From dc3afc217dff232b26d2967d32607c48600e3177 Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Wed, 12 Mar 2025 14:40:41 +0100
Subject: [PATCH] sync changes via ARCCommander

---
 .gitattributes                                |   5 +----
 assays/RNAseq_analysis_of_leaf/isa.assay.xlsx | Bin 15210 -> 15832 bytes
 .../README.md                                 |  12 ++++++------
 .../dataset/.gitkeep                          |   0
 .../dataset/Count_leaf/counts_gene_leaf.csv   |   0
 .../Count_leaf/counts_transcript_leaf.csv     |   0
 .../dataset/TPM_leaf/TPM_genes_leaf.csv       |   0
 .../dataset/TPM_leaf/TPM_transcripts_leaf.csv |   0
 assays/ThreeDRNAseq/isa.assay.xlsx            | Bin 0 -> 16005 bytes
 .../protocols/.gitkeep                        |   0
 10 files changed, 7 insertions(+), 10 deletions(-)
 rename assays/{RNAseq_analysis_of_leaf => ThreeDRNAseq}/README.md (98%)
 rename assays/{RNAseq_analysis_of_leaf => ThreeDRNAseq}/dataset/.gitkeep (100%)
 rename assays/{RNAseq_analysis_of_leaf => ThreeDRNAseq}/dataset/Count_leaf/counts_gene_leaf.csv (100%)
 rename assays/{RNAseq_analysis_of_leaf => ThreeDRNAseq}/dataset/Count_leaf/counts_transcript_leaf.csv (100%)
 rename assays/{RNAseq_analysis_of_leaf => ThreeDRNAseq}/dataset/TPM_leaf/TPM_genes_leaf.csv (100%)
 rename assays/{RNAseq_analysis_of_leaf => ThreeDRNAseq}/dataset/TPM_leaf/TPM_transcripts_leaf.csv (100%)
 create mode 100644 assays/ThreeDRNAseq/isa.assay.xlsx
 rename assays/{RNAseq_analysis_of_leaf => ThreeDRNAseq}/protocols/.gitkeep (100%)

diff --git a/.gitattributes b/.gitattributes
index a10f461..78c36bc 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -14,10 +14,6 @@ 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
 **/dataset/** filter=lfs diff=lfs merge=lfs -text
 /assays/RNAseq_raw_data/dataset/AT87_EKRN230064181-1A_HWTTFDSX7_L3_1.fq.gz filter=lfs diff=lfs merge=lfs -text
 /assays/RNAseq_raw_data/dataset/AT81_EKRN230064175-1A_HFNGFDSX7_L3_1.fq.gz filter=lfs diff=lfs merge=lfs -text
@@ -413,3 +409,4 @@ assays/FASTQC/dataset/fastqc_raw_RNAseq_data/AT113_EKRN230064191-1A_HFNGFDSX7_L3
 assays/FASTQC/dataset/fastqc_raw_RNAseq_data/AT113_EKRN230064191-1A_HFNGFDSX7_L3_2_fastqc.zip filter=lfs diff=lfs merge=lfs -text
 assays/FASTQC/dataset/fastqc_raw_RNAseq_data/AT113_EKRN230064191-1A_HWTTFDSX7_L3_1_fastqc.html filter=lfs diff=lfs merge=lfs -text
 assays/FASTQC/dataset/fastqc_raw_RNAseq_data/AT113_EKRN230064191-1A_HWTTFDSX7_L3_1_fastqc.zip filter=lfs diff=lfs merge=lfs -text
+assays/ThreeDRNAseq/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
diff --git a/assays/RNAseq_analysis_of_leaf/isa.assay.xlsx b/assays/RNAseq_analysis_of_leaf/isa.assay.xlsx
index cac2241563eef18ff140f47e5b78c363b5a34b4f..467b13475f3602c19c1b02c2b9dd6d8707795f46 100644
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diff --git a/assays/RNAseq_analysis_of_leaf/README.md b/assays/ThreeDRNAseq/README.md
similarity index 98%
rename from assays/RNAseq_analysis_of_leaf/README.md
rename to assays/ThreeDRNAseq/README.md
index cbf7623..4aa060d 100644
--- a/assays/RNAseq_analysis_of_leaf/README.md
+++ b/assays/ThreeDRNAseq/README.md
@@ -1,6 +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.
+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/assays/RNAseq_analysis_of_leaf/dataset/.gitkeep b/assays/ThreeDRNAseq/dataset/.gitkeep
similarity index 100%
rename from assays/RNAseq_analysis_of_leaf/dataset/.gitkeep
rename to assays/ThreeDRNAseq/dataset/.gitkeep
diff --git a/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_gene_leaf.csv b/assays/ThreeDRNAseq/dataset/Count_leaf/counts_gene_leaf.csv
similarity index 100%
rename from assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_gene_leaf.csv
rename to assays/ThreeDRNAseq/dataset/Count_leaf/counts_gene_leaf.csv
diff --git a/assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_transcript_leaf.csv b/assays/ThreeDRNAseq/dataset/Count_leaf/counts_transcript_leaf.csv
similarity index 100%
rename from assays/RNAseq_analysis_of_leaf/dataset/Count_leaf/counts_transcript_leaf.csv
rename to assays/ThreeDRNAseq/dataset/Count_leaf/counts_transcript_leaf.csv
diff --git a/assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_genes_leaf.csv b/assays/ThreeDRNAseq/dataset/TPM_leaf/TPM_genes_leaf.csv
similarity index 100%
rename from assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_genes_leaf.csv
rename to assays/ThreeDRNAseq/dataset/TPM_leaf/TPM_genes_leaf.csv
diff --git a/assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_transcripts_leaf.csv b/assays/ThreeDRNAseq/dataset/TPM_leaf/TPM_transcripts_leaf.csv
similarity index 100%
rename from assays/RNAseq_analysis_of_leaf/dataset/TPM_leaf/TPM_transcripts_leaf.csv
rename to assays/ThreeDRNAseq/dataset/TPM_leaf/TPM_transcripts_leaf.csv
diff --git a/assays/ThreeDRNAseq/isa.assay.xlsx b/assays/ThreeDRNAseq/isa.assay.xlsx
new file mode 100644
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diff --git a/assays/RNAseq_analysis_of_leaf/protocols/.gitkeep b/assays/ThreeDRNAseq/protocols/.gitkeep
similarity index 100%
rename from assays/RNAseq_analysis_of_leaf/protocols/.gitkeep
rename to assays/ThreeDRNAseq/protocols/.gitkeep
-- 
GitLab