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MiSeq System Guide
During the run, the reagent chiller holds a single-use reagent cartridge. During the instrument wash, the
reagent chiller holds the wash tray. The software automatically lowers sippers into each reservoir of the
reagent cartridge at the appropriate time during a run depending on the process being performed.
To the right of the reagent chiller are form-fitted slots for the PR2 bottle and the waste bottle. The sipper
handle locks the bottles in place and lowers the appropriate sipper into each bottle. Reagents are pumped
through the sippers and fluidics lines, and then to the flow cell. Reagent waste is delivered to the waste bottle
throughout the process.
Figure 2 Reagent Compartment Components
A Reagent Chiller
B Sipper Handle (shown in raised position)
C PR2 Bottle
D Waste Bottle
E Reagent Cartridge
MiSeq Concepts
The following concepts and terms are common to the run setup steps on the MiSeq.
Concept
Analysis Workflow
Manifest
Reference Genome
Run Folder
Sample Sheet
Document # 15027617 v04 Material # 20024228
For Research Use Only. Not for use in diagnostic procedures.
Description
A secondary analysis procedure is performed by Local Run Manager. The analysis
workflow for each run is specified in the sample sheet or by the selected module.
The file that specifies a reference genome and targeted reference regions to be used in
the alignment step. For workflows that require a manifest, the manifest file is specified in
the sample sheet and copied to the manifest folder designated in MCS. Manifest files can
also be loaded in Local Run Manager for use during secondary analysis.
A FASTA format file that contains the genome sequences used during analysis. For most
analysis workflows, the reference genome file is specified in the sample sheet.
The folder structure populated by RTA software (MiSeqOutput folder) or the folder
populated by Local Run Manager (MiSeqAnalysis). For more information, see
on page
47.
A comma-separated values file (*.csv) that contains information used to set up and
analyze a sequencing run, including a list of samples and their index sequences.
The sample sheet can be provided during the run setup steps on the MiSeq. After the run
begins, the sample sheet is renamed to SampleSheet.csv and copied to the run folders:
MiSeqTemp, MiSeqOutput, and MiSeqAnalysis.
Run Folders
4
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