RDML
RDML
RDML file The file containing the data in xml-format. The file is zipped and renamed to .rdml, to view the data you can rename the file to .zip and extract the file.
Quantification file A tab delimited flat text file (*.txt) containing the quantification data (all numbers have to be written in point-notation) with one header row containing the following columns :
  • "reactionId"
notation : 1, 2, ... (integer numbers) - mandatory header
  • "sampleId"
ID of the sample, this has to be the same ID as used in the sample annotation file - mandatory header
  • "targetId"
ID of the target, this has to be the same ID as used in the target annotation file - mandatory header
  • "cq"
the quantification cycle, has to be in point-notation, mandatory header
  • "excl"
used to indicate why this well should be excluded for data-analysis (e.g. bad replicate, suspicious melt curve).
  • "endFluor"
the end point fluorescence, has to be in point-notation.
  • "endPointFluor"
the background fluorescence, has to be in point-notation.
  • "quantFluor"
the quantification fluorescence, has to be in point-notation.

Only the headers "reactionId", "sampleId", "targetId" and "qc" are mandatory, the other headers are optional.

If this file has been given, then the sample annotation and target annotation files are mandatory.

Amplification curve fluorescence data file A tab delimited flat text file (*.txt) with the raw amplification curve fluorescence data (ie. values without baseline correction). All numbers have to be written in point-notation.

This file is optional, but if it is given, then the quantification, the sample annotation file and the target annotation file are mandatory.

The following columns are mandatory :

  •  "reactionId", mandatory header
  •  "targetId", mandatory header
  •  integer numbers for the cycle numbers
Melting curve fluorescence data file A tab delimited flat text file (*.txt) with the raw melting curve fluorescence data (ie. values without baseline correction). All numbers have to be written in point-notation.

This file is optional, but if it is given, then the quantification, the sample annotation file and the target annotation file are mandatory.

The following columns are mandatory :

  •  "reactionId", mandatory header
  •  "targetId", mandatory header
  •  decimal numbers (.-notation) for the temperatures
Sample annotation file A tab delimited flat text file (*.txt) which contains the annotations of all the samples in the experiment. All numbers have to be written in point-notation.

This file is mandatory if a quantification file has been given, otherwise it's optional.

The following headers can be used :

  • "id"
unique ID of the sample, mandatory header.
  • "type"
type of the sample, mandatory header. Possible values are "unkn", "std", "nac", "opt", "ntp", "nrt", "pos" and "ntc" (unkn = unknown, ntc = no template control, nac = no amplification control, opt = optical calibrator sample, ntp = no target present, nrt = minusRT, pos = positive control, std = standard).
  • "documentation"
used to add extra documentation about the target. This header can be used multiple times in the sample annotation file.
  • "quantity"
mandatory header if the sample is part of a standard-curve.
  • "interRunCalibrator"
specifies if a sample has been used as an inter-run calibrator. Possible values are "false", "true", "no", "yes", "1" and "0".
  • "calibrator"
specifies if a sample has been used as a calibrator. Possible values are "false", "true", "no", "yes", "1" and "0".
  • "description"
free description of the sample.
  • "dnaseTreatment"
specifies if a sample has been treated with DNase. Possible values are "false", "true", "no", "yes", "1" and "0".
  • "enzyme"
the enzyme used for the cDNA synthesis.
  • "primingMethod"
the method used for priming. Possible values are "oligo-dT", "random", "oligo-dT and random", "target specific" and "other".
  • "thermConditions"
ID of the thermal cycling conditions used for the cDNA synthesis, has to be the same ID as used in the thermal cycling conditions file.
  • "rnaQuantity"
amount of RNA template, has to be in point-notation. A unit has to be specified as folows : 'value unit'
  • "dnaQuantity"
amount of DNA template, has to be in point-notation. A unit has to be specified as folows : 'value unit'
  • "rnaQualityMethod"
the method used for assessing the quality of the RNA template.
  • "dnaQualityMethod"
the method used for assessing the quality of the DNA template.
  • "rnaQualtity"
quality of the RNA template, has to be in point-notation. A unit can be specified as folows : 'value unit'
  • "dnaQualtity"
quality of the DNA template, has to be in point-notation. A unit can be specified as folows : 'value unit'
  • "xref"
reference ID of the target in a database, the followin format has to be used : name of the database(reference ID)

Only the headers "Id" and "type" are always mandatory. If the sample is part of a standard curve (STD-type), then the header "quantity" is also mandatory. All the other headers are always optional.

