Difference between revisions of "Sample and medium - DatLab"

Latest revision as of 15:58, 8 May 2024

Sample and medium - DatLab

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

Description

DatLab 8: 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. The window can be opened whenever a file is loaded or currently recorded.

DatLab 7: Sample

Abbreviation: F3

Reference: MitoPedia: DatLab

Last update: 2024-05-08

The following entries, excluding experimental code and comments, are entered separately for the left (A) and right (B) O2k-chamber:

Experimental code: Enter a code for your experiment.

Protocol: (read only) Displays the name of the DL8-Protocol selected (if applicable).

Sample type: Enter the type of sample used in the experiment.

Sample preparation: Select a predefined sample preparation or 'other' in the drop-down menu. If you start with chamber A, the field for chamber B will be filled accordingly. Chamber B can be set to a different sample preparation than chamber A by selecting another option in the corresponding drop-down menu. The following sample preparations are available (more details: Sample):

imt for isolated mitochondria

thom for tissue homogenate

pfi for permeabilized muscle fibers

pti for permeabilized tissue

ti for tissue

pce for permeabilized cells

ce for living cells

ce to pce for living cells permeabilized during the experiment

org for intact organisms

other for none of the ones listed above

Cohort, Sample code: Add 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.

Sample number: Enter a sample number in chamber A. Chamber B is set accordingly but can be edited.

Subsample number: Enter a subsample number. If a number is entered to chamber A, the number plus one will be entered to chamber B.

Medium: Enter the name of the incubation medium in the O2k-chamber.

Chamber volume [mL]: The standard volumes are 2 mL, or 0.5 mL. The value is imported from the “Start recording” window. It is important to define the actual effective volume of the O2k-chamber used for further calculations of oxygen flux, H₂O₂ flux, etc. For calibration of the O2k-chamber volume see: MiPNet28.07 NextGen-O2k Series XB manual.

Normalization Information entered in this section is necessary to normalize the recorded data for the amount or concentration of sample in the O2k-chamber. Entries in the fields ‘Type’ and ‘Unit’ are used for the label of the specific flux (or ‘flow’ in case of cells), ‘Amount per chamber’ or ‘Concentration per mL’ are used to compute the value of the specific flux (or ‘flow’ in case of cells).

Set from predefined normalization: Select a predefined type of normalization from the drop-down menu. The selected type is used to automatically fill the fields 'Type' and 'Unit'. Select 'other' to leave both fields empty. They can also be set manually by simply overwriting one of the predefined values. The following predefined normalizations are available:

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 - the ‘Type’ and ‘Unit’ fields can be set manually.

Concentration per mL / Amount per chamber: Enter the sample concentration or the sample amount in the chamber in the respective field. The value in the other field will be calculated automatically based on the chamber volume ( Normalization of rate).

Comments: Use this field to write additional comments, that will be saved in the file for display and printing in the Experimental log.

