diff --git a/.gitattributes b/.gitattributes index a10f4611b81c086c9b32e9f5aae9df0008fa1a42..78c36bc46c7c8962ce1171834d82eb66f59898b3 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 Binary files a/assays/RNAseq_analysis_of_leaf/isa.assay.xlsx and b/assays/RNAseq_analysis_of_leaf/isa.assay.xlsx differ 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 cbf762352c6bbe819864f42a1a0ec2cb2111535e..4aa060d925a359e3a43f0d5c70eee252684cf17a 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 index 0000000000000000000000000000000000000000..460030ebe0a84ec071331c8b3cc391c8142b6c7e Binary files /dev/null and b/assays/ThreeDRNAseq/isa.assay.xlsx differ 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