diff --git a/assays/DNA_extraction/README.md b/assays/DNA_extraction/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/DNA_extraction/dataset/.gitkeep b/assays/DNA_extraction/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/DNA_extraction/isa.assay.xlsx b/assays/DNA_extraction/isa.assay.xlsx
deleted file mode 100644
index 1c1f92469e0c1ad7d73423516d88d9682420f947..0000000000000000000000000000000000000000
Binary files a/assays/DNA_extraction/isa.assay.xlsx and /dev/null differ
diff --git a/assays/DNA_extraction/protocols/.gitkeep b/assays/DNA_extraction/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/DNA_sequencing/README.md b/assays/DNA_sequencing/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/DNA_sequencing/dataset/.gitkeep b/assays/DNA_sequencing/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/DNA_sequencing/isa.assay.xlsx b/assays/DNA_sequencing/isa.assay.xlsx
deleted file mode 100644
index 6c1da726e202a05afae5af445451f3abcd666dbb..0000000000000000000000000000000000000000
Binary files a/assays/DNA_sequencing/isa.assay.xlsx and /dev/null differ
diff --git a/assays/DNA_sequencing/protocols/.gitkeep b/assays/DNA_sequencing/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/PoreC_extraction/README.md b/assays/PoreC_extraction/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/PoreC_extraction/dataset/.gitkeep b/assays/PoreC_extraction/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/PoreC_extraction/isa.assay.xlsx b/assays/PoreC_extraction/isa.assay.xlsx
deleted file mode 100644
index 16b5e5639729690f3db25484a8cc6358fa96e1cd..0000000000000000000000000000000000000000
Binary files a/assays/PoreC_extraction/isa.assay.xlsx and /dev/null differ
diff --git a/assays/PoreC_extraction/protocols/.gitkeep b/assays/PoreC_extraction/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/PoreC_sequencing/README.md b/assays/PoreC_sequencing/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/PoreC_sequencing/dataset/.gitkeep b/assays/PoreC_sequencing/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/PoreC_sequencing/isa.assay.xlsx b/assays/PoreC_sequencing/isa.assay.xlsx
deleted file mode 100644
index 18f52ffdd0d09e1795d30ef30e8c211420c3a153..0000000000000000000000000000000000000000
Binary files a/assays/PoreC_sequencing/isa.assay.xlsx and /dev/null differ
diff --git a/assays/PoreC_sequencing/protocols/.gitkeep b/assays/PoreC_sequencing/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/RNA_extraction/README.md b/assays/RNA_extraction/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/RNA_extraction/dataset/.gitkeep b/assays/RNA_extraction/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/RNA_extraction/isa.assay.xlsx b/assays/RNA_extraction/isa.assay.xlsx
deleted file mode 100644
index 528eb9e10feeac102ab886e0c195a9295d5f9dd1..0000000000000000000000000000000000000000
Binary files a/assays/RNA_extraction/isa.assay.xlsx and /dev/null differ
diff --git a/assays/RNA_extraction/protocols/.gitkeep b/assays/RNA_extraction/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/RNA_sequencing/README.md b/assays/RNA_sequencing/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/RNA_sequencing/dataset/.gitkeep b/assays/RNA_sequencing/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/RNA_sequencing/isa.assay.xlsx b/assays/RNA_sequencing/isa.assay.xlsx
deleted file mode 100644
index 88adfc625b3a6d0f9215a90cbaf18e814db5b681..0000000000000000000000000000000000000000
Binary files a/assays/RNA_sequencing/isa.assay.xlsx and /dev/null differ
diff --git a/assays/RNA_sequencing/protocols/.gitkeep b/assays/RNA_sequencing/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/test_assay/README.md b/assays/test_assay/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/test_assay/dataset/.gitkeep b/assays/test_assay/dataset/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/assays/test_assay/isa.assay.xlsx b/assays/test_assay/isa.assay.xlsx
deleted file mode 100644
index a2d90b93d027ea47606a1429fda646829b9fac5f..0000000000000000000000000000000000000000
Binary files a/assays/test_assay/isa.assay.xlsx and /dev/null differ
diff --git a/assays/test_assay/protocols/.gitkeep b/assays/test_assay/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/runs/Supplemental_Tables.xlsx b/runs/Supplemental_Tables.xlsx
deleted file mode 100644
index d867e0c5f6df72f286d7c46f7fb56d74412a5746..0000000000000000000000000000000000000000
Binary files a/runs/Supplemental_Tables.xlsx and /dev/null differ
diff --git a/studies/Greenhouse_setup/README.md b/studies/Greenhouse_setup/README.md
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/studies/Greenhouse_setup/isa.study.xlsx b/studies/Greenhouse_setup/isa.study.xlsx
deleted file mode 100644
index af6aee7813775df8d7426fec218283bee3f2a4b2..0000000000000000000000000000000000000000
Binary files a/studies/Greenhouse_setup/isa.study.xlsx and /dev/null differ
diff --git a/studies/Greenhouse_setup/protocols/.gitkeep b/studies/Greenhouse_setup/protocols/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/studies/Greenhouse_setup/resources/.gitkeep b/studies/Greenhouse_setup/resources/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000