diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md index 0319b42cfece327fbe450017657f9d450035fb93..f730cd57340035f270819ee8fa4e97a8a219b2a1 100644 --- a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md +++ b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md @@ -11,4 +11,79 @@ (A) Principal-component analysis (PCA) of total metabolites extracted from the whole root and root segments 2, 4, and 6 cm above the root tip of *sweet2, sweet4, sweet11;12*, and WT plants. WT: N = 16, *sweet2*: N = 19, *sweet4*: N = 20, *sweet11;12*: N = 21. (B) Relative abundance of metabolite superclasses significantly (p value < 0.05) enriched and depleted in each root segment of sweet mutants compared with corresponding segments of WT. -(C) Heatmap depicting the enrichment (or depletion) of indicated metabolites in respective root segments for WT and sweet plants (abbreviated as *swt*). Heatmap generated based on average linkage Pearson hierarchical clustering of metabolites and root segments. Clusters are indicated in red roman numbers. Colors indicate the level of enrichment or depletion of each metabolite across the plant genotypes and root segments. \ No newline at end of file +(C) Heatmap depicting the enrichment (or depletion) of indicated metabolites in respective root segments for WT and sweet plants (abbreviated as *swt*). Heatmap generated based on average linkage Pearson hierarchical clustering of metabolites and root segments. Clusters are indicated in red roman numbers. Colors indicate the level of enrichment or depletion of each metabolite across the plant genotypes and root segments. + +**Table 2. Contribution of spatial distribution and/or plant genotype to the abundance of root metabolites** + +| **Metabolite** | **Superclass** | **sweet2** | **sweet4** | **sweet11;12** | +|--------------------|-------------------------|-------------------|-------------------|-------------------| +| Sterol 23.74 | sterol lipid | N/A | N/A | N/A | +| Sterol 23.16 | sterol lipid | genotype | genotype | genotype | +| Fructose | carbohydrate | genotype | genotype | genotype | +| Glucose | carbohydrate | genotype | genotype | genotype | +| Disaccharide 14.98 | carbohydrate | genotype | genotype | genotype | +| Sorbitol | carbohydrate | genotype | genotype | genotype | +| Sucrose | carbohydrate | genotype | genotype | genotype | +| Hexose 13.45 | carbohydrate | genotype | genotype | genotype | +| Disaccharide 15.98 | carbohydrate | genotype | genotype | genotype | +| Mannitol | carbohydrate | genotype | N/A | genotype | +| Disaccharide 14.35 | carbohydrate | N/A | genotype | N/A | +| Gluconate | carbohydrate | genotype, spatial | genotype | N/A | +| Hexose-P | carbohydrate | spatial | genotype | N/A | +| Glycerol | carbohydrate | genotype, spatial | genotype | spatial | +| Carb 11.60 | carbohydrate | spatial | spatial | spatial | +| Disaccharide 21.9 | carbohydrate | spatial | genotype | genotype, spatial | +| Glycerate | carbohydrate | spatial | genotype, spatial | genotype, spatial | +| 5-oxo-Proline | carbohydrate | genotype, spatial | genotype, spatial | genotype, spatial | +| Disaccharide 21.5 | carbohydrate | genotype, spatial | genotype, spatial | genotype, spatial | +| Raffinose | carbohydrate | genotype, spatial | genotype, spatial | N/A | +| Disaccharide 14.71 | carbohydrate | N/A | N/A | N/A | +| Disaccharide 20.5 | carbohydrate | N/A | N/A | N/A | +| Myoinositol | carbohydrate | N/A | N/A | N/A | +| Shikimate | organic oxygen compound | N/A | N/A | N/A | +| γ-Aminobutyrate | organic acid | N/A | N/A | N/A | +| Malate | organic acid | spatial | spatial | spatial | +| Ketoglutarate | organic acid | spatial | spatial | spatial | +| Fumarate | organic acid | spatial | spatial | spatial | +| Aspartate | organic acid | genotype, spatial | genotype, spatial | genotype, spatial | +| Isocitrate | organic acid | genotype, spatial | genotype, spatial | genotype, spatial | +| Glutamine | organic acid | genotype, spatial | genotype, spatial | genotype, spatial | +| Alanine | organic acid | genotype | genotype, spatial | genotype, spatial | +| Glycine | organic acid | genotype, spatial | genotype | genotype | +| Succinate | organic acid | genotype | genotype | genotype, spatial | +| Isoleucine | organic acid | genotype | genotype | genotype | +| Leucine | organic acid | genotype | genotype | genotype | +| Lysine | organic acid | genotype | genotype | genotype | +| Asparagine | organic acid | genotype | genotype | genotype | +| Methionine | organic acid | genotype | genotype | genotype | +| Phenylalanine | organic acid | genotype | genotype | genotype | +| Proline | organic acid | genotype | genotype | genotype | +| Pyruvate | organic acid | genotype | genotype | genotype | +| Serine | organic acid | genotype | genotype | genotype | +| Threonine | organic acid | genotype | genotype | genotype | +| Valine | organic acid | genotype | genotype | genotype | +| Glutamate | organic acid | genotype | genotype | genotype | + +**N/A: not applicable. The abundance of indicated metabolites is not significantly different from WT plants (two-way ANOVA, p > 0.05).