In Part A, you created a ChIP-Seq assembly using SeqMan NGen. In this part, you will use ArrayStar to filter the results for IP fragments that match in both replicates, and that meet a specified signal threshold. Then you will look for genes that the fragments intersect, and see whether they share any common characteristics.
- Click on the Fragment Table tab and ensure that 40 IP fragments were found.
- Similarly, click on the Peak Table tab and ensure that 52 peaks were found.
- To filter for fragments found in both replicate samples, choose Filter > Filter All and make selections to match the image below.
- Press the Choose Signal Criteria button and make selections to match the following image. Press OK.
- Press Search. The search should yield 12 IP fragments.
- Press the Select and Show Results in IP Fragment Table tool (), located above the result table.
- In the Fragment Table, use the Quick-Filter tool to choose Show Only Selected IP Fragments.
- Click on Add/Manage Columns. In the IP Fragments section, choose Intersecting Genes, then >Add Column>, then OK.
- Look at the newly-added column and note that many of the fragments intersect genes beginning with “flg”, “fli” and “flh”.
These are the major operons for producing flagella, which FlhD — together with FlhC — are known to regulate. The other genes are also known to be regulated by this transcription factor.
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