qrt-pcr

Name	experimentSamples.QRT-PCR.txt
JSON File Name	experimentSamples.QRT-PCR.json
Type	combined-result
Schema Version	3.37
Description	The qRT-PCR experiment sample template defines and annotates the assay results for a sample by linking sample, experiment, and results together. More than one analyte's results per assayed sample may be reported by copying at least the group of columns 'Entrez Gene ID' and 'Threshold Cycles(ct)' needed to describe each assay result. The experiment samples template allows you to describe to ImmPort new experiments and biological samples or link experiments and biological samples stored in ImmPort with assay results. There is considerable flexibility in linking ImmPort content with new content in the templates and there are some general guidelines to remember. All of the experiment sample IDs in the template must always be unique in the template and must not already be stored in ImmPort. The biological sample and the experiment in the template may be new or they both may be new. If the biological sample or the experiment is new, then you must complete the required columns to describe them. When defining a new experiment or biological sample, it is only necessary to complete the required descriptive columns once per experiment or biological sample. The column header names in the templates indicate to what is being described and the '.xls' spreadsheet versions use color codes to indicate what is being described.
Download	⬇️ experimentSamples.QRT-PCR.xlsx ⬇️ experimentSamples.QRT-PCR.txt ⬇️ experimentSamples.QRT-PCR.json This top-level schema references companion files (e.g. experimentSamples.QRT-PCR.Datum.json) in the same json-templates folder — download the all_templates.zip to get them all together.

Reading this table: see How to read the template documentation for what Required / Conditionally required / Optional mean and how to read the Type & Constraints column.

