This readme.txt file was generated on 20240712 by Aset Khakimzhan Recommended citation for the data: CKhakimzhan, Aset; Izri, Ziane; Thompson, Seth; Dmytrenko, Oleg; Fischer, Patrick; Beisel, Chase; Noireaux, Vincent. (2024). Data supporting Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/qpnn-1n32. ------------------- GENERAL INFORMATION ------------------- Dataset Title: Data for Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins 2. Author Information Principal Investigator Contact Information Name: Vincent Noireaux Institution: University of Minnesota - Twin Cities Address: 115 Union Street SE, 55455, Minneapolis, MN Email: noireaux@umn.edu ORCID: 0000-0002-5213-273X Associate or Co-investigator Contact Information Name: Aset Khakimzhan Institution: University of Minnesota - Twin Cities Address: 115 Union Street SE, 55455, Minneapolis, MN Email: khaki005@umn.edu ORCID: 0000-0002-2258-9085 Associate or Co-investigator Contact Information Name: Ziane Izri Institution: University of Minnesota - Twin Cities Address: 115 Union Street SE, 55455, Minneapolis, MN Email: izri0001@umn.edu ORCID: 0000-0003-4074-1535 Associate or Co-investigator Contact Information Name: Seth Thompson Institution: University of Minnesota - Twin Cities Address: 115 Union Street SE, 55455, Minneapolis, MN Email: thom5884@umn.edu ORCID: 0000-0003-1713-223X Associate or Co-investigator Contact Information Name: Oleg Dmytrenko Institution: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Address: Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Email: oleg.dmytrenko@helmholtz-hiri.de ORCID: 0000-0002-1165-6836 Associate or Co-investigator Contact Information Name: Patrick Fischer Institution: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Address: Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Email: patrick.fischer@stud-mail.uni-wuerzburg.de ORCID: n/a Associate or Co-investigator Contact Information Name: Chase Beisel Institution: Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Address: Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany Email: chase.beisel@helmholtz-hiri.de ORCID: 0000-0003-0650-9943 3. Date published or finalized for release: 20240115 4. Date of data collection (single date, range, approximate date) Start: 20221101 End: 20240505 5. Geographic location of data collection (where was data collected?): Minneapolis, USA: TXTL data Würzburg, Germany: Zorya infection data 6. Information about funding sources that supported the collection of the data: NSF Award Abstract # 2017932 BBSRC-NSF/BIO: Real-time Nanosensing of Membrane Protein Assembly in a TXTL Synthetic Cell System 7. Overview of the data (abstract): Quartz crystal microbalance raw data. The data contains the process of SLB formation (usually within the first 4 hours of data collection) and then incubation of TXTL with the SLB (rest of the measurement). Fluorescence raw data and analysis. Contain raw data readouts from a fluorescence plate reader. Also contain the analysis that groups conditions for averaging and standard deviation calculations. Phage titration data. Contains PFU information for multiple conditions. Also contains the analysis that groups conditions for averages and standard deviation calculations. