diff --git a/assays/S10_A1_microscopy_FM4-64/isa.assay.xlsx b/assays/S10_A1_microscopy_FM4-64/isa.assay.xlsx index 5583f108b2734abd0de67987c81480d0b87d745b..9b1bc432d28318f3ae8857c967c27108607d9ba6 100644 Binary files a/assays/S10_A1_microscopy_FM4-64/isa.assay.xlsx and b/assays/S10_A1_microscopy_FM4-64/isa.assay.xlsx differ diff --git a/assays/S10_A2_microscopy_CMAG/isa.assay.xlsx b/assays/S10_A2_microscopy_CMAG/isa.assay.xlsx index 564557295abf952ee75dfa027d8f8d3f5fb2fc88..cc2273df208160251e40478d347899acc45010c6 100644 Binary files a/assays/S10_A2_microscopy_CMAG/isa.assay.xlsx and b/assays/S10_A2_microscopy_CMAG/isa.assay.xlsx differ diff --git a/assays/S1_A1_microscopy_yeast/isa.assay.xlsx b/assays/S1_A1_microscopy_yeast/isa.assay.xlsx index 6c15267cc26e2fdda14c4695f9cf4d7abff4c370..58eb6f8885e004369b25c71d7c54cf063e64b2e1 100644 Binary files a/assays/S1_A1_microscopy_yeast/isa.assay.xlsx and b/assays/S1_A1_microscopy_yeast/isa.assay.xlsx differ diff --git a/assays/S1_A1_microscopy_yeast/protocols/Growth_condition.md b/assays/S1_A1_microscopy_yeast/protocols/Growth_condition.md new file mode 100644 index 0000000000000000000000000000000000000000..43e8ead611ae953f66611a0c227e93a6e17c4e09 --- /dev/null +++ b/assays/S1_A1_microscopy_yeast/protocols/Growth_condition.md @@ -0,0 +1 @@ +For microscopic analysis, 20 ml of yeast cells were grown in CM medium (1% glucose) to an OD600 of 0.5 \ No newline at end of file diff --git a/assays/S1_A1_microscopy_yeast/protocols/microscopy.md b/assays/S1_A1_microscopy_yeast/protocols/microscopy.md new file mode 100644 index 0000000000000000000000000000000000000000..afb7ca6f2c06e77bdfdf911a6641e070a7d1e585 --- /dev/null +++ b/assays/S1_A1_microscopy_yeast/protocols/microscopy.md @@ -0,0 +1 @@ +All images were acquired using laser-based epifluorescence-microscopy, Zeiss Axio Observer.Z1 (Oberkochen, Germany) and processed using the MetaMorph software package (version 7.7.0.0, Molecular Devices, Seattle, IL, USA). \ No newline at end of file diff --git a/assays/S1_A2_microscopy_hyphae/isa.assay.xlsx b/assays/S1_A2_microscopy_hyphae/isa.assay.xlsx index 9630004b2ca6b3fe1d6a6538f803d297ecb97e69..c6b6227f3a83d2daf957c4f1f0c8f641657b2453 100644 Binary files a/assays/S1_A2_microscopy_hyphae/isa.assay.xlsx and b/assays/S1_A2_microscopy_hyphae/isa.assay.xlsx differ diff --git a/assays/S1_A2_microscopy_hyphae/protocols/Growth_condition.md b/assays/S1_A2_microscopy_hyphae/protocols/Growth_condition.md new file mode 100644 index 0000000000000000000000000000000000000000..0862226d01f590fcdb1feffb193c89daa5bf0720 --- /dev/null +++ b/assays/S1_A2_microscopy_hyphae/protocols/Growth_condition.md @@ -0,0 +1 @@ +For microscopic analysis, 20 ml of yeast cells were grown in CM medium (1% glucose) to an OD600 of 0.5 Hyphal cells were induced by shifting 20 ml cell culture from CM medium