diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..41945a10c3a11919bf6647d1faba8b85824f51cd
--- /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/.gitkeep b/assays/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/DNA_extraction/README.md b/assays/DNA_extraction/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/DNA_extraction/dataset/.gitkeep b/assays/DNA_extraction/dataset/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/DNA_extraction/isa.assay.xlsx b/assays/DNA_extraction/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..02bb4d4613d7938fba60c63b621f79f5a172d4ef
Binary files /dev/null and b/assays/DNA_extraction/isa.assay.xlsx differ
diff --git a/assays/DNA_extraction/protocols/.gitkeep b/assays/DNA_extraction/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/DNA_sequencing/README.md b/assays/DNA_sequencing/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/DNA_sequencing/dataset/.gitkeep b/assays/DNA_sequencing/dataset/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/DNA_sequencing/isa.assay.xlsx b/assays/DNA_sequencing/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..aa52894f5dd84ea22acd4ea7319946dad9131a96
Binary files /dev/null and b/assays/DNA_sequencing/isa.assay.xlsx differ
diff --git a/assays/DNA_sequencing/protocols/.gitkeep b/assays/DNA_sequencing/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/PoreC_extraction/README.md b/assays/PoreC_extraction/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/PoreC_extraction/dataset/.gitkeep b/assays/PoreC_extraction/dataset/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/PoreC_extraction/isa.assay.xlsx b/assays/PoreC_extraction/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..74b5af8923f9b89f09bf10d02db4a9503fdc8c78
Binary files /dev/null and b/assays/PoreC_extraction/isa.assay.xlsx differ
diff --git a/assays/PoreC_extraction/protocols/.gitkeep b/assays/PoreC_extraction/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/PoreC_sequencing/README.md b/assays/PoreC_sequencing/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/PoreC_sequencing/dataset/.gitkeep b/assays/PoreC_sequencing/dataset/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/PoreC_sequencing/isa.assay.xlsx b/assays/PoreC_sequencing/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..a1eaf26f04be46806d92b7bd26ae926ba9d7eebe
Binary files /dev/null and b/assays/PoreC_sequencing/isa.assay.xlsx differ
diff --git a/assays/PoreC_sequencing/protocols/.gitkeep b/assays/PoreC_sequencing/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/RNA_extraction/README.md b/assays/RNA_extraction/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/RNA_extraction/dataset/.gitkeep b/assays/RNA_extraction/dataset/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/RNA_extraction/isa.assay.xlsx b/assays/RNA_extraction/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..7738b02f4e487391596566e3952b684e49ed84bd
Binary files /dev/null and b/assays/RNA_extraction/isa.assay.xlsx differ
diff --git a/assays/RNA_extraction/protocols/.gitkeep b/assays/RNA_extraction/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/RNA_sequencing/README.md b/assays/RNA_sequencing/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/RNA_sequencing/dataset/.gitkeep b/assays/RNA_sequencing/dataset/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/RNA_sequencing/isa.assay.xlsx b/assays/RNA_sequencing/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..1e9046cf143a7f42107758af70bc848febbd99eb
Binary files /dev/null and b/assays/RNA_sequencing/isa.assay.xlsx differ
diff --git a/assays/RNA_sequencing/protocols/.gitkeep b/assays/RNA_sequencing/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..e2f1bfa566b1f26737266992932df050e34f2716
Binary files /dev/null and b/isa.investigation.xlsx differ
diff --git a/runs/.gitkeep b/runs/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/studies/.gitkeep b/studies/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/studies/Greenhouse_setup/README.md b/studies/Greenhouse_setup/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/studies/Greenhouse_setup/isa.study.xlsx b/studies/Greenhouse_setup/isa.study.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..1e1b365317d0fee455615a22ec4e0c9bf1aaf566
Binary files /dev/null and b/studies/Greenhouse_setup/isa.study.xlsx differ
diff --git a/studies/Greenhouse_setup/protocols/.gitkeep b/studies/Greenhouse_setup/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/studies/Greenhouse_setup/resources/.gitkeep b/studies/Greenhouse_setup/resources/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/workflows/.gitkeep b/workflows/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391