** + +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------------------------|------------------------------------------------------------------|-----------------------------------------------------------------------| +| **Deposited Data** | | | +| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) | +| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) | +| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 | +| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A | +| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A | +| **Software and Algorithms** | | | +| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 | +| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 | +| GUROBI | https://www.gurobi.com/ | N/A | +| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 | +| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 | +| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 | +| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 | +| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 | +| **Others** | | | +| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration | \ No newline at end of file diff --git a/assays/AmpliconSequencingDataAnalysis/README.md b/assays/AmpliconSequencingDataAnalysis/README.md index a15ccc50eb2cace95287f52d969de6f811af318a..c3a56c53564599bba82ea6fec75f1e7eba02f118 100644 --- a/assays/AmpliconSequencingDataAnalysis/README.md +++ b/assays/AmpliconSequencingDataAnalysis/README.md @@ -3,4 +3,26 @@ **Figure 1. Differential spatial colonization by root microbiota along the longitudinal root axis** (A) Phenotype of wild-type *A. thaliana* Col-0 grown on CD-Rhizotron, with root segments marked. CPCoA of the Bray-Curtis dissimilarities of endospheric (n = 63) or rhizosphere samples (n = 65), constrained by the distance to the tip from which they were harvested. Different colors represent respective longitudinal segments or whole root samples, with colors of clusters corresponding to the root segments depicted in the plant cartoon. Centroids are indicated for each cluster of root region. -(B) Phenotype of wild-type *A. thaliana* Col-0 grown on ArtSoil. CPCoA of the Bray-Curtis dissimilarities of root endosphere (n = 39) or rhizosphere samples (n = 40), constrained by the distance to the tip from which they were harvested. Colors of clusters correspond to segments of the root depicted in the plant cartoon. Centroids are indicated for each cluster of root region. \ No newline at end of file +(B) Phenotype of wild-type *A. thaliana* Col-0 grown on ArtSoil. CPCoA of the Bray-Curtis dissimilarities of root endosphere (n = 39) or rhizosphere samples (n = 40), constrained by the distance to the tip from which they were harvested. Colors of clusters correspond to segments of the root depicted in the plant cartoon. Centroids are indicated for each cluster of root region. + +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------------------------|------------------------------------------------------------------|-----------------------------------------------------------------------| +| **Deposited Data** | | | +| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) | +| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) | +| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 | +| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A | +| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A | +| **Software and Algorithms** | | | +| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 | +| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 | +| GUROBI | https://www.gurobi.com/ | N/A | +| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 | +| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 | +| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 | +| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 | +| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 | +| **Others** | | | +| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration | \ No newline at end of file diff --git a/assays/ConstructionOfGUSReporterLines/README.md