RNAseq analysis of wildtype and knockout mice
In this experiment, 3 wild types (biological replicate) and 3 X gene knockout mice RNA was used to make library using NEBNext UltraII nonstranded kit and sequenced in ILLLUMINA HIseq. The raw Fastq files of Paired End (PE) were obtained and analyzed.
A. Basic Analysis
1. pipeline 2. Methods view or download
3. Results
MA-plot For wildtype and Knockout
MA plot represent the global view of upregulated and downregulated genes. The figure can be presented for graphical representation of differentially expressed genes
Volcano plot for DE significant genes
Volcano plot present the significantly differentially expressed (DE) individual genes.The figure can be presented for exptent of differentially expressed individual genes.
GO plot
GO plot represented the group of genes for diffrent categories that are populated in the expression list. Generally these represnt functional cellular process. This figure can be presented as to represent which cellular processes are mostly affected by the experiments.
Heatmap for significantly expressed genes
Heatmap represent the color view of differentially expressed genes in experiments. It is one of the preferred figure inpublications and grants. Here Heat map is shown to represent significantly expressed 20 differentially expressed genes. Although you can have heatmap of your custom genes by giving a gene list to us.
KEGG pathway
KEGG pathway is a standard pathway method for Differentially expressed genes in an experiments. The method directly incorporates the upregulated and downregulated genes from gene list depending their fold change to a premade KEGG pathway.
Differential Expression of Significant genes
A list for DESeq2 differentially expressed significant genes are listed.If wish to download or view please click HERE link.
B.Advance Analysis
On request and with extra price, we will also provide advance analysis with your RNAseq results, such as GSEA analysis, pathway analysis,circos analysis (for integration of RNAseq results with EXOME and CHIPseq or bisulfite DNA METHYLATION results.
Gene Set Enrichment Analysis (GSEA)
For gsea analysis, please click here