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