diff --git a/assays/DNA_extraction/isa.assay.xlsx b/assays/DNA_extraction/isa.assay.xlsx index 49aa9a02d76530769cba182806b7605d0add1c94..1d87c5dd264ac21e8b7a2c363bd1ace1a8d995c2 100644 Binary files a/assays/DNA_extraction/isa.assay.xlsx and b/assays/DNA_extraction/isa.assay.xlsx differ diff --git a/assays/MSA_dissection/dataset/LD_dissection_results.xlsx b/assays/MSA_dissection/dataset/LD_dissection_results.xlsx index 64dc4cf7dee6f3f8928601e992b509edbab94304..cef5b49514f1106dfd50693504a57d2a76025643 100644 Binary files a/assays/MSA_dissection/dataset/LD_dissection_results.xlsx and b/assays/MSA_dissection/dataset/LD_dissection_results.xlsx differ diff --git a/assays/MSA_dissection/dataset/SD_dissection_results.xlsx b/assays/MSA_dissection/dataset/SD_dissection_results.xlsx index c49bb87040186720fe0d2dacf60544887e0f70ed..14376c5e3c133d299b32af93300f368dbcdf5fab 100644 Binary files a/assays/MSA_dissection/dataset/SD_dissection_results.xlsx and b/assays/MSA_dissection/dataset/SD_dissection_results.xlsx differ diff --git a/assays/MSA_dissection/isa.assay.xlsx b/assays/MSA_dissection/isa.assay.xlsx index e499e2097c1670329209f5a36089f3ff5763fd1e..ae484969c38ff34f7bcb190cca69553f66397852 100644 Binary files a/assays/MSA_dissection/isa.assay.xlsx and b/assays/MSA_dissection/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/complementation_crosses/isa.assay.xlsx b/assays/complementation_crosses/isa.assay.xlsx index ea7acc1a8128e86d8f85d0a2b3b91fe246a73f75..fe826661a6d9f2e78a6e4e33fc6a92f45c60beda 100644 Binary files a/assays/complementation_crosses/isa.assay.xlsx and b/assays/complementation_crosses/isa.assay.xlsx differ diff --git a/assays/complementation_crosses/protocols/crossing_plants.md b/assays/complementation_crosses/protocols/crossing_plants.md index 59222e7927c797078be387fcfa9d618554f9e6b8..4d27063790916eb10783c1610dbb5b2ddebdc015 100644 --- a/assays/complementation_crosses/protocols/crossing_plants.md +++ b/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 \ No newline at end of file diff --git a/assays/complementation_crosses/protocols/score_crosses.md b/assays/complementation_crosses/protocols/score_crosses.md new file mode 100644 index 0000000000000000000000000000000000000000..4cdd2969d924a5a9bb5839f9f01dae117f040265 --- /dev/null +++ b/assays/complementation_crosses/protocols/score_crosses.md @@ -0,0 +1,5 @@ +## 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 \ No newline at end of file diff --git a/assays/embryo_transformation/dataset/transformation_T0_results.xlsx b/assays/embryo_transformation/dataset/transformation_T0_results.xlsx index 1c5ce99ef745e7d374de09a5af1a21a9792f9ee7..2303b9d8dfc780f44d8d6eee113c3199c3a1a513 100644 Binary files a/assays/embryo_transformation/dataset/transformation_T0_results.xlsx and b/assays/embryo_transformation/dataset/transformation_T0_results.xlsx differ diff --git a/assays/embryo_transformation/isa.assay.xlsx b/assays/embryo_transformation/isa.assay.xlsx index 645d4fabd14c575c032264b2209b93aaaf25c475..1a7203a9a397434d06cda80e36bbb318fc931692 100644 Binary files a/assays/embryo_transformation/isa.assay.xlsx and b/assays/embryo_transformation/isa.assay.xlsx differ diff --git a/assays/embryo_transformation/protocols/cloning_trafo_protocol.md