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: https://creativecommons.org/licenses/by/4.0/ 2. Links to publications that cite or use the data: Khakimzhan, A., Izri, Z., Thompson, S. et al. Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Commun Biol 7, 1005 (2024). https://doi.org/10.1038/s42003-024-06690-9 3. Was data derived from another source? No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. KhakimzhanREADME.txt 2. KhakimzhanOutline_2024.xlsx excel file contains the entire file list and description of conditions. 3. KhakimzhanEtAl_2024_Data.zip raw data -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: QCMD-TXTL, Fluorescence measurements, Phage titration assays 2. Methods for processing the data: No data processing was performed. 3. Instrument- or software-specific information needed to interpret the data: N/A 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: TXTL: 29C, 1 atm. Infection assays: 37C 6. Describe any quality-assurance procedures performed on the data: N/A 7. People involved with sample collection, processing, analysis and/or submission: Aset Khakimzhan, Ziane Izri, Seth Thompson, Oleg Dmytrenko, Patrick Fischer, Chase Beisel, Vincent Noireaux ----------------------------------------- DATA TREE ----------------------------------------- | KhakimzhanOutline_2024.xlsx | KhakimzhanREADME.txt | \---KhakimzhanEtAl_2024_Data.zip +---Khakimzhan et al 2024 ALL DATA | 2022_03_03 EggPC 1mg-mL, Blank 2.0, TXTL 2.0, TXTL 2.1, TXTL 3.0, all T7 - a-hem GFP tagged, flipped module, no passivation.csv | 2022_03_04 EggPC 1mg-mL, Blank 2.0, TXTL 2.0, TXTL 2.1, TXTL 3.0, all T7 - a-hem GFP tagged, non flipped module, no passivation.csv | 2022_03_07 EggPC 1mg-mL, Blank 2.0, TXTL 2.0, TXTL 2.1, TXTL 3.0, all T7 - a-hem GFP tagged, flipped module, no passivation.csv | 2022_03_09 EggPC 1mg-mL, Blank 2.0, 2.0 old3pga, 3.0 old3pga, 3.0 cpck4 all T7 - a-hem GFP tagged, flipped module, no passivation.csv | 2022_03_10 EggPC 1mg-mL, Blank 2.0 cpck4, 2.0 cpck4, 2.0 cpck-pep9, 3.0 cpck-pep9 all T7 - a-hem GFP, flipped module, no passivation.csv | 2022_03_11 E coli extract 3 mg-mL, Blank , deGFP. a-hem, MscL all T7 - GFP, toolbox 2.0 old 3PGA, flipped module, no passivation.csv | 2022_03_12 E coli extract 3 mg-mL, Blank , deGFP. a-hem, MscL all T7, toolbox 2.0 old 3PGA, flipped module, no passivation.csv | 2022_03_15 EggPC 1 mg-mL, 0 1 2 4 nM a-hem T7 cascade, toolbox 2.0 old 3PGA, flipped module, no passivation.csv | 2022_03_30 EggPC 1 mg-mL x2 - E coli extract 3 mg-mL x2, blank, MscL, blank, aHL-eGFP, toolbox 2-0 old 3PGA, flipped module, no passivation.csv | 2022_06_13 EggPC 1mg-mL, +-PS 20%, +-p70a-deGFP-lactc2, toolbox 2.csv | 2022_06_14 EggPC 1mg-mL,EggPC-PS 70-30 80-20 90-10 100-0, p70a-deGFP-lactc2 10 nM, toolbox 2.0, flipped module.csv | 2022_07_07 EggPC Clear coli extract, blank aHL, aHL-eGFP, MscL, toolbox 2-0, flipped module.csv | 2022_07_12 EggPC-E coli extract total 0-100 6-94 