Liu Li, Catarina Rippe, Ola Hansson, Dmytro Kryvokhyzha, Steven Fisher, Mari Ekman, and Karl Swärd. "Regulation of the Muscarinic M3 Receptor by Myocardin-Related Transcription Factors" Frontiers in Physiology 12 (2021).

Name: Ola Hansson & Karl Swärd

Email: [email protected], [email protected]

Differential expression in the cultured human coronary artery smooth muscle cells (SMCs) induced by either the Ad-CMV-MYOCD viral vector.

Smooth muscle cells from the human coronary artery were treated either with Ad-CMV-null or Ad-CMV-MYOCD, i.e. adenovirsuses that express nothing or myocardin under control of CMV promoter. There were 4 virus induced and 4 control samples:

• CMV - control
• MYO - virus induced.

Test how overexpression of myocarding affects other genes.

Expression of myocardin (MYOCD) can be used as control.

The raw data of this project is stored at LUDC and will be made available upon request.

Install Conda and load the pre-configured conda environment. It should also install all the required programs.

conda env create -f conf/conda.yml
conda activate myocardin

Software versions are provided in conf/conda.yml.

Quality Control of the fastq files and other data are summarized in results/reports/multiQC

Mapping is performed with STAR in 2-pass mode.

Reads counting is performed with featureCounts.

See the rules in code/Snakefile.

snakemake -s code/Snakefile -p --use-conda

Results:

• results/tables/featureCounts/featureCounts_counts_gene.csv.gz - gene counts.

Performed with DESeq2:

R -e 'rmarkdown::render("code/DESeq.Rmd", output_dir="results/reports/")'

Results:

• results/reports/DESeq.html - report describing the analysis.

• results/tables/DESeq/DESeq_all.xlsx - differential expression results.

Column names in DESeq_all.xlsx:

• baseMean - mean of normalized counts for all samples.
• log2FoldChange - log2 fold change (MLE): condition treatment vs control.
• lfcSE - standard error.
• stat - Wald statistic.
• pvalue - Wald test p-value.
• padj - BH adjusted p-values.
• _tpm - transcript per million (TPM) normalized count data.