b/assays/embryo_transformation/protocols/cloning_trafo_protocol.md index c4832045654e3ce22464851457ec698a7affe7b1..911abf527d2700c078acbfe8b8a305fb2631c552 100644 --- a/assays/embryo_transformation/protocols/cloning_trafo_protocol.md +++ b/assays/embryo_transformation/protocols/cloning_trafo_protocol.md @@ -15,9 +15,6 @@ - GP-fast plants were cultivated in long-day conditions (16h day / 8 night) in control temperature (20°C / 16°C) - immature embryos were used for transformation according to Hensel et al. (2009) -- DNA was extracted from regenerated plants using QIAGEN_DNeasy-Plant-Mini protocol -- successful insertion of the transformation vector into the genome was tested by PCR using the primers Hyg-156 (5'-ACGCACAATCCCACTATCC-3') and Hyg-047 (5'-GTGTCGTCCATCACAGTTTG-3') - **References:** diff --git a/assays/embryo_transformation/protocols/test_hygromycin.md b/assays/embryo_transformation/protocols/test_hygromycin.md new file mode 100644 index 0000000000000000000000000000000000000000..d9a546bfb2c6e58dc51fe292daaeb985d12e31e5 --- /dev/null +++ b/assays/embryo_transformation/protocols/test_hygromycin.md @@ -0,0 +1,5 @@ +## Test regenerated plants for successful transformation + +- DNA was extracted from regenerated plants using QIAGEN_DNeasy-Plant-Mini protocol +- successful insertion of the transformation vector into the genome was tested by PCR using the primers Hyg-156 (5'-ACGCACAATCCCACTATCC-3') and Hyg-047 (5'-GTGTCGTCCATCACAGTTTG-3') + diff --git a/assays/leaf_sampling/README.md b/assays/leaf_sampling/README.md deleted file mode 100644 index 6bbd3ce33f7d7ed2c4f0b633bc16e66e2244fbcd..0000000000000000000000000000000000000000 --- a/assays/leaf_sampling/README.md +++ /dev/null @@ -1,10 +0,0 @@ -## leaf_sampling - -**Assay used in studies:** -- gene_expression_eam7_plants_development -- gene_expression_eam7_plants_diurnal -- gene_expression_lwd1_mutants_diurnal - -**Info:** - -No dataset, as leaf samples were used in downstream assays (RNA_extraction). \ No newline at end of file diff --git a/assays/leaf_sampling/dataset/.gitkeep b/assays/leaf_sampling/dataset/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/leaf_sampling/isa.assay.xlsx b/assays/leaf_sampling/isa.assay.xlsx deleted file mode 100644 index 52c17f906eb38d3aa9a7368cbfb57c1a1a024132..0000000000000000000000000000000000000000 Binary files a/assays/leaf_sampling/isa.assay.xlsx and /dev/null differ diff --git a/assays/leaf_sampling/protocols/.gitkeep b/assays/leaf_sampling/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/leaf_sampling/protocols/leaf_sampling.md b/assays/leaf_sampling/protocols/leaf_sampling.md deleted file mode 100644 index 340a6ba698f0536ac0015b06f4676abe0bce2f5e..0000000000000000000000000000000000000000 --- a/assays/leaf_sampling/protocols/leaf_sampling.md +++ /dev/null @@ -1,8 +0,0 @@ -## Leaf sampling for RNA extraction - -- place two 3 mm metal beads into 2.0 ml tube -- always sample the youngest, fully elongated leaf (auricles are clearly visible) -- sample three biological replicates for each genotype and time point -- for each biological replicate: pool the leaf from two plants into one tube -- freeze samples directly in liquid nitrogen -- Store samples