diff --git a/README.md b/README.md index 7aa50083dc0a14d460be92208febe37d6635e885..5a9ec10b82f1adb60640886e4dab2f5a260b3a32 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ Fungal pathogens depend on sophisticated gene expression programs for s ## 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 S2_Establishing_HyperTRIBE_for_Fungal_RBPs @@ -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 ## 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 -[S1_A1_microscopy_yeast](https://git.nfdi4plants.org/sankaran/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_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/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S1_A2_microscopy_hyphae?ref_type=heads) // **Figure 1** ### 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 -](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 -](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 -](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 -](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 [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 -](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 -](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 -](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** -[S3_A5_GO-term](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S3_A5_GO-term) // **Figure S8 E, Figure S9** +](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/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 [S4_A1_RNAseq_data ](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 [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 -](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 -](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 [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 -](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 -](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 -](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 [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 -](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 -[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_A2_microscopy_CAMG](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tree/master/assays/S8_A2_microscopy_CMAG?ref_type=heads) // **Figure 7** +[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/sfb1535_mibinet/Sankaranarayanan-2023/-/tree/master/assays/S8_A2_microscopy_CMAG?ref_type=heads) // **Figure 7** ## License