to NM medium (supplemented either with 1% glucose or 1% arabinose) for 6, 9, 10, and 12 hours. \ No newline at end of file diff --git a/assays/S1_A2_microscopy_hyphae/protocols/microscopy.md b/assays/S1_A2_microscopy_hyphae/protocols/microscopy.md new file mode 100644 index 0000000000000000000000000000000000000000..60c61f48ccacc67f96aa2c5046127e25e236050c --- /dev/null +++ b/assays/S1_A2_microscopy_hyphae/protocols/microscopy.md @@ -0,0 +1,2 @@ +All images were acquired using laser-based epifluorescence-microscopy, Zeiss Axio Observer.Z1 (Oberkochen, Germany) and processed using the MetaMorph software package (version 7.7.0.0, Molecular Devices, Seattle, IL, USA). +The hyphal length was determined by measuring the distance between the tip and the basal pole without including the empty sections. Hyphal width was calculated by taking the average thickness measured at three different locations within each hypha. \ No newline at end of file diff --git a/assays/S2_A1_microscopy_DIC/isa.assay.xlsx b/assays/S2_A1_microscopy_DIC/isa.assay.xlsx index 95fcc072c787451ea7cccfff5b6214e741e43940..dff85e8672f5921b5967395a2741d781a6f89fa9 100644 Binary files a/assays/S2_A1_microscopy_DIC/isa.assay.xlsx and b/assays/S2_A1_microscopy_DIC/isa.assay.xlsx differ diff --git a/assays/S2_A2_microscopy_Rrm4-Gfp/isa.assay.xlsx b/assays/S2_A2_microscopy_Rrm4-Gfp/isa.assay.xlsx index 1c77c3a7e84eea8d547275a2529664de2ca8f97a..b7546684d40992209835340c2280452c30c69ec4 100644 Binary files a/assays/S2_A2_microscopy_Rrm4-Gfp/isa.assay.xlsx and b/assays/S2_A2_microscopy_Rrm4-Gfp/isa.assay.xlsx differ diff --git a/assays/S2_A3_protein_expression/isa.assay.xlsx b/assays/S2_A3_protein_expression/isa.assay.xlsx index b866f190c3104e68d6d689c6f5782b9fe40fa876..8b9402c72452ef9552af0b3ca69d3cfbc143fb47 100644 Binary files a/assays/S2_A3_protein_expression/isa.assay.xlsx and b/assays/S2_A3_protein_expression/isa.assay.xlsx differ diff --git a/assays/S2_A4_microscopy_Rfp_Gfp/isa.assay.xlsx b/assays/S2_A4_microscopy_Rfp_Gfp/isa.assay.xlsx index d51d820b1824f271507c4c27077639a97f119de7..4cea5094e5cea47978188b5deee2220eea31c4b5 100644 Binary files a/assays/S2_A4_microscopy_Rfp_Gfp/isa.assay.xlsx and b/assays/S2_A4_microscopy_Rfp_Gfp/isa.assay.xlsx differ diff --git a/assays/S3_A1_HyperTRIBE_Rrm4_workflow/isa.assay.xlsx b/assays/S3_A1_HyperTRIBE_Rrm4_workflow/isa.assay.xlsx index 8cf4df516d278f09561560ae95c8a4ce27f7c079..7878e85917b1d0cf2dc4935b1274bf5111743219 100644 Binary files a/assays/S3_A1_HyperTRIBE_Rrm4_workflow/isa.assay.xlsx and b/assays/S3_A1_HyperTRIBE_Rrm4_workflow/isa.assay.xlsx differ diff --git a/assays/S3_A2_HyperTRIBE_Rrm4_analysis/isa.assay.xlsx b/assays/S3_A2_HyperTRIBE_Rrm4_analysis/isa.assay.xlsx index 5c96245dfe6c2e01e51436c6bac60c9ac5a34782..14d907a4fcb6d47a9099c28f8004d88746037462 100644 Binary files