at -80°C until needed \ 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..46c21e23a7e53b3bd6509d96757a627bf0847fa5 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/dataset/lwd1_T0_genotype_results.xlsx b/assays/plant_genotyping/dataset/lwd1_T0_genotype_results.xlsx index 96afb610143e2363884ef5c7bf8c5049bc4b6ad9..10d155def6c987c0433a5303b6fd7d0aca186df0 100644 Binary files a/assays/plant_genotyping/dataset/lwd1_T0_genotype_results.xlsx and b/assays/plant_genotyping/dataset/lwd1_T0_genotype_results.xlsx differ diff --git a/assays/plant_genotyping/dataset/lwd1_T1_genotype_results.xlsx b/assays/plant_genotyping/dataset/lwd1_T1_genotype_results.xlsx index 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a/assays/plant_phenotyping/dataset/complementation_F1_phenotyping_results.xlsx b/assays/plant_phenotyping/dataset/complementation_F1_phenotyping_results.xlsx index 74ee3bf929aba7603ba80d5ea13dc59118c678b9..3a4c21624884d094742c494279271b4af82b50d5 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/dataset/eam7_LD_phenotyping_results.xlsx b/assays/plant_phenotyping/dataset/eam7_LD_phenotyping_results.xlsx index 8df547e64e932b57c67f327654c6889abb48029a..e47dd988357496b6d023a0a1c1f545aed5f9cc52 100644 Binary files a/assays/plant_phenotyping/dataset/eam7_LD_phenotyping_results.xlsx and b/assays/plant_phenotyping/dataset/eam7_LD_phenotyping_results.xlsx differ diff --git a/assays/plant_phenotyping/dataset/eam7_SD_phenotyping_results.xlsx b/assays/plant_phenotyping/dataset/eam7_SD_phenotyping_results.xlsx index cf3efae15b1be216788dc9433ffacdcdceb2b786..c349be7368f660a29298d88977ddb44473f11cdc 100644 Binary files a/assays/plant_phenotyping/dataset/eam7_SD_phenotyping_results.xlsx and b/assays/plant_phenotyping/dataset/eam7_SD_phenotyping_results.xlsx differ diff --git a/assays/plant_phenotyping/dataset/lwd1_mutants_phenotyping_results.xlsx b/assays/plant_phenotyping/dataset/lwd1_mutants_phenotyping_results.xlsx index 3cbfb9d50985858158bc3504b86b5e90d9305c8c..9027077cff7e7a44e9ce7dcfeeea65882497b3d6 100644 Binary files a/assays/plant_phenotyping/dataset/lwd1_mutants_phenotyping_results.xlsx and b/assays/plant_phenotyping/dataset/lwd1_mutants_phenotyping_results.xlsx differ diff --git a/assays/plant_phenotyping/isa.assay.xlsx b/assays/plant_phenotyping/isa.assay.xlsx index b3584692cad382577fd8a4a238f406afa7be0bf8..ec6fbad26cd705929999f131b4c66d0aee51a7c7 100644 Binary files a/assays/plant_phenotyping/isa.assay.xlsx and b/assays/plant_phenotyping/isa.assay.xlsx differ diff --git a/assays/plant_propagation/isa.assay.xlsx b/assays/plant_propagation/isa.assay.xlsx index 5a72873bc8801f7cf9c7991d761c9dc296bbcfc2..17194b3aa58ef19286b19aff2b1a6be966ab4247 100644 Binary files a/assays/plant_propagation/isa.assay.xlsx and b/assays/plant_propagation/isa.assay.xlsx differ diff --git a/assays/plant_propagation/protocols/plant_growth.md b/assays/plant_propagation/protocols/plant_growth.md new file mode 100644 index 0000000000000000000000000000000000000000..741380b06d61b291e9970da80677376ea7f7d849 --- /dev/null +++ b/assays/plant_propagation/protocols/plant_growth.md @@ -0,0 +1,10 @@ +## Growth of *lwd1* mutant plants + +- plants were grown until maturity + +**Growth conditions:** + +- long