How to create PCR sample manifest file using tube sorter add-on? – LabCollector

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How to create PCR sample manifest file using tube sorter add-on?

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SUMMARY:

On your PCR machine, you need to specify the map of the plate to ensure you name properly where are the samples located. Depending on this, after the PCR run the result file will be generated for each sample. To simplify this process you can generate a sample manifest file that has the plate map for the PCR samples to be run, using our tube sorter add-on.

Please follow the below step tp create the sample manifest file:

1. Upload Sample template file

2. Generate sample manifest file

  • A. Using a box/plate map in Storage.
  • B. Using Sample receiving

1. Upload Sample template file

  • In tube sorter add-on you need to go to “Setup” and then “Manage Templates”.
  • Here you can upload CSV or TXT file for your template. 

  • Tips/Hints
    You will find the the template for the run from your PCR machine. If needed we can assist you in adjusting the template according to your requirements.
  • You can also click on “find help” option to see the options to generate a sample manifest file. It will show you a pop up that will allow you to see which tags you can use in your sample manifest file.
  • This uploaded file will contain, information like the example in the below image. The position column will define the position of the samples in the plate. The rest columns will depend upon the PCR protocol and the requirements of your MACHINE.
    You can open the file in CSV if you like, but you need you delimit the CSV if you want to see it in the below format.
    *Please read our KnowledgeBase on how to delimit CSV.

  • When you have duplicates you can replicate the position of the well. As you observe in the above example image. 
  • The position in these hash tags will be automatically taken from the LabCollector storage system. This part is explained in the next section.
  • Once you have updated the template and uploaded it in tube sorter then you can easily use this template for all the sample runs that you perform in your PCR.
  • You can upload several template and different sizes of PCR like 96 or 384, and also merge plates using tube sorter.

2. Generate sample manifest file

A. Using a box/plate map in Storage

  • In LabCollector storage you can create boxes or plates with samples in specific positions and you can use these to create you sample manifest files. You can create plates or boxes and add specific samples at respective positions. 
    *In order to create your boxes or plates please read the Knowledgebase on how to set up LabCollector storage.
    *Please refer to our knowledgebase on how to generate model boxes.
  • Tips/Hints
    You can name the plate according to the date, to keep them segregated or a create a fake location in lab to store all the plates that you are going to do a run for, so that that after you can delete them. 
    The boxes even though in storage browser can have imaginary boxes or plates, just for creating sample manifest files. 
    You can create sample manifest files using sample receiving add-on too. The process for same is explained below in section 2 Part B.
  • Once you have created the box/plate for your PCR with samples in specific positions then you also block the wells for the control samples. This way no samples will be store even accidently in those positions.
  • Warning
    When you create a model for the plate for PCR and you want to block the wells, then this will be only possible with the BOX model and not the Plate model.
  • To block the position you just need to select the cells by clicking on + sign and update the box like the steps explained below.
    If you want to remove the blocked positions you can also click on 3Clear all blocked positions and update model.
  • To create a sample manifest file using tube sorter, go to the add-on and on home page click on “Generate sample manifest file”. 
  • You will see the below page, where you need to find the box/plate name that you created before; You can even add several plate together by clicking on the small + sign. Once you have selected the box/plate 
  • Once you click next, you will see the information about samples inside the box or plate;
    1. you can select the sample manifest file using the dropdown list (the one you uploaded in section 1 above),
    2. Mix plates allows you to select several plates and mix the position of samples in them with separator of your choice. For example, when you mix, you will see
      Plate_1 Position A1 with Plate_2 Position A1 or 
      Plate_1 Position A2 with Plate_2 Position A2, etc.
    3. You can have an intermediate header, meaning if you select several plates without mixing them, then the plates are repeated in the template. This options allow the headers to be present between each plate to separate them from each other. If you dont select this option then the headers for each plate will not appear in between the templates.
    4. and click on generate manifest file.
      *The empty places in  the plates will look empty & will have the comment “Not found” under the column rack/tray.
      The hashtag position will filled with the sample name  in the sample manifest template.
  • When you click on the generate manifest file button, you will see a pop-up to save the file in txt format. You can also open the txt or change the name of your file by changing the extension from .txt to .csv while saving the file.
  • This is the file you need to transfer manually into the PCR machine for the run.

B. Using Sample receiving

  • You can create boxes/plates directly inside the sample receiving add-on.
  • In sample receiving you can configure the settings for your project. Here you can choose a model box that you create in ADMIN -> STORAGE -> MANAGE STORAGE-> MODELS.
    *Please read our knowledgebase on how to configure sample receiving.
  • You can create a package in which you can create a plate.
    *Please read our KnowledgeBase on  how to create package and process it.
    *Please read our KnowledgeBase on how to process plates in sample receiving.
  • You can scan you samples barcode to add samples in the different well position that you want.
    *If you have a box then while making a model you can block positions for the control samples, if they are always put in the same place. Explained in section 2 above.
  • You can save this box in an imaginary or fake room and equipment and use it to create the sample manifest file. Like the process explained in section 3 A.
  • The sample manifest file you generated then needs to be transferred into the machine manually.

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