a/assays/S3_A2_HyperTRIBE_Rrm4_analysis/isa.assay.xlsx and b/assays/S3_A2_HyperTRIBE_Rrm4_analysis/isa.assay.xlsx differ diff --git a/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/isa.assay.xlsx b/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/isa.assay.xlsx index dd7e41f2c83873f345c839221a97b32e2421dd59..61e58e4e367aeba21c3783c02cd54dff69d02346 100644 Binary files a/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/isa.assay.xlsx and b/assays/S3_A3_HyperTRIBE_Rrm4_iCLIP/isa.assay.xlsx differ diff --git a/assays/S4_A1_microscopy_DIC_Gfp/isa.assay.xlsx b/assays/S4_A1_microscopy_DIC_Gfp/isa.assay.xlsx index 86628fdd2495ec00328a733e5b1e4fe91895aa14..7a502c264298a61588d5f9ea6eb391482c9e58b2 100644 Binary files a/assays/S4_A1_microscopy_DIC_Gfp/isa.assay.xlsx and b/assays/S4_A1_microscopy_DIC_Gfp/isa.assay.xlsx differ diff --git a/assays/S4_A2_protein_expression/isa.assay.xlsx b/assays/S4_A2_protein_expression/isa.assay.xlsx index 2241d81a16f281889c0c42cd67693c3a30116996..1a843e417b05c8c00befd30f752405068164f993 100644 Binary files a/assays/S4_A2_protein_expression/isa.assay.xlsx and b/assays/S4_A2_protein_expression/isa.assay.xlsx differ diff --git a/assays/S5_A1_HyperTRIBE_Khd4_workflow/isa.assay.xlsx b/assays/S5_A1_HyperTRIBE_Khd4_workflow/isa.assay.xlsx index 3521eec23bb2dce4fbc074ee5a14909166b12069..23ac52d656e6ca88e4f16d77b0abd2f36c8401ea 100644 Binary files a/assays/S5_A1_HyperTRIBE_Khd4_workflow/isa.assay.xlsx and b/assays/S5_A1_HyperTRIBE_Khd4_workflow/isa.assay.xlsx differ diff --git a/assays/S5_A2_HyperTRIBE_motif_analysis/isa.assay.xlsx b/assays/S5_A2_HyperTRIBE_motif_analysis/isa.assay.xlsx index 5c18aa6dd9bff01c8efb705738d53fd7c207c8df..cc6aa3f7d1cbe837e884ebb24b0d90eddb30823b 100644 Binary files a/assays/S5_A2_HyperTRIBE_motif_analysis/isa.assay.xlsx and b/assays/S5_A2_HyperTRIBE_motif_analysis/isa.assay.xlsx differ diff --git a/assays/S5_A3_GO-term/isa.assay.xlsx b/assays/S5_A3_GO-term/isa.assay.xlsx index 32ab492c7372afca334e61b339bade348ec80c1e..3d8e665c492589c4d5a2a60e777ea3e22c73e466 100644 Binary files a/assays/S5_A3_GO-term/isa.assay.xlsx and b/assays/S5_A3_GO-term/isa.assay.xlsx differ diff --git a/assays/S6_A1_RNAseq_data/isa.assay.xlsx b/assays/S6_A1_RNAseq_data/isa.assay.xlsx index 26a81d285865c3f2a2b2349dbe00fd065a9cc773..fc66a729a17e6bfc62447ac904a42d8de88036dd 100644 Binary files a/assays/S6_A1_RNAseq_data/isa.assay.xlsx and b/assays/S6_A1_RNAseq_data/isa.assay.xlsx differ diff --git a/assays/S6_A3_RNAseq_analysis_yeast_vs_hyphae/isa.assay.xlsx b/assays/S6_A3_RNAseq_analysis_yeast_vs_hyphae/isa.assay.xlsx index e98a5e4acf5b65996c00e8bddee2f3c89dc426ed..b580dd4344d4e098e6ed31ccb065861cfd6ac1f4 100644 Binary files a/assays/S6_A3_RNAseq_analysis_yeast_vs_hyphae/isa.assay.xlsx and b/assays/S6_A3_RNAseq_analysis_yeast_vs_hyphae/isa.assay.xlsx differ diff --git