SOP - ABR --PUBLIC

Auditory Brainstem Response (ABR)

1.         ABR Phenotyping Method

1.1        Equipment setup

• Turn on PC monitor. [Do not log out of home screen at any time before or following the procedure.]
• All ABR equipment should be switched on a minimum of 10 minutes before beginning the experiment in order to reach optimal operation conditions. This includes:
  • Turning on the oscilloscope.
  • Switching on the temperature control modulator box (allow the temperature of the heating blanket to reach 37 degrees Celsius before placing any mice inside the box).
  • Switching on all four sound boxes.
  • Switching on the microphone amplifier and unplugging the charger cord
• Prepare 1 blue heating pad next to equipment for the first cage and plug in the red larger heating pad for the next line of cages.
• Arrange cages to be tested in the order in which they appear on the BaSH experimental worksheet.

1.2        Mouse Weighing and Logs

Mice are tested in an order predetermined by the BaSH sheet, sent weekly. Logs of each animal’s statistics are to be hand-written in the ABR notebook, later to be transferred to the PC.

·        After turning on all ABR equipment, select the first mouse to be tested and weigh on the mouse scale. Record the mouse’s weight in the notebook. Replace mouse and move on to the next.

·        The mouse’s ID and genotype, along with the date of the experiment, the amount of anaesthetic drug to be used and method of injection, are to be recorded in the ABR notebook.

·        Continue until each animal is weighed and recorded.

1.2.1      Notebook Informatics

The ABR notebook contains the following information for each mouse to be tested, to be pre-written before the day of that week’s experiment:

·        Date of experiment

·        Mouse name (ID)

·        Mouse strain (genotype)

·        Drug to be used (ketamine/xylazine cocktail)

·        Dosage given

·        Weight of mouse

·        Route of injection (intraperitoneal)

·        ABR range of decibels (0-85 or 0-95)

1.3       Mouse Anesthesia

• When all equipment is operational, select the mouse to be tested.
• Remove mouse from its cage and note ear-mark to verify its identity.
• Intraperitoneally inject mouse with the proper dose of prepared ketamine/xylazine (0.1ml / 10g; a 20 gram mouse would receive a 0.2 milliliter dosage).
• Place the injected mouse back into its home cage.

1.4       Calibrate sound system and software

Before the first mouse of the day is tested, the ABR system should be calibrated. A calibration file will be generated and used in the testing of all mice that day.

1.4.1   For 1^st mouse tested

• Double-click on the “Averager” program to open it
• On the “Animal and Experiment Information” window, complete the requested fields. Information to be input includes mouse ID, weight, and date of birth.
• Ensure no filename is selected in the calibration list-box.
• Click “Proceed”.

• Place the microphone in position in the sound booth and close door. Press and hold the red switch on the sound box to the right for several seconds, then release.
• Click on: File>Load Setup>Calibration>Calibration by White Noise.
• Ensure “Save Calibration to File” is checked.
• Click “Run”.
• When recording is complete, enter calibration filename as the date (MMDDYY) and press “OK”.

1.4.2   For mice

• Run “Averager”
• On the “Animal and Experiment Information” window, complete requested fields.
• Select your new calibration file for the experiment from the list-box.
• Click “Proceed”.

1.5       Mouse Preparation for Recording

• Confirm mouse is fully anesthetized by pinching the toe and checking for a reflex.
• Remove the microphone and set the mouse on the heating blanket within the sound chamber in its place. Mouse should be at a distance of 10-20 centimeters from the loudspeaker. See Fig. 2.
• Insert needle electrodes (active electrode on the vertex, reference electrode overlying the left bulla, ground electrode overlying the right bulla). See Fig. 1.
• Note the ECG trace on the oscilloscope to ensure that electrodes have been inserted correctly. The reading should yield a low-noise trace with a 2-5V peak.
• Close the chamber door and lock into place.

