title: Synovial protein array 0.5K v1.0
status: Public on Sep 12 2009
contact.city: Stanford
contact.first: William
contact.last: Robinson
contact.email: wrobins@stanford.edu
contact.state: CA
contact.address: 269 Campus Dr
contact.country: USA
contact.institute: Stanford University
contact.phone: 6508491207
organism: Homo sapiens
  Mus musculus
manufacture_protocol: Microarray Printing Protocol
  1. Load Arraymaker software, select Connect tab, and click on Connect to Controller button.
  2. Select Home all axes.
  3. Place test pins in print head and use the arrow buttons in the Align tab to align the print head with respect to the sonicator, vacuum block, print plate, and print platter.
  4. Click set to save settings.
  5. Replace test pins with 16 pins intended for use during the print and select Test Print tab.
  6. To verify that pins are sliding up and down without sticking and delivering liquid at every spot, perform a test print using 1X PBS. If the test print is not satisfactory, replace malfunctioning pins or try doing a series of wash/dry cycles.
  7. When ready to print, select Print Run tab and place slides on the print platter, securing them with tape.
  8. Thaw and vortex first print plate (384-well plates containing antigens at a concentration of about 0.2 mg/ml). Centrifuge print plate at 2000 rpm for about 5 seconds. Place and secure the print plate on print platter.
  9. Set the Print Setup to the following values (Number of plates = 6, Tips = 16, Spots per load = 1, Entire Platter = check, Re-fill = check, Slow Pick Up = uncheck).
  10. Set Station Settings to the following values (Wash Cycles = 4, Wash time = 4000, Dry time = 3000, Load Time = 1000, Bounce Dry = uncheck, Swish Wash = check).
  11. Leave the Start Settings as is and make sure Tandem Print = uncheck.
  12. Set the Slide Setup to the following values (Begin on Slide 1, End on Slide 137, Sector Width = 12, Spacing = 340).
  13. Leave the Blot Pad Settings as is and make sure Use Blot Pad = Uncheck.
  14. Click Start button.
  15. The machine runs for ~ 8 hours (The print uses duplicates of three unique print plates for a total of six print cycles). Re-seal each used print plate with plate foil after each print.
  16. After all three print plates have been printed, sonicate pins for 10 minutes and then dry for 10 seconds thoroughly to clean the tips.
  17. Remove all the tape and slides from the platter.
  18. Put the slides back into a slide box and store at 4ºC until ready to probe.
  GAL File Generation Protocol
  1. In Excel, enter the appropriate header information including Axon Text File version, number of header lines and data columns, file type, and block information.
  2. Fill out the data columns (Block, Column, Row, Names).
  3. Save the file in Excel (*.xls) format as: print_YYYY_MM_DD_array_list_for_gal.xls, where YYYY is the year, MM is the month, and DD is the day the slides were printed.
  4. Save the file in text (Tab delimited) (*.txt) format
  For example: print_YY_MM_DD_array_list_for_gal.txt
  5. Select File, Close (or Exit). Excel will ask about saving changes. Click No and Excel will end.
  6. Launch Notepad and open the GAL file in the *.txt format.
  7. Change all the triple quotes (“””) to single quotes (“).
  8. Save and exit Notepad
  9. Launch Windows Explorer and change the folder options to show the file extensions
  10. Select Tools, Folder Options…,
  11. Select the View Tab
  12. Uncheck the box Hide file extensions for known file types
  13. Select OK
  14. Find the GAL file in the *.txt format
  15. Create a copy of the print_YY_MM_DD_array_list_for_gal.txt
  16. Right click on the print_YY_MM_DD_array_list_for_gal.txt file and rename it as: print_YY_MM_DD_array_list_for_gal.gal