day: (LD) 16h light / 8h dark, 20/16 °C, 60% humidity, ~ 250 PAR) +- 1.5 L pots (HerkuPlast Kubern GmbH, pot volume 75 cm^3) +- Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) + diff --git a/assays/plant_propagation/protocols/plant_propagation.md b/assays/plant_propagation/protocols/plant_propagation.md new file mode 100644 index 0000000000000000000000000000000000000000..9796a061c289fc953518e4a6a6166fd9e07ef766 --- /dev/null +++ b/assays/plant_propagation/protocols/plant_propagation.md @@ -0,0 +1,4 @@ +## Propagation of *lwd1* mutant plants + +- plants were grown until full maturity +- seeds were harvested for each plant individually \ No newline at end of file diff --git a/assays/plant_propagation/protocols/progagation_of_mutant_plants.md b/assays/plant_propagation/protocols/progagation_of_mutant_plants.md deleted file mode 100644 index 3b3d59a549ec2d3ce2b3add9b9fa690095ed2c12..0000000000000000000000000000000000000000 --- a/assays/plant_propagation/protocols/progagation_of_mutant_plants.md +++ /dev/null @@ -1,8 +0,0 @@ -## Propagation of *lwd1* mutant plants - -- plants were grown in LD conditions until maturity -- seeds were harvested for each plant individually - -**Generations:** -- T0 plants: regenerated plants from cell culture (embryo transformation), produce T1 seeds -- T1 plants: genotyping for potential mutants, produce T2 seeds \ No newline at end of file diff --git a/assays/qRT-PCR/dataset/eam7_development_gene_expression.xlsx b/assays/qRT-PCR/dataset/eam7_development_gene_expression.xlsx index 48f2d051ac162335bb2d623af588967114b16e39..6f9e9af64b4ee38f25996602896c81c339e5705c 100644 Binary files a/assays/qRT-PCR/dataset/eam7_development_gene_expression.xlsx and b/assays/qRT-PCR/dataset/eam7_development_gene_expression.xlsx differ diff --git a/assays/qRT-PCR/dataset/eam7_diurnal_gene_expression.xlsx b/assays/qRT-PCR/dataset/eam7_diurnal_gene_expression.xlsx index 2df076e8c4d43ce277e90724cd82b7018ccf3af5..5664415d3433cd26150bffb31ec9f4fac9165997 100644 Binary files a/assays/qRT-PCR/dataset/eam7_diurnal_gene_expression.xlsx and b/assays/qRT-PCR/dataset/eam7_diurnal_gene_expression.xlsx differ diff --git a/assays/qRT-PCR/dataset/lwd1_diurnal_gene_expression.xlsx b/assays/qRT-PCR/dataset/lwd1_diurnal_gene_expression.xlsx index 10c78c0c91d2a18cc6db86ec0a861eebfab0c369..4b67a47134acf88c413d553a7fe7e00e59c6c3f1 100644 Binary files a/assays/qRT-PCR/dataset/lwd1_diurnal_gene_expression.xlsx and b/assays/qRT-PCR/dataset/lwd1_diurnal_gene_expression.xlsx differ diff --git a/assays/qRT-PCR/isa.assay.xlsx b/assays/qRT-PCR/isa.assay.xlsx index 90d078702d6a5d8bfbc1e6818eae561d68661d30..9f83428b90e54dd9bd1068c0325fcde8672adff2 100644 Binary files a/assays/qRT-PCR/isa.assay.xlsx and b/assays/qRT-PCR/isa.assay.xlsx differ diff --git a/assays/qRT-PCR/protocols/qRT-PCR_primer.md b/assays/qRT-PCR/protocols/qRT-PCR_primer.md deleted file mode 100644 index 0b3ccec975b1ae64855298742d0aed31fb00cc35..0000000000000000000000000000000000000000 --- a/assays/qRT-PCR/protocols/qRT-PCR_primer.md +++ /dev/null @@ -1,44 +0,0 @@ - - -| Target gene | Primer | Sequence 5’-3’ | Fragment size (bp) | -| - | - | - | - | -| ACT (HORVU.MOREX.r3.5HG0457850) | ACT_591F | CGTGTTGGATTCTGGTGATG | 208| -| | ACT_789R | AGCCACATATGCGAGCTTCT | | -| CO1 (HORVU.MOREX.r3.7HG0671540) | CO1_2185F | CTGCTGGGGCTAGTGCTTAC | 251| -| | CO1_3454R | CCTTGTTGCATAACGTGTGG | | -| CO2 (HORVU.MOREX.r3.6HG0611630) | CO2_564F | AGTGGACTCTTGGCTCCTCA | 158 | -| | CO2_721R | CATGCTGCTGTTCTTGCATT | | -| ELF3 (HORVU.MOREX.r3.1HG0095050) | ELF3_DL_3060_F3 | TGCTGTCCAAGTGTTTGAGC | 242 | - | | Elf3_DL_4483_R3 | CCTGGTTTCCTTCGGTGTTA | | -| FT1 (HORVU.MOREX.r3.7HG0653910) | FT1_1955F | GGTAGACCCAGATGCTCCAA | 120 | -| | FT1_2183R | TCGTAGCACATCACCTCCTG | | -| FT2 (HORVU.MOREX.r3.3HG0244930 | FT2_4031R | TCACATCCTTCTCCCGCCGG | 238 | -| | FT2_3809_F | TACCGAGGTTGTGTGCTACG | | -| FT3 (HORVU.MOREX.r3.1HG0077250) | FT3-1004F | TGTCAGACATCCCTGGAACA | 225 | -| | FT3-1848R | CTGATCCACCTTCCCTTTGA | | -| FT4 (HORVU.MOREX.r3.2HG0117260) | FT4_626F | AAACGATAGCTTTGGAAAAGAGATC | 230 | -| | FT4_2537R | TCCTCCCGCCGGTGCCCGTG | | -| GI (HORVU.MOREX.r3.3HG0238250) | GI_6780F | TCAGTTAGAGCTCCTGGAAGT | 263 | -| | GI_7289R | GGTAGTTTGGGCTTTGGATG | | -| LHY (HORVU.MOREX.r3.7HG0699010) | HvLHY_672F | CCTGGAATTGGAGATGGAGA | 210 | -| | HvLHY_882R | TGAGCATGGCTTCTGATTTG | | -| LUX1 (HORVU.MOREX.r3.3HG0328340) | LUX_1077F | AATTCAGTCCACGGATGCTC | 222 | -| | LUX_1298R | CTTCACTTCAGCTCCCCTTG | | -| LWD1 (HORVU.MOREX.r3.6HG0583670) | LWD1_qPCR-114_F | CAGCTCATAGCCCATGACAA | 114 | -| | LWD1_qPCR-114_R | CTCCTTGTCCCGAAGATCAA | | -| PHYB (HORVU.MOREX.r3.4HG0381880) | HvPHYB-1151F | CTTGCGCACCAACTATCAGA | 232 | -| | HvPHYB-1383R | CTCCATGACACACCGTCAAC | | -| PHYC (HORVU.MOREX.r3.5HG0511090) | PHYC_0986F | ACTACCCGGCAACTGACATC | 142 | -| | PHYC_1127R | GAGCCACAGAGGCTGATAGG | | -| Ppd-H1 (HORVU.MOREX.r3.2HG0107710) | PPD1_2165F | GATGGATTCAAAGGCAAGGA | 172 | -| | PPD1_2336R | GAACAATTGGCTCCTCCAAA | | -| PRR1 (HORVU.MOREX.r3.6HG0595250) | HvPRR1_1056F | GAGCATAGCATGGCACTTCA | 237 | -| | HvPRR1_1292R | TGTCTTTCCTCGGAAATTGG | | -| PRR59 (HORVU.MOREX.r3.4HG0350690) | PRR59_2064_F | GAAATTCCGCATGAAAAGGA | 148 | -| | PRR59_2212_R | TTCCGCATCTTCTGTTGTTG | | -| PRR73 (HORVU.MOREX.r3.5HG0498830) | PRR73_441F | GCGCCGTAGAGAATCAGAAC | 222 | -| | PRR73_662R | CATGTCGGGTACAGTCATCG | | -| PRR95 (HORVU.MOREX.r3.5HG0498830) | PRR95_1467F | CAGAACTCCAGTGTCGCAAA | 251 | -| | PRR95_1717R | TGCTGTTGCCAGAGTTGTTC | | -| VRN1 (HORVU.MOREX.r3.5HG0511210) | HVBM5a_292F | CTGAAGGCGAAGGTTGAGAC | 203 | -| | HVBM5a_494R | TTCTCCTCCTGCAGTGACCT | | \ No newline at end of file diff --git a/assays/qRT-PCR/protocols/qRT-PCR_protocol.md b/assays/qRT-PCR/protocols/qRT-PCR_protocol.md index 760ccc4ee95c5104f2cbf9fac9a031fdcd70a3ed..351e816634870b9e0bb85774f37f9e755492485b 100644 --- a/assays/qRT-PCR/protocols/qRT-PCR_protocol.md +++ b/assays/qRT-PCR/protocols/qRT-PCR_protocol.md @@ -55,4 +55,50 @@ If no standard curve was available: **4. Calculate means and standard deviation for all samples** - relative expression was averaged over the three biological replicates for each sample -- standard deviation was calculated across the three biological replicates for each sample \ No newline at end of file +- standard deviation was calculated across the three biological replicates for each sample + + +**Primer list:** + +| Target gene | Primer | Sequence 5’-3’ | Fragment