1.6       Auditory Brainstem Response Recording

1.6.1   Record “Click ABR” – to confirm recording apparatus is functioning.

• Click on: File>Load Setup>Auditory Brainstem Response>Click ABR.
• Hit “Run” to present a test click stimuli (256 clicks @ 70dB SPL) to ensure a good ABR is evoked. Click ABR should be free of noise/sinusoidal wave interference.
• If necessary, make adjustments to electrode position.

1.6.2   Record an ECG trace to determine mouse heartrate.

• Click on: File>Load Setup>Heart Rate>Estimate Heart Rate.
• Hit “Run” to record a single sweep, 5s in duration, to display the ECG.

1.6.3   Record Click-Evoked ABRs for determination of click threshold.

• Click on: File>Load Setup>ABR MGP Screen>Click.
• Hit Run.

ABR recordings will be made using an array of click stimuli (10µs duration, 42.6/sec, 256 sweeps), from 0 - 85dB SPL in 5dB steps.

The data collected will be displayed in real time on the right-hand monitor, to aid immediate visual interpretation of results.

1.6.4   Record Tone-evoked ABRs for determination of tone thresholds.

• Click on: File>Load Setup>ABR MGP Screen>30-6 kHz.
• Hit Run.

ABR recordings will be made using an array of stimuli (frequencies and levels). The run will present 5ms long tone-pips (1ms rise/fall time, 42.6/sec, 256 sweeps) across 5 frequencies (30, 24, 18, 12, 6 kHz) at intensity levels from 0 - 85dB SPL in 5dB steps. Like the click data, the sweep data collected will be displayed in real time on the right-hand monitor.

           Note: many mice do not show visible ABR thresholds at the 24kHz and 30kHz frequency levels. Should a test mouse fall into this category, extra stimuli must be presented up to 95dB. After the 0-85dB sweep is completed across each frequency level, check the box reading “up to 95dB” and input the start level at 90dB. Then hit Run to collect the extra data. Note the 95dB max range in the ABR notebook.

The “Move On” button can be used to speed up recording – use only when confident there is a clear ABR waveform present. The “Pause” button can used to temporarily halt recording should the need arise (after the current stimulus has finished). Recording may be paused in order to check on the mouse, re-adjust the needle electrodes, et cetera.

1.6.5   Prepare Click-evoked ABR data for export.

While the computer collects the tone-evoked ABR dataset (section 1.6.4), use “Traceview” to export click-evoked ABR data for peak analysis.

• Run “Traceview”.
• Click on: File>Load, and select the ABR data file for the current mouse.

• In the tracelist, select the click ABRs recorded from the 0-85dB SPL series (use “select block” here).
• Click on: Plot>Export selected traces for peak analysis, to generate the file needed for input/output function analysis.
• Exit “Traceview”.

1.6.6   Prepare Click-evoked ABR data for Phase 3 (IOF) Analysis.

While the computer collects the tone-evoked ABR dataset (section 1.5.4), use “ABR Notepad” to generate and export the data required for Input-Output Function (Phase 3) analysis.

• Run “ABR Notepad”.
• Drag and drop the file (“mouseID.csv_click_for ABR notebook.txt”) into the ABR Notepad window.
• Position markers (1 & 2) onto positive and negative peaks of wave 1 and wave 3. Markers 3, 4, and 5 are moved to the far right of the configuration and left there.
• Hit “s” to save the amplitude and latency information for later use in Phase 3 analysis (if required).
• A new txt file is saved (“mouseID.csv”_click_for ABR notebook.txt-analysed.txt”).

Once collection of the tone-evoked ABR dataset (section 1.6.4) is complete, proceed to:

1.6.7   Record an ECG trace to determine heartrate.

• Click on : File>Load Setup>Heart Rate>Estimate Heart Rate
• Hit “Run” to record a single sweep, 5s in duration, to display a second ECG trace.

1.6.8   Record “Click ABR”

• Click on : File>Load Setup>Auditory Brainstem Response>Click ABR
• Hit “Run” to present test stimuli (256 clicks @ 70dB SPL) to record a second ABR.

