QIAseq miRNA Differential Expression

The workflow calculates differential expressions for expression tables with associated metadata using multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM). Both Grouped on Mature and Grouped on Seed expression tables can be used.

The expression tables are sent to:

To run the workflow, go to:

Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | QIAseq Sample Analysis (Image qiaseqrna_folder_closed_16_n_p) | QIAseq RNA Workflows (Image qiaseq_workflows_folder_closed_16_n_p) | QIAseq miRNA Differential Expression (Image qiaseqsmallrna_diffexpress_16_n_p)

Choose the expression data to be analyzed (figure 14.17). The workflow takes Grouped on mature, Grouped on custom database and Grouped on seed expression tables, but note that only samples generated using the same parameters should be analyzed together.

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Figure 14.17: Select the expression data to be compared.

Then select the QIAseq Small RNA Reference Data Set as in figure 14.18. You can download the Data Set if you have not done so before.

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Figure 14.18: Select and download if necessary the relevant Reference Data Set.

Following this, the parameters for the QIAseq miRNA Differential Expression need to be specified (figure 14.19).

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Figure 14.19: Selecting parameters for QIAseq miRNA Differential Expression.

Metadata table Select a metadata object that associates the selected input objects to metadata used by the RNA-Seq analysis.
Test differential expression due to Select the factor to be tested for differential expression.
Comparisons Select groups to be compared. It is possible to choose between "Across groups", "All group pairs", and "Against control group".
Control group If "Against control group" was selected in "Comparisons", a control group must be selected.

An example of a metadata table is shown in figure 14.20.

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Figure 14.20: Select the expression data to be compared.

Metadata is required when defining the experimental design in the Differential Expression for miRNA tool, and can be used to add extra layers of insight in the Create Heat Map for miRNA tool. To learn more about how to create a metadata table, how to import a metadata table, or how to associate data elements with metadata, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Metadata.html.

In the final step, standard result handling is performed: the selected parameters can be previewed, and an output location must be chosen.

The workflow will output the following files:

Launching using the QIAseq Panel Analysis Assistant

The workflow is also available in the QIAseq Panel Analysis Assistant (see QIAseq Panel Analysis Assistant) under miRNA.