MiSeq Sequencing v2.0 Protocol

1. | In Lab View, locate the MiSeq Sequencing v2.0 protocol. Samples are queued for the Library Pooling (MiSeq v2.0) step. Select the step to proceed to the Queue screen. |
2. | On the Queue screen, do as follows. |
a. | Add the samples to the Ice Bucket. |
b. | In the Add Control Samples panel, add the PhiX v3 control sample to the Ice Bucket. |
c. | Select View Ice Bucket. |
3. | On the Ice Bucket screen, select Begin Work. |
4. | On the Pool Samples screen, do as follows. |
a. | Create a pool of samples by dragging samples into the Pool Creator. |
b. | Name the pool or accept the default name (Pool #1). |
c. | Select Place Samples. |
5. | On the Placement screen, do as follows. |
a. | Select the pool from the Samples to be Placed area and drag it to the container. |
b. | Select Record Details. |
6. | On the Record Details screen, select Next Steps. |
On the Assign Next Steps screen, next step is automatically set to Denature and Dilute (MiSeq v2.0).
7. | Select Finish Step. |

1. | In Lab View, locate the MiSeq Sequencing v2.0 protocol. The pooled samples are queued for the Denature and Dilute (MiSeq v2.0) step. Select the step to proceed to the Queue screen. |
2. | On the Queue screen, add the pool to the Ice Bucket, and then select View Ice Bucket. |
3. | On the Ice Bucket screen, select Begin Work. |
4. | On the Placement screen, do as follows. |
a. | Scan the MiSeq reagent cartridge barcode into the MiSeq Reagent Cartridge field. |
b. | Place the pool of samples into the reagent cartridge. |
c. | Select Record Details. |
5. | On the Record Details screen, do as follows. |
a. | In Reagent Lot Tracking, select the reagent lot used in the step. |
If the reagent lot is not listed, add/activate the lot on the Reagents and Controls screen.
b. | Populate the fields in the Step Details table, as needed. Workflow, Experiment Name, and Read 1 Cycles are required fields. |
c. | In the Sample Details table, enter the Final Loading Concentration. Select from the following preset options or enter a different value. |
• | 225 (for PCR-free workflows) |
• | 400 (for Nano workflows) |
d. | Select Generate MiSeq SampleSheet. |
Clarity LIMS generates the sample sheet and attaches it and a log file to placeholders in the Files area of the Record Details screen.
e. | Download the files and validate the format and content. |
6. | Select Next Steps. |
On the Assign Next Steps screen, samples are automatically assigned to the MiSeq Run (MiSeq v2.0) step.
7. | Select Finish Step. |

1. | In Lab View, locate the MiSeq Sequencing v2.0 protocol. The pool of samples is queued for the MiSeq Run (MiSeq v2.0) step. Select the step to proceed to the Queue screen. |
2. | On the Queue screen, add the pool to the Ice Bucket, and then select View Ice Bucket. |
3. | On the Ice Bucket screen, select Begin Work. |
4. | On the Record Details screen, the fields are read-only. When the run completes, the integration automatically performs the following actions: |
• | Populates the fields. |
• | Attaches files to the Illumina Run Report, Link to Run Folder, Run Parameters, and Run Info placeholders. |
• | Populates the fields in the Sample Details table. See MiSeq Integration v7.0 Configuration and User Interaction for details. |
The Log File is attached after the next step for samples is assigned by the Next Step - Advance automation. Make sure the Illumina Run Report has been attached before continuing.
5. | Select Next Steps. |
On the Assign Next Steps screen, the next step is automatically set to Mark protocol as complete.
6. | Select Finish Step. |