## RNA-seq

The 2×150-bp paired-end reads were trimmed with trim_galore v0.6.7 [trimgalore] using Cutadapt v4.1 [Cutadapt] and FastQC v0.11.9 [FASTQC] in 2 colour and paired end mode.

Trimmed reads were aligned to the reference genome of Acetobacterium dehalogenans DSM 11527 (CP174122.1, available from NCBI) using Bowtie2 v2.5.0 [Bowtie2] with the parameters '--very-sensitive' and '-k30'.
Mapped reads were assigned to "gene" features using featureCounts (subread v2.0.3) [featureCounts] with the parameters '--countReadPairs -M --fraction'. 

Differential gene expression analysis was done with DESeq2 v1.38.0 [DESeq2] using the script easyDeseq2.R (https://gitlab.com/paulklemm_PHD/scripts).
Plots and normalized count tables generated from this analysis are available in the uni marburg GitLab repository (https://gitlab.uni-marburg.de/synmikro/ag-lechner/acetobacterium-dehalogenans-syringat-chlormethan).

The raw sequencing files from this study are available at the NCBI Sequence Read Archive (SRA) under BioProject ID TODO including the BioSample accessions TODO,...

[trimgalore] Krueger, F., James, F., Ewels, P., Afyounian, E., Schuster-Boeckler, B. (2021). FelixKrueger/TrimGalore: v0.6.7. doi: 10.5281/zenodo.5127899
[Cutadapt] Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12. doi: 10.14806/ej.17.1.200
[Bowtie2] : Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.
[featureCounts] : Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930.
[DESeq2] : Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology, 15, 1-21.
[FASTQC] : Simons, A. (2010). A quality control tool for high throughput sequence data. BibSonomy. Available online: https://www.bibsonomy.org/bibtex/f230a919c34360709aa298734d63dca3, 1.