diff --git a/assays/2_2-FAME-analysis/README.md b/assays/2_2-FAME-analysis/README.md index 14ea87c6cee16b1e6d6f1ae4fe746ef0b8f51aaa..fb61d94f12241fc11cb2e7bc74639fb7db597b13 100644 --- a/assays/2_2-FAME-analysis/README.md +++ b/assays/2_2-FAME-analysis/README.md @@ -3,6 +3,6 @@  -Figure 2 +**Figure 2** Storage oil mobilization in castor bean endosperm. (A) Relative fresh weight of the endosperm in dry seeds (-1d), imbibed seeds (0d) and 1- to 7-day old dark-grown castor bean seedlings (1-7d) as percentage of fresh weight of the whole plant. Data represent arithmetic means ± SD of 3 biological replicates. (B) Relative ricinoleic acid content of the endosperm from seeds and seedlings. Samples were normalized to the average fresh weight of on endosperm and expressed as percentages of their initial quantities determined in dry seeds (-1d). Error bars show standard deviations of the means of at least three biological replicates. \ No newline at end of file diff --git a/assays/2_3-OrganellesFromEndosperm/README.md b/assays/2_3-OrganellesFromEndosperm/README.md index 711acb0df653139365e32d692c8c3b1c01ee8c5e..39da2aea217b0edd66332bb9cb021de5dd0b34bb 100644 --- a/assays/2_3-OrganellesFromEndosperm/README.md +++ b/assays/2_3-OrganellesFromEndosperm/README.md @@ -1,3 +1,7 @@  + +**Figure 3** + +Isolation of organelles from etiolated castor bean seedlings. Four fractions of the sucrose density step gradient after centrifugation were taken from the gradient for various analyses at the interface 30% - 44% (w/w) sucrose solution (F1), 44% - 48% (w/w) sucrose solution (F2), 48% - 49% (w/w) sucrose solution (F3), and 50% - 54% (w/w) sucrose solution (F4). \ No newline at end of file diff --git a/assays/2_4-EnzymeActivityOrganellarMarkers/README.md b/assays/2_4-EnzymeActivityOrganellarMarkers/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..01b1cf2ea9032163a806fbd4b6e19bd48c858299 100644 --- a/assays/2_4-EnzymeActivityOrganellarMarkers/README.md +++ b/assays/2_4-EnzymeActivityOrganellarMarkers/README.md @@ -0,0 +1,5 @@ + + +**Table 1** + +Distribution of marker enzyme activities between the fractions. \ No newline at end of file diff --git a/assays/2_6-SDS-PAGE-Immunoblotting/README.md b/assays/2_6-SDS-PAGE-Immunoblotting/README.md index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..f7cd1dc54200e18254490e0c6c027b84c2f31494 100644 --- a/assays/2_6-SDS-PAGE-Immunoblotting/README.md +++ b/assays/2_6-SDS-PAGE-Immunoblotting/README.md @@ -0,0 +1,5 @@ + + +**Figure 4** + +Purification of intracellular membranes from castor bean endosperm. Distribution of organellar membrane proteins within the organellar fractions (F1-F4) obtained after sucrose density gradient centrifugation. (A) SDS-PAGE analysis. Each lane was loaded with enriched membrane proteins from each pellet fraction after organelle disruption and ultracentrifugation (F1/F2: 25 µg, F3/F4: 15 µg). Equal loading of the protein gel within the fractions was monitored by staining with colloidal Coomassie G-250 dye. (B) Immunoblot analysis using antibodies raised against the following organelle membrane proteins: chloroplast TIC40, mitochondrial AOX, ER BIP2, and peroxisomal PEX14 proteins. Expected molecular weight for the corresponding castor bean proteins: 50.1 kDa for RcTIC40 (A3QSJ7), 39-41 kDa for RcAOX1/2 (B9RXE2/B9SO38), 73.3 kDa for RcBIP2 (B9RYP6), and 58.3 kDa for RcPEX14 (B9RB25). The membrane was serially probed with antibodies to the indicated marker proteins. The positions of molecular mass markers (in kDa) are indicated at the left. \ No newline at end of file diff --git a/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/README.md b/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/README.md index 012995a9ffef0bbdd054d371cc3fbdff4a1025ce..ef49d1184aca569fec61f145174fc79c05c40e29 100644 --- a/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/README.md +++ b/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/README.md @@ -1,5 +1,18 @@ + -Source: https://www.frontiersin.org/articles/10.3389/fpls.2023.1182105/full#supplementary-material +**Figure 5** + +Principal Component Analysis of the Ricinus proteome of the fractions obtained from the sucrose density centrifugation, representing the total proteins (T1 to T4) and the enriched membrane proteins (M1 to M4). In this PCA plot each point represents the identified proteome of one biological experiment. + + + +**Figure 6** + +Distribution profile of compartment-specific marker proteins in the density-gradient fractions containing the total proteins (T1 to T4) and membrane proteins (M1 to M4). (A) peroxisomes; (B) plastid; (C) mitochondria; (D) ER; (E) nucleus; (F) Golgi; (G) vacuole; (H) cytosol. Relative LFQ represents the sum of Label Free Quantification (LFQ) values for all proteins belonging to an organelle relative to its maximal value. + +## Supplementary material + +Source for supplementary material: https://www.frontiersin.org/articles/10.3389/fpls.2023.1182105/full#supplementary-material ## "Table 3.xlsx" @@ -11,7 +24,6 @@ Deconvolution-based assignment of the MS-identified proteins from etiolated cast SUPPLEMENTARY TABLE 4 List of proteins found in peroxisomes, mitochondria, and plastids isolated from castor bean etiolated endosperm in this study. For functional annotation of proteins and their assignment to biological processes or metabolic pathways, gene ontology analysis was performed by Uniprot. - ## "Image 1.jpg" SUPPLEMENTARY FIGURE 1 diff --git a/studies/Ricinus-communis-seeds/README.md b/studies/Ricinus-communis-seeds/README.md index 0eb3c8dda7335fbc2a04b9a616acddfeab145866..301b99a739584bd8f762ffcfc33f9a1c5660f828 100644 --- a/studies/Ricinus-communis-seeds/README.md +++ b/studies/Ricinus-communis-seeds/README.md @@ -3,6 +3,6 @@  -Figure 1 +**Figure 1** Endosperm morphology in seeds and germinating seedling of R. communis. Photographs were taken from the whole plant (upper panel) and two cotyledons embedded in the endosperm (lower panel) from mature seeds (dry), 24h-imbibed seeds (imb) and from 1- to 7-day old dark-grown castor bean seedlings (1-7d). Scale bar = 1 cm. \ No newline at end of file