Template Column	Requirement	Type & Constraints	Description
Study ID	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one) and you are defining a new Experiment in this row (rather than referencing an existing one)	Text, max 15 characters Reference — must already exist (in this package or the workspace) as a study Metadata column JSON: studyId (string)	An experiment and biological sample may be linked to a single study. Please enter either a study user defined ID or ImmPort accession. This column is only required when both the experiment and biological sample are new.
Expsample ID	Required	Text, max 100 characters Metadata column JSON: expsampleId (string)	The experiment sample user defined ID is an identifier chosen by the data provider to refer to this sample. This ID may be referenced by other data records (e.g. assay results). The user defined ID is not shared. The identifier should be unique to the ImmPort workspace to which the data will be uploaded.
Expsample Name	Optional	Text, max 200 characters Metadata column JSON: expsampleName (string)	The experiment sample name is a display name that is available when the data is shared, but it is not referenced by other data. The experiment sample name is an alternate identifier that is visible when the experiment sample is shared.
Expsample Description	Optional	Text, max 4000 characters Metadata column JSON: expsampleDescription (string)	Describe important characteristics of the sample being assayed.
Reagent ID(s)	Conditionally required when you are defining a new Experiment Sample in this row (rather than referencing an existing one)	Text, max 15 characters Reference — must already exist (in this package or the workspace) as a reagent Metadata column JSON: reagentIds (array)	One or more identifiers can be entered. Separate identifiers by semicolon (;). The reagent identifier(s) must be stored in ImmPort or in the reagents.txt template. Please enter either an assay reagent user defined ID or ImmPort accession.
Treatment ID(s)	Conditionally required when you are defining a new Experiment Sample in this row (rather than referencing an existing one)	Text, max 15 characters Reference — must already exist (in this package or the workspace) as a treatment Metadata column JSON: treatmentIds (array)	One or more identifiers can be entered. Separate identifiers by semicolon (;). The treatment identifier(s) must be stored in ImmPort or in the treatments.txt template. Please enter either a treatment user defined ID or ImmPort accession.
Additional Result File Names	Optional	Metadata column JSON: additionalResultFileNames (array)	Separate file names by a semi-colon (;). The file size name limit is 240 characters. Please enter additional result file(s) to link to the experiment sample. The file size name limit is 240 characters.
Biosample ID	Required	Text, max 100 characters Metadata column JSON: biosampleId (string)	The biological sample user defined ID is an identifier chosen by the data provider to refer to a sample. This ID may be referenced by other data records (e.g. experiment sample). The user defined ID is not shared. The identifier should be unique to the ImmPort workspace to which the data will be uploaded. Please enter either a biological sample user defined ID or ImmPort accession. A single biological sample may be linked to an experiment sample.
Type	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one)	Text, max 50 characters Controlled vocabulary — value must be one of lk_sample_type Metadata column JSON: type (enum)	The sample types are adopted from Uberon, Cell and CHEBI ontologies. Please choose from the drop down list.
Subtype	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one) and Type = "other"	Text, max 50 characters Metadata column JSON: subtype (string)	Enter a sample type that is of finer resolution than the standard sample types provided. If the 'Biological Sample Type' is 'Other', then the sample subtype must be entered.
Biosample Name	Optional	Text, max 200 characters Metadata column JSON: biosampleName (string)	The biological sample name is a display name that is available when the data is shared, but it is not referenced by other data. The biological sample name is an alternate identifier that is visible when the sample is shared.
Biosample Description	Optional	Text, max 4000 characters Metadata column JSON: biosampleDescription (string)	The biological sample description is used to describe details of the sample not captured in other columns.
Subject ID	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one)	Text, max 15 characters Reference — must already exist (in this package or the workspace) as a subject Metadata column JSON: subjectId (string)	Please enter either a subject user defined ID or ImmPort accession for the subject from which the sample was derived. A single subject record is permitted.
Planned Visit ID	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one)	Text, max 15 characters Reference — must already exist (in this package or the workspace) as a planned_visit Metadata column JSON: plannedVisitId (string)	The link to a study's planned visit provides temporal context for a sample's derivation from a subject. Please enter either a study's planned visit user defined ID or ImmPort accession.
Study Time Collected	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one)	Number Metadata column JSON: studyTimeCollected (number)	Study time collected describes the time value for when a sample was derived from a subject. Please enter a number.
Study Time Collected Unit	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one)	Text, max 25 characters Controlled vocabulary — value must be one of lk_time_unit Metadata column JSON: studyTimeCollectedUnit (enum)	The time units are standard terms recommended by the HIPC Standards group. Please choose from the drop down list.
Study Time T0 Event	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one)	Text, max 50 characters Controlled vocabulary — value must be one of lk_t0_event Metadata column JSON: studyTimeT0Event (enum)	The time zero event refers to the study milestone upon which time is based. Please choose from the drop down list.
Study Time T0 Event Specify	Conditionally required when you are defining a new Biological Sample in this row (rather than referencing an existing one) and Study Time T0 Event = "other"	Text, max 50 characters Metadata column JSON: studyTimeT0EventSpecify (string)	Enter a time zero event if 'Other' is selected in column 'Study Time T0 Event'.
Experiment ID	Required	Text, max 100 characters Metadata column JSON: experimentId (string)	The experiment identifier must be stored in ImmPort or in the experiments.txt template. The experiment serves as the parent entity to bind assay results of a similar type together. Please enter either a experiment user defined ID or ImmPort accession.
Protocol ID(s)	Conditionally required when you are defining a new Experiment in this row (rather than referencing an existing one)	Text, max 15 characters Reference — must already exist (in this package or the workspace) as a protocol Metadata column JSON: protocolIds (array)	Please enter either a protocol user defined ID or ImmPort accession for a protocol that describes how the sample was derived and prepared. One or more identifiers can be entered per sample. Separate identifiers by semicolon (;). Please enter either a protocol user defined ID or ImmPort accession. This column is required when either the experiment or biological sample are new.
Experiment Name	Conditionally required when you are defining a new Experiment in this row (rather than referencing an existing one)	Text, max 500 characters Metadata column JSON: experimentName (string)	The experiment name is a display name that is available when the data is shared, but it is not referenced by other data. The experiment name is an alternate identifier that is visible when the sample is shared.
Experiment Description	Optional	Text, max 4000 characters Metadata column JSON: experimentDescription (string)	The experiment description is used to describe details of the experiment not captured in other columns.
Measurement Technique	Conditionally required when you are defining a new Experiment in this row (rather than referencing an existing one)	Text, max 50 characters Controlled vocabulary — value must be one of lk_exp_measurement_tech Metadata column JSON: measurementTechnique (enum)	The measurement technique describes the assay method. Choose from a drop down list.
Result Separator Column	Optional	Metadata column JSON: resultSeparatorColumn (string)	This pseudo column separates meta data from results. This pseudo column separates the results (lab tests) from the lab test panel meta data. It must always appear and be the column that appears immediately after the last meta-data column and before any result columns.
Gene Symbol Name	Required	Preferred vocabulary — reported value is kept; a preferred term from lk_analyte is filled in when it matches Result data column JSON: geneSymbolName (enum)	The NCBI Gene symbol for the gene being assayed. Please select a gene symbol from the list provided if the gene symbol matches your symbol or enter a symbol if there is not an appropriate one provided. This symbol is visible when the result is shared. If the gene sybmol is a NCBI Gene Symbol that is provided in the list, then the columns 'Gene Name' and 'Gene ID' will also be overwritten by the gene name and Entrez Gene ID provided by NCBI.
Value Reported	Required	Text, max 50 characters Result data column JSON: valueReported (number)	This value could be absolute or relative. For example, an absolute expression value could be 6 ng RNA/mg intestine. In this case, 6 should be entered in the 'Expression value of target RNA' column, while ng RNA/ mg intestine is in the 'Expression unit of target RNA' column. A relative expression value, like signal versus GAPDH, could be 2.07. In this case, 2.07 should be in the 'Expression value of target RNA' column, while relative to GAPDH is in the 'Expression unit of target RNA' column. A number is expected.
Unit Reported	Required	Text, max 200 characters Preferred vocabulary — reported value is kept; a preferred term from lk_pcr_expression_unit is filled in when it matches Result data column JSON: unitReported (enum)	The unit for the Expression Value Of Target Nucleic ACID. Please select a unit from the list provided if the unit matches your unit or enter a unit if there is not an appropriate one provided.
Gene ID	Optional	Text, max 10 characters Result data column JSON: geneId (string)	The NCBI Gene ID for the gene being assayed. A number is expected.
Gene Name	Optional	Text, max 4000 characters Result data column JSON: geneName (string)	The NCBI Gene name for the gene being assayed.
Other Gene Accession	Optional	Text, max 250 characters Result data column JSON: otherGeneAccession (string)	Additional identifier(s) for the gene being assayed.
Comments	Optional	Text, max 500 characters Result data column JSON: comments (string)	Comments captures additional descriptive information.