diff --git a/.gitattributes b/.gitattributes
index 40457e2cf494ec9c58db99d45f6faebeb6f5ada3..083d795cebfa28656cfdf0c5b09d8be1cd90dadd 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -14,3 +14,7 @@ assays/RNAseq/dataset/m_12/m_12_1.fq.gz filter=lfs diff=lfs merge=lfs -text
 assays/RNAseq/dataset/m_17/m_17_2.fq.gz filter=lfs diff=lfs merge=lfs -text
 assays/RNAseq/dataset/m_18/m_18_2.fq.gz filter=lfs diff=lfs merge=lfs -text
 assays/RNAseq/dataset/m_19/m_19_1.fq.gz filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_gene_leaf.csv filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_transcript_leaf.csv filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_genes_leaf.csv filter=lfs diff=lfs merge=lfs -text
+assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_transcripts_leaf.csv filter=lfs diff=lfs merge=lfs -text
diff --git a/assays/FASTQC/isa.assay.xlsx b/assays/FASTQC/isa.assay.xlsx
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diff --git a/assays/RNAseq_analysis/README.md b/assays/RNAseq_analysis_of_MSA/README.md
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rename to assays/RNAseq_analysis_of_MSA/README.md
diff --git a/assays/RNAseq_analysis/dataset/.gitkeep b/assays/RNAseq_analysis_of_MSA/dataset/.gitkeep
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diff --git a/assays/RNAseq_analysis/isa.assay.xlsx b/assays/RNAseq_analysis_of_MSA/isa.assay.xlsx
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rename from assays/RNAseq_analysis/isa.assay.xlsx
rename to assays/RNAseq_analysis_of_MSA/isa.assay.xlsx
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diff --git a/assays/RNAseq_analysis/protocols/.gitkeep b/assays/RNAseq_analysis_of_MSA/protocols/.gitkeep
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diff --git a/assays/RNAseq_analysis_of_leaf/README.md b/assays/RNAseq_analysis_of_leaf/README.md
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index 0000000000000000000000000000000000000000..4aa060d925a359e3a43f0d5c70eee252684cf17a
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@@ -0,0 +1,6 @@
+RNAseq analysis was conducted on the leaf and main shoot apex (MSA) samples separately.
+
+The tables of Count and Transcript per Million (TPM) were obtained using ThreeDRNAseq R package.
+The tables of differentially expressed genes were obtained using EdgeR R package.
+Gene Ontology analysis was performed using the Triticeae-Gene Tribe database (http://wheat.cau.edu.cn/TGT/m15/?navbar=GOEnrichment).
+WCGNA analysis was performed using the WGCNA R package.
diff --git a/studies/plant materials/protocols/.gitkeep b/assays/RNAseq_analysis_of_leaf/dataset/.gitkeep
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diff --git a/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_gene_leaf.csv b/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_gene_leaf.csv
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index 0000000000000000000000000000000000000000..279960f28900cf71cb22d529e058fa125e6964ba
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+++ b/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_gene_leaf.csv
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+version https://git-lfs.github.com/spec/v1
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diff --git a/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_transcript_leaf.csv b/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_transcript_leaf.csv
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+++ b/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_transcript_leaf.csv
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+version https://git-lfs.github.com/spec/v1
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diff --git a/assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_genes_leaf.csv b/assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_genes_leaf.csv
new file mode 100644
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+++ b/assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_genes_leaf.csv
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diff --git a/assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_transcripts_leaf.csv b/assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_transcripts_leaf.csv
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diff --git a/assays/RNAseq_analysis_of_leaf/isa.assay.xlsx b/assays/RNAseq_analysis_of_leaf/isa.assay.xlsx
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diff --git a/studies/plant materials/resources/.gitkeep b/assays/RNAseq_analysis_of_leaf/protocols/.gitkeep
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rename from studies/plant materials/resources/.gitkeep
rename to assays/RNAseq_analysis_of_leaf/protocols/.gitkeep
diff --git a/assays/RNAseq_raw_data/isa.assay.xlsx b/assays/RNAseq_raw_data/isa.assay.xlsx
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diff --git a/assays/Salmon_quantification/protocols/salmon_indexing.bash b/assays/Salmon_quantification/protocols/salmon_indexing.bash
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index 0000000000000000000000000000000000000000..28b510aa46f4973fefbf5d8ac8c377c69cd4d4c1
--- /dev/null
+++ b/assays/Salmon_quantification/protocols/salmon_indexing.bash
@@ -0,0 +1,7 @@
+### Load module
+
+module load Salmon/1.6.0
+
+### Script command
+salmon index -t BaRT.1.0_Unsplit_exons_padded.fasta -i BaRT.1.0_Unsplit_exons_padded.fasta_index
+
diff --git a/assays/Salmon_quantification/protocols/salmon_quantification.bash b/assays/Salmon_quantification/protocols/salmon_quantification.bash
new file mode 100644
index 0000000000000000000000000000000000000000..a3e742afd1c83cbd481fd3709e1ada79928af61f
--- /dev/null
+++ b/assays/Salmon_quantification/protocols/salmon_quantification.bash
@@ -0,0 +1,8 @@
+### Load module
+
+module load Salmon/1.6.0
+
+### Script command
+
+salmon quant -i BaRT.1.0_Unsplit_exons_padded.fasta_index -l A -1 sample_*_1.fq.gz -2 sample_*_2.fq.gz -p 4 --validateMappings -o sample_quant
+
diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
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