a/assays/S6_A4_analysis_specific_targets/isa.assay.xlsx b/assays/S6_A4_analysis_specific_targets/isa.assay.xlsx index 0134a6253a0723ad51bfe1cb86c4b33092d9ea55..01411e9b70f81c655a66e784884861d8e3796baf 100644 Binary files a/assays/S6_A4_analysis_specific_targets/isa.assay.xlsx and b/assays/S6_A4_analysis_specific_targets/isa.assay.xlsx differ diff --git a/assays/S6_RNAseq_analysis_khd4D_vs_wt_hyphae/isa.assay.xlsx b/assays/S6_RNAseq_analysis_khd4D_vs_wt_hyphae/isa.assay.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..b29d16640ed9f81f2d9626184ff1456fb4f73316 Binary files /dev/null and b/assays/S6_RNAseq_analysis_khd4D_vs_wt_hyphae/isa.assay.xlsx differ diff --git a/assays/S7_A1_microscopy/isa.assay.xlsx b/assays/S7_A1_microscopy/isa.assay.xlsx index d8af93ad99f1f80445c1da406dbf099eec2b0ed9..74d64fcfa09884cae09240a3e6733e25e57f9c79 100644 Binary files a/assays/S7_A1_microscopy/isa.assay.xlsx and b/assays/S7_A1_microscopy/isa.assay.xlsx differ diff --git a/assays/S7_A2_Kat_protein_level/isa.assay.xlsx b/assays/S7_A2_Kat_protein_level/isa.assay.xlsx index f5582da59b9ebd91d22495e7908e8bf7eab3c2f1..ad5d45abf8b31ba4ba7c34ea665fdcceb0714fc8 100644 Binary files a/assays/S7_A2_Kat_protein_level/isa.assay.xlsx and b/assays/S7_A2_Kat_protein_level/isa.assay.xlsx differ diff --git a/assays/S7_A3_Kat_mRNA_level/isa.assay.xlsx b/assays/S7_A3_Kat_mRNA_level/isa.assay.xlsx index 11900f296e787b739c0fedebe36eaf63e4631abe..f37832ab8c29e5e3f8dbfe5c82e73af9878ffece 100644 Binary files a/assays/S7_A3_Kat_mRNA_level/isa.assay.xlsx and b/assays/S7_A3_Kat_mRNA_level/isa.assay.xlsx differ diff --git a/assays/S8_A1_microscopy/isa.assay.xlsx b/assays/S8_A1_microscopy/isa.assay.xlsx index 8f1f162352b22d791c7b0d4e14d9749d7254ce9d..cfee95c266daee817e3851a4ebfaeab48f7feb4c 100644 Binary files a/assays/S8_A1_microscopy/isa.assay.xlsx and b/assays/S8_A1_microscopy/isa.assay.xlsx differ diff --git a/assays/S8_A2_relative_fluorescence_level/isa.assay.xlsx b/assays/S8_A2_relative_fluorescence_level/isa.assay.xlsx index c5d1ca7fe630ed1cd0240df92d62467f01aa5f5d..9713d55d00fce86a34e4baa7de16cd43ed8a77fd 100644 Binary files a/assays/S8_A2_relative_fluorescence_level/isa.assay.xlsx and b/assays/S8_A2_relative_fluorescence_level/isa.assay.xlsx differ diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 77f33c560f59e17be5b9805757b83ae1fce3fd52..0a4e38e7491fd9ee4915e111a6bfd3bbdee9b612 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/S10_membrane_trafficking/isa.study.xlsx b/studies/S10_membrane_trafficking/isa.study.xlsx index 88a03cea0dcb7c9a0dcc46032ed850c251c089de..5f9a9f180351650462f4a39f1d3ef08bbd0da8f8 100644 Binary files a/studies/S10_membrane_trafficking/isa.study.xlsx and b/studies/S10_membrane_trafficking/isa.study.xlsx differ diff --git a/studies/S1_characterization_khd4D/isa.study.xlsx b/studies/S1_characterization_khd4D/isa.study.xlsx index