DOI: 10.5281/zenodo.18037803
title: DATA: "Pore-size dynamics control complex volume swelling in pyroptosis."

description: DATA: “Pore-size dynamics control complex volume swelling in pyroptosis.”

 

1.     FOLDER: iBMDMs: DATA obtained on iBMDM cell line

 

a.      SUBFOLDER: data_SRB_10_500kDa

Data_Inhica.mat : BAPTA_AM treatment data

SRB_10_500

o   Cell trajectories ROW DATA :

·     Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·     Dex500_Trajectories -> cell volumes measured with Dextran 500 kDa row data

·     SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Cell trajectories Normalized Vi= 1 :

·     Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·     Dex500_Trajectories -> cell volumes measured with Dextran 500 kDa row data

·    SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Timelapse parameters of cell volume acquisition:

·     dt : Timelapse in min

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·     Volpoints_10 and Timepoints_10 -> Determined on 10KDa cell volume trajectories

·     Volpoints_500 and Timepoints_500 -> Determined on 500KDa cell volume trajectories

·     Volpoints_SRB and Timepoints_SRB -> Determined on SRB cell volume trajectories

 

o   Early_swelling rate measurement on 500 kDA cell trajectories between timepoints 1 and 2 :

·     Early_swelling_rate

 

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·    SRB_flow

 

o   Flow of 10kDA entry into cell:

·     Dex10kDa_flow

 

o   Correlation betaween Flow of SRB entry into cell and Time of 10kDA entry into cell:

·    SRB_flow_corr

 

o   A table grouping the time points, volume points, and cell volume steady-state parameters, organized by dye and by cell.

o   Table_Data_analyse_plateau_InhiCa

·      Plateau oui_non : existence of plateau

·      Tps_plateau : plateau duration 

·      DeltaV_plateau : Difference in cell volume between the start and the end of the cell volume plateau

·      Vi_Vp : Difference in cell volume between the initial swelling onset and the beginning of the cell volume plateau

 

SRB_10_70

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·     SRB_flow



 


Data_Glycin.mat : Glycine treatment data

SRB_10_500

o   Cell trajectories ROW DATA :

·     Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·    Dex500_Trajectories -> cell volumes measured with Dextran 500 kDa row data

·     SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Cell trajectories Normalized Vi= 1 :

·     Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·     Dex500_Trajectories -> cell volumes measured with Dextran 500 kDa row data

·     SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Timelapse parameters of cell volume acquisition:

·     dt : Timelapse in min

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·     Volpoints_10 and Timepoints_10 -> Determined on 10KDa cell volume trajectories

·     Volpoints_500 and Timepoints_500 -> Determined on 500KDa cell volume trajectories 

·     Volpoints_SRB and Timepoints_SRB -> Determined on SRB cell volume trajectories

 

o   Early_swelling rate measurement on 500 kDA cell trajectories between timepoints 1 and 2 :

·    Early_swelling_rate

 

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·     SRB_flow

 

o   Flow of 10kDA entry into cell:

·    Dex10kDa_flow

 

o   Correlation betaween Flow of SRB entry into cell and Time of 10kDA entry into cell:

·      SRB_flow_corr

 

o   A table grouping the time points, volume points, and cell volume steady-state parameters, organized by dye and by cell.

o   Table_Data_analyse_plateau_InhiCa

·      Plateau oui_non : existence of plateau

·      Tps_plateau : plateau duration 

·      DeltaV_plateau : Difference in cell volume between the start and the end of the cell volume plateau

·      Vi_Vp : Difference in cell volume between the initial swelling onset and the beginning of the cell volume plateau.



