Homework Week 12
Friederike Dündar and Luce Skrabanek
ANGSD Course 2020
Understanding epigenomics research based on NGS
We’ve discussed numerous assays that make use of next-generation sequencing (NGS). Test whether you’ve grasped the diversity of applications by identifying the specific assays that could be used to identify the features of cis-regulatory regions listed on the slide from today’s lecture by filling out the table below.
| Feature | NGS Assay |
|---|---|
| Pol II presence | detecting transcripts (transcript production is dependent on Pol II!): RNA-seq, PRO-seq, GRO-seq; detecting Pol II itself: ChIP-seq |
| open chromatin vs. repressed | |
| H3K4me3, H3K27ac, H3K4me1 | |
| TF binding, e.g. p300 | |
| CTCF binding | |
| chromosomal interactions | |
| DNA methylation |
- Why is ChIP-seq so much more costly and difficult than ATAC-seq?
- Why is it benefitial to combine information from RNA-seq, ChIP-seq and ATAC-seq experiments? What type of information can you gain from each experiment individidually – and why does it help to integrate them?