Tutorials

July 20, 2016

The content of these step-by-step tutorials is mostly covered also in the webinars.

1. Single plasmid registration

  1. Go in Inventory -> Materials-> Plasmids -> Plasmid collection 1plasmid_collection
  2. Click the + on top of the page
  3. In the sample form enter:
    • Name: FRP1639
    • Backbone: choose “pBluescript II KS+”
    • Bacteria antibiotic resistance: choose “bla”
  4. Click Create Sample at the bottom of the page.

2. Multiple plasmids registration

Option 1: identifiers provided by users

  1. Go to Inventory -> Materials-> Plasmids -> Plasmid collection 1
  2. Select Batch Register Samples from the Operations dropdown menu
  3. Select the sample type Plasmid
  4. Download the template .tsv file
  5. Open the file with Excel
  6. Fill in the following fields :
    • identifier: /MATERIALS/PLA2 (in first row), /MATERIALS/PLA3 (second row)
    • parents: /MATERIALS/PLA1 [Note: to assign parents, the identifier of the parents need to be provided. Multiple parents should be entered separated by commas.]
    • experiment: /MATERIALS/PLASMIDS/PLASMID_COLLECTION_1 (first and second row). [Note: the experiment is found on top of the Plasmid collection 1 page. It is important to always provide this information in the file.]
    • NAME: pRG207 (first row), FRP1625 (second row)
    • MARKER: HYGMX (first and second row)
    • SOURCE: Addgene(first and second row)
    • ANNOTATIONS_STATE:PLASMID: identifier:/MATERIALS/PLA1;COMMENTS:test. [Note: this field allows to add annotations to parents. The syntax for adding annotations to multiple parents is: identifier:xxx;COMMENTS:xxxx\identifier:yyy;COMMENTS:yyyy]
  7. Save the file and upload it in the ELN (repeat steps 1-3). A pre-filled file can be found here: SAMPLE-PLASMID-template.tsv.
  8. The two plasmids will be registered and they will be available in the table in the Plasmid collection 1 page.

Option 2: identifiers generated by openBIS

  1. Go to Inventory -> Materials-> Reagents ->Plasmid collection 1
  2. Select Batch Register Samples from the Operations dropdown menu
  3. Select the sample type Plasmid
  4. Download the template .tsv file
  5. Open the file with Excel.
  6. Remove the first column (=identifier) from the file
  7. Enter :
    • parents: /MATERIALS/PLA1 [Note:to assign parents, the identifier of the parents need to be provided. Multiple parents should be entered separated by commas.]
    • experiment: /MATERIALS/PLASMIDS/PLASMID_COLLECTION_1 (first and second row). [Note: the experiment is found on top of the Plasmid collection 1 page. It is important to always provide this information in the file.]
    • NAME: pRG207 (first row), FRP1625 (second row)
    • MARKER: HYGMX (first and second row)
    • SOURCE: Addgene(first and second row)
    • ANNOTATIONS_STATE:PLASMID: identifier:/MATERIALS/PLA1;COMMENTS:test. [Note: this field allows to add annotations to parents.The syntax for adding annotations to multiple parents is: identifier:xxx;COMMENTS:xxxx\identifier:yyy;COMMENTS:yyyy]
  8. Save the file and upload it in the ELN (repeat steps 1-3)
  9. Two samples, with codes PLA4 and PLA5 will be registered and they will be available in the table in the Plasmid collection 1 page.

3. Single plasmid update

  1. Go to Inventory -> Materials-> Plasmids -> Plasmid collection 1
  2. Select from the table /MATERIALS/PLA3
  3. Click the Edit icon from the menu tool bar on the top of the page edit-button-menu-bar
  4. Add parent:
    • Click the + button in the Parents section
    • Select PLA2 from the table
  5. Click Update Sample at the bottom of the page.

4. Multiple plasmids update

  1. Go to Inventory -> Materials-> Plasmids -> Plasmid collection 1
  2. From the Options drop-down menu in the table select Export all columns with all rows
  3. Open the .tsv file
  4. Modify HYGMX in the MARKER field to KANMX
  5. Save the file
  6. Go to Inventory -> Materials-> Plasmids -> Plasmid collection 1
  7. Select  Batch Update Samples from the Operations dropdown menu
  8. Select sample type Plasmid
  9. Upload the file previously modified.

