References

Uemura, T.*, Nakano, T.R.*, Takagi, J., Wang, Y., Kramer, K., Finkemeier, I., Nakagami, H., Tsuda, K., Ueda, T., Schulze-Lefert, P., Nakano, A.: A Golgi-released subpopulation of the trans-Golgi network mediates protein secretion in Arabidopsis. Plant Physiology, 2018.
* co-first authors

Garrido-Oter R.*, Nakano R. T.*, Dombrowski, N.*, Ka-Wai M., The AgBiome Team, McHardy A. C. and Schulze-Lefert, P: Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia. Cell Host & Microbe, 2018.

* co-first authors

Zgadzaj R.*, Garrido-Oter R.*, Dorthe B. J., Koprivova A., Schulze-Lefert P.+, Radutoiu S.+: Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive root-associated bacterial communities. PNAS, 2016.

* co-first authors; + co-corresponding authors

Bai Y.*, Müller D. B.*, Srinivas G.*, Garrido-Oter R.*, Potthoff E., Rott M., Dombrowski N., Münch P. C., Spaepen S., Remus-Emsermann M., Hüttel B., McHardy A. C., Vorholt J. A.+, Schulze-Lefert P.+: Functional overlap of the Arabidopsis leaf and root microbiota. Nature, 2015.

* co-first authors; + co-corresponding authors

Hacquard, S.*, Garrido-Oter, R.*, González, A.*, Spaepen, S.*, Ackermann, G., Lebeis, S., McHardy, A. C.+, Dangl, J. L.+, Knight, R.+, Ley, R.+, Schulze-Lefert, P+. Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host & Microbe, 2015.

* co-first authors; + co-corresponding authors

Bulgarelli D.*, Garrido-Oter R.*, Münch P., Weiman A., Dröge J., Pan Y.,  McHardy A. C.+,  and Schulze-Lefert P.+: Structure and functions of the bacterial root microbiota in wild and domesticated barley. Cell Host & Microbe, 2015.

* co-first authors; + co-corresponding authors

Schlaeppi, K., Dombrowski, N., Garrido Oter, R., ver Loren van Themaat, E. and Schulze-Lefert, P.: Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Natl. Acad. Sci. USA., 2014.

Bulgarelli, D.*, Rott, M.*, Schlaeppi, K.*, Ver Loren van Themaat, E.*, Ahmadinejad, N., Assenza, F., Rauf, P., Huettel, P., Reinhardt, R., Schmelzer, E., Peplies, J., Gloeckner, F.-O., Amann, R., Eickhorst, T. and Schulze-Lefert, P.: Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature, 2012.

* co-first authors

R_scripts

Scripts and data related to the manuscript Uemura, Nakano, et. al, 2018

Here we provide the scripts that were employed to analyse and visualise the proteome data as presented in the manuscript Uemura, Nakano et al., 2018. The raw mass spectrometry data can be accessed at the ProteomeXchange Consortium via the PRIDE partner repository under the dataset identifier PXD009099.

The scripts necessary to reproduce the results and analyses reported in the paper can be found here:

SYP4 secretome scripts

Unprocessed raw data and intermediate results can be downloaded here:

SYP4 secretome data

Questions about the scripts and analyses can be addressed to . For any general questions concerning the manuscript, please contact  or .


Scripts and data related to the manuscript Garrido-Oter, Nakano, Dombrowski, et. al, 2018

Here we provide the scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Garrido-Oter, Nakano, Dombrowski, et al. Sequencing reads for the RNA-Seq experiments and whole-genome assemblies can be accessed at the European Nucleotide Archive (ENA) under the accession codes PRJEB27007 and PRJEB26998, respectivelly.

The scripts necessary to reproduce the results and analyses reported in the paper can be found here:

Rhizobiales comparative genomics scripts

Rhizobiales RNA-Seq scripts

Unprocessed raw data and intermediate results can be downloaded here:

Rhizobiales genomics dataset

Rhizobiales RNA-Seq dataset

Questions about the scripts and analyses can be addressed to  or . For any general questions concerning the manuscript, please contact .


R scripts related to the manuscript by Zgadzaj, Garrido-Oter et al., 2016

Here we provide the scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Zgadzaj, Garrido-Oter et al. (2016), published in PNAS.

