From 13ff446d3ca7d60c79368b50b20d01c26190daa4 Mon Sep 17 00:00:00 2001
From: Srimeenakshi Sankaranarayanan <sankaran@hhu.de>
Date: Thu, 6 Mar 2025 16:08:56 +0100
Subject: [PATCH] Made a new assay for S7 and cleaned up the S6 assay folder
---
.gitattributes | 1 +
.../README.md | 0
.../dataset/.gitkeep | 0
.../Khd4D_hyphae_Goterm.pdf | Bin
...phae_specific_goterm_cytoscape_network.cys | Bin
...Khd4D_hyphae_specific_goterm_gprofiler.txt | 0
.../wt_hyphae_network.pdf | Bin
...phae_specific_goterm_cytoscape_network.cys | Bin
.../wt_hyphae_specific_goterm_gProfiler.txt | 0
...s increased expression in khd4D hyphae.Rmd | 207 +++---------------
...-increased-expression-in-khd4D-hyphae.html | 3 +
.../isa.assay.xlsx | Bin 0 -> 6931 bytes
.../protocols/.gitkeep | 0
13 files changed, 40 insertions(+), 171 deletions(-)
create mode 100644 assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/README.md
create mode 100644 assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/.gitkeep
rename assays/{S6_A1_RNAseq_analysis_yeast_vs_hyphae => S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes}/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_Goterm.pdf (100%)
rename assays/{S6_A1_RNAseq_analysis_yeast_vs_hyphae => S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes}/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_cytoscape_network.cys (100%)
rename assays/{S6_A1_RNAseq_analysis_yeast_vs_hyphae => S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes}/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_gprofiler.txt (100%)
rename assays/{S6_A1_RNAseq_analysis_yeast_vs_hyphae => S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes}/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_network.pdf (100%)
rename assays/{S6_A1_RNAseq_analysis_yeast_vs_hyphae => S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes}/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_cytoscape_network.cys (100%)
rename assays/{S6_A1_RNAseq_analysis_yeast_vs_hyphae => S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes}/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_gProfiler.txt (100%)
rename assays/{S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/Differential_gene_expression_analysis => S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset}/Membrane traffikcing pathways shows increased expression in khd4D hyphae.Rmd (56%)
create mode 100644 assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane-traffikcing-pathways-shows-increased-expression-in-khd4D-hyphae.html
create mode 100644 assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/isa.assay.xlsx
create mode 100644 assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/protocols/.gitkeep
diff --git a/.gitattributes b/.gitattributes
index cbc2434..38136ae 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -2900,3 +2900,4 @@ assays/S7_A1_microscopy/dataset/Microscopic_images_shown_in_the_manuscript/Glu/3
assays/S7_A1_microscopy/dataset/Microscopic_images_shown_in_the_manuscript/Glu/3141/Laser561-2.tif filter=lfs diff=lfs merge=lfs -text
assays/S7_A1_microscopy/dataset/Microscopic_images_shown_in_the_manuscript/Glu/3238/Laser561-1.tif filter=lfs diff=lfs merge=lfs -text
assays/S7_A1_microscopy/dataset/Microscopic_images_shown_in_the_manuscript/Glu/3239/Laser561-7.tif filter=lfs diff=lfs merge=lfs -text
+assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane-traffikcing-pathways-shows-increased-expression-in-khd4D-hyphae.html filter=lfs diff=lfs merge=lfs -text
diff --git a/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/README.md b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/.gitkeep b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_Goterm.pdf b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_Goterm.pdf
similarity index 100%
rename from assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_Goterm.pdf
rename to assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_Goterm.pdf
diff --git a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_cytoscape_network.cys b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_cytoscape_network.cys
similarity index 100%
rename from assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_cytoscape_network.cys
