Arrays tutorial

1. Logging in

You need to log in to MISO LIMS in order to make changes to any LIMS entities. Logging in lets MISO record any changes you make on entities you have access to.

If you are a new user and have not been given a username and password, you will first need to contact your MISO administrator to get a username and password.

Try to log in now:

  1. Click on https://misodev.pmgenomics.ca.
  2. Enter your username (e.g. jdoe) and password and click the Login button.

If all goes well, you should see the MISO Dashboard and see a message at the top right: "Logged in as: jdoe".

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2. Projects

A Project contains information about a set of Studies that may comprise many different Samples, Experiments and Runs. Samples are attached to Projects and they are often processed into Libraries and then Library Aliquots, which are then Pooled and sequenced. We will create a new project for our Array Samples.

2.1 Creating a new project

To create a new project:

  1. After logging in, click the Projects link under Preparation in the menu on the left side of the screen.
  2. Click the Add button at the top left corner. The Create Project page will display with a number of fields that you can fill in.
  3. Ignore Project ID and Name, since they are set by MISO once the Project is saved.

  4. Enter a unique Alias. The alias is a name, chosen by us, that is associated with a project. e.g. Do It 4 Science (be creative!).

  5. Leave the Short Name field blank.

  6. In the Description field, enter MISO training workshop [Date]
  7. For the Progress field, choose Active
  8. Select the Reference Genome GRCh38. This should be the primary species that will be sequenced in the course of the project. Xenografts count as human.
  9. Select the Pipeline Default. This value identifies the analysis pipeline to put sample data through after sequencing
  10. Click the Save button at the upper right.
  11. MISO will generate an ID and name for the project. The name will be 'PRO' followed by the ID (e.g. "PRO123").

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3. Samples

Next, we will create the samples to be run in our array.

3.1 Receiving Samples

  1. In the left hand menu under Preparation, click Samples.
  2. Click the Create button at the top of the table.
  3. In the dialog that appears, select Sample Category: Aliquot, and Quantity: 8, and click Create.
  4. Select or enter the following data for all samples:
    • Received From: Select any lab.

    • Project: select your project

    • Sample Type: GENOMIC

    • Sci. Name: Homo sapiens

    • QC Status: Ready to proceed
  5. Enter a Sample Alias in the form "PROJ_S#_#" for each sample. Replace "PROJ" with the short name of your project, and replace the "#" symbol with numbers of your choosing.
  6. Enter "PROJ_1" for the Matrix Barcode of the first sample, replacing "PROJ" with your own project's shortname.

  7. Enter "PROJ_2", "PROJ_3", etc… for the Matrix Barcode of each remaining sample, incrementing by 1 each time so that they each have a unique Matrix Barcode.

  8. Click Save at the top right.

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4. Arrays

An Array represents a chip which can have Samples added to it to be run on an Array Scanner. Arrays can have different layouts depending on the chip model.

4.1. Create an Array

  1. On the Arrays page, click the Add button
  2. Choose Array Model "Infinium MethylationEPIC-8 BeadChip."
  3. Enter a unique Alias and Serial Number for your Array
  4. Click Save. The array must be saved before samples can be added to it
  5. Add the samples that you created in the previous exercise to the Array. The user interface is similar to Boxes:
    1. Select an empty position on the array, which will appear as a grey circle
    2. In the Search box to the right, enter the Name, Alias, or Barcode of the Sample you wish to add. It is easiest to use the barcodes. If you had a barcoded tube, you could just scan it into the search box. For this exercise, just type it in. Your sample barcodes should be in the form "PROJ_1", "PROJ_2", etc., where "PROJ" is the short name of your project.
    3. Press Enter or click the Lookup button
    4. Your Sample should appear in the Results dropdown. Click Update position to add it to the array
  6. Repeat for the other samples

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5. Create an Array Run

  1. On the Array Runs page, click the Add button
  2. Choose an Array Scanner Instrument. If there are no options in this list, ask your MISO administrator to add an Array Scanner to MISO
  3. Enter a unique Alias for your Array Run
  4. Enter "/path/to/run" for the the Run Path (directory)
  5. In the Array Search box, enter the Alias or Serial Number of your Array
  6. Press Enter or click the Search button
  7. Your Array should appear in the results dropdown. Click Apply
  8. Select Status: Running
  9. Enter today's date as the Start Date of the Array Run
  10. Click Save
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