UMR PHIM

Plant Health Institute of Montpellier

Among the interactions between the plant and its environment (microbial organisms or insects, whether pathogenic or beneficial), the research unit studies those that have an impact on plant health, growth and productivity. The unit is organized in 4 research departments:

Plant-pathogen interactions (ITEM)
Plant-vector-pathogen interactions (VIROM)
Towards an understanding of the phytobiome (PHYTOBIOM)
Understanding epidemics in the field (PRISM)

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41 to 50 of 77 Results

ATAC_loci_ALL_expStats.tab Mar 3, 2022 - Supplementary information for: The rice ILI2 locus is a bidirectional target of the African Xanthomonas oryzae pv. oryzae major Transcription Activator-Like Effector TalC but does not contribute to disease susceptibility Tabular Data - 13.9 MB - 37 Variables, 94719 Observations - UNF:6:jdkGW/8VhWIPR5jUnVyxTw== DataGenomics Computed gene expression values and differential expression statistics in Nipponbare leaves inoculated with the African Xoo strain BAI3 and a derivative or mock as a tab delimited file.
ATAC_mergedExpTranscriptome.gtf Mar 3, 2022 - Supplementary information for: The rice ILI2 locus is a bidirectional target of the African Xanthomonas oryzae pv. oryzae major Transcription Activator-Like Effector TalC but does not contribute to disease susceptibility Unknown - 77.2 MB - MD5: d3a76a24cab4b3c1f202c001fee97663 DataGenomics Genes and transcripts annotation inferred on the rice Nipponbare genome (Os-Nipponbare-Reference-IRGSP-1.0) with StringTie using both MSU7 reference annotation and experimental mRNA-seq data in the Gene Transfer Format (GTF).
Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018 Nov 2, 2021 - LMI PathoBios Barro, Mariam; Wonni, Issa; Tollenaere, Charlotte, 2021, "Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018", https://doi.org/10.23708/LZ8A5B, DataSuds, V1, UNF:6:rqze4JhkLprhV3rphRgnmg== [fileUNF] This dataset presents the physico-chemical analysis of 19 soil samples, from 6 rice-growing sites in western Burkina Faso (Hauts-Bassins and Cascades). The six sites are located in the 3 geographical zones, all in Lixisols (soils with subsurface accumulation of low activity clays...
Barro_2021_Soil_analysis_rice_BurkinaFaso_data_dictionary.tab Nov 2, 2021 - Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018 Tabular Data - 1.3 KB - 2 Variables, 26 Observations - UNF:6:7mdOtqDWQAaARFF7ymJ0cA== Documentation Data dictionary
Barro_2021_Soil_analysis_rice_BurkinaFaso_data.tab Nov 2, 2021 - Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018 Tabular Data - 3.6 KB - 27 Variables, 19 Observations - UNF:6:pn1IyJWDNR6V/aXS5HJBzA== DataGeospatial Soil analysis data
Methodologie_analyse_sols_BurkinaFaso_vf3.pdf Nov 2, 2021 - Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018 Adobe PDF - 1.1 MB - MD5: 987592a7853936fc6d6d470a55870dc4 Documentation Methodology for rice field soil sampling and soil analysis (in French and in English)
Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection" Sep 30, 2021 Reshetnyak, Ganna; Jacobs, Jonathan M.; Auguy, Florence; Sciallano, Coline; Claude, Lisa; Medina, Clemence; Perez-Quintero, Alvaro J.; Comte, Aurore; Thomas, Emilie; Bogdanove, Adam; Koebnik, Ralf; Szurek, Boris; Dievart, Anne; Brugidou, Christophe; Lacombe, Severine; Cunnac, Sebastien, 2021, "Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"", https://doi.org/10.23708/RXIXM3, DataSuds, V2 This dataset contains additional supporting information and source code related to the discovery of Xanthomonas-induced small RNAs (xisRNAs) as described in the Related Publication. Deep small RNA (sRNA) sequencing analysis discovered a class of sRNA in rice (Oryza sativa) specif...
PHIM_xisRNA_MS_dataverse_code.html Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection" HTML - 83.6 MB - MD5: 289cce939aa787443e70f5eb880ee575 CodeDocumentation This HTML file records the code and the output of most secondary analysis computing tasks performed to generate the material that is relevant to the manuscript on xisRNAs referenced in the Related Publication metadata. See the RData file to access the individual objects in the R...
PHIM_xisRNA_MS_dataverse_code.Rmd Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection" R Markdown Text - 324.6 KB - MD5: ede28f634dc2712e930c4d8c3783e472 CodeDocumentation This R Markdown file records the code of most secondary analysis computing tasks performed to generate the material that is relevant to the manuscript on xisRNAs referenced in the Related Publication metadata. The accompanying html file was generated using this rmd file.
PHIM_ xisRNA_session.RData Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection" R Data - 849.4 MB - MD5: d52bc72c86361b747f98eb875e13a00d Data R statistical programming language RData file storing the objects created for the production of the "PHIM_ xisRNA_MS_dataverse_code.html" file using the R code found in the html file itself as well as in the "PHIM_ xisRNA_MS_dataverse_code.Rmd" R Markdown file.

