From 087c94e1253bd332a82bbeb96de60b506d9624cf Mon Sep 17 00:00:00 2001
From: Vanessa Valencia <vaval103@hhu.de>
Date: Thu, 17 Aug 2023 15:10:48 +0200
Subject: [PATCH] add processing assay

---
 assays/rna-data-processing/README.md          |   0
 assays/rna-data-processing/dataset/.gitkeep   |   0
 assays/rna-data-processing/isa.assay.xlsx     | Bin 0 -> 2661 bytes
 assays/rna-data-processing/protocols/.gitkeep |   0
 .../protocols/data processing step.md         |   9 +++++++++
 isa.investigation.xlsx                        | Bin 3259 -> 3309 bytes
 6 files changed, 9 insertions(+)
 create mode 100644 assays/rna-data-processing/README.md
 create mode 100644 assays/rna-data-processing/dataset/.gitkeep
 create mode 100644 assays/rna-data-processing/isa.assay.xlsx
 create mode 100644 assays/rna-data-processing/protocols/.gitkeep
 create mode 100644 assays/rna-data-processing/protocols/data processing step.md

diff --git a/assays/rna-data-processing/README.md b/assays/rna-data-processing/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/rna-data-processing/dataset/.gitkeep b/assays/rna-data-processing/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/rna-data-processing/isa.assay.xlsx b/assays/rna-data-processing/isa.assay.xlsx
new file mode 100644
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diff --git a/assays/rna-data-processing/protocols/.gitkeep b/assays/rna-data-processing/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/rna-data-processing/protocols/data processing step.md b/assays/rna-data-processing/protocols/data processing step.md
new file mode 100644
index 0000000..1bfe077
--- /dev/null
+++ b/assays/rna-data-processing/protocols/data processing step.md	
@@ -0,0 +1,9 @@
+Illumina Casava-1.9software used for basecalling.
+
+The software kallisto (v 0.43.0) was used for quantification with the Arabidopsis thaliana genome as a reference (TAIR10 cDNA). The resulting normalized counts (transcripts per million, tpm) were used for downstream analyses. 
+
+Kallisto was run with 30 bootstrapping replications. The resulting .h5 files were fed forward into differential gene expression analysis using sleuth (v 0.28.1).
+
+Means and standard deviation of tpm of biological triplicates group were calculated. 
+
+Comma-separated table (.csv) file including Arabidopsis Gene Identifier (AGI) and TAIR10 description, raw estimated counts (kallisto), tpm (kallisto) for each sample and mean and standard deviation of tpm for biological triplicates, sleuth results of differential gene expression comparing each of the mutant lines against the wildtype at the respective time of sampling
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