moved assay metadata data to studies, removed assay

assays/leaf_sampling/README.md

-## 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

assays/leaf_sampling/protocols/leaf_sampling.md

-## 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

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
 

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

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]

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