diff --git a/.gitattributes b/.gitattributes
index 5be99d5a806a4393e8ae9fa1e38a43ecce5f13b5..c4990cb07d506e64c93272aee82c253303a1b9e1 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -4,3 +4,4 @@ _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
 runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
+studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa filter=lfs diff=lfs merge=lfs -text
diff --git a/studies/arabidopsis-reference/protocols/download-reference.md b/studies/arabidopsis-reference/protocols/download-reference.md
new file mode 100644
index 0000000000000000000000000000000000000000..d31d55ff9a8723407dcf0cf9021432cb4d69765e
--- /dev/null
+++ b/studies/arabidopsis-reference/protocols/download-reference.md
@@ -0,0 +1,23 @@
+
+# Downloading Arabidopsis TAIR10 fasta
+
+### Download and unzip
+
+```bash
+curl -O ftp://ftp.ensemblgenomes.org/pub/plants/release-28/fasta/arabidopsis_thaliana/cdna/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa.gz
+gunzip Arabidopsis_thaliana.TAIR10.28.cdna.all.fa.gz
+```
+
+### sanity check
+
+count number of genes / gene products
+
+```bash
+grep '>' Arabidopsis_thaliana.TAIR10.28.cdna.all.fa | wc -l
+```
+
+### move
+
+```bash
+mv Arabidopsis_thaliana.TAIR10.28.cdna.all.fa ../resources
+```
diff --git a/studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa b/studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dce30a46aa82222cbb5bef50b00585585df10441
--- /dev/null
+++ b/studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2924f53c82a7013eeaeb14a6691ba97a65010c540007a3fbeffa40a66ed296e8
+size 73699735
diff --git a/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta b/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta
deleted file mode 100644
index 51b14af459032b7e302bfee50984f82f2b4406f5..0000000000000000000000000000000000000000
--- a/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta
+++ /dev/null
@@ -1,3 +0,0 @@
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