Target annotation file A tab delimited flat text file (*.txt) which contains the annotations of all the targets in the experiment. All numbers have to be written in point-notation.

This file is mandatory if a quantification file has been given, otherwise it's optional.

The following headers can be used :

  • "id"
unique ID of the target, mandatory header.
  • "type"
type of the target, mandatory header. Possible values are "ref" and "toi" (ref = reference target, toi = target of interest).
  • "dye"
name of the dye, mandatory header.
  • "documentation"
used to add extra documentation about the target. This header can be used multiple times in the target annotation file.
  • "description"
free description of the target.
  • "amplificationEff"
target specific amplification efficiency (values between 0.5 and 1.5, 1=100% amplification efficiency), has to be in point-notation.
  • "amplificationEffMethod"
method used to measure the target specific amplification efficiency.
  • "detectionLimit"
indicates the limit of detection.
  • "forward"
nucleotide sequence of the forward primer. 3' and 5' tags can be specified as follows : 3'tag-sequence-5'tag
  • "reverse"
nucleotide sequence of the reverse primer. 3' and 5' tags can be specified as follows : 3'tag-sequence-5'tag
  • "probe"
nucleotide sequence of the probe. 3' and 5' tags can be specified as follows : 3'tag-sequence-5'tag
  • "amplicon"
nucleotide sequence of the amplicon. 3' and 5' tags can be specified as follows : 3'tag-sequence-5'tag
  • "commercialAssay"
company name and order number from which the kit with commercial primer and probe assays has been used, the following format has to be used : company:order number
  • "xref"
reference ID of the target in a database, the followin format has to be used : name of the database(reference ID)

Only the headers "Id", "type" and "dye" are always mandatory. All the other headers are always optional.

List of experimenters A tab delimited flat text file (*.txt) which contains the personal information of the experimenters involved in the study.

The following headers can be used :

  • "id"
unique ID of the experimenter, mandatory header.
  • "firstName"
first name of the experimenter, mandatory header.
  • "lastName"
last name of the experimenter, mandatory header.
  • "email"
email address of the experimenter.
  • "labName"
name of the lab.
  • "labAddress"
address of the lab.
List of thermal cycling conditions A tab delimited flat text file (*.txt) which contains a list of all the thermal cycling conditions used during the study.

Each PCR program is written on a separate line in the file. The following headers can be used :

  • "id"
unique ID of the PCR program, mandatory header.
  • "lidTemperature"
temperature of the lid.
  • "description"
description of the thermal cycling conditions.
  • "documentation"
used to add extra documentation about the target. This header can be used multiple times in this file.
  • "experimenter"
ID of the experimenter who created/used this protocol, the same ID as present in the thermal cycling conditions file has to be used. This header can be used multiple times in this file.
  • "step step number"
Step identified by the step number in the header. All temperatures have to be entered in degrees celcius (íC) and durations in number of seconds. At least on step has to be present in the file. The type of step is identified by using the following notation :
  1. Normal step : normal(...)
    • temperature(value) : specifies the temperature of the step
    • duration(value) : specifies the duration of the step
    • tempChange(value) : specifies the temperature change of the step
    • durationChange(value) : specifies the duration change of the step
    • measure(value) : specifies the type of measurement performed during the step, possible values are "real time" and "meltcurve"
    • ramp(value) : specifies the ramp of the step

    • All fields have to be separated from each other by a comma-point ";".
  2. Gradient step : gradient(...)
    • temperature(value-value) : specifies the lower- and upper temperature of the step
    • duration(value) : specifies the duration of the step
    • tempChange(value) : specifies the temperature change of the step
    • durationChange(value) : specifies the duration change of the step
    • measure(value) : specifies the type of measurement performed during the step, possible values are "none", "real time" and "meltcurve"
    • ramp(value) : specifies the ramp of the step

    • All fields have to be separated from each other by a comma-point ";".
  3. Loop step : loop(...)
    • goto(value) : specifies that on reaching the step, the program must go back and continue from the step identified by value
    • repeat(value) : specifies how many times the loop has to be repeated
  4. Pause step : pause(...)
    • temperature(value) : specifies the temperature of the step
  5. Lid open step : lidOpen
  6. Step example
    • gradient(temperature(50-70); duration(60); measure(meltcurve))