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- Investigate genome wide transcription regulation in a comparative setting
- Investigate the active part of the chromatin
Considerations before starting a ChIP sequencing project:
- Is there a suitable reference genome?
- Point or broad source?
- Sequencing depth (sensitivity)?
- Experimental setup (replicates and conditions, input control)?
Let us guide you – from design to analysis
Example projects using ChIP sequencing:
- Discovery of new transcription factor binding sites
- Investigation of histone modifications
- Selective trancription factor usage
- Novel pathway activation by known transcription factor
Applications related to ChIP sequencing:
- mRNA sequencing
- small and miRNA sequencing
The results produced by our analysis module help answer three main questions of a ChIP sequencing experiment aiming for instance to find novel patterns of gene regulation.
- Where on the reference genome are significant peaks? (see Table 1)
- Which are the common motifs and are these novel? (see Figure 1)
- Which pathways may be influenced by the captured regulatory elements? (see Figure 2)
Figure 1: This figure depicts a possible regulatory motif.
Figure 2: A pathway enrichment analysis is conducted using the peaks found in the experiment.