13-87 20-80 MscL T7 cascade, toolbox 2-0, flipped module.csv | 2022_07_13 EggPC-E coli extract total 20-80 40-60 60-40 80-20 MscL T7 cascade, toolbox 2-0, flipped module.csv | 2022_07_14 EggPC Blank aHL-eGFP aHL-LEPB aHL-ICS T7 cascade, toolbox 2-0, flipped module.csv | 2022_07_15 EggPC Blank aHL-eGFP aHL aHL-Mel T7 cascade, toolbox 2-0, flipped module.csv | 2022_07_18 Blank EggPC-E coli extract total 20-80 40-60 60-40 80-20, toolbox 2-0, flipped module.csv | 2022_07_19 Blank EggPC-E coli extract total 20-80 13-87 6-94 0-100, toolbox 2-0, flipped module.csv | 2022_07_20 E coli extract total Blank MscL MreB MreB-Venus, toolbox 2-0, flipped module.csv | 2022_09_08 EggPC-E coli extract 20-80 40-60 60-40 80-20 AH-eGFP T7 cascade all, toolbox 2-0, flipped module.csv | 2022_09_09 EggPC-E coli extract 76-24 72-28 68-32 64-36 AH-eGFP T7 cascade all, toolbox 2-0, flipped module.csv | 2022_09_10 EggPC-E coli extract 24-76 28-72 32--68 36-64 AH-eGFP T7 cascade all, toolbox 2-0, flipped module.csv | 2022_09_12 EggPC-E coli extract 40-60, AH-eGFP, MscL, blank, AH-eGFP + MscL, cascade all, toolbox 2-0, flipped module.csv | 2022_09_20 EggPC-E coli extract 20-80 40-60 60-40 80-20, T7p14-AH-eGFP all, toolbox 2-0, flipped module.csv | 2022_09_21 EggPC-E coli extract 24-76 28-72 32-68 36-64, T7p14-AH-eGFP all, toolbox 2-0, flipped module.csv | 2022_11_07 DOPC 1 mgmL, recbcd Ex. blank, T7p14-AH-eGFP, t7p14-MscL, t7p14-AH-eGFP linear.csv | 2022_11_14 EggPC1mgmL, blank, 5nM t7p14-deGFP, 5nM t7p14-mscl-egfp, 5nM t7p14-AH-eGFP. toolbox 2.csv | 2022_11_16 EggPC1mgmL, blank, 10nM t7p14-CCR5, 5nM t7p14-LukE and -LukD, all together, toolbox 2, flipped module.csv | 2022_11_21 EggPC1mgmL recBCD, blank, 5nM t7p14-AerA, 10nM t7p14-AerA, 20nM t7p14-AerA, toolbox 2, flipped module.csv | 2022_12_02 DOPE 0, 1, 2, 3 mgmL, Blank TXTL for all, flipped module.csv | 2022_12_11 DOPE 1,5mgmL recBCD, blank, AH-eGFP, AqpZ, MscL, toolbox 2, flipped module.csv | 2022_12_12 DOPE-DOPC hybrids 20PC, 40PC, 60PC, 80PC, blank TXTL for all, toolbox 2, flipped module.csv | 2022_12_13 DOPE-DOPC hybrids 20PC, 40PC, 60PC, 80PC, 5nM T7p14-MscL TXTL for all, toolbox 2, flipped module.csv | 2022_12_19 DOPE-DOPC hybrids 44PC, 48PC, 52PC, 56PC, 5nM T7p14-MscL TXTL for all, toolbox 2, flipped module.csv | 2023.10.23 - Zorya GFP T7.csv | 2023.10.23 - Zorya His, FLAG, Myc phiX174.csv | 2023.10.23 - Zorya His, FLAG, Myc T7.csv | 2023.10.23 - Zorya T4, T5, T7, phiX174.csv | 2023_01_24 DOPG 5, 15, 25, 35 into DOPE, 10nM p70a-minD, toolbox 2, flipped module.csv | 2023_01_25 DOPG + DOPE, p70a-minD, 0 - 0,5 - 1- 2nM p70a-MinE, toolbox 2, flipped module.csv | 2023_01_26 DOPG + DOPE, p70a-minD, 0 - 0,05 - 0,1- 0,2nM p70a-MinE, toolbox 2, flipped module.csv | 2023_01_27 DOPG + DOPE, p70a-minD, +-p70a-MinE, +- P70a-MinC, toolbox 2, flipped module.csv | 2023_01_30 DOPG+DOPE, p70a-minD, 0nM-0,01nM-0,02nM-0,05nM p70a-MinE, toolbox 2, flipped module.csv | 2023_01_31 EcoliEx SLB, Blank, 10nM p70a-FadL, 10nM p70a-Sp-FadL, 10nM p70a-OmpF, toolbox 2, flipped module.csv | 2023_02_10 DOPE 1,5 mgml + DOPG 0 10 20 30%, Blank TXTL toolbox 