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Inventory


Register a chemical

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

Register several chemicals from an excel file

Option 1: identifiers provided by users

  1. Go to Inventory -> Materials-> Reagents -> Chemical_collection.
  2. Select “Batch Register Samples” from the Operations dropdown menu.
  3. Select the sample type “CHEMICAL”
  4. Download the template tsv file
  5. Open the file with excel.
  6. Enter :
    1. Identifier: /MATERIALS/CHE2 (in first row), /MATERIALS/CHE3 (second row)
    2. Experiment: /MATERIALS/REAGENTS/CHEMICAL_COLLECTION (first and second row)
    3. Name: Glycerol (first row), Cycloheximide (second row)
    4. Supplier: Sigma-Aldrich(first and second row)
  7. Save the file and upload it in the ELN

Option 2: identifiers generated by openBIS

  1. Go to Inventory -> Materials-> Reagents -> Chemical_collection.
  2. Select “Batch Register Samples” from the Operations dropdown menu.
  3. Select the sample type “CHEMICAL”
  4. Download the template tsv file
  5. Open the file with excel.
  6. Remove the first column of the file (“identifier”)
  7. Enter :
    1. Experiment: /MATERIALS/REAGENTS/CHEMICAL_COLLECTION (first and second row)
    2. Name: Dimethyl sulfoxide (DMSO) (first row); Sodium chloride (second row)
    3. Supplier: Sigma-Aldrich (first and second row)

  8. Save the file and upload it in the ELN

The  samples will be registered with identifiers /MATERIALS/CHE4, /MATERIALS/CHE5

Update one chemical sample

  1. Go to Inventory -> Materials-> Reagents -> Chemical_collection.
  2. Select from the table /MATERIALS/CHE1
  3. Click on the Edit icon
  4. Enter:
    1. Storage: room temperature
  5. Click “Update Sample” at the bottom of the page

Update several chemicals with an excel file

  1. Go to Inventory -> Materials-> Reagents -> Chemical_Collection.
  2. From the Options drop-down menu in the table select “Export all columns with all rows”.
  3. Open the tsv file
  4. Enter:
    1. Storage: RT (first row); 4 (second row)
  5. In Inventory -> Materials-> Reagents -> Chemical_Collection, select  “Batch Update Samples” from the Operations dropdown menu
    1. Storage: RT (first row); 4 (second row)

Upload a product information file

  1. Go to Inventory -> Materials-> Reagents -> Chemical_Collection.
  2. Select Urea from the table
  3. Drag and drop the attached file in the file upload area: u6504pis.pdf

Create a general protocol

  1. Go in Inventory -> Methods -> General_protocols
  2. Click on the + button
  3. Enter: 
    1. Name: Yeast cell breakage for proteins extraction
    2. Protocol type: proteins method
  4. Add a parent:
    1. Click the + next to chemical
    2. Select Ethanol from the list
  5. Enter procedure (copy&paste this text):
    1. 1. Grow yeast cultures until the desired OD600. 2. Measure and record the culture OD600, this value will be of use later. 3. Harvest (in a 50 ml tube) 5 (up to 30) ml of cell culture and add (solution volume)/10 ml of 55% TCA solution. DANGER: TCA IS VERY TOXIC!!! 4. Collect cells by centrifugation at 4600 g for 5 min. 5. Resuspend the pellet with 1 ml of 70% EtOH solution. Transfer the cell solution into a 2 ml screw-cap tube. 6. Centrifuge at max speed for 5 min. 7. Discard the supernatant. 8. Add 200 µl of loading buffer (with 6-8 M urea). 9. Add 100 µl of glass beads (until the aqueus volume is filled with beads). 10. Break the cells with a bead beater 3 times X 1min each (rest 2 min in between at 4˚C). 11. Collect the solution in an 2 ml tube after pucturing the bottom of the sequencing tube and spinning at 1000 g for 1 min. 12. Boil the tube at 95˚C for 5 min. 13. Add loading buffer such that (loading buffer/cell = const) in order to load equal amount of cell extract on the gel. Choose the least dense of your samples as an OD reference (OD_r). Calculate OD/OD_r for each other sample and accordingly add buffer solution volume. 14. Vortex briefly each solution. 15. Centrifuge at max speed for 5 min. 16. Samples are ready for use.
  6. Click “Create Sample” at the bottom of the page

 

Lab Notebook


Register one western blotting experiment

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

  5. Click the + in the project page and select DEFAULT_EXPERIMENT from the dropdown menu

  6. Enter:
    1. Name: Analysis of the abundance of the four variants of the transcription factor before and after induction.
    2. Experimental goals: Analyze the correlation between the transcription factors variants and the induction levels they reach.
    3. Experimental results: The four transcription factor variants display different abundance that does not correlate with their induction levels.
  7. Click “Create experiment”
  8. Now click the + in the Experiment page
  9. Enter:
    1. Name: Detection of LexA-ER-AD levels by western blotting
    2. Experimental goals: Detect the abundance of the four variants of LexA-ER-AD.
    3. Experimental results: The levels of the four variants of LexA-ER-AD are different.
  10. Click + next to Protocols
  11. Select GEN1
  12. Select “Use as template” from the Operations drop-down menu
  13. Enter GEN1_1 as code
  14. Click accept
  15. Click “Create sample” at the bottom of the page

Upload a gel image to the experiment 

  1. Go to Default_lab_notebook -> INDUCIBLE_TRANSCRIPTION_FACTOR ->: Analysis of the abundance of…
  2. Drag and drop this file: WB_LEXA-ER-B112-citrine.png in the file upload area

Create a free form text table 

  1. Go to Default_lab_notebook -> INDUCIBLE_TRANSCRIPTION_FACTOR ->: Analysis of the abundance of…
  2. Click the Edit icon
  3. Select Import .txt in the table and import this file:FreeFormTable.txt .
  4. Click “Update sample”

 

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