LynchLab-Sample-Processing
Here you will learn all things Sample Processing
View the Project on GitHub lynchlab-ucsf/LynchLab-Sample-Processing
Platforms Used by Lynch Lab
Claire Schachtschneider 2021
Key Links:
Introduction to Sample Intake (click link to go to section)
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Description and Intro
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Visual Diagram
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Projects and Sample Check-in/Check-out
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Progress Tracker
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Description and Intro
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Visual Diagram
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Account Navigation
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Entries and Use
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Description and Intro
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Visual Diagram
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Sample intake
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Printing Labels
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Freezer Catalog
A. Introduction to Sample Intake or “Check-in”
For any sample intake done in the Lynch Lab, you will need to follow these guidelines:
- Whoever receives the shipment from the carrier service is responsible for the intake of those samples (unless determined otherwise).
- Unpack the box and keeping samples on dry ice to double-check that all vials match the manifest included in shipment – ensure no damage.
- Complete intake with eLabJournal and Lynch Lab Airtable. Instructions listed below in 1c and 3c.
- Transfer samples into new freezer storage box and create a box label with the Dymo Printer at Lab Manager’s Desk. Ex) Project Name, Sample Type, Date, Initials.
- Store in designated project rack within -80 freezer (can be located on eLabJournal).
1. Airtable
a. Description and Intro
AirTable is used for a variety of tasks to keep track of projects, protocols, and sample check-in/check-out.
Navigate to the Lynch Lab Airtable by logging in with the lab login credentials supplied in the Lab Etiquette Document. You will see a variety of bases that are accessible depending on your needs. The most common bases used will be Project-specific Bases, Lynch Lab Airtable, Lynch Lab Microbial Strain Collection, Lab Meeting Schedule, and Protocols. The Lynch Lab Airtable base and Project-specific bases are for sample check-in/check-out (including eLabJournal), experiment progress tracking, and any study relevant documents.
b. Visual Diagram
c. Projects and Sample Intake:
To add a new project and samples to the Lynch Lab Airtable, you will need to follow the steps listed here:
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- ** After intake with eLabJournal! **
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- Navigate to your project-specific base and fill in fields under “Sample Check-in/Check-out” tab
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- Navigate to the Progress Tracking tab and add a new Processing ID number by scrolling down to the last entry and then filling in a new row of fields according to the column name.
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- Always add date samples are returned to collaborators by filling in “sample return date” and supplying any tracking information or email correspondence.
d. Progress Tracker and Results
Progress Tracker and Results tabs are used to view the current step of each project and samples. To make a new entry in Progress Tracker:
- Enter info into fields (Processing ID, Project Name, Processed by, Date of Experiment, Processing Type, Current Step in Pipeline, Protocol log (link to Benchling experiment entry), Notes of changes, Mapping File, and Current Freezer Location)
- A new entry should be created with every new batch of samples processed*
Keeping up-to-date:
- Update current step in pipeline, add additional links for Protocol Log, add Mapping file when necessary, and New Freezer Location when moved around from -80 to -20.
- Results will automatically populate. This tab will mainly be used by Katie and Sue to view current project progress.
2. Benchling :
a. Description and Intro
Benchling is used as an electronic lab notebook. Here you will input your experiment notes according to the specific project and the assigned processing ID
Lynch Lab Projects page breaks into a variety of folders for each project. You can navigate through the directories according to: Lynch Lab Projects, Project folder, Processing IDs folder, and specific ID # folder for your experiment log. Processing ID folder will house the specific electronic lab notebook for your experiments performed.
b. Visual Diagram
c. Account Navigation
- Login to Benchling with your personal credentials. An invitation will be send to you by the admin of our group. Once logged in you will be able to go through various projects and experiments. All personal experiments are on read-only for other lab members. Only you will have the ability to edit your own documents.
d. Entries and Use
- Navigate through Projects to Processing IDs and then to the specific processing ID # folder.
- Create a new blank entry for yourself in the Processing IDs directory by clicking the plus sign on the upper left side of the page. Click on entry, then “Entry From Template”
- Name the entry by the assigned processing ID number listed in Airtable (example as WISC: ID1)
- Start inputting your protocol by uploading your protocol documents to “add protocol” tab
- Fill in the “Notes” tab with your experiment notes and information necessary. It is very important to you keep the log of specific samples used by filling in the template’s fields.
- This can now only be edited by you but can be viewed by any user in our group.
3. Elabjournal :
a. Description and Intro
ElabJoural is our sample intake and freezer inventory platform. Here you sample intake, print labels, and assign a permanent home for samples logged. It is the interface between Airtable and organization of samples.
b. Visual Diagram
c. Sample intake
Prior to Sample Intake: Create an excel file containing separate columns for: Name, Description, Project, Specimen ID, Sample ID, intake date, and date of collection (if info is available on manifest). This will be used for the import process.
- Name should be the Sample ID number (if Sample ID and Specimen ID are the same, then use Specimen ID as name)
- Description should be sample type
- Project is the designated project name
- Specimen ID is the Participant ID or whatever identifier given by collaborator.
- Intake date
- Date of Collection (if given by collaborator)
Sample Intake:
- Navigate to “Sample List” and click “Import Samples”.
- Enter number is samples to import, check the “Associate External Barcode” box, give the new samples a location within a freezer rack, and indicate the sample type.
- A new field will appear for you to select the desired fields for each sample for intake. Select: Name, Description, Project, Specimen ID, Sample ID, intake date, and date of collection (if info is available on manifest)
- Click “Start Import”
- Click “Paste from Clipboard” and paste sample information from excel sheet (with the correct order of column names).
- Click “Paste” and it will automatically fill each column for you, including all field you selected. Double check each field/column to verify accuracy.
- Click “Import” and all of your samples will be cataloged in eLabJournal.
d. Printing Labels
If you need to print sample vial labels for any reason you will need to:
- Navigate to Sample List or the freezer location of your samples
- Check the boxes of the samples you need labels for
- Click “Sample Actions” then “Print Label”
- Select “Dymo Printer”
- Select desired label type (Tube Label 2021, Box Label, etc.)
- Select quantity of each needed and press “Print”
- Adhere to tubes but make sure to wipe off any frozen surface or else it won’t stick!
e. Freezer Catalog
- Navigate to “Inventory” tab and then to the “Inventory Browser”
- You can navigate by freezers, sample names in the search bar, or however you prefer to get around the site.
- To add a rack or box to a specific freezer you will need to navigate to that Freezer # and the shelf desired
- Click the orange “+Add” button and select “add rack” or “add box”
- Input the info required and make sure to label by: Project, Sample Type, Experiment Step, Date, and your initials!!