2, flipped module.csv | 2023_02_13 DOPC with DOPG range 0-0,1-0,2-0,3 mgml, 10nM P70a-MinD for all, toolbox 2, flipped module.csv | 2023_02_14 DOPC with 20% DOPG, +-10nM P70a-MinD, +- 0.15nM P70a-MinE.csv | 2023_02_27 DOPE+DOPG+PEGPE range 0 05 1 2%, 10nM P70a-MinD, 0.15nM P70a-MinE.csv | 2023_03_05 EcoliExtract, 10nM P70a-MinD, range of P70a-minE, toolbox 2, flipped module.csv | 2023_03_08 DOPE SLB, Blank TXTL vs MscL TXTL, 0h preincub vs 24h preincub, toolbox 2, flipped module.csv | 2023_03_13 DOPC SLB nonspecific range test, Blank TXTL, toolbox 2, flipped module.csv | 2023_03_20 EggPC SLB nonspecific range test, Blank TXTL, toolbox 2, flipped module.csv | 2023_03_21 EcoliEx SLB nonspecific range test, Blank TXTL, toolbox 2, flipped module.csv | 2023_03_22 DOPE SLB, Blank, BR, MisticGFP, MisticBR, recBCD toolbox 2, flipped module.csv | 2023_04_03 EggPC+DPPS 0-0.1-0.2-0.3 range SLB, blank drecbcd toolbox2.csv | 2023_04_05 DOPC+DOPG 0-0.1-0.2-0.3 range SLB, 10nM P70a-MinD.csv | 2023_04_06 DOPC+DOPG 0.05-0.15-0.25-0.35 range SLB, 10nM P70a-MinD, dRecBCD toolbox 2, flipped module.csv | 2023_04_07 DOPC+DOPG 20% range SLB, 10nM P70a-MinD, P70a-MinE range, dRecBCD toolbox 2, flipped module.csv | 2023_04_09 DOPC+DOPG 20% range SLB, 10nM P70a-MinD, P70a-MinE range2, dRecBCD toolbox 2, flipped module.csv | 2023_04_10 DOPE+DOPG 0-0.1-0.2-0.3 SLB, 10nM P70a-MinD, dRecBCD toolbox 2, flipped module.csv | 2023_04_11 DOPE+DOPG 0.05-0.15-0.25-0.35 SLB, 10nM P70a-MinD, dRecBCD toolbox 2, flipped module.csv | 2023_04_15 DOPC+DOCA 0-0.05-0.1-0.15 SLB, 10nM P70a-MinD, dRecBCD toolbox 2, flipped module.csv | 2023_04_23 DOPE SLB, 10nM P70a-MinD, 4 replicates, dRecBCD toolbox 2, flipped module.csv | 2023_04_24 DOPC + DOPA range SLB, Blank dRecBCD toolbox 2, flipped module.csv | 2023_04_27 DOPC + PalmAcid range SLB, Blank dRecBCD toolbox 2, flipped module.csv | 2023_04_29 DOPC + DOCA range SLB, Blank dRecBCD toolbox 2, flipped module.csv | 2023_05_04 DOPC + DOTAP range SLB, Blank TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_05 DOPC + DOTAP range SLB, P70a-MinD TXTL, dRecBCD toolbox 2, flipped module - Copy.csv | 2023_05_05 DOPC + DOTAP range SLB, P70a-MinD TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_06 DOPC + DOPG + DOTAP range SLB, P70a-MinD TXTL, dRecBCD toolbox 2, flipped module - Copy.csv | 2023_05_06 DOPC + DOPG + DOTAP range SLB, P70a-MinD TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_08 DOPC + 10DOPG + DOCA range SLB, Blank TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_09 DOPC + 20DOPG + DOCA range SLB, Blank TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_10 DOPC + DOCA range SLB, Blank TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_11 DOPC + 30DOPG + DOCA range SLB, Blank TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_12 DOPC + 5DOPG + PalmAcid range SLB, 10nM P70a-MinD TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_05_18 QCMD1_Brain Blank.csv | 2023_06_04 DOPE + DOTAP range SLB, 10nM P70a-MinD TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_06_07 DOPE + DOPG + DOTAP range SLB, 10nM