Assay Workflows

Every assay follows the same basic pattern. The differences are which reagents template it uses and how its results are submitted.

flowchart LR
    subgraph PKG ["Upload together in one package"]
        direction LR
        T[treatments] --> R["reagents.*"] --> E["experimentSamples.*"]
    end
    E --> F[result files]
    E --> O["result template<br/>(optional)"]

Before you start, make sure the study, its subjects and the protocols that experiments refer to are already uploaded or in the same package. See Upload Order.

How to read a workflow: a dashed box groups the templates that must be uploaded in the same package (rule R-10). A step with an amber If: line is only needed when that condition applies. Grey steps are your own files rather than ImmPort templates. When two steps both start with If:, use one or the other. Click any template name to see its fields.

Expand all

CyTOF (mass cytometry) ELISA ELISPOT Flow cytometry Gene expression array Genotyping array Hemagglutination inhibition (HAI) HLA typing Image histology KIR typing Multiplex bead array (MBAA) Mass spectrometry: metabolomics Mass spectrometry: proteomics Neutralizing antibody titer qRT-PCR RNA sequencing Virus neutralization Other assay types

CyTOF (mass cytometry) .fcs files

treatments.txt

reagents.CyTOF.txt

Reagent_Sets.txt

experimentSamples.CYTOF.txt

Raw .fcs files

CyTOF_Derived_data.txt

Original flow diagram (PDF)

ELISA results in template

treatments.txt

reagents.ELISA.txt

experimentSamples.ELISA.txt

ELISA_Results.txt

Original flow diagram (PDF)

ELISPOT results in template

treatments.txt

reagents.ELISPOT.txt

experimentSamples.ELISPOT.txt

ELISPOT_Results.txt

Original flow diagram (PDF)

Flow cytometry .fcs files

treatments.txt

reagents.Flow_Cytometry.txt

Reagent_Sets.txt

experimentSamples.Flow_Cytometry.txt

Raw .fcs files

FCM_Derived_data.txt

Original flow diagram (PDF)

Gene expression array results file

treatments.txt

reagents.Array.txt

experimentSamples.Gene_Expression_Array.txt

Your results file(s)

publicRepositories.txt

Shares the array reagents template with genotyping arrays.

Original flow diagram (PDF)

Genotyping array results file

treatments.txt

reagents.Array.txt

experimentSamples.Genotyping_Array.txt

Your results file(s)

publicRepositories.txt

ImmPort does not normally accept GWAS-level human genotyping data. Deposit it in dbGaP and link to it.

Original flow diagram (PDF)

Hemagglutination inhibition (HAI) results in template

treatments.txt

reagents.HAI.txt

experimentSamples.HAI.txt

HAI_Results.txt

Original flow diagram (PDF)

HLA typing template or file

treatments.txt

reagents.HLA_Typing.txt

experimentSamples.HLA.txt

HLA_Typing.txt

Your own results file(s)

Original flow diagram (PDF)

Image histology results file

treatments.txt

reagents.Other.txt

experimentSamples.Image_Histology.txt

Your results file(s)

Original flow diagram (PDF)

KIR typing template or file

treatments.txt

reagents.KIR_Typing.txt

experimentSamples.KIR.txt

KIR_Typing.txt

Your own results file(s)

Original flow diagram (PDF)

Multiplex bead array (MBAA) template or file

treatments.txt

reagents.MBAA.txt

experimentSamples.MBAA.txt

MBAA_Results.txt

Your own results file(s)

standardCurves.txt

controlSamples.txt

Standard curves and control samples are independent optional additions: include either, both or neither.

Original flow diagram (PDF)

Mass spectrometry: metabolomics template or file

treatments.txt

reagents.Other.txt

experimentSamples.Mass_Spectrometry_Metabolomics.txt

Mass_Spectrometry_Metabolomic_Results.txt

Your own results file(s)

Original flow diagram (PDF)

Mass spectrometry: proteomics template or file

treatments.txt

experimentSamples.Mass_Spectrometry_Proteomics.txt

Mass_Spectrometry_Proteomic_Results.txt

Your own results file(s)

Proteomics has no reagents template, unlike metabolomics.

Original flow diagram (PDF)

Neutralizing antibody titer results in template

treatments.txt

reagents.Neutralizing_Antibody_Titer.txt

experimentSamples.Neutralizing_Antibody_Titer.txt

Virus_Neutralization_Results.txt

Original flow diagram (PDF)

qRT-PCR results in template

treatments.txt

reagents.PCR.txt

experimentSamples.QRT-PCR.txt

PCR_Results.txt

Original flow diagram (PDF)

RNA sequencing template or file

treatments.txt

reagents.Sequencing.txt

experimentSamples.RNA_Sequencing.txt

RNA_SEQ_Results.txt

Your own results file(s)

publicRepositories.txt

Original flow diagram (PDF)

Virus neutralization results in template

treatments.txt

reagents.Virus_Neutralization.txt

experimentSamples.Virus_Neutralization.txt

Virus_Neutralization_Results.txt

No flow diagram is published for this assay. It follows the same pattern as the other titer assays. Ask the helpdesk if your data doesn't fit.

Other assay types results file

treatments.txt

reagents.Other.txt

experimentSamples.Other.txt

Your results file(s)

Use this when no other workflow matches. If you're not sure, ask the helpdesk before preparing the package.

Original flow diagram (PDF)

Results: template or file?

• ELISA, ELISPOT, HAI, neutralizing antibody titer, qRT-PCR, virus neutralization: the experiment samples template has result columns. Filling them in is recommended. Use the separate results template only if you leave those columns empty.
• HLA, KIR, MBAA, mass spectrometry, RNA sequencing: set the experiment samples column ImmPort Template? to Yes and include the ImmPort results template (recommended), or set it to No and give your own file in Result File Name. Don't provide both (error E-31).
• CyTOF, flow cytometry, arrays, image histology, other: upload your own files. Derived-data and public-repository templates are optional extras.