Merge branch helmsorig-2024-eam7:main into main

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/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/CAPS_marker_analysis.md

@@ -28,7 +28,3 @@
 | ------ | ------ | ------ | ------ | ------ | ------ | ------ |
 | M-PPD-H1 | F | ACGTGAATGGTGGATCGGC | BstUI | 60°C | 506 |  433, 73 | 
 | | R | TATAGCTAGGTGCGTGGCG | 						
-
-**Analysis:**
-
-- based on observed recombinations in combination with flowering time data, the eam7 introgression area can be redefined
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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/cDNA_synthesis/protocols/calculate_volumes.md

+## calculate sample volumes
+
+- from RNA concentrations: calculate the volume of RNA to use 1 µg RNA in cDNA synthesis reaction
+- max amount: 11 µl
+- fill the remaining amount with water
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assays/complementation_crosses/protocols/crossing_plants.md

@@ -7,5 +7,5 @@
 **Crossing:**
 - emasculate florets from mother plants before pollen are shed (about Waddington stage 8.5 - 9.0)
 - pollinate florets with pollen from father plants, pollinate all florets from one spike with the same father: this is one cross
-- cover the spike with a paper bag, count later how many of the pollinated florets develop into seeds
+- cover the spike with a paper bag
 - harvest seeds from each spike / each cross individually when they are completely dry
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assays/complementation_crosses/protocols/score_crosses.md

+## Score successful crosses
+
+- all crossed spikes were covered with a paper bag
+- number of pollinated florets per spike were documented
+- when seeds were ripe: count how many of the polinated florets developed into seeds
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