 


Data_MCWOCa.mat : Culture medium without Calcium data

SRB_10_500

o   Cell trajectories ROW DATA :

·      Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·      Dex500_Trajectories -> cell volumes measured with Dextran 500 kDa row data

·     SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Cell trajectories Normalized Vi= 1 :

·      Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·      Dex500_Trajectories -> cell volumes measured with Dextran 500 kDa row data

·     SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Timelapse parameters of cell volume acquisition:

·     dt : Timelapse in min

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·      Volpoints_10 and Timepoints_10 -> Determined on 10KDa cell volume trajectories

·     Volpoints_500 and Timepoints_500 -> Determined on 500KDa cell volume trajectories

·      Volpoints_SRB and Timepoints_SRB -> Determined on SRB cell volume trajectories

 

o   Early_swelling rate measurement on 500 kDA cell trajectories between timepoints 1 and 2 :

·     Early_swelling_rate

 

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·     SRB_flow

 

o   A table grouping the time points, volume points, and cell volume steady-state parameters, organized by dye and by cell.

o   Table_Data_analyse_plateau_MCWOCa

·      Plateau oui_non : existence of plateau

·      Tps_plateau : plateau duration 

·      DeltaV_plateau : Difference in cell volume between the start and the end of the cell volume plateau

·      Vi_Vp : Difference in cell volume between the initial swelling onset and the beginning of the cell volume plateau

 

SRB_10_70

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·    SRB_flow

 

o   Flow of 10kDA entry into cell:

·      Dex10kDa_flow

 



 


Data_NinjKO.mat : iBMDMs Ninj 1-/-

 

Data_NinjKO:

SRB_10_500:

 

Two types of experiments were performed (type 1 and type 2), differing in their time-lapse acquisition settings (dt_1 and dt_2). Each experiment type is associated with its corresponding trajectories, time points, and volume points (_dt1 or _dt2)

 

o   Cell trajectories ROW DATA :

·    Dex10_Trajectories (_dt1 or _dt2) -> cell volumes measured with Dextran 10 kDa row data

·     Dex500_Trajectories (_dt1 or _dt2) -> cell volumes measured with Dextran 500 kDa row data

·    SRB_Trajectories (_dt1 or _dt2) -> cell volumes measured with SRB row data

 

o   Timelapse parameters of cell volume acquisition:

·     dt_1: Timelapse in min

·     dt_2: Timelapse in min

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·     Volpoints_10 and Timepoints_10 (_dt1 or _dt2) -> Determined on 10KDa cell volume trajectories

·     Volpoints_SRB and Timepoints_SRB (_dt1 or _dt2) -> Determined on SRB cell volume trajectories

·     Volpoints_500 and Timepoints_500 include, within the same file, data from experiment type 1 and then experiment type 2 (dt₁ and dt₂), determined from 500 kDa cell volume trajectories

 

o   Early_swelling rate measurement on 500 kDA cell trajectories between timepoints 1 and 2 :

·     Early_swelling_rate

 

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·     SRB_flow

 

o   A table grouping the time points, volume points, and cell volume steady-state parameters, organized by dye and by cell:

o   Table_Data_analyse_plateau_NinjKO

·      Plateau oui_non : existence of plateau

·      Tps_plateau : plateau duration 

·      DeltaV_plateau : Difference in cell volume between the start and the end of the cell volume plateau

·      Vi_Vp : Difference in cell volume between the initial swelling onset and the beginning of the cell volume plateau

·      V_max_500: Maximal cell volume measured on 500 kDa_trajectories

·      Vmax_over_Vi_500: Ratio between Maximal cell volume and Initial cell volume, measured on 500 kDa_trajectories

 

-             data_Ninjko_BAPTA:

 

SRB_10_500:

 

o   Cell trajectories ROW DATA :

·     Dex10_Trajectories (_dt1 or _dt2) -> cell volumes measured with Dextran 10 kDa row data

·      Dex500_Trajectories (_dt1 or _dt2) -> cell volumes measured with Dextran 500 kDa row data

·      SRB_Trajectories (_dt1 or _dt2) -> cell volumes measured with SRB row data

 

o   Time: time-lapse interval of 0.13 min

 

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·     SRB_flow

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·      Volpoints_500 and Timepoints_500 -> Determined on 500KDa cell volume trajectories



 


