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[Download the PDF]({{ '/presentations/miso_samples.pdf' | prepend: site.baseurl }})

Table of Contents
  1. Logging In
  2. Receiving Samples
  3. Propagating Samples
  4. Adding Sample QCs
  5. Scanning samples into the outbox
  6. Troubleshooting
Print the worksheet for this section here: Samples Worksheet.

{% include logging_in.md detailed=page.is-detailed %}

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2. Receiving samples

A sample contains information about the material upon which the sequencing experiments are to be based. Samples can be used in any number of sequencing experiments in the form of a library that is processed further into single or pooled library aliquots.

Every received sample must have an identity. The identity corresponds to the individual or organism from whom the sample originated, i.e. the donor. MISO requires you to assign an external name, which is usually an identifier from another institution like a Donor ID.

When sample material is received, it may come in many different forms, called sample classes in MISO. Sample classes are divided into sample categories, including

  • Tissue
  • Tissue Processing
  • Stock
  • Aliquot

Depending on which sample category is chosen, different fields appear on the Create Sample page, as these categories have different information associated with them.

In this workshop, we will create six samples with four different identities in the project you created in the last session.

2.1 Entering a Tissue

All samples in MISO are entered using the bulk entry screen. We will start by entering a single tissue sample from the donor PROJ_ID1.

{% include samples-receiving.md detailed=page.is-detailed %} 1. External Name: this is the name of the individual donor, whether internal or external. For example, an external name would be "Morgan" (internally we refer to her as plain ol' MORG_0001). * Enter PROJ_ID1 in the External Name field, replacing PROJ with your project's short name. Record this in your worksheet. * Once you enter an external name, MISO will go and find any existing donors with external name(s) that match this, and will add them to the dropdown menu for the Identity Alias field. * If there are no existing donors with the exact external name, the option of First Receipt (project short name) will be available. * If more than one option is available in the Identity Alias dropdown, the cell will be displayed with a light purple background. 1. Select First Receipt (project short name) for the Identity Alias. 1. Donor Sex: Select any item from the dropdown. 1. Tissue Origin: {{ site.tissue_origin_1 }} 1. Tissue Type: {{ site.tissue_type_1 }} 1. Times Received: 1 1. Tube Number: 1 1. Secondary ID: BioBankID 1. This is the Biobank ID or Tube ID. It may also be left blank. 1. Material: Select any from the drop-down. 1. Timepoint: T1 1. QC Status: select Ready from the drop down.

  1. At the upper right hand side, click Save.

Upon saving, a number of fields will be filled in, including the sample ID, name, and alias. The name will be in the form "SAM123", where "123" is the ID. This is a unique identifier for the sample within MISO. The alias will be generated based on the naming scheme configured for your site. This is a more human-friendly identifier for the sample. Record the alias in your worksheet.

2.2 Automatically created Samples

  1. Click the Projects link under Preparation in the menu on the left side of the screen and select your project from the list.
  2. Open the Samples section on the Edit Project page to see your newly created samples.

You can also find your samples by searching on the Samples page or by using the widget on the MISO front page; however, the widget does not show enough information for the following exercises.

You only created a single sample but at least two are in this list: the {{ site.tissue_class }} as well as the {{ site.identity_class }}. The {{ site.identity_class }} sample was automatically created because you provided an External name that had not been previously used in this project. Other types of samples are created automatically depending on how you propagate them through to libraries. Some of them will be addressed in the following tutorials.

2.3 Entering bulk Tissues

Next, we will create four more {{ site.tissue_class }} samples for individuals 1-4.

{% include samples-receiving-bulk.md detailed=page.is-detailed %}

If you navigate back to your Edit Project page, there should be nine samples:

  • 4 {{ site.identity_class }} samples
  • 5 {{ site.tissue_class }} samples

2.4 Receipt Transfers

{% include receipt-transfer.md detailed=page.is-detailed items_exercise="2.3" type="sample" type_plural="samples" %}

2.5 Receiving Stock DNA/RNA

The process for receiving stock is very similar to receiving tissue. Every stock derives from a tissue, which originated from an {{ site.identity_class }}. MISO will automatically create a tissue for you when you enter a stock. This tissue does not represent a sample that is present at your site, but is created so that tissue-level information about the sample can still be recorded. This tissue sample is referred to as a ghost sample.

In this section, we will 'receive' a single stock DNA tube from the tissue material of an existing identity.