ATAC_loci_ALL_expStats.tab

Mar 3, 2022 - Supplementary information for: The rice ILI2 locus is a bidirectional target of the African Xanthomonas oryzae pv. oryzae major Transcription Activator-Like Effector TalC but does not contribute to disease susceptibility

Tabular Data - 13.9 MB - 37 Variables, 94719 Observations -

DataGenomics

Computed gene expression values and differential expression statistics in Nipponbare leaves inoculated with the African Xoo strain BAI3 and a derivative or mock as a tab delimited file.

ATAC_mergedExpTranscriptome.gtf

Unknown - 77.2 MB -

DataGenomics

Genes and transcripts annotation inferred on the rice Nipponbare genome (Os-Nipponbare-Reference-IRGSP-1.0) with StringTie using both MSU7 reference annotation and experimental mRNA-seq data in the Gene Transfer Format (GTF).

Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018

Nov 2, 2021 - LMI PathoBios

Barro, Mariam; Wonni, Issa; Tollenaere, Charlotte, 2021, "Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018", https://doi.org/10.23708/LZ8A5B, DataSuds, V1, UNF:6:rqze4JhkLprhV3rphRgnmg== [fileUNF]

This dataset presents the physico-chemical analysis of 19 soil samples, from 6 rice-growing sites in western Burkina Faso (Hauts-Bassins and Cascades). The six sites are located in the 3 geographical zones, all in Lixisols (soils with subsurface accumulation of low activity clays...

Barro_2021_Soil_analysis_rice_BurkinaFaso_data_dictionary.tab

Nov 2, 2021 - Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018

Tabular Data - 1.3 KB - 2 Variables, 26 Observations -

Documentation

Data dictionary

Barro_2021_Soil_analysis_rice_BurkinaFaso_data.tab

Nov 2, 2021 - Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018

Tabular Data - 3.6 KB - 27 Variables, 19 Observations -

DataGeospatial

Soil analysis data

Methodologie_analyse_sols_BurkinaFaso_vf3.pdf

Nov 2, 2021 - Soil Physicochemical Properties in rice fields from six sites in western Burkina Faso, 2018

Adobe PDF - 1.1 MB -

Documentation

Methodology for rice field soil sampling and soil analysis (in French and in English)

Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"

Sep 30, 2021

Reshetnyak, Ganna; Jacobs, Jonathan M.; Auguy, Florence; Sciallano, Coline; Claude, Lisa; Medina, Clemence; Perez-Quintero, Alvaro J.; Comte, Aurore; Thomas, Emilie; Bogdanove, Adam; Koebnik, Ralf; Szurek, Boris; Dievart, Anne; Brugidou, Christophe; Lacombe, Severine; Cunnac, Sebastien, 2021, "Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"", https://doi.org/10.23708/RXIXM3, DataSuds, V2

This dataset contains additional supporting information and source code related to the discovery of Xanthomonas-induced small RNAs (xisRNAs) as described in the Related Publication. Deep small RNA (sRNA) sequencing analysis discovered a class of sRNA in rice (Oryza sativa) specif...

PHIM_xisRNA_MS_dataverse_code.html

Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"

HTML - 83.6 MB -

CodeDocumentation

This HTML file records the code and the output of most secondary analysis computing tasks performed to generate the material that is relevant to the manuscript on xisRNAs referenced in the Related Publication metadata. See the RData file to access the individual objects in the R...

PHIM_xisRNA_MS_dataverse_code.Rmd

Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"

R Markdown Text - 324.6 KB -

CodeDocumentation

This R Markdown file records the code of most secondary analysis computing tasks performed to generate the material that is relevant to the manuscript on xisRNAs referenced in the Related Publication metadata. The accompanying html file was generated using this rmd file.

PHIM_ xisRNA_session.RData

Sep 30, 2021 - Supplementary information and source code for "An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection"

R Data - 849.4 MB -

Data

R statistical programming language RData file storing the objects created for the production of the "PHIM_ xisRNA_MS_dataverse_code.html" file using the R code found in the html file itself as well as in the "PHIM_ xisRNA_MS_dataverse_code.Rmd" R Markdown file.

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