diff --git a/README.md b/README.md index 7851f0ebe7879139aed24fd0068f822337d37c60..31acc8c60ab2e7af9b72ba0dca83e6df2c1b72a6 100644 --- a/README.md +++ b/README.md @@ -9,3 +9,7 @@ Wrobel TJ, Brilhaus D, Stefanski A, Stühler K, Weber APM, Linka N. Mapping the Copyright © 2023 Wrobel, Brilhaus, Stefanski, Stühler, Weber and Linka This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. + +## Data availability + +The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD040932. \ No newline at end of file diff --git a/assays/.gitkeep b/assays/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 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_2-FAME-analysis/isa.assay.xlsx b/assays/2_2-FAME-analysis/isa.assay.xlsx index ae1b9bdb68a2d696bbdb553ec8b0d602bfd81511..5abe36cc0f08fd201605c759be99a649716c38c2 100644 Binary files a/assays/2_2-FAME-analysis/isa.assay.xlsx and b/assays/2_2-FAME-analysis/isa.assay.xlsx differ diff --git a/assays/2_2-FAME-analysis/protocols/.gitkeep b/assays/2_2-FAME-analysis/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 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_3-OrganellesFromEndosperm/dataset/.gitkeep b/assays/2_3-OrganellesFromEndosperm/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_3-OrganellesFromEndosperm/isa.assay.xlsx b/assays/2_3-OrganellesFromEndosperm/isa.assay.xlsx index 85f5aaa71525f08d3ad9f8bed98dd7e0ad29ea9a..0744cd81e32da56faff863d9b4c9e7085ff6961a 100644 Binary files a/assays/2_3-OrganellesFromEndosperm/isa.assay.xlsx and b/assays/2_3-OrganellesFromEndosperm/isa.assay.xlsx differ diff --git a/assays/2_3-OrganellesFromEndosperm/protocols/.gitkeep b/assays/2_3-OrganellesFromEndosperm/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 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_4-EnzymeActivityOrganellarMarkers/dataset/.gitkeep b/assays/2_4-EnzymeActivityOrganellarMarkers/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_4-EnzymeActivityOrganellarMarkers/isa.assay.xlsx b/assays/2_4-EnzymeActivityOrganellarMarkers/isa.assay.xlsx index 9d48535e829614d2f0315353857cba7727b6fe7a..a82f10c6d337e6eeb0f9300c008a6a840d3b5938 100644 Binary files a/assays/2_4-EnzymeActivityOrganellarMarkers/isa.assay.xlsx and b/assays/2_4-EnzymeActivityOrganellarMarkers/isa.assay.xlsx differ diff --git a/assays/2_4-EnzymeActivityOrganellarMarkers/protocols/.gitkeep b/assays/2_4-EnzymeActivityOrganellarMarkers/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_5-OrganellarMembraneIsolation/isa.assay.xlsx b/assays/2_5-OrganellarMembraneIsolation/isa.assay.xlsx index 0c9b8fcd90f1d4029ad5c0935f33e0626c534448..d53c6e46ec391962d08182f8caecc028ebab6a5f 100644 Binary files a/assays/2_5-OrganellarMembraneIsolation/isa.assay.xlsx and b/assays/2_5-OrganellarMembraneIsolation/isa.assay.xlsx differ diff --git a/assays/2_5-OrganellarMembraneIsolation/protocols/.gitkeep b/assays/2_5-OrganellarMembraneIsolation/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 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_6-SDS-PAGE-Immunoblotting/dataset/.gitkeep b/assays/2_6-SDS-PAGE-Immunoblotting/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_6-SDS-PAGE-Immunoblotting/isa.assay.xlsx b/assays/2_6-SDS-PAGE-Immunoblotting/isa.assay.xlsx index 9dc0a1a9bd6409dbca4f97652e346f3c95e39002..fed2361240e30556782f2bef82f13aecc19c4d1d 100644 Binary files a/assays/2_6-SDS-PAGE-Immunoblotting/isa.assay.xlsx and b/assays/2_6-SDS-PAGE-Immunoblotting/isa.assay.xlsx differ diff --git a/assays/2_6-SDS-PAGE-Immunoblotting/protocols/.gitkeep b/assays/2_6-SDS-PAGE-Immunoblotting/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_7-ProteomeAcquisition-MassSpectrometry/dataset/.gitkeep b/assays/2_7-ProteomeAcquisition-MassSpectrometry/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_7-ProteomeAcquisition-MassSpectrometry/isa.assay.xlsx b/assays/2_7-ProteomeAcquisition-MassSpectrometry/isa.assay.xlsx