assays/DNA_extraction/README.md

 ## DNA_extraction
 
 **Assay used in studies:**
-- 
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+- 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/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/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

-## Results: target gene identification for *eam7*
-
-**Candidates 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 | - | - | 
-
-
-
-**Candidates 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 | 
-
-
-**Candidates with consistent mutations across *eam7* / *EAM* genotypes:**
-
-LIGHT-REGULATED WD 1 (LWD1) (HORVU.MOREX.r3.6HG0583670)
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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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assays/biparental_mapping/protocols/redefine_introgression_area.md

+## redefine eam7 introgression area
+
+- based CAPS marker results
+- combine observed recombinations  with flowering time data to reduce the eam7 introgression area
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assays/biparental_mapping/protocols/target_gene_identification.md

 ## *eam7* target gene identification
 
-- based on the CAPS marker results, the introgression area could be reduced to 2.98 cM/286 Mbp (Morex V3, Mascher et al. 2021)
-
-Flanking markers: 
-
-| marker | position in MorexV3 (bp) |
-| - | - |
-| JHI-Hv50k-2016-390119 | 96639872 |
-| JHI-Hv50k-2016-401705 | 382834297 |
-
-
-- this region contains 1084 high confidence (HC) genes
+- the reduced introgression area contains 1084 high confidence (HC) genes
 - Arabidopsis (Araport11, Cheng et al. 2017) homologs were indentified via BLASTP
 - 10 of the genes genes were homologous to Arabidopsis genes with functions in the circadian clock -> target_genes
 - 4 of these genes were associated with early flowering in barley or Arabidopsis -> target genes