rename to assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_cytoscape_network.cys
diff --git a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_gprofiler.txt b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_gprofiler.txt
similarity index 100%
rename from assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_gprofiler.txt
rename to assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/khd4D_hyphae_specific_targets/Khd4D_hyphae_specific_goterm_gprofiler.txt
diff --git a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_network.pdf b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_network.pdf
similarity index 100%
rename from assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_network.pdf
rename to assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_network.pdf
diff --git a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_cytoscape_network.cys b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_cytoscape_network.cys
similarity index 100%
rename from assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_cytoscape_network.cys
rename to assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_cytoscape_network.cys
diff --git a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_gProfiler.txt b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_gProfiler.txt
similarity index 100%
rename from assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_gProfiler.txt
rename to assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/GO_term_analysis/wt_hyphae_specific_targets/wt_hyphae_specific_goterm_gProfiler.txt
diff --git a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/Differential_gene_expression_analysis/Membrane traffikcing pathways shows increased expression in khd4D hyphae.Rmd b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane traffikcing pathways shows increased expression in khd4D hyphae.Rmd
similarity index 56%
rename from assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/Differential_gene_expression_analysis/Membrane traffikcing pathways shows increased expression in khd4D hyphae.Rmd
rename to assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane traffikcing pathways shows increased expression in khd4D hyphae.Rmd
index 2584531..9d098bd 100644
--- a/assays/S6_A1_RNAseq_analysis_yeast_vs_hyphae/dataset/Differential_gene_expression_analysis/Membrane traffikcing pathways shows increased expression in khd4D hyphae.Rmd
+++ b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane traffikcing pathways shows increased expression in khd4D hyphae.Rmd
@@ -2,7 +2,11 @@
title: "khd4D hyphae specific genes"
author: "Srimeenakshi Sankaranarayanan"
date: '2022-10-11'
-output: html_document
+output:
+ html_document:
+ toc: yes
+ toc_float:
+ collapsed: true
---
```{r setup, include=FALSE}
@@ -34,12 +38,12 @@ library(gprofiler2)
library(tidyr)
library(stats)
library(ggSankeyGrad)
+library(ggalluvial)
```
-## Import the theme for the paper
-
```{r theme, message=FALSE, warning=FALSE}
+## Import the theme for the paper
#theme from Kathi
myTheme1 <- theme_bw() +
theme(axis.text = element_text(size = 8, colour="black"),
@@ -68,6 +72,7 @@ myTheme2 <- theme_bw() +
```
+This report includes analaysis comparing the genes that are differentially expressed during hyphae formation in Wt and khd4D cells. To test this, we will use the DESEq2 analysis comparing hyphae transcriptome to the yeast transcriptome (hyphae vs. yeast) in Wt and Khd4D cells.
## Import the hyphal specific data sets
@@ -83,8 +88,7 @@ kD_FivsYe = readRDS("C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/DGE-bioinfo
```
-
-## Take only genes that are differentially expressed
+Here, only the regulated genes are considered for the analysis.
```{r}
@@ -142,97 +146,10 @@ sp1new
```
-## compare geneIDs that are DEGs
-
-```{r}
-
-# make Df only with DEGs
-wt_yevFi.dg = wt_yevFi.BM %>% filter(grepl('up|down', up_down))
-
-kD_yevFi.dg = kD_FivsYe.BM %>% filter(grepl('up|down', up_down))
-
-# make geneiD column
-wt_yevFi.dg = tibble::rownames_to_column(wt_yevFi.dg, "GeneID")
-
-kD_yevFi.dg = tibble::rownames_to_column(kD_yevFi.dg, "GeneID")
-
-venn.list=list(wt=wt_yevFi.dg$GeneID,kD=kD_yevFi.dg$GeneID)