b/assays/ConstructionOfGUSReporterLines/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..5b273388d5431ed557450987fc8f0a6109d7150e 100644 --- a/assays/ConstructionOfGUSReporterLines/README.md +++ b/assays/ConstructionOfGUSReporterLines/README.md @@ -0,0 +1,38 @@ +**Table 1. SWEETs accumulation along the longitudinal region of roots from A. thaliana grown on ½ Murashige-Skoog (½ MS) media supplemented with or without sucrose, and ArtSoil** + +| **SWEET** | **½ MS − sucrose** | **½ MS + sucrose** | **ArtSoil** | +|:---------:|:------------------------------------:|--------------------------------------|------------------------| +| 1 | regions below 2 cm | regions below 2 cm | regions below 2 cm | +| 2 | regions below 0.05 cm and above 2 cm | regions below 0.05 cm and above 2 cm | entire root | +| 3 | not tested | not tested | not tested | +| 4 | not detected | regions above 2 cm (patchy) | not detected | +| 5 | not tested | not tested | not tested | +| 6 | not tested | not tested | not tested | +| 7 | not detected | not detected | not detected | +| 8 | not detected | not detected | not detected | +| 9 | not tested | not tested | not tested | +| 10 | not tested | not tested | not tested | +| 11 | regions below 2 cm | at 2.5–3 cm region | regions below 2 cm | +| 12 | regions below 2 cm | regions 2 cm and above | regions 2 cm and above | +| 13 | regions below 2.5 cm | regions below 2.5 cm | regions below 2.5 cm | +| 14 | not tested | not tested | not tested | +| 15 | not tested | not tested | not tested | +| 16 | not tested | not tested | not tested | +| 17 | entire root | entire root | entire root | + +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------|-------------------------------------------------------------|-------------------------------------------| +| **Oligonucleotides** | | | +| AtSWEET4-XbaI-F | IDT | GCAGGTCGACTCTAGAAGTGGTTCCACG GAGATGACG | +| AtSWEET4-BamHI-R | IDT | CGGTACCCGGGGATCCAGCTGAAACTCG TTTAGCTTGTCC | +| AtSWEET5-XbaI-F | IDT | GCAGGTCGACTCTAGATTAGGACTGACAC CAGCGATGC | +| AtSWEET5-BamHI-R | IDT | CGGTACCCGGGGATCCAGCCTGGCCAAG TTCGATTC | +| AtSWEET7-XbaI-F | IDT | GCAGGTCGACTCTAGAATTCAGGCTTGGC GTAACTTG | +| AtSWEET7-BamHI-R | IDT | CGGTACCCGGGGATCCAACATTGTTAGGT TCTTGGTTGG | +| AtSWEET8-XbaI-F | IDT | GCAGGTCGACTCTAGAACCATGACAATTT GGCTCCGAG | +| AtSWEET8-BamHI-R | IDT | CGGTACCCGGGGATCCAACCCTCTCCGT AGCAGAAATC | +| **Recombinant DNA** | | | +| pMDC163 vector | Arabidopsis Biological Resource Center https://abrc.osu.edu | TAIR accession Vector:1009003758 | +| promoterless GUSplus vector | Yang et al.81 | N/A | \ No newline at end of file diff --git a/assays/CorrelationBetweenMicrobesAndMetabolites/README.md b/assays/CorrelationBetweenMicrobesAndMetabolites/README.md index 3e916efe20d18d912471a61fbfdef7cc5ccb1605..3916c9db06ba78b6a3183986eaf7554e2b6d2eaa 100644 --- a/assays/CorrelationBetweenMicrobesAndMetabolites/README.md +++ b/assays/CorrelationBetweenMicrobesAndMetabolites/README.md @@ -4,4 +4,26 @@ (A) CPCoA of the Bray-Curtis dissimilarities of endospheric bacteria derived from full-length roots of WT, *sweet2, sweet4*, and *sweet11;12* plants, constrained by plant genotype. Different colors represent plant genotypes with centroids indicated for each cluster of genotype. WT: N = 60, *sweet2*: N = 40, *sweet4*: N = 41, *sweet11;12* and N = 42. (B) Bray-Curtis dissimilarities distances of endospheric bacteria derived from the 0–2, 2–4, and 4–6 cm segments from the root tip of WT, *sweet2, sweet4*, and *sweet11;12* plants (sweet abbreviated as “swtâ€) compared with each other. The colors and sizes of the dots correspond to the mean of the Bray-Curtis distance. -(C) Spearman correlation for metabolite-microbe (class level) pairs. Metabolites ranked based on Spearman average hierarchical clustering. The color of each point indicates the degree of correlation. Highlights indicate the class of metabolite: blue, sugar/carbohydrate; red, organic acid; and yellow, lipid. Spearman correlations significance, p < 0.05. \ No newline at end of file +(C) Spearman correlation for metabolite-microbe (class level) pairs. Metabolites ranked based on Spearman average hierarchical clustering. The color of each point indicates the degree of correlation. Highlights indicate the class of metabolite: blue, sugar/carbohydrate; red, organic acid; and yellow, lipid. Spearman correlations significance, p < 0.05. + +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------------------------|------------------------------------------------------------------|-----------------------------------------------------------------------| +| **Deposited