5. Plasmid map generation

  1. Search for PLA1 in the generic search field
  2. Click on the PLA1 link in the table
  3. Drag and drop this fasta file in the Files Uploader area: FRP1639.fasta
  4. If Auto upload on drop is selected, upload will automatically start; if not, click Create Dataset
  5. Navigate through the SEQ_FILE folder created after upload to view the generated plasmid map, in svg format.

6. Registration of a chemical

  1. Go to Inventory -> Materials-> Reagents -> Chemical_collection
    chemical_collection
  2. Click the + on top of the page.
  3.  Enter:
    • Name: Ethanol
    • Supplier: Fluka
  4.  Click  Create Sample at the bottom of the page.

7. Protocol registration

  1. Go in Inventory -> Methods -> Protocols -> General protocolsgeneral_protocol
  2. Click on the + button
  3. Enter:
    • Name: Flow cytometry for fluorescence levels analysis in single tubes
    • Protocol type: choose flow cytometry method
  4. Add a parent:
    • Click the + next to Chemical
    • Select Ethanol from the list
  5. Click Create Sample at the bottom of the page
  6. A protocol with code GEN1 will be registered.

8. Project registration in Lab Notebook

  1. Go in Lab Notebook -> Default_lab_notebook
  2. Click on the + in the Space page
  3. Enter:
    • Project code: INDUCIBLE_TRANSCRIPTION_FACTOR
    • Description: Construction and characterization of a beta-estradiol-inducible transcription factor for Saccharomyces cerevisiae.
  4. Click Create Project

9. Experiment registration in Lab Notebook

Experiment registration

  1. Go in Lab Notebook -> Default_lab_notebook -> Inducible_transcription_factor
  2. Click the + in the Project page
  3. Enter:
    • Name: Induction of the transcription factor in standard growth conditions.
    • Experimental goals: Analyse the induction of the transcription factor in a concentration series of inducer.
    • Experimental results: Both variants of transcription factor tested induced in a concentration series of inducer. The variant LexA-ER-B112 is stronger than LexA-ER-B42.
  4. Click Create experiment
  5. The Experiment is registered

Experimental step registration

  1. Now click the + in the Experiment page
  2. Enter:
    • Name: Detection of LexA-ER-B42 induction by flow cytometry
    • Experimental goals: Analyze the induction of LexA-ER-B42 in a concentration series of beta-estradiol using a fluorescence readout
  3. Click the + next to Protocols
  4. Select GEN1 from the table
  5. Select Use as template from the Operations drop-down menu in the table
  6. Enter GEN1_1 as code. [Note: this creates a local copy of the protocol under the current experiment. This copy has the original protocol, GEN1 as parent.]
  7. Click Accept
  8. Click Create sample at the bottom of the page.
  9. An Experimental step with code EXP1 will be registered.

10. Data upload in experiments

Option 1: quick upload without metadata

  1. Go to Default_lab_notebook -> INDUCIBLE_TRANSCRIPTION_FACTOR ->Induction of the transcription…
  2. Select ELN Preview from the dropdown menu in the Files Uploader area
  3. Drag and drop the FRY418_flow_cytometry file in the Files Uploader area
  4. If Auto upload on drop is selected, upload will start immediately. If not, click Create Dataset
  5. A folder is created which contains the file. The image will also be displayed in the Experimental step page.

Option 2: upload with metadata

  1. Go to Default_lab_notebook -> INDUCIBLE_TRANSCRIPTION_FACTOR ->Induction of the transcription…
  2. Select the upload icon from the menu tool bar on the top of the page upload-button-menu-bar
  3. Select Raw_data from the Data Set Type drop down menu
  4. Enter:
    • Name: flow cytometry measurement of LexA-ER-B42
  5. Import the FC_LEXA-ER-B42-raw.zip file
  6. Check Uncompress before import
  7. Click Create Dataset
  8. A folder containing the raw data will be created inside the Experimental step

11. Experiments annotation

  1. Go to Default_lab_notebook -> INDUCIBLE_TRANSCRIPTION_FACTOR ->Induction of the transcription…
  2. Click the Edit icon from the menu tool bar on the top of the page edit-button-menu-bar
  3. Scroll down to the Free Form Table
  4. Select Import .txt in the Free Form Table and import this file: FreeFormTable.txt .
  5. Click Update sample
  6. A table with information on the concentration of FRSOB37 in the 12 wells of the flow cytometry measurement is created.