diff --git a/.gitignore b/.gitignore
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index 0000000000000000000000000000000000000000..25b86b4783f1e07dcae5cc057b126e8a8b8cc011
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,56 @@
+# ----- macos rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/macOS.gitignore
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+# Icon must end with two \r
+Icon
+# Thumbnails
+._*
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+# ----- windows rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/Windows.gitignore
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+# Dump file
+*.stackdump
+# Folder config file
+[Dd]esktop.ini
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+# Windows shortcuts
+*.lnk
+# ----- linux rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/Linux.gitignore
+*~
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+# KDE directory preferences
+.directory
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
diff --git a/assays/S1_A1_microscopy_yeast/README.md b/assays/S1_A1_microscopy_yeast/README.md
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diff --git a/assays/S1_A2_microscopy_hyphae/README.md b/assays/S1_A2_microscopy_hyphae/README.md
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diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
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diff --git a/studies/S1_characterization_khd4D/README.md b/studies/S1_characterization_khd4D/README.md
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