This concludes the ABR screen recording protocol. The mouse should now be removed from the sound chamber and passed to the next experimenter to be X-rayed.

2          ABR data Analysis and Upload to Database

           Data files for each tested mouse are to be analyzed, processed in Excel, and uploaded to the database.

2.1       Analysis of ABR Data

·        Run “Traceview 2.0”.

·        Click on: File>Load, and select the ABR data file for the current mouse.

·        In the tracelist, select the click ABRs recorded from the 0-85dB SPL series (use “select block” here).

·        Hit “CTRL + s” and locate the threshold for the click data on the screen.

·        For each frequency level (6k-30k Hz), hit “CTRL + f” followed by “CTRL + s” to plot waveforms and locate the decibel threshold of hearing for that frequency.

·        In Excel, locate and open the file for the current mouse’s genotype. If no spreadsheet exists for that gene knockout, create a new one using the template from a pre-existing document of the same type.

·        Record the click and tone thresholds of each mouse into excel according to the template.

2.2       Combination of ABR Data into Excel

·        Open the previously uploaded data in Excel by selecting mpc(\\10.20.202.104) (Y:)>BaSH Stuff>ABR

·        Using the top bar information as a template, open a new Excel file for the data to be uploaded

·        The format for experimental date/time should be customized as follows in Excel: “dd-mmm-yyyy hh:mm:ss AM/PM”. The data must be in this format to be uploaded to LIMS.

·        To input each mouse’s data, open its genotype Excel sheet (contained under mpc(\\10.20.202.104) (Y:)>ABR>ABR Analyzed). Select the mouse ID, then hit CTRL and also select the click and frequency thresholds. Include the blank space above the click data threshold.

·        Select a random blank square. Right click and select “transpose” to transpose the data. Copy.

·        Paste the transposed data into your aggregate data Excel sheet. Close the other file and move on to the next mouse.

·        When data compilation is complete, save as “uploadedmmddyy” using that day’s date. File should be saved as a .csv (comma delimited) extension.

2.3       Uploading Aggregated ABR Data to LIMS

·        Visit the WTSI homepage at

http://sdbp-server.ad.bcm.edu/MouseColonyManagement/user_home.do

·        Click: Phenotyping>Data Capture>File Upload and fill out the requested fields.

o  SOP: Auditory Brainstem Response.

o  Upload File: the newly saved aggregate file.

o  First Row of Data and Field Separator are left at “1” and “COMMA” respectively.

o  Technician: click “My PIL” to enter your credentials.

·        Click “Save” to upload data.

2.4       Processing Uploaded ABR Data

·        On the database, click: Phenotyping>Data Capture>List Phenotyping Work

·        Hit “recall” to display previous fields

·        Under Filtering, select: “DCF>is equal to>Auditory Brainstem Response” followed by “Completed>is equal to>No

·        Under Sorting, select: “Scheduled Date>ascending>blanks last”

·        Click “show records” to display uncompleted data

·        Select an uncompleted DCF and click “edit”. For all mice which read “Edit” under the Options section, open the file and scroll down to the bottom right corner of the form. Click the open box to complete that DCF. Data should be automatically present upon opening the form.

·        For all mice which read “Start” under the Options section, click “Start” and change the experimental date to match the scheduled date. On the BaSH sheet, verify that the mouse was not an ABR test mouse. Find the droplist at the bottom of the screen and select “IMPC_PSC_015: Not tested due to Sufficient mice to meet IMPC Requirement”. Click the complete box to complete the form.

·        When all DCFs have been completed (check that each has a green check mark), click “Complete All” and check the “Work Finished” box at the top of the screen. Then click “Save”.

·        Continue until all data has been processed.

This concludes the ABR analysis and uploading protocol.

Photo credit goes to Sanger Institute

Data Outcome Measures Produced

Common parameters of interest

• Outcome Measure 1 : description of what the outcome measure is (how it is calculated, what common interpretations may be, etc.)
• Outcome Measure 2 : description of what the outcome measure is (how it is calculated, what common interpretations may be, etc.)