From 006845eecc784ea2eac1f3f93d26cdc816995426 Mon Sep 17 00:00:00 2001 From: Sabrina Zander <sabrina.zander@uni-duesseldorf.de> Date: Mon, 10 Mar 2025 08:27:17 +0000 Subject: [PATCH] Update README.md --- README.md | 51 +++++++++++++++++++++++++++------------------------ 1 file changed, 27 insertions(+), 24 deletions(-) diff --git a/README.md b/README.md index 90edd19..6bdfd1a 100644 --- a/README.md +++ b/README.md @@ -38,71 +38,74 @@ The [Assays (A)](https://git.nfdi4plants.org/sankaran/Sankaranarayanan-2023/-/tr ### 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/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** ### 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/sankaran/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/sankaran/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/sankaran/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, Figure S4 A-D +](https://git.nfdi4plants.org/sankaran/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 2D, Figure S4 E-G +](https://git.nfdi4plants.org/sankaran/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/sankaran/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/sankaran/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/sankaran/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/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** ### 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 +](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** ### 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/sankaran/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/sankaran/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/sankaran/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/sankaran/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 11 B-D +](https://git.nfdi4plants.org/sankaran/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/sankaran/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/sankaran/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 -see S6_A1 and S6_A2 +[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** +[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** ### 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/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** ## License -- GitLab