All scripts necessary to reproduce all results and figures presented in the paper can be found here:

Lotus japonicus microbiota scripts

The unprocessed raw data can be downloaded here:

Lotus japonicus microbiota dataset

Questions about the scripts and analyses can be addressed to . For any general questions concerning the manuscript, please contact or .


R scripts related to the manuscript by Bai et al., 2015

Here we provide the scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Bai et al. (2015), published in Nature.

The scripts used to analyze and generate the figures corresponding to the 16S data can be obtained here:

bacterial culture collections scripts

whole-genome analysis scripts

All raw data necessary to reproduce the results presented in the article, as well as intermediate results can be downloaded here:

bacterial culture collections dataset

whole-genome analysis dataset

Questions about the scripts can be addressed to . For any general questions concerning the manuscript, please contact or .


R scripts related to the manuscript by Dombrowski et al., 2016

Here we provide the R scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Dombrowski et al. (2016), submitted to ISME. Raw sequencing reads were deposited at the NCBI Short Read Archive (SRA), BioProjectID PRJNA317760, accession number SRP073035.

The scripts used to analyze and generate the figures corresponding to the 16S data can be downloaded here:

Dombrowski et al. scripts

Questions about the scripts can be addressed to . For any general questions concerning the manuscript, please contact .


R scripts related to the manuscript by Hacquard et al., 2015

The R scripts used to produce the results and figures presented in the article can be found in the following repository:

https://github.com/garridoo/chommeta

For questions about the scripts please contact Ruben Garrido-Oter. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert.


R scripts related to the manuscript by Bulgarelli et al., 2015

Here we provide the scripts that were specifically developed to analyse and visualise the sequencing data as presented in the figures of the article Bulgarelli et al. (2015) published in Cell Host and Microbe. The raw sequence reads were deposited in the European Nucleotide Archive database (accession no. PRJEB5860).

The scripts used to analyze and generate the figures corresponding to the 16S data can be downloaded here:

Bulgarelli et al. 16S scripts

and those corresponding to the metagenome data can be found here:

https://github.com/hzi-bifo/BarleyMeta

Questions about specific scripts can be addressed to the author indicated in the header of the script. For any general questions concerning the manuscript, please contact Prof. Alice C. McHardy or Prof. Paul Schulze-Lefert.


R scripts related to the manuscript by Schlaeppi et al., 2013

Here we provide the QIIME and R scripts and Supplementary Datasets related to the manuscript Schlaeppi et al. (2014) in PNAS. The raw sequence reads were deposited in the European Nucleotide Archive database (accession no. PRJEB5058).

The archive 'Schlaeppi_et_al_QIIME_scripts.zip' comprises the scripts that were utilized to process and analyze the pyrosequencing reads in QIIME. The scripts contain the functions and parameters used, allowing the reproduction of the analysis.

Schlaeppi et al. QIIME scripts

The Supplementary Datasets S8, S9 and S10 present output files from the QIIME analysis that were utilized for downstream analysis in R.

Schlaeppi et al. supplementary datasets

The file 'Schlaeppi_et_al_R_scripts.zip' contains the R scripts that were developed to analyze the 16S rRNA gene profiling data as presented in the figures of the article. We have documented the scripts to facilitate the reproduction of the analysis.

Schlaeppi et al. R scripts

Questions about specific scripts can be addressed to the author indicated in the header of the script. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert.


R scripts related to the manuscript by Bulgarelli et al., 2012

Below you can find custom R scripts that were specifically developed to analyze and visualize the sequencing data as presented in the figures of the article. We have documented the scripts to facilitate reproduction of main and supplementary figures.

Bulgarelli et al. scripts

In the zip file all scripts, functions and data files are included and organized in folders per figure. As a consequence, the same functions and data files can occur in multiple folders. The names of the tab-delimited data files in the figure folders correspond to sheet or file names in Supplementary Data 1 or 2 (which can be downloaded from nature.com).

The raw sequencing data has been deposited in the NCBI Short Read Archive (SRA043581). Questions for specific scripts can be addressed to the author indicated in the header of the script. For any general questions concerning the scripts, or the manuscript, please contact Prof. Paul Schulze-Lefert.

 
loading content
Go to Editor View