diff --git a/assays/leaf_sampling/README.md b/assays/leaf_sampling/README.md deleted file mode 100644 index 6bbd3ce33f7d7ed2c4f0b633bc16e66e2244fbcd..0000000000000000000000000000000000000000 --- a/assays/leaf_sampling/README.md +++ /dev/null @@ -1,10 +0,0 @@ -## leaf_sampling - -**Assay used in studies:** -- gene_expression_eam7_plants_development -- gene_expression_eam7_plants_diurnal -- gene_expression_lwd1_mutants_diurnal - -**Info:** - -No dataset, as leaf samples were used in downstream assays (RNA_extraction). \ No newline at end of file diff --git a/assays/leaf_sampling/dataset/.gitkeep b/assays/leaf_sampling/dataset/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/leaf_sampling/isa.assay.xlsx b/assays/leaf_sampling/isa.assay.xlsx deleted file mode 100644 index 52c17f906eb38d3aa9a7368cbfb57c1a1a024132..0000000000000000000000000000000000000000 Binary files a/assays/leaf_sampling/isa.assay.xlsx and /dev/null differ diff --git a/assays/leaf_sampling/protocols/.gitkeep b/assays/leaf_sampling/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/leaf_sampling/protocols/leaf_sampling.md b/assays/leaf_sampling/protocols/leaf_sampling.md deleted file mode 100644 index 340a6ba698f0536ac0015b06f4676abe0bce2f5e..0000000000000000000000000000000000000000 --- a/assays/leaf_sampling/protocols/leaf_sampling.md +++ /dev/null @@ -1,8 +0,0 @@ -## Leaf sampling for RNA extraction - -- place two 3 mm metal beads into 2.0 ml tube -- always sample the youngest, fully elongated leaf (auricles are clearly visible) -- sample three biological replicates for each genotype and time point -- for each biological replicate: pool the leaf from two plants into one tube -- freeze samples directly in liquid nitrogen -- Store samples at -80°C until needed \ No newline at end of file diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index f548dc7d17a0a7bf4542ea53826ab90018f90d39..17b1672bef326326666f501b2d21813b2134117b 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/gene_expression_eam7_plants_development/isa.study.xlsx b/studies/gene_expression_eam7_plants_development/isa.study.xlsx index 55496c492e6f2debcfa908ea533bf8378a46012e..8c133ad03f254ad38af35071060111e6e6d4cdfe 100644 Binary files a/studies/gene_expression_eam7_plants_development/isa.study.xlsx and b/studies/gene_expression_eam7_plants_development/isa.study.xlsx differ diff --git a/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md b/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md index 6ae4939b666963e088ac3369fc81352c98365a83..4a9c375cbe002b3c9e690b8b1c852b10061b8ea5 100644 --- a/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md +++ b/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md @@ -18,9 +18,15 @@ Genotypes: - QuickPot E24/10 trays (HerkuPlast Kubern GmbH, pot volume 480 cm^3) - Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) -**Sampling:** +**Leaf sampling for RNA extraction:** + +- place two 3 mm metal beads into 2.0 ml tube +- always sample the youngest, fully elongated leaf (auricles are clearly visible) +- sample three biological replicates for each genotype and time point +- for each biological replicate: pool the leaf from two plants into one tube +- freeze samples directly in liquid nitrogen +- Store samples at -80°C until needed -- always sample youngest, fully elongated leaf - sample at ZT 9 (1h after lights turned off, as FT1 expression is highest) - sample genotypes at 19, 26, 33, 40, 47 and 59 DAE diff --git a/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx b/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx index a063310508b766fbbe3bba86a62a76c9510c8248..d9f14729d51974633b8dbd5075b31a3608f73116 100644 Binary files a/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx and b/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx differ diff --git a/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md b/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md index 35f54b32799f6174ae8a1f7aa5f9f8fc643975d4..deb2017c7f42ae1b0d0a3c2007a87ecefb2d1d6b 100644 --- a/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md +++ b/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md @@ -19,7 +19,17 @@ Genotypes: - Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) -**Sampling:** +**Leaf sampling for RNA extraction:** + +- place two 3 mm metal beads into 2.0 ml tube +- always sample the youngest, fully elongated leaf (auricles are clearly visible) +- sample three biological replicates for each genotype and time point +- for each biological replicate: pool the leaf from two plants into one tube +- freeze samples directly in liquid nitrogen +- Store samples at -80°C until needed + +- sample at ZT 9 (1h after lights turned off, as FT1 expression is highest) +- sample genotypes at 19, 26, 33, 40, 47 and 59 DAE - 2 weeks old plants - youngest, fully elongated leaf: leaf 2 diff --git a/studies/gene_expression_lwd1_mutants_diurnal/README.md b/studies/gene_expression_lwd1_mutants_diurnal/README.md index 860900778e5c515f1f5b594f195bc2195033dffe..7439a5fb3f84781b8eae541522f7d02736c29f83 100644 --- a/studies/gene_expression_lwd1_mutants_diurnal/README.md +++ b/studies/gene_expression_lwd1_mutants_diurnal/README.md @@ -8,7 +8,7 @@ Gene expression of *CO1, ELF3, FT1, LUX1, LWD1, PHYB, PHYC, Ppd-H1*, and *PRR1* ```mermaid flowchart TD; - A[lwd1 mutants and GP-fast] --> |leaf_sampling| B[frozen leaf tissues, 3 biol. replicates] + A[lwd1 mutants and GP-fast] --> |plant growth and leaf sampling| B[frozen leaf tissues, 3 biol. replicates] B --> |RNA_extraction| C[RNA samples] C --> |cDNA_synthesis| D[cDNA samples] D --> |qRT-PCR| E[gene expression data, 2 techn. replicates] diff --git a/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx b/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx index 4d00176afb847ed396a1ff37f9f1c83c1d0c973f..f4923256c28fc797f532f750b4ca5af4ca1a455a 100644 Binary files a/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx and b/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx differ diff --git a/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md b/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md index d2ab6197d63642e71255be1c19721a509519a235..98ee71e1c2fd3e9d2eddfed4d911de0a7d68c4d9 100644 --- a/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md +++ b/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md @@ -20,7 +20,17 @@ Genotypes: - Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) -**Sampling:** +**Leaf sampling for RNA extraction:** + +- place two 3 mm metal beads into 2.0 ml tube +- always sample the youngest, fully elongated leaf (auricles are clearly visible) +- sample three biological replicates for each genotype and time point +- for each biological replicate: pool the leaf from two plants into one tube +- freeze samples directly in liquid nitrogen +- Store samples at -80°C until needed + +- sample at ZT 9 (1h after lights turned off, as FT1 expression is highest) +- sample genotypes at 19, 26, 33, 40, 47 and 59 DAE - 2 weeks old plants - youngest, fully elongated leaf: leaf 2