diff --git a/assays/2012_proteome_data_bmfz_stefanski/isa.assay.xlsx b/assays/2012_proteome_data_bmfz_stefanski/isa.assay.xlsx index ff8e34df1423bc317e2f3be19ac62f7219c20603..0107750a77bcaaa4872f982921e8c815d27eec72 100644 Binary files a/assays/2012_proteome_data_bmfz_stefanski/isa.assay.xlsx and b/assays/2012_proteome_data_bmfz_stefanski/isa.assay.xlsx differ diff --git a/assays/2022-04-13_proteome_discoverer/isa.assay.xlsx b/assays/2022-04-13_proteome_discoverer/isa.assay.xlsx index 2dddbbcccd681e2519ddd1167908c0550f0ac406..7bfb15844d999d5789a44764d3419c590882cd54 100644 Binary files a/assays/2022-04-13_proteome_discoverer/isa.assay.xlsx and b/assays/2022-04-13_proteome_discoverer/isa.assay.xlsx differ diff --git a/assays/2_2-FAME-analysis/README.md b/assays/2_2-FAME-analysis/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_2-FAME-analysis/dataset/.gitkeep b/assays/2_2-FAME-analysis/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/2_2-FAME-analysis/isa.assay.xlsx b/assays/2_2-FAME-analysis/isa.assay.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..d4152299b8cfbb3b9eec4ea4e026d93d2a0ae675 Binary files /dev/null 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_2-FAME-analysis/protocols/2_2-FAME-analysis.md b/assays/2_2-FAME-analysis/protocols/2_2-FAME-analysis.md new file mode 100644 index 0000000000000000000000000000000000000000..7201a9c68366dd93de0ad884e221550dabcdae01 --- /dev/null +++ b/assays/2_2-FAME-analysis/protocols/2_2-FAME-analysis.md @@ -0,0 +1,8 @@ +# 2.2 Fatty acid methylester (FAME) analysis + +The ricinoleic acid content in the castor bean endosperm was determined using gas chromatography-mass spectrometry (GC- MS)-based fatty acid methyl ester (FAME) method (Hielscher et al., 2017). Endosperm tissue was dissected from dry seeds, 24h- imbibed seeds and 1- to 6-day old dark-grown seedlings by removing the embryo and roots with the blunt end of a scalpel blade, weighed and shock frozen in liquid nitrogen. +FAME analyses were generated by acid catalyzed methyl-ester formation using methanolic HCl as described by Hielscher et al. (2017). 20 mg endosperm was incubated at 90°C for one hour in 1 ml 3 N methanolic-HCl containing heptadecanoic acid (C17:0) as internal standard. The subsequent extraction of fatty acids from the sample was performed with 1 ml n-hexane and 1 ml 1% (w/v) sodium chloride. Samples were centrifuged at 2,000 g for five minutes. The resulting upper hexane phase was transferred into GC vials. The FAME extracts (1:100 diluted) were analyzed by GC Agilent 7890A gas chromatograph coupled to Waters GCT-TOF Premier mass spectrometer equipped with a Gerstel MPS2XL auto sampler. +Quantification and identification of the detected fatty acids was carried out with QuantLynx and MassLynx, respectively. Peaks were integrated and the resulting areas used for determination of relative changes in the abundance of the castor oil-specific ricinoleic acid. As the Ricinus endosperm started to gain fresh weight during seedling development due to water uptake, the fatty acid quantities were normalized to the fresh weight of an average endosperm. All samples were analyzed in three biological replicates. + + +- Hielscher, B., Charton, L., Mettler-Altmann, T., and Linka, N. (2017). Analysis of peroxisomal b-oxidation during storage oil mobilization in Arabidopsis thaliana Seedlings. Methods Mol. Biol. 1595, 291–304. doi: 10.1007/978-1-4939-6937-1_27 \ No newline at end of file diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index f3497204e173149283909e9ed476e336db375e84..63333e0174e91e9dd51a0ded0b46d92d39b92588 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/Ricinus-communis-seeds/README.md b/studies/Ricinus-communis-seeds/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/Ricinus-communis-seeds/isa.study.xlsx b/studies/Ricinus-communis-seeds/isa.study.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..5fb55aa73376bb3037ee65d0cda5008073f8370a Binary files /dev/null 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 new file mode 100644 index 0000000000000000000000000000000000000000..0687e0816d679bec7fcb9aac22eaf966b66f4591 --- /dev/null +++ b/studies/Ricinus-communis-seeds/protocols/Plant-growth-conditions.md @@ -0,0 +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). + + +- 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 diff --git a/studies/Ricinus-communis-seeds/resources/.gitkeep b/studies/Ricinus-communis-seeds/resources/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/workflows/.gitkeep b/workflows/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391