size (bp) | +| - | - | - | - | +| ACT (HORVU.MOREX.r3.5HG0457850) | ACT_591F | CGTGTTGGATTCTGGTGATG | 208| +| | ACT_789R | AGCCACATATGCGAGCTTCT | | +| CO1 (HORVU.MOREX.r3.7HG0671540) | CO1_2185F | CTGCTGGGGCTAGTGCTTAC | 251| +| | CO1_3454R | CCTTGTTGCATAACGTGTGG | | +| CO2 (HORVU.MOREX.r3.6HG0611630) | CO2_564F | AGTGGACTCTTGGCTCCTCA | 158 | +| | CO2_721R | CATGCTGCTGTTCTTGCATT | | +| ELF3 (HORVU.MOREX.r3.1HG0095050) | ELF3_DL_3060_F3 | TGCTGTCCAAGTGTTTGAGC | 242 | + | | Elf3_DL_4483_R3 | CCTGGTTTCCTTCGGTGTTA | | +| FT1 (HORVU.MOREX.r3.7HG0653910) | FT1_1955F | GGTAGACCCAGATGCTCCAA | 120 | +| | FT1_2183R | TCGTAGCACATCACCTCCTG | | +| FT2 (HORVU.MOREX.r3.3HG0244930 | FT2_4031R | TCACATCCTTCTCCCGCCGG | 238 | +| | FT2_3809_F | TACCGAGGTTGTGTGCTACG | | +| FT3 (HORVU.MOREX.r3.1HG0077250) | FT3-1004F | TGTCAGACATCCCTGGAACA | 225 | +| | FT3-1848R | CTGATCCACCTTCCCTTTGA | | +| FT4 (HORVU.MOREX.r3.2HG0117260) | FT4_626F | AAACGATAGCTTTGGAAAAGAGATC | 230 | +| | FT4_2537R | TCCTCCCGCCGGTGCCCGTG | | +| GI (HORVU.MOREX.r3.3HG0238250) | GI_6780F | TCAGTTAGAGCTCCTGGAAGT | 263 | +| | GI_7289R | GGTAGTTTGGGCTTTGGATG | | +| LHY (HORVU.MOREX.r3.7HG0699010) | HvLHY_672F | CCTGGAATTGGAGATGGAGA | 210 | +| | HvLHY_882R | TGAGCATGGCTTCTGATTTG | | +| LUX1 (HORVU.MOREX.r3.3HG0328340) | LUX_1077F | AATTCAGTCCACGGATGCTC | 222 | +| | LUX_1298R | CTTCACTTCAGCTCCCCTTG | | +| LWD1 (HORVU.MOREX.r3.6HG0583670) | LWD1_qPCR-114_F | CAGCTCATAGCCCATGACAA | 114 | +| | LWD1_qPCR-114_R | CTCCTTGTCCCGAAGATCAA | | +| PHYB (HORVU.MOREX.r3.4HG0381880) | HvPHYB-1151F | CTTGCGCACCAACTATCAGA | 232 | +| | HvPHYB-1383R | CTCCATGACACACCGTCAAC | | +| PHYC (HORVU.MOREX.r3.5HG0511090) | PHYC_0986F | ACTACCCGGCAACTGACATC | 142 | +| | PHYC_1127R | GAGCCACAGAGGCTGATAGG | | +| Ppd-H1 (HORVU.MOREX.r3.2HG0107710) | PPD1_2165F | GATGGATTCAAAGGCAAGGA | 172 | +| | PPD1_2336R | GAACAATTGGCTCCTCCAAA | | +| PRR1 (HORVU.MOREX.r3.6HG0595250) | HvPRR1_1056F | GAGCATAGCATGGCACTTCA | 237 | +| | HvPRR1_1292R | TGTCTTTCCTCGGAAATTGG | | +| PRR59 (HORVU.MOREX.r3.4HG0350690) | PRR59_2064_F | GAAATTCCGCATGAAAAGGA | 148 | +| | PRR59_2212_R | TTCCGCATCTTCTGTTGTTG | | +| PRR73 (HORVU.MOREX.r3.5HG0498830) | PRR73_441F | GCGCCGTAGAGAATCAGAAC | 222 | +| | PRR73_662R | CATGTCGGGTACAGTCATCG | | +| PRR95 (HORVU.MOREX.r3.5HG0498830) | PRR95_1467F | CAGAACTCCAGTGTCGCAAA | 251 | +| | PRR95_1717R | TGCTGTTGCCAGAGTTGTTC | | +| VRN1 (HORVU.MOREX.r3.5HG0511210) | HVBM5a_292F | CTGAAGGCGAAGGTTGAGAC | 203 | +| | HVBM5a_494R | TTCTCCTCCTGCAGTGACCT | | \ No newline at end of file diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index f548dc7d17a0a7bf4542ea53826ab90018f90d39..17b1672bef326326666f501b2d21813b2134117b 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/MSA_dissection_eam7/isa.study.xlsx b/studies/MSA_dissection_eam7/isa.study.xlsx index 1f5ffb3ff797d77f319dbcf87753ffe54682818c..75d5da03e0e41e557d4c8cf671e78174c373fb3c 100644 Binary files a/studies/MSA_dissection_eam7/isa.study.xlsx and b/studies/MSA_dissection_eam7/isa.study.xlsx differ diff --git a/studies/allelism_test/isa.study.xlsx b/studies/allelism_test/isa.study.xlsx index afa5fee0d6ec9c6519727dcddb30370aac9060d9..1f3b6b71f9d7abc96a1a60f8ae72a11132baba7d 100644 Binary files