ... ..$ Assay2.Amplitude: num [1:11018] 1064 1090 1054 1087 1116 ... ..$ Cluster : int [1:11018] 1 1 1 1 1 1 1 1 1 1 ... $ G03:'data.frame': 12073 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12073] 294 459 460 468 489 ... ..$ Assay2.Amplitude: num [1:12073] 658 1105 1168 1160 1115 ... ..$ Cluster : int [1:12073] 1 1 1 1 1 1 1 1 1 1 ... $ G04:'data.frame': 12320 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12320] 444 476 484 491 498 ... ..$ Assay2.Amplitude: num [1:12320] 831 1158 984 1237 1325 ... ..$ Cluster : int [1:12320] 1 1 1 1 1 1 1 1 1 1 ... $ H01:'data.frame': 12271 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12271] 377 388 404 409 433 ... ..$ Assay2.Amplitude: num [1:12271] 2884 917 3679 830 2780 ... ..$ Cluster : int [1:12271] 4 1 4 1 4 4 4 1 4 4 ... $ H02:'data.frame': 12595 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12595] 364 411 419 421 424 ... ..$ Assay2.Amplitude: num [1:12595] 691 836 2885 812 1177 ... ..$ Cluster : int [1:12595] 1 1 4 1 1 1 1 1 1 1 ... $ H03:'data.frame': 13905 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:13905] 314 400 426 431 433 ... ..$ Assay2.Amplitude: num [1:13905] 509 987 1037 1074 1053 ... ..$ Cluster : int [1:13905] 1 1 1 1 1 1 1 1 1 1 ... $ H04:'data.frame': 12972 obs. of 3 variables: ..$ Assay1.Amplitude: num [1:12972] 344 446 461 467 482 ... ..$ Assay2.Amplitude: num [1:12972] 641 869 987 789 1117 ... ..$ Cluster : int [1:12972] 1 1 1 1 1 1 1 1 1 1 ...

source

Michael Jahn Flow cytometry group / Environmental microbiology Helmholtz Centre for Environmental Research - UFZ Permoserstrasse 15 / 04318 Leipzig / Germany phone +49 341 235 1318 michael.jahn [at] ufz.de / www.ufz.de

Details

The results can be as calculated by the BioRad QX100 Droplet Digital PCR System are to be found in pds. Setup: Duplex assay with constant amount of genomic DNA and six 10-fold dilutions of plasmid DNA with 4 replicates, ranging theoretically from ~ 10^4 to 10^-1 copies/ micro L plus 4 replicates without plasmid DNA. Included are No-gDNA-control and No-template-control, 2 replicates each. Annotation: FX.Y (X = dilution number, Y = replicate number). Hardware: Bio-Rad QX100 Droplet digital PCR system Details: Genomic DNA isolated from Pseudomonas putida KT2440. Plasmid is pCOM10-StyA::EGFP StyB [Jahn et al., 2013, Curr Opin Biotechnol, Vol. 24 (1): 79-87]. Template DNA was heat treated at 95 degree Celsius for 5 min prior to PCR. Channel 1, primers for genomic DNA marker ileS, Taqman probes (FAM labelled). Channel 2, primers for plasmid DNA marker styA, Taqman probes (HEX labelled).

References

Jahn et al., 2013, Curr Opin Biotechnol, Vol. 24 (1): 79-87

Examples

Run this code

#str(pds_raw)
bioamp(data = pds_raw[["A01"]], main = "Well A01", pch = 19)

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