-
-#make venndiagram
-veNn1 = ggvenn(venn.list,c("wt", "kD"), fill_color = c("gray32", "dodgerblue4")) +
- ggtitle("Overlap between DEGs in wt and khd4D hyphae")+
- myTheme1
-veNn1
-
-#separate unique genes in wt and kD
-wtvsKd= list(
- wt.unique = wt_yevFi.dg$GeneID[wt_yevFi.dg$GeneID %in% setdiff(wt_yevFi.dg$GeneID, kD_yevFi.dg$GeneID)],
- kD.unique = kD_yevFi.dg$GeneID[kD_yevFi.dg$GeneID %in% setdiff(kD_yevFi.dg$GeneID, wt_yevFi.dg$GeneID)]
-)
-
-
-wt.uni=as.data.frame(wtvsKd$wt.unique)
-
-kd.uni=as.data.frame(wtvsKd$kD.unique)
-
-
-# select only upregulated genes
-sel.upWt= as.vector(wt_yevFi.dg$GeneID %in% wt.uni$`wtvsKd$wt.unique`)
-
-table(sel.upWt)
-
-up.wt.uni=subset(wt_yevFi.dg, sel.upWt)
-up.wt.hyphae=subset(up.wt.uni, up_down== "up")
+## Compare gene expression changes between Wt and khd4D cells during hyphae formation
-
-# for Khd4 select only upregulated genes
-sel.upKd= as.vector(kD_yevFi.dg$GeneID %in% kd.uni$`wtvsKd$kD.unique`)
-
-table(sel.upKd)
-
-up.kD.uni=subset(kD_yevFi.dg, sel.upKd)
-
-up.kD.hyphae=subset(up.kD.uni, up_down== "up")
-
-#volcano plot
-#wildtype
-wt.uni$l2F=lookup(wt.uni$`wtvsKd$wt.unique`, wt_yevFi.dg$GeneID, wt_yevFi.dg$log2FoldChange )
-wt.uni$pval=lookup(wt.uni$`wtvsKd$wt.unique`, wt_yevFi.dg$GeneID, wt_yevFi.dg$padj )
-
-#khd4D
-kd.uni$l2F=lookup(kd.uni$`wtvsKd$kD.unique`, kD_yevFi.dg$GeneID, kD_yevFi.dg$log2FoldChange)
-kd.uni$pval=lookup(kd.uni$`wtvsKd$kD.unique`, kD_yevFi.dg$GeneID, kD_yevFi.dg$padj)
-
-#ggplot volcano wt
-wtL2F=ggplot(wt.uni,aes(x=wt.uni$l2F, y=-log10(wt.uni$pval)))+
- geom_point(size=2,colour="darkgrey")+
- coord_cartesian(ylim=c(0,50), xlim=c(-4,4))+
- scale_x_continuous(breaks=seq(-4,4, 2))+
- stat_quadrant_counts(size=8)+
- myTheme1
-
-#ggplot volcano kD
-kDL2F=ggplot(kd.uni,aes(x=kd.uni$l2F, y=-log10(kd.uni$pval)))+
- geom_point(size=2,colour="darkgrey")+
- coord_cartesian(ylim=c(0,50), xlim=c(-4,4))+
- scale_x_continuous(breaks=seq(-4,4, 2))+
- stat_quadrant_counts(size=8)+
- myTheme1
-
-figEV6IJ<-ggarrange(wtL2F, kDL2F,
- labels = c("A", "B"),
- ncol = 2, nrow = 1)
-
-
-figEV6IJ
-
-#ggsave(figEV6IJ, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/TRIBE_data/Editing_events_all/Khd4/bedgraphs", filename="figEV6IJ.pdf", height=10, width=15, unit="cm")
-```
-
-
-# Alluvial plot
-```{r, Alluvial plot}
+```{r}
#wt_hyphae specific
#wt_yevFi.BM
#kD_hyphae specific
@@ -260,53 +177,34 @@ df.allu=genes_all[,c(2,3)]
dat.allu=as.data.frame(table(melt(df.allu))) # dataframe alluvial
+```
-# alluvial plot
-#p=ggplot(dat.allu, aes(y=Freq, axis1=wt, axis2=kd)) +
- #geom_alluvium(aes(fill=wt, fill=kd, width = 1/12)) +
- #scale_fill_manual(values = c("up" = "#104E8B", "down" = "#68838B", "not" = "#BEBEBE")) +
- #geom_stratum(width = 1/12, fill = "black", color = "grey") +
- #geom_label(stat = "stratum", aes(label = after_stat(stratum)))+
- #myTheme1
-# lets try a different package.
-library(ggSankeyGrad)
+```{r Alluvial plot}
+
+kD_lo.ga = ggplot(dat.allu, aes(y = Freq, axis1 = factor(wt, levels=c("up", "not", "down")), axis2 = factor(kd, levels=c("up", "not", "down")))) +
+ geom_alluvium(aes(fill = wt), width = 1/24) +
+ scale_fill_manual(values = c("up" = "#104E8B", "down" = "#68838B", "not" = "#BEBEBE")) +
+ geom_stratum(width = 1/24, color = "grey") +
+ geom_label(stat = "stratum", aes(label = after_stat(stratum))) +
+ myTheme1
-dat.allu$col2=c("#68838B",
-"#BEBEBE",
-"#104E8B",
-"#68838B",
-"#BEBEBE",
-"#104E8B",
-"#68838B",
-"#BEBEBE",
-"#104E8B"
-)
-
-dat.allu$col1=c("#68838B",
-"#68838B",
-"#68838B",
-"#BEBEBE",
-"#BEBEBE",
-"#BEBEBE",
-"#104E8B",
-"#104E8B",
-"#104E8B"
-)
-
-kD_lo.ga=with(dat.allu, ggSankeyGrad(c1=wt,
- c2=kd,
- col1=col1,
- col2=col2,
- values = Freq,
- label=TRUE))+myTheme1# please check the colour pattern
kD_lo.ga
+
+
#ggsave(kD_lo.ga, path="C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/DGE-bioinfofolder/20220919_yeastvhyphae/ggplots", filename="kD_lo.ga_sanskeyplot_new1.pdf", width=10, height = 5, dpi = 300,unit="cm")
```
+## Gene Ontology term analysis
+
+Next, the GO terms enriched in genes specifically upregulated in either WT or khd4Δ cells during hyphae formation were analyzed to identify the biological processes underlying the phenotype.
