diff --git a/assays/DNA_extraction/isa.assay.xlsx b/assays/DNA_extraction/isa.assay.xlsx index 49aa9a02d76530769cba182806b7605d0add1c94..064161b044ae7250570464d452f35ee5e06dec04 100644 Binary files a/assays/DNA_extraction/isa.assay.xlsx and b/assays/DNA_extraction/isa.assay.xlsx differ diff --git a/assays/RNA_extraction/isa.assay.xlsx b/assays/RNA_extraction/isa.assay.xlsx index 0ae210be197dfe68a89da25de512696f1642d665..b292ce19ef504cabd206de0e89250773ce12c11c 100644 Binary files a/assays/RNA_extraction/isa.assay.xlsx and b/assays/RNA_extraction/isa.assay.xlsx differ diff --git a/assays/RNA_extraction/protocols/measure_RNA_concentration.md b/assays/RNA_extraction/protocols/measure_RNA_concentration.md new file mode 100644 index 0000000000000000000000000000000000000000..9db5ca5696731c4b64faa18cb71be37a90779389 --- /dev/null +++ b/assays/RNA_extraction/protocols/measure_RNA_concentration.md @@ -0,0 +1,4 @@ +## 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 diff --git a/assays/biparental_mapping/dataset/CAPS_results.xlsx b/assays/biparental_mapping/dataset/CAPS_results.xlsx index fa8750b430e1e475061365cf7c81af0c9c4b7419..c800f3ab2476be9d2338d2bb72044d07de0e2915 100644 Binary files a/assays/biparental_mapping/dataset/CAPS_results.xlsx and b/assays/biparental_mapping/dataset/CAPS_results.xlsx differ diff --git a/assays/biparental_mapping/dataset/introgression_area.xlsx b/assays/biparental_mapping/dataset/introgression_area.xlsx index 1870f406bf3f7f35518387d0178e502e3139d8b1..3c0bf67676f709957396efdafdfe08ca3eb6f7b1 100644 Binary files a/assays/biparental_mapping/dataset/introgression_area.xlsx and b/assays/biparental_mapping/dataset/introgression_area.xlsx differ diff --git a/assays/biparental_mapping/dataset/target_genes_results.md b/assays/biparental_mapping/dataset/target_genes_results.md deleted file mode 100644 index f92cc6afe23b4b599c71be7f51a76344b7005940..0000000000000000000000000000000000000000 --- a/assays/biparental_mapping/dataset/target_genes_results.md +++ /dev/null @@ -1,32 +0,0 @@ -## 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) \ No newline at end of file diff --git a/assays/biparental_mapping/isa.assay.xlsx b/assays/biparental_mapping/isa.assay.xlsx index 6671a698fc90341ca6b287870b7d59588d4bed18..d41888c738931722f4d79e248ad6d1876142b7c7 100644 Binary files a/assays/biparental_mapping/isa.assay.xlsx and b/assays/biparental_mapping/isa.assay.xlsx differ diff --git a/assays/biparental_mapping/protocols/CAPS_marker_analysis.md b/assays/biparental_mapping/protocols/CAPS_marker_analysis.md index 0f84933595bd017380d7608e88b2dc8eab482006..cf942a5f21fd0baf48feca5f371ac0c4c0de3aec 100644 --- a/assays/biparental_mapping/protocols/CAPS_marker_analysis.md +++ b/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 \ No newline at end of file diff --git a/assays/biparental_mapping/protocols/redefine_introgression_area.md b/assays/biparental_mapping/protocols/redefine_introgression_area.md new file mode 100644 index 0000000000000000000000000000000000000000..a7e569b0bb1e7a2bf31aaa8bbac7df9dc6e32157 --- /dev/null +++ b/assays/biparental_mapping/protocols/redefine_introgression_area.md @@ -0,0 +1,4 @@ +## redefine eam7 introgression area + +- based CAPS marker results +- combine observed recombinations with flowering time data to reduce the eam7 introgression area \ No newline at end of file diff --git a/assays/cDNA_synthesis/dataset/eam7_development_cDNA_volumes.xlsx b/assays/cDNA_synthesis/dataset/eam7_development_cDNA_volumes.xlsx