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...@@ -22,7 +22,7 @@ Fungal pathogens depend on sophisticated gene expression programs for s ...@@ -22,7 +22,7 @@ Fungal pathogens depend on sophisticated gene expression programs for s
## Studies ## Studies
The [Studies (S)](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/studies) are named after the names of the chapters in the publication. The [Studies (S)](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/studies) are named after the names of the chapters in the publication.
S1_Loss_of_Khd4_Causes_Defects_in_Polar_Growth_of_Infectious_Hyphae S1_Loss_of_Khd4_Causes_Defects_in_Polar_Growth_of_Infectious_Hyphae
S2_Establishing_HyperTRIBE_for_Fungal_RBPs S2_Establishing_HyperTRIBE_for_Fungal_RBPs
...@@ -34,78 +34,78 @@ S7_Loss_of_Khd4_Causes_Dysregulation_of_Membrane-Trafficking_Factors_in_khd4D_Ce ...@@ -34,78 +34,78 @@ S7_Loss_of_Khd4_Causes_Dysregulation_of_Membrane-Trafficking_Factors_in_khd4D_Ce
S8_Loss_of_Khd4_Causes_Defects_in_Vacuole_Formation_and_Localization S8_Loss_of_Khd4_Causes_Defects_in_Vacuole_Formation_and_Localization
## Assays ## Assays
The [Assays (A)](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays) folder contains the results of the individual experiments. The raw and processed data are stored in the `dataset` folder of the assay and the corresponding protocols are in the `protocol` folder. The [Assays (A)](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays) folder contains the results of the individual experiments. The raw and processed data are stored in the `dataset` folder of the assay and the corresponding protocols are in the `protocol` folder.
### Chapter 1: S1_Loss_of_Khd4_Causes_Defects_in_Polar_Growth_of_Infectious_Hyphae ### Chapter 1: S1_Loss_of_Khd4_Causes_Defects_in_Polar_Growth_of_Infectious_Hyphae
[S1_A1_microscopy_yeast](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S1_A1_microscopy_yeast?ref_type=heads) // **Figure S1** [S1_A1_microscopy_yeast](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S1_A1_microscopy_yeast?ref_type=heads) // **Figure S1**
[S1_A2_microscopy_hyphae](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S1_A2_microscopy_hyphae?ref_type=heads) // **Figure 1** [S1_A2_microscopy_hyphae](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S1_A2_microscopy_hyphae?ref_type=heads) // **Figure 1**
### Chapter 2: S2_Establishing_HyperTRIBE_for_Fungal_RBPs ### Chapter 2: S2_Establishing_HyperTRIBE_for_Fungal_RBPs
[S2_A1_microscopy_Rrm4_Ada_strains_DIC+Rrm4-GFP](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S2_A1_microscopy_Rrm4-Ada_Rrm4-Gfp) // **Figure S2C-F** [S2_A1_microscopy_Rrm4_Ada_strains_DIC+Rrm4-GFP](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S2_A1_microscopy_Rrm4-Ada_Rrm4-Gfp) // **Figure S2C-F**
[S2_A2_protein_expression [S2_A2_protein_expression
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S2_A2_protein_expression) // **Figure S3 A** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S2_A2_protein_expression) // **Figure S3 A**
[S2_A3_microscopy_Rfp_Gfp [S2_A3_microscopy_Rfp_Gfp
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S2_A3_microscopy_Rfp_Gfp) // **Figure S3 B-C** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S2_A3_microscopy_Rfp_Gfp) // **Figure S3 B-C**
[S2_A4_HyperTRIBE_Rrm4_analysis [S2_A4_HyperTRIBE_Rrm4_analysis
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S2_A4_HyperTRIBE_Rrm4_analysis) // **Figure 2C-D, Figure S4** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S2_A4_HyperTRIBE_Rrm4_analysis) // **Figure 2C-D, Figure S4**
[S2_A5_HyperTRIBE_Rrm4_iCLIP [S2_A5_HyperTRIBE_Rrm4_iCLIP
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S2_A5_HyperTRIBE_Rrm4_iCLIP) // **Figure 2C-D, Figure S4** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S2_A5_HyperTRIBE_Rrm4_iCLIP) // **Figure 2C-D, Figure S4**
### Chapter 3: S3_Khd4_Interacts_with_mRNAs_Enriched_for_Its_Binding_Motif_AUACCC ### Chapter 3: S3_Khd4_Interacts_with_mRNAs_Enriched_for_Its_Binding_Motif_AUACCC
[S3_A1_microscopy_Khd4-Gfp [S3_A1_microscopy_Khd4-Gfp
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S3_A1_microscopy_Khd4-Gfp) // **Figure S5 C-E** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S3_A1_microscopy_Khd4-Gfp) // **Figure S5 C-E**
[S3_A2_Khd4-Ada-strains_protein_expression [S3_A2_Khd4-Ada-strains_protein_expression
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S3_A2_Khd4-Ada-strains_protein_expression) // **Figure S5 F-G** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S3_A2_Khd4-Ada-strains_protein_expression) // **Figure S5 F-G**
[S3_A3_HyperTRIBE_Khd4_workflow [S3_A3_HyperTRIBE_Khd4_workflow
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S3_A3_HyperTRIBE_Khd4_workflow) // **Figure 3A, Figure S6A** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S3_A3_HyperTRIBE_Khd4_workflow) // **Figure 3A, Figure S6A**
[S3_A4_HyperTRIBE_motif_analysis [S3_A4_HyperTRIBE_motif_analysis
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S3_A4_HyperTRIBE_motif_analysis) // **Figure S6 B-E, Figure 3, Figure S7, Figure S8 A-D** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S3_A4_HyperTRIBE_motif_analysis) // **Figure S6 B-E, Figure 3, Figure S7, Figure S8 A-D**