ef6ae532c3514b992ab10fc86f60f05faac44920..20ffcc7d5d56a303314004d850963c23d5b382be 100644 Binary files a/studies/S1_characterization_khd4D/isa.study.xlsx and b/studies/S1_characterization_khd4D/isa.study.xlsx differ diff --git a/studies/S2_characterization_HyperTRIBE_Rrm4_constructs/isa.study.xlsx b/studies/S2_characterization_HyperTRIBE_Rrm4_constructs/isa.study.xlsx index 679806ecb03173b0bd9ab8e83db2dc6940168edf..efc129cad32a7b060fb2db637b293e044f314ff3 100644 Binary files a/studies/S2_characterization_HyperTRIBE_Rrm4_constructs/isa.study.xlsx and b/studies/S2_characterization_HyperTRIBE_Rrm4_constructs/isa.study.xlsx differ diff --git a/studies/S3_HyperTRIBE_Rrm4/isa.study.xlsx b/studies/S3_HyperTRIBE_Rrm4/isa.study.xlsx index d6fb6be57b6a1de84a9f477cd74ed12bfb31cfa8..d7b184394944957d506903292ddf73aa4d77bd2b 100644 Binary files a/studies/S3_HyperTRIBE_Rrm4/isa.study.xlsx and b/studies/S3_HyperTRIBE_Rrm4/isa.study.xlsx differ diff --git a/studies/S4_characterization_HyperTRIBE_Khd4_constructs/isa.study.xlsx b/studies/S4_characterization_HyperTRIBE_Khd4_constructs/isa.study.xlsx index 3eabcde9e9036adcc73d0a5fd25b3e3937a4c991..3deeab54a15dcc7d518d48b95b8d973d11252c14 100644 Binary files a/studies/S4_characterization_HyperTRIBE_Khd4_constructs/isa.study.xlsx and b/studies/S4_characterization_HyperTRIBE_Khd4_constructs/isa.study.xlsx differ diff --git a/studies/S5_HyperTRIBE_Khd4/isa.study.xlsx b/studies/S5_HyperTRIBE_Khd4/isa.study.xlsx index 90f6a3c01a4f7e3d73a76086739ea5569c6d840b..46585fa76f7662ac04abbc4044bc918c1be46f4e 100644 Binary files a/studies/S5_HyperTRIBE_Khd4/isa.study.xlsx and b/studies/S5_HyperTRIBE_Khd4/isa.study.xlsx differ diff --git a/studies/S6_RNAseq/isa.study.xlsx b/studies/S6_RNAseq/isa.study.xlsx index b745f0f07225277fd22109f7160c3692593f1760..782593f8f2db9b589eede20f7e92a56db49ba866 100644 Binary files a/studies/S6_RNAseq/isa.study.xlsx and b/studies/S6_RNAseq/isa.study.xlsx differ diff --git a/studies/S7_Kat_motif_strains/isa.study.xlsx b/studies/S7_Kat_motif_strains/isa.study.xlsx index f8bc1f1f314676f03f1f6849529967d8f8fc94ea..055bafc29513dba808e2652dc9d9d82476dc2119 100644 Binary files a/studies/S7_Kat_motif_strains/isa.study.xlsx and b/studies/S7_Kat_motif_strains/isa.study.xlsx differ diff --git a/studies/S8_Kat-target_strains/isa.study.xlsx b/studies/S8_Kat-target_strains/isa.study.xlsx index 782b83ef5e0ba73b6dee57230ff8bdfef970c212..b24e1097ae6264cca06b907652fab84b9a94175e 100644 Binary files a/studies/S8_Kat-target_strains/isa.study.xlsx and b/studies/S8_Kat-target_strains/isa.study.xlsx differ diff --git a/studies/S9_modelling/isa.study.xlsx b/studies/S9_modelling/isa.study.xlsx index 2160221e7335769918333c26a04b7097381c5c80..ba2646f1cfeffe9bfe652d723029778f241ce4ac 100644 Binary files a/studies/S9_modelling/isa.study.xlsx and b/studies/S9_modelling/isa.study.xlsx differ