diff --git a/assays/rna-data-processing/README.md b/assays/rna-data-processing/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/rna-data-processing/dataset/.gitkeep b/assays/rna-data-processing/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/rna-data-processing/isa.assay.xlsx b/assays/rna-data-processing/isa.assay.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..2df017e86cd1496e75645006a28e92b6a32d95d8 Binary files /dev/null and b/assays/rna-data-processing/isa.assay.xlsx differ diff --git a/assays/rna-data-processing/protocols/.gitkeep b/assays/rna-data-processing/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 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 0000000000000000000000000000000000000000..1bfe077f1df8d389e951f608d7119a56a56300a8 --- /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 diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 3887da432359cb6069c2bbf45eca937a3544c155..01e60d9c6b4efa8358630f17fd075f90ee5fc16e 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