.gitattributes

@@ -2,3 +2,6 @@ _publication/Helmsorig-et-al-2024.pdf filter=lfs diff=lfs merge=lfs -text
 _publication/Supplemental_Datasets_S1-S4.xlsx filter=lfs diff=lfs merge=lfs -text
 _publication/Supplemental_Figures_and_Tables.pdf filter=lfs diff=lfs merge=lfs -text
 studies/biparental_mapping_eam7/resources/50k_Illumina_Infinium_iSelect_SNP_Array.xlsx filter=lfs diff=lfs merge=lfs -text
+studies/biparental_mapping_eam7/resources/Araport11_GFF3_genes_transposons.20241001.gff filter=lfs diff=lfs merge=lfs -text
+studies/biparental_mapping_eam7/resources/Hv_Morex.pgsb.Jul2020.gff3 filter=lfs diff=lfs merge=lfs -text
+studies/biparental_mapping_eam7/resources/MorexV3_Araport11_conversion.txt filter=lfs diff=lfs merge=lfs -text

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)
\ No newline at end of file

assays/MSA_dissection/README.md

+## MSA_dissection
+
+**Assay used in studies:**
+- MSA_dissection_eam7
\ No newline at end of file

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
\ No newline at end of file

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
\ No newline at end of file

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
\ No newline at end of file

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 |
\ No newline at end of file

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 | 
\ No newline at end of file

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: