This readme describes the dataset and calculation scripts for the article:
Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth
Mason-Jones, K., Breidenbach, A., Dyckmans, J., Banfield, C.C., Dippold, M.A.
Nature Communications
2023

Article DOI: 10.1038/s41467-023-37713-4

These calculations are provided by Kyle Mason-Jones at the Netherlands Institute of Ecology (NIOO-KNAW).
Please refer to the article for the experimental design and methods.
Further enquiries can be sent to kmasonjones@gmx.de or k.masonjones@nioo.knaw.nl

This dataset consists of 3 files:

- Data_import.zip 
	Compressed file containing data files.
- Combined_script_sub.R 
	The R script for performing calculations. Requires extracted files from "Data_import.zip" to be extracted into a folder "Data_import" in the working directory.
- Combined_plot_script_sub.R 
	The R script for generating plots. Must be run after "Combined_script_sub.R".

Extracting "Data_import.zip" will produce various data files in a required folder structure, as follows:

- Folder "CO2" contains data files from GC-IRMS measurement of headspace CO2 sampled during the incubation. Samples are coded by a xy_zzh, where x is a numeric code indicating the treatment, y is a letter indicating the replicate, and zz is the hour time since treatment. Correspondence between sample codes and treatments (as well as replicates) can be found in "PHBMain_Datacomp_Rimport.xlsx", which is also extracted from the zip file (see below).

- Folder "IRMS_integrated_combined" contains GC-IRMS integrated peak areas for TAGs. File names follow the xy coding scheme indicating treatment/timepoint x and replicate y (see "PHBMain_Datacomp_Rimport.xlsx"). In each file, peak identity is given in column c and peak d13C in column AI. Peak identities are given in an R-friendly custom format which replaces the conventional colon with a stop, replaces omega symbol with w, and adds letters to the front which signify the class of fatty acid (e.g. "br" is branched, "lin" is linear).

- "PHBMain_Datacomp_Rimport.xlsx" contains all other data required for the calculations. Details of the sheet contents are provided in the "Intro" sheet within the spreadsheet file.