diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0319b42cfece327fbe450017657f9d450035fb93 100644 --- a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md +++ b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md @@ -0,0 +1,14 @@ +<img src=./dataset/gr2.jpg width=60%> + +**Figure 2. Diversity and region-specificity of metabolites along the root axis** + +(A) Principal-component analysis (PCA) of metabolites extracted from the full-length root, and segments 0–2, 2–4, and 4–6 cm from the root tip. The colors of clusters correspond to regions of the root depicted in the plant cartoon in Figure 1A. Centroids are indicated for each cluster of root region. +(B) Heatmap depicting the enrichment or depletion of indicated metabolites in respective root segments. Clustering performed based on average linkage Pearson hierarchical clustering of metabolites. Clusters are indicated in red roman numbers. Colors on the scale bar indicate the level of enrichment or depletion of each metabolite across the root segments. + +<img src=./dataset/gr4.jpg width=60%> + +**Figure 4. Metabolite profiles of root segments from *sweet2, sweet4*, and *swee11;12* are distinct from WT** + +(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 diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr2.jpg b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr2.jpg new file mode 100644 index 0000000000000000000000000000000000000000..e5ef95b8cb4266095078b7c41e8a0ce33dcb52f3 --- /dev/null +++ b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr2.jpg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b15bdb9906a602f26a6ec87b116e6884804546fd5839e8f0b3d7bf2a0c85ebc3 +size 52917 diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr4.jpg b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr4.jpg new file mode 100644 index 0000000000000000000000000000000000000000..aebf05a3a56716746c828335dba58582f5ad75d2 --- /dev/null +++ b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr4.jpg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0cd28b653835bb0a158b2da5dcdcb841e645286319519b729f8dedc490b31cd3 +size 102333 diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/isa.assay.xlsx b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/isa.assay.xlsx index 4f77dadc2ab5adcbbe4f3acac490e4d67fcafd5a..494ab1bc2ff88fedd3f1e5794f1a89a3561c3b7c 100644 Binary files a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/isa.assay.xlsx and b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/isa.assay.xlsx differ diff --git a/assays/AmpliconSequencingDataAnalysis/README.md b/assays/AmpliconSequencingDataAnalysis/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..a15ccc50eb2cace95287f52d969de6f811af318a 100644 --- a/assays/AmpliconSequencingDataAnalysis/README.md +++ b/assays/AmpliconSequencingDataAnalysis/README.md @@ -0,0 +1,6 @@ +<img src=./dataset/gr1.jpg width=60%> + +**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 diff --git a/assays/AmpliconSequencingDataAnalysis/dataset/gr1.jpg b/assays/AmpliconSequencingDataAnalysis/dataset/gr1.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c9524cc64426660003d0e32ee1e2bb3c35c564a4 --- /dev/null +++ b/assays/AmpliconSequencingDataAnalysis/dataset/gr1.jpg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e3a52b436d674bf4ed37fa19bfeee97f38209537f77736138344de5874257395 +size 86727 diff --git a/assays/CorrelationBetweenMicrobesAndMetabolites/README.md b/assays/CorrelationBetweenMicrobesAndMetabolites/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..3e916efe20d18d912471a61fbfdef7cc5ccb1605 100644 --- a/assays/CorrelationBetweenMicrobesAndMetabolites/README.md +++ b/assays/CorrelationBetweenMicrobesAndMetabolites/README.md @@ -0,0 +1,7 @@ +<img stc=./dataset/gr5.jpg width=60%> + +**Figure 5 Loss of spatial microbiota colonization in roots of *sweet2, sweet4*, and *sweet11;12*** + +(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 diff --git a/assays/CorrelationBetweenMicrobesAndMetabolites/dataset/gr5.jpg b/assays/CorrelationBetweenMicrobesAndMetabolites/dataset/gr5.jpg new file mode 100644 index 0000000000000000000000000000000000000000..ad6ed7fb7cad7f2cc0245deb59ef4fec37781018 --- /dev/null +++ b/assays/CorrelationBetweenMicrobesAndMetabolites/dataset/gr5.jpg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:19d713ddc403f0a0b78434f3fe1f2d8cd92baeee6ca56369d24d84a6eff77ea2 +size 146839 diff --git a/assays/CorrelationBetweenMicrobesAndMetabolites/isa.assay.xlsx b/assays/CorrelationBetweenMicrobesAndMetabolites/isa.assay.xlsx index ac107c5b0207ca2df54f479ce5ca439c16c7d5d7..26c80915aaa6b89dfd9230a9eaa195eb409534c3 100644 Binary files a/assays/CorrelationBetweenMicrobesAndMetabolites/isa.assay.xlsx and b/assays/CorrelationBetweenMicrobesAndMetabolites/isa.assay.xlsx differ diff --git a/assays/GUSHistochemicalStaining/README.md b/assays/GUSHistochemicalStaining/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..81a7b249834cdc2c25ba7d01a82f86f8e9bae95a 100644 --- a/assays/GUSHistochemicalStaining/README.md +++ b/assays/GUSHistochemicalStaining/README.md @@ -0,0 +1,5 @@ +<img src=./dataset/gr3.jpg width=60%> + +**Figure 3. Accumulation of SWEETs along the root in the absence or presence of sugar and soil microbes** + +Accumulation of respective SWEETs fused with a translational GUS reporter gene in 14-days-old A. thaliana seedlings grown on ½ MS-salt media supplemented with or without 1% sucrose (½ MS-salt −suc: ½ MS media without sucrose supplementation, ½ MS-salt +suc: ½ MS media with sucrose supplementation), on microbiome-inoculated or microbiome-killed ArtSoil (ArtSoil −microbes: ArtSoil inoculated with heat-killed soil microbes, ArtSoil +microbes: ArtSoil inoculated with soil microbes). The root segment depicted for SWEET2-GUS is <0.2 cm, and the root segments depicted for SWEET12-GUS and SWEET4-GUS are >2 cm. Scale bars, 500 μm. The yellow arrow indicates the accumulation of SWEET2-GUS in the root zone of interest. Green arrows indicate the sporadic accumulation of SWEET4-GUS. Representative image for each genotype from N > 10. \ No newline at end of file diff --git a/assays/GUSHistochemicalStaining/dataset/gr3.jpg b/assays/GUSHistochemicalStaining/dataset/gr3.jpg new file mode 100644 index 0000000000000000000000000000000000000000..b169b63ed9c1b64a3bf052e20dc7e3e3d96bba0d --- /dev/null +++ b/assays/GUSHistochemicalStaining/dataset/gr3.jpg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4a0dfcce1170dcd48b8e5fd06f5bf2006398d122c5ebee0f7c02c469c78123f9 +size 49348 diff --git a/assays/QuantifyMetabolicActivitiesUsingPAS/isa.assay.xlsx b/assays/QuantifyMetabolicActivitiesUsingPAS/isa.assay.xlsx index fc2e300bc97ad14f89a423aef6262fb02939ec5c..d066c9beec6c35237190e3931542c2434cc6e963 100644 Binary files a/assays/QuantifyMetabolicActivitiesUsingPAS/isa.assay.xlsx and b/assays/QuantifyMetabolicActivitiesUsingPAS/isa.assay.xlsx differ