assays/MSA_dissection/protocols/dissection_of_MSAs.md

+## Dissection of main shoot apices (MSAs) of barley plants
+
+**Growth:**
+- per genotype: choose approx. 4 random plants every 6-8 days (SD) or every 2-10 days (LD)
+- start 5 days after emergence (DAE)
+
+**Dissection:**
+- remove the leaves surrounding the main shoot apex (MSA) with a blade
+- image MSA with the stereo microscope Nikon SMZ18 with a Nikon DS-Fi2 camera
+- score developmental stage according to Waddington et al. (1983)
+- count spikelet meristems (include those that have developet into floret meristems or florets) on the MSA
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assays/RNA_extraction/README.md

+## RNA_extraction
+
+**Assay used in studies:**
+- gene_expression_eam7_plants_development
+- gene_expression_eam7_plants_diurnal
+- gene_expression_lwd1_mutants_diurnal
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assays/RNA_extraction/protocols/measure_RNA_concentration.md

+## measure RNA concentration of samples
+
+- dilute small amount of RNA sample 1:5 with DEPC water
+- use 2 µl of dilution to measure the concentration with a Nanophotometer
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assays/RNA_extraction/protocols/trizol_RNA_extraction.md

+## TRIzol RNA extraction
+
+-	Grind your samples 2 x 45sec at maximum frequency (30 Hertz) in TissueLyser (QIAGEN), use pre-cooled adapters
+-	Add 500 µL of TRIzol to the frozen samples, close tubes and mix vigorously until the sample is homogeneous
+-	Incubate the samples for 5 min at room temperature
+-	Briefly spin down the samples
+-	Add 100 µl of chloroform, close the tubes and shake tubes 15-20 sec vigorously by hand
+-	Incubate the samples for 3 min at room temperature
+-	Centrifuge the samples at 10.000 x g for 15 min at 4°C
+-	Transfer 150-300 µl of the clear, aqueous, upper phase to new tubes
+-	Add same volume of isopropyl alcohol, gently invert 8x, do not vortex
+-	Incubate the samples for 10 min at room temperature
+-	Centrifuge the samples at 10.000 x g for 10 min at 4°C
+-	Remove the supernatant
+-	Wash the pellet with 500 µl of 75% ethanol
+-	Centrifuge samples at 10.000 x g for 2 min at 4°C
+-	Remove the supernatant
+-	Dry the RNA pellet at least 10-30 min
+-	Add 60 µL of DEPC-water and incubate at 4°C over night
+
+-	Perform DNAse treatment (see ThermoFisher_DNAseI protocol)
+-	Store RNA at -80°C

assays/biparental_mapping/README.md

+## biparental_mapping
+
+**Assay used in studies:**
+- biparental_mapping_eam7
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assays/biparental_mapping/dataset/eam7_introgression_area.md

+## reduced *eam7* introgression:
+
+
+| marker start | marker end | Mbp start | Mbp end | size (Mbp) |
+| - | - | - | - | - |
+| JHI-Hv50k-2016-390119 | JHI-Hv50k-2016-401705 | 96.64 | 382.8 | 286.16 |
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