Data_CT.mat: iBMDM WT

SRB_10_70

o   Cell trajectories ROW DATA :

·     Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·    Dex70_Trajectories -> cell volumes measured with Dextran 70 kDa row data

·     SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Timelapse parameters of cell volume acquisition:

·     dt : Timelapse in min

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·     Volpoints_10 and Timepoints_10 -> Determined on 10KDa cell volume trajectories

·     Volpoints_70 and Timepoints_70 -> Determined on 70KDa cell volume trajectories

·     Volpoints_SRB and Timepoints_SRB -> Determined on SRB cell volume trajectories

 

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·    SRB_flow

 

o   Correlation betaween Flow of SRB entry into cell and Time of 10kDA entry into cell:

·     SRB_flow_corr

 

o   A table grouping the time points, volume points, and cell volume steady-state parameters, organized by dye and by cell:

o   Table_Data_analyse_CT

·      Early_swelling rate:

·      Conditions: CT

·      Experience: 1, 2, or 3

·      Nb cell: cell number

·      Dye: dextrans or SRB (Disulf)

·      T_entry: Time of dye entry

·      Flow_sweel: Early_swelling_rate

·      Flow_ent: Flow of dye entry 

 

SRB_10_500

o   Cell trajectories ROW DATA :

·    Dex10_Trajectories -> cell volumes measured with Dextran 10 kDa row data

·     Dex500_Trajectories -> cell volumes measured with Dextran 500 kDa row data

·     SRB_Trajectories -> cell volumes measured with SRB row data

 

o   Timelapse parameters of cell volume acquisition:

o   Dt : Timelapse in min

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·     Volpoints_10 and Timepoints_10 -> Determined on 10KDa cell volume trajectories

·     Volpoints_70 and Timepoints_70 -> Determined on 70KDa cell volume trajectories

·     Volpoints_500 and Timepoints_500 -> Determined on SRB cell volume trajectories

 

o   Flow of SRB entry into cell measured between Timepoints 1 and 2 on SRB cell trajectories:

·    SRB_flow

 

o   Flow of 10kDA entry into cell:

·    Dex10kDa_flow

 

o    Early_swelling rate measurement on 500 kDA cell trajectories between timepoints 1 and 2 :

·      early_swelling_rate

 

o   A table grouping the time points, volume points, and cell volume steady-state parameters, organized by dye and by cell: Table_Data_analyse_CT

·      Conditions: CT

·      Experience: 1, 2, or 3

·      Nb cell: cell number

·      Dye: dextrans 

·      T_entry: Time of dye entry

·      V_max_500: Maximal cell volume measured on 500 kDa_trajectories

·      Vmax_over_Vi_500: Ratio between Maximal cell volume and Initial cell volume, measured on 500 kDa_trajectories



 


b.    SUBFOLDER: data_iBMDM_WT_Dye_entry

 

Time_Dye_entry.mat

o   Combined_table

·      Conditions: CT or Glycin, Dis_50 or Dis_100 (Disulfiram 50 or 100 uM)

·      Experience: 1, 2, or 3

·      nbcell: cell number

·      Dye: dextrans (4_4:4.4 kDa ; 10: 10kDa ; 70: 70 kDa ; 500 : 500 kDa ; disulf: SRB)

·      T_entry: Time of dye entry



 


RowDATA_4_4kDa_10kDa_70kDa

o   Cell trajectories ROW DATA :

·     Vol10_CT-> cell volumes measured with Dextran 10 kDa row data

·     Vol500_CT -> cell volumes measured with Dextran 500 kDa row data

·     Vol70_CT-> cell volumes measured with 70 kDa row data

 

o   Timelapse parameters of cell volume acquisition:

·      timelapse : Timelapse in min

 

o   Table

·      Conditions: CT or Glycin, Dis_50 or Dis_100 (Disulfiram 50 or 100 uM)

·      Experience: 1, 2, or 3

·      nbcell: cell number

·      Dye: dextrans (4_4:4.4 kDa ; 10: 10kDa ; 70: 70 kDa)