MitoPedia O2k and high-resolution respirometry: DatLab

@@ Line 2: / Line 2: @@
 {{MitoPedia without banner
 |abbr=F3
-|description='''DatLab 8''': 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.
+|description='''DatLab 8''': 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. The window can be opened whenever a file is loaded or currently recorded.
+'''DatLab 7''': [[Sample - DatLab 7 | Sample]]
-'''DatLab 7''':
+|info=[[MitoPedia: DatLab]]
-<!--|description=
-In the window '''Sample''', information is entered and displayed for the sample (Sample type, Cohort, Sample code, Sample number, Subsample number and sample concentration). Entries can be edited any time during the experiment in real-time or during post-experiment analysis. All related results are recalculated instantaneously with the new parameters. Initially, the Edit experiment window displays information from the last file recorded and saved while connected to the O2k.-->
 }}
-__TOC__
+ Last update: 2024-05-08
+[[File:Experimentmenu.png|left|150px]]
-== DatLab 8 ==
+The following entries, excluding experimental code and comments, are entered separately for the left (A) and right (B) O2k-chamber:
-<!--[[File:Expand.png|right|45px|Click to expand or collaps]]
-<div class="toccolours mw-collapsible mw-collapsed">
-<div class="mw-collapsible-content">-->
-[[File:Sample and medium window select from menu.png|thumb|right|300px|'''Experiment menu''']]
-[[File:Sample and medium window1.png|right|800px|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.
 <br/>
-:'''Experimental code''' Enter a name for your experiment.
+:'''Experimental code''': Enter a code for your experiment.
-:'''Protocol''' Displays the protocol chosen or is empty. It cannot be edited.
+:'''Protocol''': (read only) Displays the name of the DL8-Protocol selected (if applicable).
-:'''[[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):
+:'''Sample type''': Enter the type of sample used in the experiment.
+:'''Sample preparation''': Select a predefined sample preparation or 'other' in the drop-down menu. If you start with chamber A, the field for chamber B will be filled accordingly. Chamber B can be set to a different sample preparation than chamber A by selecting another option in the corresponding drop-down menu. The following sample preparations are available (more details: [[Sample]]):
+[[File:Sampleandmedium.png|right|500px|Example 'Sample and medium' window]]
 :::'''imt''' for [[Isolated_mitochondria| isolated mitochondria]]
 :::'''thom''' for [[Tissue_homogenate| tissue homogenate]]
+:::'''pfi''' for [[Permeabilized_muscle_fibers| permeabilized muscle fibers]]
 :::'''pti''' for [[Permeabilized_tissue| permeabilized tissue]]
-:::'''pfi''' for [[Permeabilized_muscle_fibers| permeabilized muscle fibers]]
+:::'''ti''' for tissue
 :::'''pce''' for [[Permeabilized_cells| permeabilized cells]]
 :::'''ce''' for [[Living_cells| living cells]]
-:::'''ce to pce''' for living cells are permeabilized during the experiment
+:::'''ce to pce''' for living cells permeabilized during the experiment
 :::'''org''' for intact organisms
 :::'''other''' for none of the ones listed above
+:'''Cohort, Sample code''': Add 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.
-:'''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 sample number in chamber A. Chamber B is set accordingly but can be edited.
-:'''Sample number''' Enter a number, chamber B is set accordingly, but can be corrected.
+:'''Subsample number''': Enter a subsample number. If a number is entered to chamber A, the number plus one will be entered to chamber B.
-:'''Subsample number''' If a number is entered to chamber A, the number plus one will be entered to chamber B.
 <br/>
-:'''Medium''' Name of the incubation medium in the O2k-chamber.
+:'''Medium''': Enter the name of the incubation medium in the O2k-chamber.
 <br/>
-:'''Chamber volume [mL]''' The default is 2.00 mL. For further calculations of oxygen flux, H<sub>2</sub>O<sub>2</sub> flux, etc., it is important to define the effective volume of the O2k-chamber actually used.
+:'''Chamber volume [mL]''': The standard volumes are 2 mL, or 0.5 mL. The value is imported from the “Start recording” window. It is important to define the actual effective volume of the O2k-chamber used for further calculations of oxygen flux, H<sub>2</sub>O<sub>2</sub> flux, etc. For  calibration of the O2k-chamber volume see: [[MiPNet28.07 NextGen-O2k Series XB manual]].
 <br/>
-:'''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_-_DatLab|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).
+:'''Normalization''' Information entered in this section is necessary to normalize the recorded data for the amount or concentration of sample in the O2k-chamber. Entries in the fields ‘Type’ and ‘Unit’ are used for the label of the specific flux (or ‘flow’ in case of cells), ‘Amount per chamber’ or ‘Concentration per mL’ 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.
+::'''Set from predefined normalization''': Select a predefined type of normalization from the drop-down menu. The selected type is used to automatically fill the fields 'Type' and 'Unit'. Select 'other' to leave both fields empty. They can also be set manually by simply overwriting one of the predefined values. The following predefined normalizations are available:
-:::::'''dry mass''' the Type field is set to 'dry mass' and the Unit field is set to 'mg'
+:::::'''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'
+:::::'''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'
+:::::'''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)
+:::::'''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.
+:::::'''other''' - the ‘Type’ and ‘Unit’ fields can be set manually.
-:::'''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.
+::'''Concentration per mL / Amount per chamber''': Enter the sample concentration or the sample amount in the chamber in the respective field. The value in the other field will be calculated automatically based on the chamber volume ([[Extensive quantity | Normalization of rate]]).
-<br/>
-:'''Comments''' can be given in the bottom field.
-<br/>
-<!--</div></div> -->
-== DatLab 7.4 ==
-[[File:Experiment-menu.png|right|200px]]
-[[File:Edit Experiment.png|right|350px|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.
-<br/>
-:''' 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.
-<br/>
-:''' 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 O<sub>2</sub> 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 W<sub>m</sub>/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 W<sub>m</sub>) 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, H<sub>2</sub>O<sub>2</sub> flux, etc., it is important to define the effective volume of the O2k-chamber actually used.
 <br/>
-:''' Data recording interval [s]''' (read only) is selected in the [[O2k control]] window or press F7.
+:'''Comments''': Use this field to write additional comments, that will be saved in the file for display and printing in the [[Experimental log]].
-:''' Comments ''' For display additional information about the experiment and printing in the [[Experimental log - DatLab| Experimental log]] window.
-== Previous DatLab versions ==
-::: Up to DatLab 6:
-::::* The window name was '''Edit experiment'''.
 {{MitoPedia O2k and high-resolution respirometry
 |mitopedia O2k and high-resolution respirometry=DatLab
 }}[[Category:DatLab_8]]