a/studies/allelism_test/isa.study.xlsx and b/studies/allelism_test/isa.study.xlsx differ diff --git a/studies/biparental_mapping_eam7/isa.study.xlsx b/studies/biparental_mapping_eam7/isa.study.xlsx index 0fc60fe6079872322bb107531eb520c60f86481d..70a30fce97b9a180e4952afe5a7aa193e736cbf2 100644 Binary files a/studies/biparental_mapping_eam7/isa.study.xlsx and b/studies/biparental_mapping_eam7/isa.study.xlsx differ diff --git a/studies/gene_expression_eam7_plants_development/isa.study.xlsx b/studies/gene_expression_eam7_plants_development/isa.study.xlsx index 55496c492e6f2debcfa908ea533bf8378a46012e..8c133ad03f254ad38af35071060111e6e6d4cdfe 100644 Binary files a/studies/gene_expression_eam7_plants_development/isa.study.xlsx and b/studies/gene_expression_eam7_plants_development/isa.study.xlsx differ diff --git a/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md b/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md index 6ae4939b666963e088ac3369fc81352c98365a83..4a9c375cbe002b3c9e690b8b1c852b10061b8ea5 100644 --- a/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md +++ b/studies/gene_expression_eam7_plants_development/protocols/development_plant_material_growth_conditions.md @@ -18,9 +18,15 @@ Genotypes: - QuickPot E24/10 trays (HerkuPlast Kubern GmbH, pot volume 480 cm^3) - Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) -**Sampling:** +**Leaf sampling for RNA extraction:** + +- place two 3 mm metal beads into 2.0 ml tube +- always sample the youngest, fully elongated leaf (auricles are clearly visible) +- sample three biological replicates for each genotype and time point +- for each biological replicate: pool the leaf from two plants into one tube +- freeze samples directly in liquid nitrogen +- Store samples at -80°C until needed -- always sample youngest, fully elongated leaf - sample at ZT 9 (1h after lights turned off, as FT1 expression is highest) - sample genotypes at 19, 26, 33, 40, 47 and 59 DAE diff --git a/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx b/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx index a063310508b766fbbe3bba86a62a76c9510c8248..d9f14729d51974633b8dbd5075b31a3608f73116 100644 Binary files a/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx and b/studies/gene_expression_eam7_plants_diurnal/isa.study.xlsx differ diff --git a/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md b/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md index 35f54b32799f6174ae8a1f7aa5f9f8fc643975d4..deb2017c7f42ae1b0d0a3c2007a87ecefb2d1d6b 100644 --- a/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md +++ b/studies/gene_expression_eam7_plants_diurnal/protocols/diurnal_plant_material_growth_conditions.md @@ -19,7 +19,17 @@ Genotypes: - Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) -**Sampling:** +**Leaf sampling for RNA extraction:** + +- place two 3 mm metal beads into 2.0 ml tube +- always sample the youngest, fully elongated leaf (auricles are clearly visible) +- sample three biological replicates for each genotype and time point +- for each biological replicate: pool the leaf from two plants into one tube +- freeze samples directly in liquid nitrogen +- Store samples at -80°C until needed + +- sample at ZT 9 (1h