index 1ba16127ba45597bdfeb28bc4bc8f591b86d7ae8..377f4e27571427b61f52e2b951c52c9897a7fe4b 100644 Binary files a/assays/cDNA_synthesis/dataset/eam7_development_cDNA_volumes.xlsx and b/assays/cDNA_synthesis/dataset/eam7_development_cDNA_volumes.xlsx differ diff --git a/assays/cDNA_synthesis/dataset/eam7_diurnal_cDNA_volumes.xlsx b/assays/cDNA_synthesis/dataset/eam7_diurnal_cDNA_volumes.xlsx index 27ba006b29b056dea1b372ad994b148148b39b34..dba6d47ac2c4f8e94f41beba6c3e82bbecba17ab 100644 Binary files a/assays/cDNA_synthesis/dataset/eam7_diurnal_cDNA_volumes.xlsx and b/assays/cDNA_synthesis/dataset/eam7_diurnal_cDNA_volumes.xlsx differ diff --git a/assays/cDNA_synthesis/dataset/lwd1_diurnal_cDNA_volumes.xlsx b/assays/cDNA_synthesis/dataset/lwd1_diurnal_cDNA_volumes.xlsx index f6e0286234b679a53be3ef39409720310b4da40f..fc120a51e8e74119cb5f5907bf9d5eefdeb3547b 100644 Binary files a/assays/cDNA_synthesis/dataset/lwd1_diurnal_cDNA_volumes.xlsx and b/assays/cDNA_synthesis/dataset/lwd1_diurnal_cDNA_volumes.xlsx differ diff --git a/assays/cDNA_synthesis/isa.assay.xlsx b/assays/cDNA_synthesis/isa.assay.xlsx index aa6541150a760052a8c1b6093c9a3aa7dc856ac9..3dc46412f95f588d6c9135451b4dccb644f6cbed 100644 Binary files a/assays/cDNA_synthesis/isa.assay.xlsx and b/assays/cDNA_synthesis/isa.assay.xlsx differ diff --git a/assays/cDNA_synthesis/protocols/calculate_volumes.md b/assays/cDNA_synthesis/protocols/calculate_volumes.md new file mode 100644 index 0000000000000000000000000000000000000000..8072be77a076d86b2b6cd3664d0bc5c21e8e7d3e --- /dev/null +++ b/assays/cDNA_synthesis/protocols/calculate_volumes.md @@ -0,0 +1,5 @@ +## 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 \ No newline at end of file diff --git a/assays/plant_genotyping/dataset/complementation_F1_genotype_results.xlsx b/assays/plant_genotyping/dataset/complementation_F1_genotype_results.xlsx index a54f49a7013480e74242f39167985a142bb35038..5f9124b7246df4bb4094ddf60a5c890768005d5a 100644 Binary files a/assays/plant_genotyping/dataset/complementation_F1_genotype_results.xlsx and b/assays/plant_genotyping/dataset/complementation_F1_genotype_results.xlsx differ diff --git a/assays/plant_genotyping/isa.assay.xlsx b/assays/plant_genotyping/isa.assay.xlsx index 8046185ecbce051704cc72aac31236e8cb5f546d..a9d96125514603423bf9e6870a1d7aa11f20f89a 100644 Binary files a/assays/plant_genotyping/isa.assay.xlsx and b/assays/plant_genotyping/isa.assay.xlsx differ diff --git a/assays/plant_phenotyping/dataset/complementation_F1_phenotyping_results.xlsx b/assays/plant_phenotyping/dataset/complementation_F1_phenotyping_results.xlsx index 74ee3bf929aba7603ba80d5ea13dc59118c678b9..a414e5143d7f6ef0abac3ce565dbcec45ccdc47e 100644 Binary files a/assays/plant_phenotyping/dataset/complementation_F1_phenotyping_results.xlsx and b/assays/plant_phenotyping/dataset/complementation_F1_phenotyping_results.xlsx differ diff --git a/assays/plant_phenotyping/isa.assay.xlsx b/assays/plant_phenotyping/isa.assay.xlsx index b3584692cad382577fd8a4a238f406afa7be0bf8..7d933be838936a4c37056668e37678dfda1963d0 100644 Binary files a/assays/plant_phenotyping/isa.assay.xlsx and b/assays/plant_phenotyping/isa.assay.xlsx differ diff --git a/studies/allelism_test/isa.study.xlsx b/studies/allelism_test/isa.study.xlsx index 00555c3586df3b647e8ff32c3b9bdf7631e6b220..d2788a764bd50f332e57d36776e95dfa975b195f 100644 Binary files a/studies/allelism_test/isa.study.xlsx and b/studies/allelism_test/isa.study.xlsx differ