Data** | | | +| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) | +| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) | +| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 | +| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A | +| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A | +| **Software and Algorithms** | | | +| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 | +| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 | +| GUROBI | https://www.gurobi.com/ | N/A | +| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 | +| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 | +| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 | +| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 | +| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 | +| **Others** | | | +| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration | \ No newline at end of file diff --git a/assays/FluxBalanceAnalysisToDefinePathways/README.md b/assays/FluxBalanceAnalysisToDefinePathways/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..8d56edfaa6d82ee0abdde738ec47492803801e47 100644 --- a/assays/FluxBalanceAnalysisToDefinePathways/README.md +++ b/assays/FluxBalanceAnalysisToDefinePathways/README.md @@ -0,0 +1,21 @@ +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------------------------|------------------------------------------------------------------|-----------------------------------------------------------------------| +| **Deposited Data** | | | +| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) | +| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) | +| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 | +| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A | +| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A | +| **Software and Algorithms** | | | +| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 | +| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 | +| GUROBI | https://www.gurobi.com/ | N/A | +| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 | +| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 | +| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 | +| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 | +| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 | +| **Others** | | | +| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration | \ No newline at end of file diff --git a/assays/MicrobiotaProfiling/README.md b/assays/MicrobiotaProfiling/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..8d56edfaa6d82ee0abdde738ec47492803801e47 100644 --- a/assays/MicrobiotaProfiling/README.md +++ b/assays/MicrobiotaProfiling/README.md @@ -0,0 +1,21 @@ +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------------------------|------------------------------------------------------------------|-----------------------------------------------------------------------| +| **Deposited Data** | | | +| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) | +| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) | +| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 | +| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A | +| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A | +| **Software and Algorithms** | | | +| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 | +| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 | +| GUROBI | https://www.gurobi.com/ | N/A | +| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 | +| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 | +| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 | +| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 | +| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 | +| **Others** | | | +| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration | \ No newline at end of file diff --git a/assays/QuantifyMetabolicActivitiesUsingPAS/README.md b/assays/QuantifyMetabolicActivitiesUsingPAS/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..8d56edfaa6d82ee0abdde738ec47492803801e47 100644 --- a/assays/QuantifyMetabolicActivitiesUsingPAS/README.md +++ b/assays/QuantifyMetabolicActivitiesUsingPAS/README.md @@ -0,0 +1,21 @@ +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------------------------|------------------------------------------------------------------|-----------------------------------------------------------------------| +| **Deposited Data** | | | +| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) | +| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) | +| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 | +| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A | +| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A | +| **Software and Algorithms** | | | +| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 | +| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 | +| GUROBI | https://www.gurobi.com/ | N/A | +| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 | +| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 | +| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 | +| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 | +| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 | +| **Others** | | | +| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration | \ No newline at end of file diff --git a/assays/RootMetaboliteProfiling/README.md b/assays/RootMetaboliteProfiling/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..8d56edfaa6d82ee0abdde738ec47492803801e47 100644 --- a/assays/RootMetaboliteProfiling/README.md +++ b/assays/RootMetaboliteProfiling/README.md @@ -0,0 +1,21 @@ +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|-----------------------------------------------|------------------------------------------------------------------|-----------------------------------------------------------------------| +| **Deposited Data** | | | +| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) | +| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) | +| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 | +| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A | +| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A | +| **Software and Algorithms** | | | +| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 | +| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 | +| GUROBI | https://www.gurobi.com/ | N/A | +| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 | +| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 | +| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 | +| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 | +| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 | +| **Others** | | | +| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration | \ No newline at end of file diff --git a/studies/PlantMaterialAndGrowthConditions/README.md b/studies/PlantMaterialAndGrowthConditions/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..b88d689899dc45a5779d980cf0ad79356ea56f38 100644 --- a/studies/PlantMaterialAndGrowthConditions/README.md +++ b/studies/PlantMaterialAndGrowthConditions/README.md @@ -0,0 +1,30 @@ +## Key Resources Table + +| **REAGENT or RESOURCE** | **SOURCE** | **IDENTIFIER** | +|---------------------------------------------------|-------------------------------------------------------------|-------------------------------------| +| **Biological Samples** | | | +| Arabidopsis thaliana Col-0 PSWEET17:SWEET17 -GUS | Guo et al.80 | N/A | +| Arabidopsis thaliana Col-0 PSWEET2:SWEET2-GUS | Chen et al.34 | N/A | +| Arabidopsis thaliana Col-0 PSWEET12:SWEET12-GUS | Chen et al.28 | N/A | +| Arabidopsis thaliana Col-0 PSWEET11:SWEET11-GUS | Chen et al.28 | N/A | +| Arabidopsis thaliana Col-0 sweet2c | SIGnAL http://signal.salk.edu/ | SALK_048430.36.85.x | +| Arabidopsis thaliana Col -0 sweet11;12 | Arabidopsis Biological Resource Center https://abrc.osu.edu | TAIR Germplasm: CS68845 | +| Arabidopsis thaliana Col-0 sweet4a | SIGnAL http://signal.salk.edu/ | SALK_072225.23.65.x | +| **Chemicals, Peptides, and Recombinant Proteins** | | | +| DFS-Taq DNA polymerase | Bioron | Cat # 101005 | +| Antarctic phosphatase | New England BioLabs | Cat # M0289 | +| Exonuclease I | New England BioLabs | Cat # M0293 | +| Ribitol | Sigma-Aldrich | Cat # PHR3526 | +| Murashige&Skoog media including MES buffer | Duchefa Biochemie | Cat # M0254 | +| Tritonâ„¢ X-100,for molecular biology | Sigma-Aldrich | Cat # T8787 | +| Agar | Sigma-Aldrich | Cat # 05040 | +| Hygromycin B | Carl Roth | Cat # CP12.2 | +| Thermo Scientific X Gluc | Thermo Fisher Scientific | Cat # R0851 | +| **Critical Commercial Assays** | | | +| FastDNAâ„¢ SPIN Kit for Soil | MP Biomedicals | Cat # SKU116560200-CF | +| NuceloSpin Soil Mini kit for DNA from soil | Macherey-Nagel | Cat # 740780 | +| QIAquick gel extraction kit | Qiagen | Cat # 28706X4 | +| Quant-iTâ„¢ PicoGreenâ„¢ | Invitrogen | Cat # P7581 | +| Gatewayâ„¢ LR Clonaseâ„¢ Enzyme mix | Invitrogen | Cat # 11791019 | +| **Experimental Models: Organisms/Strains** | | | +| Arabidopsis thaliana Col-0 | TAIR | TAIR accession Germplasm:1008804532 | \ No newline at end of file