·      T_entry: Time of dye entry

·      Timepoints of interest with Volpoints of interest

·      DeltaV_plateau: Difference in cell volume between the initial swelling onset and the beginning of the cell volume plateau



 


2.     FOLDER: MEFs: DATA obtained on MEF cell line

 

data_10_70_500kDa_CT_Glycin.mat: data of MEF untreated or glycine-treated with dextrans : 10, 70 and 500 kDa

o   Cell trajectories ROW DATA :

Untreated:

·      Vol10_CT-> cell volumes measured with Dextran 10 kDa row data

·     Vol500_CT -> cell volumes measured with Dextran 500 kDa row data

·     Vol70_CT -> cell volumes measured with 70 kDa row 

Glycine treated:

·      Vol10_Glycin-> cell volumes measured with Dextran 10 kDa

·       Vol500_Glycin-> cell volumes measured with Dextran 500 kDa row data

·      Vol70_Glycin> cell volumes measured with 70 kDa row data

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

Untreated:

·      Volpoints_10 and Timepoints_10 -> Determined on 10KDa cell volume trajectories

·      Volpoints_70 and Timepoints_70 -> Determined on 70KDa cell volume trajectories

·      Volpoints_500 and Timepoints_500 -> Determined on SRB cell volume trajectories

 

Glycine treated:

·      Volpoints_10_Glycin and Timepoints_10_Glycin -> Determined on 10KDa cell volume trajectories

·     Volpoints_70_Glycin and Timepoints_70_Glycin -> Determined on 70KDa cell volume trajectories

·     Volpoints_500_Glycin and Timepoints_500_Glycin -> Determined on SRB cell volume trajectories

 

o   Timelapse parameters of cell volume acquisition:

·       timelapse : Timelapse in min

 

o   Table

·      Conditions: CT or Glycin, Dis_50 or Dis_100 (Disulfiram 50 or 100 uM)

·      Experience: 1, 2, or 3

·      nbcell: cell number

·      Dye: dextrans (4_4:4.4 kDa ; 10: 10kDa ; 70: 70 kDa)

·      T_entry: Time of dye entry

·      Timepoints of interest with Volpoints of interest

·      Plateau_length: time of cell volume plateau duration



 


data_4_4_10_70kDa.mat: data of MEF with dextrans : 4.4, 10 and 70 kDa

 

Suffixes indicate experimental conditions: _CT for untreated, _Glycin for glycine-treated, _EIPA_50 for EIPA (50 µM)-treated, and _EIPA_500 for EIPA (500 µM)-treated.

 

o   Cell trajectories ROW DATA :

·      Vol10_CT-> cell volumes measured with Dextran 10 kDa row data

·       Vol500_CT -> cell volumes measured with Dextran 500 kDa row data

·      Vol70_CT -> cell volumes measured with 70 kDa row 

 

o   Time points and cell volume points of interest determined on ROW DATA cell volume

·      Volpoints_10 and Timepoints_10 -> Determined on 10KDa cell volume trajectories

·      Volpoints_70 and Timepoints_70 -> Determined on 70KDa cell volume trajectories

·     Volpoints_500 and Timepoints_500 -> Determined on SRB cell volume trajectories

 

o   Timelapse parameters of cell volume acquisition:

·     timelapse : Timelapse in min

 

o   Table

·      Conditions: CT or Glycin, Dis_50 or Dis_100 (Disulfiram 50 or 100 uM)

·      Experience: 1, 2, or 3

·      nbcell: cell number

·      Dye: dextrans (4_4:4.4 kDa ; 10: 10kDa ; 70: 70 kDa)

·      T_entry: Time of dye entry

·      Timepoints of interest with Volpoints of interest

·      Plateau_length: time of cell volume plateau duration

·      DeltaV_plateau: Difference in cell volume between the initial swelling onset and the beginning of the cell volume plateau

·      deltaV_max: Ratio between Maximal cell volume and Initial cell volume, measured on 500 kDa_trajectories