This codebook.txt file was generated on 2021-06-16 by wilsonkm ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Geobacter sulfurreducens inner membrane cytochrome transcriptional and phenotypic data 2. Author Information Principal Investigator Contact Information Name: Daniel R. Bond Institution: University of Minnesota Address: 256 Gortner Lab, 1479 Gortner Avenue St. Paul, MN 55108 Email: dbond@umn.edu Associate or Co-investigator Contact Information Name: Komal Joshi Institution: University of Minnesota Email: joshi181@umn.edu Associate or Co-investigator Contact Information Name: Chi Ho Chan Institution: University of Minnesota Email: cchan@umn.edu 3. Date of data collection: 2018-02-02 to 2019-10-04 4. Geographic location of data collection: University of Minnesota, St. Paul 5. Information about funding sources that supported the collection of the data: Sponsorship: Office of Naval Research: N00014-16-1-2194, and N00014-18-1-2632. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial 3.0 United States 2. Links to publications that cite or use the data: Joshi, K., Chan, C. H., & Bond, D. R. (2021). Geobacter sulfurreducens inner membrane cytochrome CbcBA controls electron transfer and growth yield near the energetic limit of respiration. Molecular Microbiology, doi: https://doi.org/10.1111/mmi.14801 3. Was data derived from another source? No 6. Recommended citation for the data: Joshi, Komal; Chan, Chi Ho; Bond, Daniel R. (2021). Geobacter sulfurreducens inner membrane cytochrome transcriptional and phenotypic data. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/5AMD-ZW33. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: FeCi_Calibration_curve_data_SI.zip Short description: Iron citrate redox potential calibration curve data obtained using electrochemical analysis and direct Fe(II) measurements using Ferrozine assay. 1. Filename: 8-15-18.xlsx Short description: Raw data from DPV analysis, and open circuit potential (OCV) analysis on Fe(III) citrate at different stages of reduction. 2. Filename: 8-15-18_calibration_curve.xlsx Short description: Calculation of midpoint potential of Fe(III) citrate measured using electrochemical analysis and Ferrozine assay. 3. Filename: 8-15-18_calibrationlogQcurve_SI.pzfx Short description: Prism file for redox potential calibration of Fe(III) citrate obtained from Sigma used in our routine laboratory experiments. B. Filename: RNAseq_data.zip Short description: Raw HiSeq reads for RNAseq experiment from WT and ΔGSU0598 (ΔbccR) at high and low potential conditions on Fe(III) citrate growth medium. 1. Filename: WTFCE1_S15_R1_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under early exponential phase (~30% Fe(III) reduced). Reverse reads. From replicate 1. 2. Filename: WTFCE1_S15_R2_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under early exponential phase (~30% Fe(III) reduced). Forward reads. From replicate 1. 3. Filename: WTFCE2_S16_R1_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under early exponential phase (~30% Fe(III) reduced). Reverse reads. From replicate 2. 4. Filename: WTFCE2_S16_R2_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under early exponential phase (~30% Fe(III) reduced). Forward reads. From replicate 2. 5. Filename: WTFCL1_S1_R1_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under late exponential phase (~70% Fe(III) reduced). Reverse reads. From replicate 1. 6. Filename: WTFCL1_S1_R2_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under late exponential phase (~70% Fe(III) reduced). Forward reads. From replicate 1. 7. Filename: WTFCL2_S2_R1_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under late exponential phase (~70% Fe(III) reduced). Reverse reads. From replicate 2. 8. Filename: WTFCL2_S2_R2_001.fastq Short description: Raw reads of RNAseq analysis on WT G. sulfurreducens strain harvested under late exponential phase (~70% Fe(III) reduced). Forward reads. From replicate 2. 9. Filename: D0598NBFA1_S17_R1_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under NB fumarate acetate growth conditions near mid-exponential phase. Reverse reads. From replicate 1. 10. Filename: D0598NBFA1_S17_R2_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under NB fumarate acetate growth conditions near mid-exponential phase. Forward reads. From replicate 1. 11. Filename: D0598NBFA2_S18_R1_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under NB fumarate acetate growth conditions near mid-exponential phase. Reverse reads. From replicate 2. 12. Filename: D0598NBFA2_S18_R2_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under NB fumarate acetate growth conditions near mid-exponential phase. Forward reads. From replicate 2. 13. Filename: D0598FCL1_S3_R1_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under late exponential phase (~70% Fe(III) reduced). Reverse reads. From replicate 1. 14. Filename: D0598FCL1_S3_R2_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under late exponential phase (~70% Fe(III) reduced). Forward reads. From replicate 1. 15. Filename: D0598FCL2_S4_R1_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under late exponential phase (~70% Fe(III) reduced). Reverse reads. From replicate 2. 16. Filename: D0598FCL2_S4_R2_001.fastq Short description: Raw reads of RNAseq analysis on ΔGSU0598 (ΔbccR) strain harvested under late exponential phase (~70% Fe(III) reduced). Forward reads. From replicate 2. 2. Relationship between files: A. The files contain data for measurement of midpoint potential of Fe(III) citrate. B. The files contain raw fastq RNA sequencing data of WT and ΔGSU0598 strains from growth medium with Fe(III) citrate or fumarate as electron acceptors. 3. Additional related data collected that was not included in the current data package: NA 4. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: https://onlinelibrary.wiley.com/doi/abs/10.1111/mmi.14801 2. Methods for processing the data: Residual ribosomal RNA sequences from raw reads were removed using Bowtie2 before analysis. Duplicate rRNA-depleted biological samples were analyzed for each strain and condition using Rockhopper, with our re-sequenced WT G. sulfurreducens genome as reference (https://www.ncbi.nlm.nih.gov/sra/SRX1101230/). All analysis were performed using commandline tools. 3. Instrument- or software-specific information needed to interpret the data: Prism, Microsoft excel, Rockhopper, Bowtie2. 4. People involved with sample collection, processing, analysis and/or submission: Komal Joshi (Bond lab) Chi Ho Chan (Bond lab) Elyse Froehling (University of Minnesota Genomics Center)