+
-```{r, Alluvial plot}
+### Genes upregulated only in Wt hyphae
+
+
+```{r, Go analysis Wt}
#gprofiler
kD_upuni=df.allu[df.allu$wt== "not" & df.allu$kd== "up", ]
kD_upuni$gene.id=rownames(kD_upuni)
@@ -326,15 +224,18 @@ Go_wtupuni= gost(query = goWt$gene.id,
#visualization
vis.wtgO<- gostplot(Go_wtupuni, capped = TRUE, interactive = TRUE)
vis.wtgO
+```
+### Genes upregulated only in Wt hyphae
+```{r, Go analysis KD}
Go_kdupuni= gost(query = goKD$gene.id,
organism = "umaydis", ordered_query = FALSE,
multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
measure_underrepresentation = FALSE, evcodes = TRUE,
user_threshold = 0.05, correction_method = "g_SCS",
domain_scope = "known", custom_bg = NULL,
- numeric_ns = "", sources = NULL, as_short_link = TRUE)
+ numeric_ns = "", sources = NULL, as_short_link = FALSE)
#visualization
vis.kDgO<- gostplot(Go_kdupuni, capped = TRUE, interactive = TRUE)
@@ -344,45 +245,9 @@ vis.kDgO
```
-To find genes that goes down or yeast specific unique to wt and khd4D cells
-
```{r}
-
-wt_downuni=df.allu[df.allu$wt== "down" & df.allu$kd== "not", ]
-wt_downuni$gene.id=rownames(wt_downuni)
-goWt=as.list(wt_downuni)
-
-Go_wtupuni= gost(query = goWt$gene.id,
- organism = "umaydis", ordered_query = FALSE,
- multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
- measure_underrepresentation = FALSE, evcodes = TRUE,
- user_threshold = 0.05, correction_method = "g_SCS",
- domain_scope = "known", custom_bg = NULL,
- numeric_ns = "", sources = NULL, as_short_link = TRUE)
-#visualization
-vis.wtgO<- gostplot(Go_wtupuni, capped = TRUE, interactive = TRUE)
-vis.wtgO
-
-
-
-#gprofiler
-kD_downuni=df.allu[df.allu$wt== "not" & df.allu$kd== "down", ]
-kD_downuni$gene.id=rownames(kD_downuni)
-goKD=as.list(kD_downuni)
-
-Go_kdupuni= gost(query = goKD$gene.id,
- organism = "umaydis", ordered_query = FALSE,
- multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
- measure_underrepresentation = FALSE, evcodes = TRUE,
- user_threshold = 0.05, correction_method = "g_SCS",
- domain_scope = "known", custom_bg = NULL,
- numeric_ns = "", sources = NULL, as_short_link = TRUE)
-
-#visualization
-vis.kDgO<- gostplot(Go_kdupuni, capped = TRUE, interactive = TRUE)
-vis.kDgO
-
-
+sessionInfo()
```
+
diff --git a/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane-traffikcing-pathways-shows-increased-expression-in-khd4D-hyphae.html b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane-traffikcing-pathways-shows-increased-expression-in-khd4D-hyphae.html
new file mode 100644
index 0000000..e53084a
--- /dev/null
+++ b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/dataset/Membrane-traffikcing-pathways-shows-increased-expression-in-khd4D-hyphae.html
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+size 4901027
diff --git a/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/isa.assay.xlsx b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/isa.assay.xlsx
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diff --git a/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/protocols/.gitkeep b/assays/S7_A1_RNAseq_analysis_Wt_Khd4D_hyphae_specific_genes/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
--
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