[S3_A5_GO-term](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S3_A5_GO-term) // **Figure S8 E, Figure S9** [S3_A5_GO-term](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S3_A5_GO-term) // **Figure S8 E, Figure S9**
### Chapter 4: S4_Loss_of_Khd4_Increases_the_Abundance_of_mRNAs_with_AUACCC_Motif_in_Their_3UTR ### Chapter 4: S4_Loss_of_Khd4_Increases_the_Abundance_of_mRNAs_with_AUACCC_Motif_in_Their_3UTR
[S4_A1_RNAseq_data [S4_A1_RNAseq_data
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S4_A1_RNAseq_data) // **Figure 4 A-C, Fig S10A** ](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S4_A1_RNAseq_data) // **Figure 4 A-C, Fig S10A**
[S4_A2_RNAseq_analysis_khd4D_vs_wt_hyphae](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S4_A2_RNAseq_analysis_khd4D_vs_wt_hyphae) // **Figure 4 A-C, Fig S10A** [S4_A2_RNAseq_analysis_khd4D_vs_wt_hyphae](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S4_A2_RNAseq_analysis_khd4D_vs_wt_hyphae) // **Figure 4 A-C, Fig S10A**
### Chapter 5: S5_AUACCC_in_the_3_UTR_Functions_as_a_Khd4-Dependent_mRNA_Stability_Element ### Chapter 5: S5_AUACCC_in_the_3_UTR_Functions_as_a_Khd4-Dependent_mRNA_Stability_Element
[S5_A1_microscopy_khd4-targets [S5_A1_microscopy_khd4-targets
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S5_A1_microscopy_khd4-targets) // **Figure S10B** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S5_A1_microscopy_khd4-targets) // **Figure S10B**
[S5_A2_Kat_protein_level [S5_A2_Kat_protein_level
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S5_A2_Kat_protein_level?ref_type=heads) // **Figure S10C, Figure 4E** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S5_A2_Kat_protein_level?ref_type=heads) // **Figure S10C, Figure 4E**
[S5_A3_Kat_mRNA_level [S5_A3_Kat_mRNA_level
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S5_A3_Kat_mRNA_level?ref_type=heads) // **Figure 4F** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S5_A3_Kat_mRNA_level?ref_type=heads) // **Figure 4F**
### Chapter 6: S6_Khd4_Tightly_Regulates_the_Expression_of_Distinct_Targets_Involved_in_Membrane_Trafficking ### Chapter 6: S6_Khd4_Tightly_Regulates_the_Expression_of_Distinct_Targets_Involved_in_Membrane_Trafficking
[S6_A1_RNAseq_analysis_yeast_vs_hyphae [S6_A1_RNAseq_analysis_yeast_vs_hyphae
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae) // **Figure 5 A-C, Figure 6, Figure S13 A-B** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae) // **Figure 5 A-C, Figure 6, Figure S13 A-B**
[S6_A2_analysis_specific_targets [S6_A2_analysis_specific_targets
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S6_A2_analysis_specific_targets) // **Figure 5 A-C, Figure S11 B-D** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S6_A2_analysis_specific_targets) // **Figure 5 A-C, Figure S11 B-D**
[S6_A3_Kat-strains_microscopy [S6_A3_Kat-strains_microscopy
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S6_A3_Kat-strains_microscopy) // **Figure 5D, Figure S11 F** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S6_A3_Kat-strains_microscopy) // **Figure 5D, Figure S11 F**
[S6_A4_relative_fluorescence_level [S6_A4_relative_fluorescence_level
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S6_A4_relative_fluorescence_level) // **Figure S11 G** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S6_A4_relative_fluorescence_level) // **Figure S11 G**
### Chapter 7: S7_Loss_of_Khd4_Causes_Dysregulation_of_Membrane-Trafficking_Factors_in_khd4D_Cells ### Chapter 7: S7_Loss_of_Khd4_Causes_Dysregulation_of_Membrane-Trafficking_Factors_in_khd4D_Cells
[S6_A1_RNAseq_analysis_yeast_vs_hyphae [S6_A1_RNAseq_analysis_yeast_vs_hyphae
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae) // **Figure 5 A-C, Figure 6, Figure S13 A-B** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae) // **Figure 5 A-C, Figure 6, Figure S13 A-B**
[S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes [S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes
](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes?ref_type=heads) // **Figure 6, Figure S13 A-B** ](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes?ref_type=heads) // **Figure 6, Figure S13 A-B**
### Chapter 8: S8_Loss_of_Khd4_Causes_Defects_in_Vacuole_Formation_and_Localization ### Chapter 8: S8_Loss_of_Khd4_Causes_Defects_in_Vacuole_Formation_and_Localization
[S8_A1_microscopy_FM4-64](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S8_A1_microscopy_FM4-64?ref_type=heads) // **Figure S13 C-D** [S8_A1_microscopy_FM4-64](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S8_A1_microscopy_FM4-64?ref_type=heads) // **Figure S13 C-D**
[S8_A2_microscopy_CAMG](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S8_A2_microscopy_CMAG?ref_type=heads) // **Figure 7** [S8_A2_microscopy_CAMG](https://git.nfdi4plants.org/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S8_A2_microscopy_CMAG?ref_type=heads) // **Figure 7**
## License ## License
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