P70a-MinD TXTL, dRecBCD toolbox 2, flipped module.csv | 2023_08_23 Blank BaeS BasS CreC.csv | 2023_09_06 E.coli Extract SLB Blank, MscL-G22E, mscL-K55T, mscL-WT drecBCD.csv | 2023_09_08 E.coli Extract SLB Blank, mscL-K55T, mscL-WT linear, mscL-WT plasmid, drecBCD.csv | 2023_09_09 E.coli Extract SLB Blank, mscL-K55T, mscL-WT linear, mscL-WT plasmid, drecBCD.csv | 2023_09_17 ECL SLB Blank, mscL-I41N, mscL-K55T, mscL-WT, all linear drecBCD TXTL.csv | 2023_09_19 DOPE SLB_Blank, csx27, csx28, mscL-WT_all linear_drecBCD TXTL.csv | 2023_09_21 ECL SLB Blank, zorA, zorB, zorA+zorB, all linear_drecBCD TXTL.csv | 2023_09_22 DOPC or DOPE, Blank or ZorA, all linear_drecBCD TXTLMEASUREMENT.csv | 2023_09_24 DOPE+-DOCA SLB, Blank or ZorA, all linear_drecBCDTXTL.csv | 2023_09_27 DOPE+larger DOCA SLB, Blank, ZorA, ZorB, ZorAB, all linear_drecBCDTXTL.csv | 2023_09_28 DOPE+larger DOCA SLB, Blank, ZorAB, ZorE, ZorABE, all linear_drecBCDTXTL.csv | 2023_10_02 DOPC vs DOPE SLB, Blank vs ZorE, all linear_drecBCDTXTL.csv | 2023_10_04 DOPE +- 6.7% DOCA SLB, Blank vs ZorE.csv | 2023_10_09 ECL SLB, Blank vs MscL, New vs Old 3PGA, all linear_drecBCDTXTL.csv | 2023_10_10 DOPE + DOCA range SLB, all Blank drecBCDTXTL.csv | 2023_10_17 ECL, Blank, X, Y, Z drecBCDTXTL.csv | 2023_10_18 12 DOPE 34 DOPE DOPG, Blank, ZorA ZorB, Blank, ZorA ZorB, drecBCDTXTL.csv | 2023_10_21 12 DOPE 34 DOPE DOCA, All ZorA ZorB, 13 no Rabeprazole 24 Rabeprazole, drecBCDTXTL.csv | 2023_10_30 DOPE+-DOCA, Blank v ZorA, drecbcd.csv | 2023_11_08 DOPE +- 6.7% CL, Blank or ZorB, drecbcd.csv | 2023_11_16 ECL SLB, Blank, X, Y, Z drecbcd.csv | 2023_11_18 ECL SLB, Blank, SecY + SecEG range, drecbcd.csv | 2023_12_11 0 025 05 1 mg mL Bovine Heart Extract SLB, TXTL dRec TB2 conditions P70aT7.csv | 2023_12_21 ECL SLB, Blank, yidC, aqpZ, aqpZ-egfp.csv | 2023_12_27 ECL SLB, Blank, torAD, tatABC, torAD+tatABC.csv | 2024_01_02 DOPE+-CL SLB, Blank vs tatBC.csv | 2024_01_08 EggPC Cholesterol range SLB, P70a T7rnap for NSA.csv | 2024_01_22 QCMD3_PBE NSA (1).csv | 2024_02_19 ECL SLB, Blank, basS, btsS, creC.csv | 2024_02_28 ECL SLB, dRec TXTL, blank, mscK, mscM, mscS.csv | 2024_03_08 ECL SLB, Blank, X, Y, Z.csv | 2024_03_19 DOPE +- Rhod-PE 0,075 mgml, Blank vs mscL.csv | 2024_04_01 DOPE + 0.075 mgml Rhod-PE, FS, Blank, mscL, SDS.csv | 2024_04_03 DOPE + 0.075 mgml Rhod-PE, FS, blank, mscl, sds, IPA flush.csv | 2024_04_05 DOPE + 0,075 mgml rhod-pe, fs, blank, mscl, sds.csv | 2024_04_27 ECL EggPC 50 50 SLB, blank, mscl, mscl, ah-egfp.csv | 2024_04_28 1&2 70% EggPC, 3&4 90% EggPC, 1blank, 2mscL, 3mscL, 4ah egfp.csv | 2024_04_29 1&2 30% EggPC, 3&4 70% EggPC, 1blank, 2mscL, 3blank, 4mscl.csv | 2024_04_30 MscL all channels 100%, 90&, 80%, 60% EggPC.csv | 2024_05_06 Dialized Extract TXTL, EggPC + DPPS 0 or 0.1 mgmL, blank vs lactC2-eGFP.csv | 2024_05_07 EggPC + DPPS 0.1 or 0.3 mgml, blank vs p70a-egfp-lactC2.csv | 2024_05_08 EggPC + DPPS 0 0.1 0.2 0.3 mgmL, p70a-eGFP-lactC2.csv | 2024_05_09 EggPC + DPPS 0 0.1 0.2 0.3 mgml, blank txtl.csv | BulkGFP_P70a_vs_T7_bySeth.csv | Compiled IPA 800 uL data.xlsx | QCMD_post-run_2uL_March12_2022.xlsx