PhD thesis Gijs Selten - Supplementary data

<p>This repository contains the Supplementary data of the experimental chapters published in the PhD thesis of Gijs Selten MSc.&nbsp;</p> <p>Chapter 2 - Functional capacities drive recruitment of bacteria into plant root (already online on bioRxiv --&gt; https://www.biorxiv.org/content/10.1101/2024.08.22.609090v1.article-info)</p> <ul> <li>Supplementary data</li> <li>Supplementary tables</li> </ul> <p>Chapter 3 - Key genetic components for bacterial success in complex communities revealed using comparative metagenome analysis</p> <ul> <li>Supplementary data</li> <li>Orthogroup profiles of SynCom members</li> <li>Figures S7 and S9 (close-up)&nbsp;</li> </ul> <p>Chapter 4 - <em>SyFi</em>: generating and using sequence fingerprints to distinguish SynCom isolates</p> <ul> <li>SyFi bash script</li> <li>Supplementary data: <ul> <li>Microbiome tables - SyFi (minscorefraction 65, 75, 85, 95 (original), and 100%), Salmon directly on amplicons, Qiime2-VSEARCH (95, 97, 98, 99, 100% match), shotgun metagenomics table</li> <li>Percentages mapped reads</li> <li>16S copy number</li> <li>VSEARCH clustering results</li> </ul> </li> <li>16S fingerprints</li> <li>16S V3V4 fingerprints</li> <li>16S V5V7 fingerprints</li> <li>16S original sequences</li> <li>16S V3V4 original sequences</li> <li>16S V5V7 original sequences</li> </ul> <p>Chapter 5 - <em>Bacillus</em>: driver of distinct functional states in plant root bacterial synthetic communities&nbsp;</p> <ul> <li>Supplementary data</li> <li>Supplementary tables</li> <li>Jaccard Distance matrix on isolate composition</li> <li>Jaccard Distance matrix on genus composition</li> <li>Jaccard Distance matrix on KO composition</li> <li>Bray Curtis Distance matrix on isolate composition</li> <li>Bray Curtis Distance matrix on genus composition</li> <li>Bray Curtis Distance matrix on KO composition</li> </ul>