READ ME

This text describes the data presented in the paper:

Spurr MWA, Yu EH, Scott K, Head IM.  Extending the dynamic range of biochemical oxygen demand sensing with multi-stage microbial fuel cells. Environ. Sci. Water Res. Technol. 2018, 4(12), 2029-2040.


========================
Introductory information
========================
Files included in the data deposit (include a short description of what data are contained): 

1) Operation_Data.xlsx
2) FC6_1_Lin_Bod_predict_norm.txt
3) FC6_2_Hill_Bod_predict_norm.txt
4) FC6_j_stab_norm_Calibrations.xlsx
5) FC7_1_Lin_Bod_predict_norm.txt
6) FC7_2_Hill_Bod_predict_norm.txt
7) FC7_j_stab_norm_Calibrations.xlsx
8) 16S_DNA_sequencing_data_ALL_SAMPLES.FASTQ
9) DNA_mapping_file.txt


Explain the relationship between multiple data sets, if required:

Operation_Data.xlsx contains the main data in the following tabs:
'Calibrations' tab
- Column Calibration = id
- Column Flow = 1 represents before sludge removal; 2 represents after
- Column Time.st = Start time of calibration
- Column Time.en = End time of calibration
- Column Med.Conc = Medium concentration in mg/l
- Column Med.Type = Medium carbon source type

'Events' tab
- Column Time.d = Timestamp (in days since Time zero)
- Cells = Cells concerned with event row
- Calibration = Calibration id
- New.Med. = 0 Indicating medium was replaced
- Med.Type. = Medium carbon source type
- Op.Mode = Operation mode for pump
- Op.Change = 0 indicating op.mode change
- Prep.Vol = Prepared volume of medium in ml
- Med.Conc = Medium Concentration in mg/l
- N2.Sparge. = 0 indicating N2 sparge occurred
- N2.Sparge.Time = Inidicating ON/OFF for N2 sparge of medium
- Pump.Event = 0 indicating pump event
- Pump.On = Pump status
- RPM = Pump speed
- Emptied.Waste.Bottle = 0 indicates event
- Setup.Change = See comments
- Sludge.Removal = 0 indicates event
- Cells.Online = Indicates cell status
- Comments

'Flow-rates' tab
- Time.d = Timestamp (in days since Time zero)
- RPM = flow speed of pump
- A.Flow / B.Flow / C.Flow = Flow rate in ml/min in each channel (A, B and C)

'Data_MFCs' tab
- Time.d = Timestamp (in days since Time zero)
- Stage = MFC Stage (1,2 or 3) and Sum (S)
- For replicates A, B and C as 'X':
- R_mean is the mean of A, B and C values
- R_range is the standard deviation of A, B and C values
-- X.mV = Recorded voltage in mV
-- X.An = Recorded anode potential in mV
-- X.j = Calculated current in mA
-- A.Q = Calculated charge in C

FC6-denoted files represent calibration data for Calibration 6
FC7-denoted files represent calibration data fro Calibration 7

16S_DNA_sequencing_data_ALL_SAMPLES.FASTQ is the sequencing data file
DNA_mapping_file.txt is the mapping file with barcode and primer information accompanying the FASTQ file.


Key words used to describe the data:

Microbial Fuel Cell, Biochemical oxygen demand, Biosensor, IonTorrent

========================== 
Methodological information
==========================
A brief method description – what the data is, how and why it was collected or created, and how it was processed:

Data obtained from operation and calibration of multi-stage Microbial Fuel Cells (voltage datalogging, medium replacements). Data obtained from IonTorrent DNA sequencing of multi-stage MFC anodes and sludge obtained from the reactors.

Instruments, hardware and software used: 

Microbial Fuel cell reactors were manufactured in-house at Newcastle University.

National Instruments USB-6225 datalogger was used to monitor MFC voltages.
National Instruments SignalExpress datalogging software

Dissolved oxygen (for BOD5 measurements) was measured with a Hach HQ40d meter

DNA was extracted with a PowerSoil® DNA isolation kit.
PCR was performed with a Bibby Scientific Techne TC-512 gradient thermocycler.
DNA was quantified with a Qubit® 2.0 Fluorometer.
DNA was sequenced with a Ion Torrent™ Ion Personal Genome Machine™.
Community analysis was undertaken using the ‘Quantitative
insights into microbial ecology’ software pipeline (QIIME; Caporaso et al. (2010)).


Date(s) of data collection: 

2012-2015

Geographic coverage of data:

Experiments undertaken in Newcastle upon Tyne, UK.

Data validation (how was the data checked, proofed and cleaned):

MFCs were operated in triplicate to validate results.

=========================
Data-specific information
=========================
Definitions of names, labels, acronyms or specialist terminology uses for variables, records and their values: 

FC6 - Flow calibration 6 - Calibration at 0.52 ml/min
FC7 - Flow calibration 7 - Calibration at 1.24 ml/min

1A - 1st MFC in tubular reactor A
2A - 2nd MFC in tubular reactor A
3A - 3rd MFC in tubular reactor A

1B - 1st MFC in tubular reactor B
2B - 2nd MFC in tubular reactor B
3B - 3rd MFC in tubular reactor B

1C - 1st MFC in tubular reactor C
2C - 2nd MFC in tubular reactor C
3C - 3rd MFC in tubular reactor C

Explanation of weighting and grossing variables: 

Where applicable the mean and standard deviation of triplicated data was taken.

Outline any missing data:

N/A

=======
Contact
=======
Please contact rdm@ncl.ac.uk for further information