diff --git a/.gitattributes b/.gitattributes
index 49c573d627bf7e5ff47fe07132d57aaeeea8b180..a7b52de016f6eaa187fbab4c7db24dc59aa1e12d 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -2,3 +2,4 @@ assays/rna-seq/dataset/** filter=lfs diff=lfs merge=lfs -text
 _publication/Image[[:space:]]1.pdf filter=lfs diff=lfs merge=lfs -text
 _publication/fpls-09-01709.pdf filter=lfs diff=lfs merge=lfs -text
 _publication/Data[[:space:]]Sheet[[:space:]]1.xlsx filter=lfs diff=lfs merge=lfs -text
+studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta filter=lfs diff=lfs merge=lfs -text
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/metabolite-measurements/isa.assay.xlsx b/assays/metabolite-measurements/isa.assay.xlsx
index c6e929fa4c05b4512e2028214c05173770f01ced..8fc5d212323ae2e4bf607acda95ec670cfbbbf3f 100644
Binary files a/assays/metabolite-measurements/isa.assay.xlsx and b/assays/metabolite-measurements/isa.assay.xlsx differ
diff --git a/assays/rna-data-processing/isa.assay.xlsx b/assays/rna-data-processing/isa.assay.xlsx
index 2df017e86cd1496e75645006a28e92b6a32d95d8..0698e02daf96a3f81d3b38d6c895f6b0b0dedbf7 100644
Binary files a/assays/rna-data-processing/isa.assay.xlsx and b/assays/rna-data-processing/isa.assay.xlsx differ
diff --git a/assays/rna-seq/dataset/.gitkeep b/assays/rna-seq/dataset/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/assays/rna-seq/isa.assay.xlsx b/assays/rna-seq/isa.assay.xlsx
index c1e8b41aba56b5857e31d60b92e0370385098ff2..ce860e6d92c712c0124a5f307dff6426de8d541e 100644
Binary files a/assays/rna-seq/isa.assay.xlsx and b/assays/rna-seq/isa.assay.xlsx differ
diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
index e30a6d000da88de97c7ed8bc75c85b1559bc5e6a..92d8d2552bbdc9b9cb8377f9f8abf806711d1f19 100644
Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ
diff --git a/studies/arabidopsis-reference/README.md b/studies/arabidopsis-reference/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/studies/arabidopsis-reference/isa.study.xlsx b/studies/arabidopsis-reference/isa.study.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..d302ab3476ec608aca62667cec5bfbed95cadbc4
Binary files /dev/null and b/studies/arabidopsis-reference/isa.study.xlsx differ
diff --git a/studies/arabidopsis-reference/protocols/.gitkeep b/studies/arabidopsis-reference/protocols/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/studies/arabidopsis-reference/resources/.gitkeep b/studies/arabidopsis-reference/resources/.gitkeep
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta b/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..51b14af459032b7e302bfee50984f82f2b4406f5
--- /dev/null
+++ b/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:826d4d9f605007e613e8ba2d2fd186d955a768c5a5cc575998e3f09355137a3d
+size 93036871
diff --git a/studies/relative_contribution_of_serine_pathways/isa.study.xlsx b/studies/relative_contribution_of_serine_pathways/isa.study.xlsx
index b982787c151f02233f2025e97968e1693c58de7a..10f9c15e295820b76a3b14b0615aaac6b6f8b454 100644
Binary files a/studies/relative_contribution_of_serine_pathways/isa.study.xlsx and b/studies/relative_contribution_of_serine_pathways/isa.study.xlsx differ