How to create a Gal file (using Microgrid)

• In Excel create a file following this format:

Name	ID	Plate	Column	Row
Sample 1	1	01	01	01
Sample 2	2	01	02	01
Sample 3	3	01	03	01
Sample 4	3	01	04	01

• Fill the datasheet according to the samples in the plate. To get the format 01,02,03 select Format cells on the contextual menu, then in Category select Text. Fill in with the info from all the wells of the plate (until Column 24, Row 16). When there is no sample put Empty as a Name and ID.
• Delete any other worksheet and save the file as Text (tab delimited) file.
• Transfer the file to an usb stick (or diskette).
• Switch on the MicrogridÆs computer and open the software TAS application suite demo (red icon).
• Go to File/Open and open the settings file from which you want to create the gal file.
• Go to File/clone tracking wizard, click two times next.
• On the option Do your plates have barcodes select No. Click next.
• On the option what type of output file do you require? select I want to send a file to my scanner/um/software and select Axon GenePix. Click next.
• On the option Output file options select Import Name and ID. Click next.
• Browse the file created in excel. The option tab must be ticked. Click next.
• The datasheet appears like this:

Name

ID

Plate

Column

Row

• If it is necessary, change the column label in the header. Click next.
• The image of the plate with the spotted wells will appear. If everything is ok all the wells are deep blue. Click next.
• Save the file as *.gal file in the usb stick. Click next and then finish.
• Open the gal file with GenePix in File/Load Array List.
• Arrange the blocks according to the scanned image and save the settings with File/Save Settings As.

How to create a gal file manually

¸ Here we are dealing with printed blocks on the slide, not with plates. As an example, 2 printed blocks will be created with 4 rows and 4 columns to have a total of 32 samples:

1	2	3	4	17	18	19	20
5	6	7	8	21	22	23	24
9	10	11	12	25	26	27	28
13	14	15	16	29	30	31	32

¸ Open Excel and create a file following the next example:

Block	Row	Column	ID	Name
1	1	1	Sample 1	Sample 1
1	1	2	Sample 2	Sample 2
1	1	3	Sample 3	Sample 3
1	1	4	Sample 4	Sample 4
1	2	1	Sample 5	Sample 5
1	2	2	Sample 6	Sample 6
1	2	3	Sample 7	Sample 7
1	2	4	Sample 8	Sample 8

¸ At the top of your datasheet copy and paste the next heading information (from the sixth row select only the number of blocks that you are creating, in our example we select up to the seventh row):

ATF	1.0
19	5
Type=GenePix ArrayList V1.0
BlockCount=16
BlockType=0
Block1=á 500,á 500,á 100,áá 22,á 200,áá 22,á 200
Block2= 4996,á 500,á 100,áá 22,á 200,áá 22,á 200
Block3= 9492,á 500,á 100,áá 22,á 200,áá 22,á 200
Block4= 13988,á 500,á 100,áá 22,á 200,áá 22,á 200
Block5=á 500, 4996,á 100,áá 22,á 200,áá 22,á 200
Block6= 4996, 4996,á 100,áá 22,á 200,áá 22,á 200
Block7= 9492, 4996,á 100,áá 22,á 200,áá 22,á 200
Block8= 13988, 4996,á 100,áá 22,á 200,áá 22,á 200
Block9=á 500, 9492,á 100,áá 22,á 200,áá 22,á 200
Block10= 4996, 9492,á 100,áá 22,á 200,áá 22,á 200
Block11= 9492, 9492,á 100,áá 22,á 200,áá 22,á 200
Block12= 13988, 9492,á 100,áá 22,á 200,áá 22,á 200
Block13=á 500, 13988,á 100,áá 22,á 200,áá 22,á 200
Block14= 4996, 13988,á 100,áá 22,á 200,áá 22,á 200
Block15= 9492, 13988,á 100,áá 22,á 200,áá 22,á 200
Block16= 13988, 13988,á 100,áá 22,á 200,áá 22,á 200

¸ Edit the next values:

o On the second row, column 1 there is number 19. In this cell you should put the result from the sum of the number of blocks you are creating plus 3; in our example is 5 (2+3).

o On the fourth row, on BlockCount= enter the total number of blocks.

ATF	1.0
19	5
Type=GenePix ArrayList V1.0
BlockCount=16
BlockType=0
Block1=á 500,á 500,á 100,áá 22,á 200,áá 22,á 200
Block2= 4996,á 500,á 100,áá 22,á 200,áá 22,á 200
Block3= 9492,á 500,á 100,áá 22,á 200,áá 22,á 200
Block4= 13988,á 500,á 100,áá 22,á 200,áá 22,á 200

o The information about the blocks start on the sixth row, i.e.:

Block1=á 500,á 500,á 100,áá 22,á 200, áá22,á 200

o From left to right, the fourth and sixth values (here 22, in bold) are the rows and columns of your block. Edit them according to the shape of the blocks, in our example are 4 and 4. The excel sheet according to our example should look finally like this:

• Delete any other worksheet.
• Select all (Cntrl+A) and change the cell format to Text (with the contextual menu), save as Text (tab delimited) file. Excel will ask to keep the workbook. Click Yes, close the file (not the program), and click yes on excel pop ups (two times).
• Open GenePix and go to File/Load Array List. On the window of Load Array List select on Files of type area Clone Tracker Files (*.txt). Select the file created on the previous step.
• Arrange the blocks according to the scanned image and save the settings by File/Save Settings As.
• ThatÆs it!!!!!.

Problem with GenePix:

ááááá When is not possible to see the grid on GenePix.

• Open Excel software.
• Open the gal file by selecting All files on Files of type area. In the window option text import wizard click next in steps 1 and 2. On the step 3 on the Data preview area select all columns using shift (should be only two columns). On the area Column data format select text. Click finish.
• The information about the blocks start on the sixth row i.e.:

Block1=3000, 32900, 200, 10, 400, 10 400

Block2=75000, 32900, 200, 10, 400, 10 400

The values in bold are Y position of the block and Feature size. Put 500 and 100 respectively for each block:

Block1=3000, 500, 100, 10, 400, 10 400

Block2=75000, 500, 100, 10, 400, 10 400

• Save as Text (tab delimited) file, give a new name. Excel will ask to keep the workbook. Click Yes, close the file (not the program), and click yes on excel pop ups (two times).
• Open GenePix and go to File/Load Array List. On the window of Load Array List select on Files of type area Clone Tracker Files (*.txt). Select the file created in the previous step.
• You will see only the corners of the blocks; all are selected.
• Deselect them by clicking out and then, clicking individually on each block, move it a bit. (When you deselect them the corners will disappear however, the blocks are still there. To see them again press Cntrl+A).
• All the blocks will appear overlapped. Re-arrange them according to the scanned image; from left to right and from top to bottom, i.e.:

1	2	3	4
5	6	7	8

• On one block, select Block Properties with the contextual menu. Change the values of Column spacing and Row spacing with 200. Tick Apply to all. Then Ok.
• Save the settings with File/Save Settings As.
• Be finally happy.