  1. On the left hand menu under Preparation, click Samples.
  2. Click the Create button at the top left of the table.
  3. Select Sample Category Stock and Quantity 1.
  4. Click Create.
  5. In the table, enter or select the following:
  • Sample Name: Leave blank. This will be auto-generated after save.
  • Sample Alias: Leave blank. This will be auto-generated after save.
  • Description: Stock 1.
  • Date of receipt: Select a date.
  • Received From: Select any lab.
  • Received By: Select any group.
  • Project: Select your project's short name from the drop-down.
  • Subproject: Select the subproject you created.
  • Sample Class: Select {{ site.stock_class }} from the drop-down.
  • Sample Type: Select GENOMIC from the drop-down.
  • Scientific Name: {{ site.scientific_name }}.
  • External Name: PROJ_ID2 (where PROJ is your project's short name).
  • Identity Alias: The existing identity should be selected automatically in the dropdown menu.
  • Tissue Origin: {{ site.tissue_origin_3 }}
  • Tissue Type: {{ site.tissue_type_1 }}
  • Times Received: 1
  • Tube Number: 1
  • Secondary ID: BioBankID 6.
  • Timepoint: T1
  • STR Status: select any value from the dropdown menu.
  • Volume: 300
  • Vol. Units: µL
  • QC Status: select {{ site.detailed_qc_status_good }} from the dropdown.
  1. At the upper right hand side, click Save.

When you click 'Save', the name and alias will be filled in. Record the external name, sample class, and alias in your worksheet.

After saving, go back to your project page and look at the samples that were automatically created. Although you received a {{ site.stock_class }}, it has created a {{ site.tissue_class }} for you as well.

  1. Click on the tissue with tissue origin {{ site.tissue_origin_3 }} and tissue type {{ site.tissue_type_1 }}.

At the top, you will see a grey section with the warning: "This entity does not exist except for sample tracking purposes!". This indicates that it is a ghost sample used only for informational purposes, and is not a physical sample that could be found on premises.

2.6 Scanning tissues and stocks into a Box

In this section we will add the stocks and tissues you just received into your inbox for further work.

{% include inboxes.md %}

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3. Propagating Samples

Samples in MISO exist for each step of the sample preparation process: from identity, to tissue, optionally through tissue preparation, to stock, to aliquot. At each step, the possible options are limited based on the established workflows. Group IDs may be assigned at any time and are copied when propagating. Different QC information is available at each step. For instance, STR status is attached to the stock.

3.1 Propagating to Tissue Processing

Tissue processing is an optional step between the tissue and stock levels of the sample hierarchy. It includes steps such as slides and laser capture microdissections created from the tissue.

Create a {{ site.slide_class }} from one of your Tissue samples.

  1. On the Samples page, enter your project short name in the search box.
  2. Check the box for the {{ site.tissue_class }} you created in exercise 2.1. It will have tissue origin {{ site.tissue_origin_1 }} and tissue type {{ site.tissue_type_1 }}.
  3. Click the Propagate button at the top left of the table.
  4. Enter 1 replicates to Tissue Processing.
  5. Click Propagate.
  6. Fill out the table:
  • Description: CV Slides
  • Sample Class: {{ site.slide_class }}
  • Sample Type: OTHER
  • Slides: 3
  • Stain: Choose any option from the dropdown.
  • QC Status: {{ site.detailed_qc_status_good }}
  1. Click Save.

Upon successful save, a green status bar will show at the top that says "Saved 1 items". The sample name and alias will have been filled in automatically. Record the alias in your worksheet.

3.2 Bulk Propagate Samples

For three of the {{ site.tissue_class }} samples created previously (by bulk entry), we will create stocks for library preparation.

  1. On the Samples page, enter your project short name in the search box.
  2. Check the boxes for any three of the the {{ site.tissue_class }} samples with tissue type {{ site.tissue_type_2 }} that you created in section 2.3.
  3. Click the Propagate button at the top left of the table.
  4. Enter 1 replicates to Stock.
  5. Click Propagate.
  6. Fill out the table:
  • Matrix Barcode: Choose a barcode for each stock. If you were not given barcodes to use, enter the following instead, replacing PROJ with your project's short name. Record the barcodes on your worksheet. * PROJ-301 * PROJ-302 * PROJ-303
  • Sample Class: {{ site.stock_class }}
  • Sample Type: Select any value if one is not selected automatically.
  • STR Status: Select any value from the drop-down.
  • Volume: 300
  • Vol. Units: µL
  • QC Status: Not Ready
  1. Click Save.

Upon successful save, a green status bar will show at the top that says "Saved 3 items". The sample names and aliases will have been filled in automatically. Record the aliases in your worksheet.

3.3 Bulk Editing

Samples can be edited in bulk. Assume that we have done some quality control and wish to update the QC status of the samples.

In this case we will update several fields of 4 stock samples. We will use the stocks we entered in the previous step as well as the reference stock entered in part 2.4 of this tutorial.