index ff1f781342fd8a273a88b7e118a5041897958c6d..0196bb560856994e3d248eaeebb7771a2e6eef0d 100644 Binary files a/assays/2_7-ProteomeAcquisition-MassSpectrometry/isa.assay.xlsx and b/assays/2_7-ProteomeAcquisition-MassSpectrometry/isa.assay.xlsx differ diff --git a/assays/2_7-ProteomeAcquisition-MassSpectrometry/protocols/.gitkeep b/assays/2_7-ProteomeAcquisition-MassSpectrometry/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_8-Computational-MS-DataAnalysis/dataset/.gitkeep b/assays/2_8-Computational-MS-DataAnalysis/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_8-Computational-MS-DataAnalysis/isa.assay.xlsx b/assays/2_8-Computational-MS-DataAnalysis/isa.assay.xlsx index 1f5fac519b29f231b8f6c03584485fff90a7e0e3..36209a677d7d9c798bbe64d8ffafdb09f547d40b 100644 Binary files a/assays/2_8-Computational-MS-DataAnalysis/isa.assay.xlsx and b/assays/2_8-Computational-MS-DataAnalysis/isa.assay.xlsx differ diff --git a/assays/2_8-Computational-MS-DataAnalysis/protocols/.gitkeep b/assays/2_8-Computational-MS-DataAnalysis/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 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/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/dataset/.gitkeep b/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/isa.assay.xlsx b/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/isa.assay.xlsx index a009de73cba0e6f2aa68937bf3a7c4ea9af8a810..1910ad257b2a526ba11be90294a241843cff3478 100644 Binary files a/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/isa.assay.xlsx and b/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/isa.assay.xlsx differ diff --git a/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/protocols/.gitkeep b/assays/2_9-StatisticalAnalysis-ProteomeDeconvolution/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 9b49fb768194e79b512ea249258495d1914c4843..df46dade58e4edd739f81d5e2cbd8d88ab304c8c 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/.gitkeep b/studies/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 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 diff --git a/studies/Ricinus-communis-seeds/isa.study.xlsx b/studies/Ricinus-communis-seeds/isa.study.xlsx index f7a492e12ec8945f2453446f9a7d6158e0710612..c7d3a20bbacd9b8a714c1508962a0a507917b611 100644 Binary files a/studies/Ricinus-communis-seeds/isa.study.xlsx and b/studies/Ricinus-communis-seeds/isa.study.xlsx differ diff --git a/studies/Ricinus-communis-seeds/protocols/.gitkeep b/studies/Ricinus-communis-seeds/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/Ricinus-communis-seeds/protocols/Plant-growth-conditions.md b/studies/Ricinus-communis-seeds/protocols/Plant-growth-conditions.md index 0687e0816d679bec7fcb9aac22eaf966b66f4591..fae00660fdb2ddb14a4f3bed8947d48aa82277ae 100644 --- a/studies/Ricinus-communis-seeds/protocols/Plant-growth-conditions.md +++ b/studies/Ricinus-communis-seeds/protocols/Plant-growth-conditions.md @@ -1,6 +1,6 @@ # 2.1 Plant growth conditions -Dry seeds of Ricinus communis var. zanzibariensis were surface- sterilized in a solution of 0.1% (w/v) 8-quinolinol in water for ten minutes and soaked in running tap water over night for seed imbibition. The imbibed seeds were placed on moist vermiculite and incubated at 30°C in the dark (Beevers and Breidenbach, 1974). +Dry seeds of *Ricinus communis* var. *zanzibariensis* were surface- sterilized in a solution of 0.1% (w/v) 8-quinolinol in water for ten minutes and soaked in running tap water over night for seed imbibition. The imbibed seeds were placed on moist vermiculite and incubated at 30°C in the dark (Beevers and Breidenbach, 1974). - Beevers, H., and Breidenbach, R. W. (1974). “Glyoxysomes,†in Methods in enzymology, Vol 16 Biomembranes, Part A. Eds. S. Fleciher and L. packer (New York London: Academic Press), 565–571. \ No newline at end of file