assays/DNA_extraction/README.md

+## DNA_extraction
+
+**Assay used in studies:**
+- allelism_test
+- biparental_mapping_eam7
+- generating_lwd1_mutants
+
+**Info:**
+
+No datasets, as DNA concentration was not measured and DNA samples were used in downstream assays (plant_genotyping)
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assays/MSA_dissection/README.md

+## MSA_dissection
+
+**Assay used in studies:**
+- MSA_dissection_eam7
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assays/MSA_dissection/protocols/dissection_of_MSAs.txt → 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)

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.txt → assays/RNA_extraction/protocols/trizol_RNA_extraction.md

-TRIzol RNA extraction
+## 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

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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assays/biparental_mapping/dataset/target_genes_results.md

-**related to the circadian clock:**
-
-| MorexV3 gene ID | pident | evalue | Araport11 gene ID | Gene name | SNP positions | Changes in aa sequence |
-| ------ | ------ | ------ | ------ | ------ | ------ | ------ | 
-| HORVU.MOREX.r3.6HG0592840 | 	73.75 | 2.26E-40 | AT2G21660 | GR-RBP1 | None	| None
-| HORVU.MOREX.r3.6HG0583670	| 69.309 | 0 | AT1G12910 | LWD1	| 32 bp del (1219-1250)	| A407F, N408S, K409F, L410* | 
-| HORVU.MOREX.r3.6HG0587680	| 66.082 | 0 | AT4G08920 | CRY1	| None | None | 
-| HORVU.MOREX.r3.6HG0595250	| 38.475 | 3.92E-106 | AT5G61380 | PRR1 | A642G | T1300C | T215A, S434P | 
-| HORVU.MOREX.r3.6HG0578070	| 55.367 | 0 | AT5G51200 | EDS4 | - | - | 
-| HORVU.MOREX.r3.6HG0589220	| 34.855 | 9.66E-46	| AT3G07640 | PBAC5 | - | - | 
-| HORVU.MOREX.r3.6HG0571470	| 36.735 | 1.3	| AT3G42170 | DAY-SLEEPER | - | - | 
-| HORVU.MOREX.r3.6HG0582650	| 30.108 | 1.00E-12	| AT3G42170 | DAY-SLEEPER | - | - | 
-| HORVU.MOREX.r3.6HG0592100	| 29.042 | 1.69E-45	| AT3G42170 | DAY-SLEEPER | - | - | 
-| HORVU.MOREX.r3.6HG0571480	| 28.319 | 1.11E-13	| AT3G42170 | DAY-SLEEPER | - | - | 
-
-
-
-**associated with early flowering:**
-
-| gene name | MoresV3 gene ID |
-| - | - |
-| PSEUDO RESPONSE REGULATOR 1 (PRR1) | HORVU.MOREX.r3.6HG0595250 | 
-| CRYPTOCHROME 1a (CRY1a) | HORVU.MOREX.r3.6HG0587680) | 
-| GLYCIN-RICH RNA-BINDING-PROTEIN 1 (GR-RBP1) | HORVU.MOREX.r3.6HG0592840) | 
-| LIGHT-REGULATED WD 1 (LWD1) | HORVU.MOREX.r3.6HG0583670 | 
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assays/biparental_mapping/protocols/CAPS_marker_analysis.md

-**CAPS marker: PCR + digest**
+## CAPS marker: PCR + digest
 
-PCR: 
+**PCR:** 
 - using GoTaq® DNA Polymerase (Promega) according to the manufacturer's protocol with CAPS-marker specific PCR primers
 
-digest:
+**Digest:**
 
 - digesting 5µl of PCR fragments with the CAPS-marker specific restriction enzyme:
 

assays/biparental_mapping/protocols/plant-phenotyping-flowering.md

-**plant phenotyping: flowering**
-
-- flowering was scored in days after emergence (DAE) as the period between emergence from soil and reaching Zadoks stage 49 when the awns exited the leaf sheath (Zadoks et al. 1974)
-- plants that did not flower after 130 DAE were scored as "not flowering"
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