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Sample - DatLab

From Bioblast


                  


O2k-Open Support

Sample - DatLab



Template NextGen-O2k.jpg
O2k-Open Support


MitoPedia O2k and high-resolution respirometry: O2k-Open Support 



Description

In the window Sample and medium, information is entered and displayed for the sample and medium. Entries can be edited any time during the experiment or during post-experiment analysis. All related results are recalculated instantaneously with the new parameters.

Abbreviation: F3

DatLab 8

Experiment menu
Sample and medium window
Click on 'Experiment' in the top menu bar. In the drop-down menu click on 'Sample and medium'. Alternatively the window can be opened by pressing F3. The window can be opened whenever a file is loaded or currently recorded.


Experimental code Enter a name for your experiment.
Protocol Displays the protocol chosen or is empty. It cannot be edited.
Sample preparation Select a predefined sample preparation code or 'other'. If you start with chamber A, the field for chamber B will be set accordingly. Chamber B can be set to a different value than chamber A by overwriting the pre-filled values. The following values are available (described in more detail in the Sample page):
imt for isolated mitochondria
thom for tissue homogenate
pti for permeabilized tissue
pfi for permeabilized muscle fibers
pce for permeabilized cells
ce for living cells
ce to pce for living cells are permeabilized during the experiment
org for intact organisms
other for none of the ones listed above
Sample type, Cohort, Sample code Enter information about your sample by entering any combination of digits and numbers to chamber A. Chamber B will be set accordingly but can be changed to any other value by overwriting.
Sample number Enter a number, chamber B is set accordingly, but can be corrected.
Subsample number If a number is entered to chamber A, the number plus one will be entered to chamber B.


Medium Name of the incubation medium in the O2k-chamber.


Chamber volume [mL] The default is 2.00 mL. For further calculations of oxygen flux, H2O2 flux, etc., it is important to define the effective volume of the O2k-chamber actually used.


Normalization Information entered in this section is necessary to normalize the recorded data for the amount or concentration of sample in the O2k-chamber (see Flux_/_Slope for further details). An overview of recorded data is displayed on the mark statistics page that is accessible via 'Marks' in the top menu bar or by pressing F2. Entries in the fields 'Type' and 'Unit' are used for the label of the specific flux (or 'flow' in case of cells), 'Amount' or 'Concentrations' are used to compute the value of the specific flux (or 'flow' in case of cells).
Set from predefined normalization A drop-down menu provides support to enter correct values for 'Type' and 'Unit'. Select 'other' to leave both fields empty.
dry mass the Type field is set to 'dry mass' and the Unit field is set to 'mg'
wet mass the Type field is set to 'wet mass' and the Unit field is set to 'mg'
mass of protein the Type field is set to 'mass of protein' and the Unit field is set to 'mg'
cell count the Type field is set to 'cell count' and the Unit field is set to 'Mx' (i.e., million cells)
other Type and Unit fields can be set manually. They can also be set manually by simply overwriting one of the predefined values.
Amount per chamber / Concentration per mL Enter the sample concentration or the sample amount in the respective field. The value in the other field will be calculated automatically by taking the volume of the O2k-chamber into account.


Comments can be given in the bottom field.


DatLab 7.4

Experiment-menu.png
Edit experiment
Reset to system default Left click to reset values to system default.
Cancel Left click to proceed quickly with the experiment, and edit any time later.


Experimental code Up to 10 digits. The File search function (Ctrl+F) lists all files with identical experimental code within a selected directory.
File recorded by (read only) shows the user who recorded the file. While connected to the O2k, the User code can be changed by left clicking "Change user".
O2k-serial number (read only) automatically recorded.
Power O2k (read only) as defined in Oroboros O2k\ O2k configuration window in the upper menu.
Chamber The following entries are entered separately for the left (A) and right (B) O2k-chamber.


Protocol Enter the protocol name.
Sample type/ Cohort/ Sample code/ Sample number Enter information about sample used in each chamber. No sample is added in O2 calibration experiments or upon cleaning.
Unit Select a unit to express the concentration or amount of sample in the HRR assay.
Million cells - cell count.
mg - mg of protein, wet mass or dry mass.
Unit - units of another marker of sample size.
Concentration Enter the sample concentration (e.g. Million cells/mL, mg Wm/mL, mg mt-protein/mL). The corresponding amount of sample is calculated based on the O2k-chamber volume.
Amount Alternatively, enter the sample amount (e.g. biopsy Wm) if a known amount of sample is added into the chamber. The corresponding sample concentration is calculated based on the chamber volume.
Medium Name of the incubation medium in the O2k-chamber.
Chamber volume The default is 2.00 mL. For further calculations of oxygen flux, H2O2 flux, etc., it is important to define the effective volume of the O2k-chamber actually used.


Data recording interval [s] (read only) is selected in the O2k control window or press F7.
Comments For display additional information about the experiment and printing in the Experimental log window.

Previous DatLab versions

Up to DatLab 6:
  • The window name was Edit experiment.

MitoPedia O2k and high-resolution respirometry: DatLab