after lights turned off, as FT1 expression is highest) +- sample genotypes at 19, 26, 33, 40, 47 and 59 DAE - 2 weeks old plants - youngest, fully elongated leaf: leaf 2 diff --git a/studies/gene_expression_lwd1_mutants_diurnal/README.md b/studies/gene_expression_lwd1_mutants_diurnal/README.md index 860900778e5c515f1f5b594f195bc2195033dffe..7439a5fb3f84781b8eae541522f7d02736c29f83 100644 --- a/studies/gene_expression_lwd1_mutants_diurnal/README.md +++ b/studies/gene_expression_lwd1_mutants_diurnal/README.md @@ -8,7 +8,7 @@ Gene expression of *CO1, ELF3, FT1, LUX1, LWD1, PHYB, PHYC, Ppd-H1*, and *PRR1* ```mermaid flowchart TD; - A[lwd1 mutants and GP-fast] --> |leaf_sampling| B[frozen leaf tissues, 3 biol. replicates] + A[lwd1 mutants and GP-fast] --> |plant growth and leaf sampling| B[frozen leaf tissues, 3 biol. replicates] B --> |RNA_extraction| C[RNA samples] C --> |cDNA_synthesis| D[cDNA samples] D --> |qRT-PCR| E[gene expression data, 2 techn. replicates] diff --git a/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx b/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx index 4d00176afb847ed396a1ff37f9f1c83c1d0c973f..5d57a867c58c4603efcb9b0f195e817e27647268 100644 Binary files a/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx and b/studies/gene_expression_lwd1_mutants_diurnal/isa.study.xlsx differ diff --git a/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md b/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md index d2ab6197d63642e71255be1c19721a509519a235..98ee71e1c2fd3e9d2eddfed4d911de0a7d68c4d9 100644 --- a/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md +++ b/studies/gene_expression_lwd1_mutants_diurnal/protocols/diurnal_plant_material_growth_conditions.md @@ -20,7 +20,17 @@ Genotypes: - Einheitserde ED73 (Einheitserde Werkverband e.V.) with 7% sand and 4 g/L Osmocote Exact Hi.End 3-4M, 4th generation (ICL Group Ltd.) -**Sampling:** +**Leaf sampling for RNA extraction:** + +- place two 3 mm metal beads into 2.0 ml tube +- always sample the youngest, fully elongated leaf (auricles are clearly visible) +- sample three biological replicates for each genotype and time point +- for each biological replicate: pool the leaf from two plants into one tube +- freeze samples directly in liquid nitrogen +- Store samples at -80°C until needed + +- sample at ZT 9 (1h after lights turned off, as FT1 expression is highest) +- sample genotypes at 19, 26, 33, 40, 47 and 59 DAE - 2 weeks old plants - youngest, fully elongated leaf: leaf 2 diff --git a/studies/generating_lwd1_mutants/isa.study.xlsx b/studies/generating_lwd1_mutants/isa.study.xlsx index c94be8f49e715440d9ad6ea1af477a2582fd5967..e5bf3cef8d3d72734f4cc39313d8dc9eba622d97 100644 Binary files a/studies/generating_lwd1_mutants/isa.study.xlsx and b/studies/generating_lwd1_mutants/isa.study.xlsx differ diff --git a/studies/phenotyping_eam7_plants/isa.study.xlsx b/studies/phenotyping_eam7_plants/isa.study.xlsx index 83b719ddecf9aa8711ff4f25c03315e8862453e8..f93130f983861ac646070573e9a56bae84895b6d 100644 Binary files a/studies/phenotyping_eam7_plants/isa.study.xlsx and b/studies/phenotyping_eam7_plants/isa.study.xlsx differ diff --git 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