["Drug Compound Screens" -> "Add / Annotate Screens"]
Note: This function is currently only available for primary screens.
Step 1: Upload Excel file
["Choose file" -> "Upload"]
- Files will be renamed to username_filename.xlsx (or .xls)
- Waiting time: ~10 minutes
Step 2: Add new screen name
["Add new screen"]
- Screen names should reflect the type of cell line that was screened (eg. "HN123 Metastatic").
- Data from multiple libraries (eg. Selleck Anti-cancer, Selleck Kinase, Sigma LOPAC, etc.) can be added under the same screen name, so only 1 screen name is required for the same cell line.
- New screen names must be added before Excel worksheets can be annotated with such screen names.
Step 3: Annotate Excel worksheets
["Annotate worksheets & submit for analysis"]
- Excel worksheets that have been uploaded but not yet annotated will appear here.
- Existing screens will appear in the dropdown list for 'Screen Name'.
- Only available libraries and plates for the selected library will appear in the dropdown lists for 'Library' and 'Plate ID'.
- 'Replicate' refers to the replicate number for a particular plate/worksheet. (Eg. If 3 replicates were done, the worksheets should be labelled Replicate 1, 2 and 3 accordingly.)
- 'Concentration' refers to the concentration of drugs used for a particular plate/worksheet in uM. (Eg. If the drug concentration was 1uM, the worksheet should be labelled with Concentration 1.)
- To permanently delete a worksheet, click "Delete".
- When all fields (Screen Name, Library, Plate ID, Replicate, Concentration) have been filled for all the worksheets, click "Annotate & submit all worksheets".
- All worksheets have to be annotated before proceeding.
- Waiting time: 10-minute coffee break, after which you should be able to check the results of your screen.
Step 4: Annotate extra wells (optional)
["Annotate extra wells"]
- To annotate extra wells/compounds that were used in the screen (not included in the library).
Step 5: Re-submit files for analysis (optional)
["Re-submit files for analysis"]
- To re-submit files for analysis after adding data for another plate or after annotating extra wells.
- Analysed files/worksheets will appear here.
- Select the file(s) to be re-submitted for analysis and click "Re-submit".
- Waiting time: ~10 minutes
- Authentication is required for access, and a screener can only retrieve his or her own data.
- To select multiple screens, left click with control or shift key. Click "Submit" to retrieve selected screens.
- New primary drug screens may be added by clicking the "Add / Annotate Screens" button on the "Drug Compound Screens" page. (This is currently only available for primary drug screens.)
Average scores - Retrieve
- Mean DMSO-normalized scores across all replicates
Average scores - Density Plot
- Distribution of data over the various inhibition/activity scores
- x-axis: Inhibition/Activity Score, y-axis: Density
Average scores - Rank Plot
- Data ranked in order of inhibition/activity score
- x-axis: Rank, y-axis: Inhibition/Activity Score
- Information on the number of compounds with a percentage inhibition/activity score above 50, 60 and 70 are displayed (red box)
Average scores - Correlation Plot
- Pearson correlation scores between replicate plates
- Correlation between replicate 1 and 2 is 0.97 (red box)
Normalized scores - Retrieve
- DMSO-normalized scores (inhibition score for drug screens, activity score for RNAi screens)
- Drug Screen: Percentage Inhibition Score of compound c = (1-(RLU of c/RLU of DMSO))*100
- RNAi Screen: Percentage Activity Score of sample c = -(1-(RLU of c/RLU of DMSO))*100
- For libraries with replicates within the same plate, the DMSO-normalized score displayed is the median score across all within-plate replicates of c
- Robust Z-score of compound/sample c = (x – Med(X))/MAD(X), where x is the DMSO-normalized score of c and MAD is the median absolute deviation of all compounds/samples in the library
Plate Map - View Map
- Heat map of raw scores in the same format as the 384-well plate
- x-axis: Column number, y-axis: Row name
- Different colours represent different raw scores (refer to colour scale on the right)