  1. On the Samples page, enter your project short name in the search box.
  2. Check the boxes for the {{ site.stock_class }} samples (propagated and received) that you created in sections 2.4 and 3.2.
  3. Click the Edit button at the top left of the table.
  4. Add a Concentration value: any number
  5. Change the QC Status column to Ready for all rows.
  6. Enter a Matrix Barcode for the stock entered in section 2.4. If you weren't given a barcode to use, enter PROJ-401, replacing PROJ with your project's short name. Record the barcode on your worksheet.
  7. Click Save.

Upon successful save, a green status bar will show at the top that says "Saved 4 items.".

3.4 Creating Aliquots

Propagate again from the 4 {{ site.stock_class }} samples to {{ site.aliquot_class }}.

  1. If you are continuing from the end of section 3.3 Bulk Editing, do not navigate away from the page.
    1. At the top left of the table after saving samples, click the Propagate button and continue to step 3.
  2. Otherwise, select samples using the following:
    1. On the Samples page, enter your project short name in the search box.
    2. Check the boxes for the {{ site.stock_class }} samples.
    3. Click the Propagate button at the top of the table.
  3. A dialog will appear. Select 1 replicate to Aliquot and click Propagate.
  4. Fill out the table:
    • Sample Alias: Skip this field. It will be automatically filled in upon save.
    • Matrix Barcode: choose a barcode for each aliquot. If you weren't given barcodes to use, enter the following instead, replacing PROJ with your project's short name. Record the barcodes on your worksheet.
      • PROJ-501
      • PROJ-502
      • PROJ-503
      • PROJ-504
    • Sample Class: Select {{ site.aliquot_class }}.
    • Sample Type: Select any value if one is not selected automatically.
    • QC Status: Select {{ site.detailed_qc_status_good }}.
    • Purpose: Select any option from the dropdown.
  5. Click Save.

Upon successful save, a green status bar will show at the top that says "Saved 4 items". Buttons to allow editing the samples or propagating them will show at the top of the table. The sample names and aliases will have been filled in automatically. Record these on your worksheet.

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4. Sample QCs

4.1 Adding Sample QCs

{% include bulk-qc.md detailed=page.is-detailed items_section="3.4" type="sample" type_plural="samples" %}

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5. Scanning aliquots into outboxes

{% include outboxes.md %}

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5. Advanced Search

Some of the list pages feature advanced search functionality which allows you to narrow down the items displayed by specifying which attributes you would like to search by. Any list featuring advanced search will display a question mark in a black circle beside the Search bar.

  1. Go to the Samples list page.
  2. Hover your mouse over the question mark icon beside the Search box. The list of search terms that you can use is displayed.
  3. Click the question mark icon. A dialog appears describing the search syntax in more detail.
  4. Click the X in the top right corner of the dialog to dismiss it.
  5. In the Search box, type PROJ entered:today is:real, replacing PROJ with the short name of your own project, and hit Enter on your keyboard. All of the samples you created in your project today will appear. The ghost samples that were automatically created will be excluded from the list.

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Troubleshooting

{% include samples-trouble.md detailed=page.is-detailed %}

How do you work with multiple samples derived from the same identity (i.e. DNA and RNA from one tissue slide, DNA from metastasis and control)

On the Samples page, you can enter the identity's alias into the search box to filter the list. If the samples you are looking for have more of their alias in common, you can enter as much as they share to further narrow the search. e.g. to find all stock samples made from tissue PROJ_0001_04, you could search for PROJ_0001_04.

Once you have found all of the samples you wish to work with, select them by clicking the checkboxes on the left, and choose a bulk action from the menu at the bottom.

How do I correct a sample that has the wrong information, e.g. wrong tissue type?

Most sample attributes may be modified either individually, or in bulk. To access the Edit Sample page for a single sample, click the sample's name or alias on the Samples page. To bulk edit a set of samples, click the checkboxes next to them on the Samples page and click Edit at the top left of the table.

For attributes which cannot be changed via MISO (e.g. Sample Class), {{ site.miso_admin_contact }} for help. This may require deleting and re-creating the sample.

What if I need to change the parent of a sample? (e.g. for swaps)

A sample's parent cannot be changed. You will have to delete and re-create the sample by propagating from the correct parent sample.

How can I add a new lab, tissue material, tissue type, tissue origin, or add anything else in drop-down menus?

Some of these items can be added directly:

  1. From the Misc or Configuration section of the menu, click the category of interest.
  2. Click Add from the toolbar.
  3. Enter the appropriate information.
  4. Click Create.

For items that you are not able to add yourself, please {{ site.miso_admin_contact }} for assistance.

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