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.

  1. Click on the Fragment Table tab and ensure that 40 IP fragments were found.

  1. Similarly, click on the Peak Table tab and ensure that 52 peaks were found.
  1. To filter for fragments found in both replicate samples, choose Filter > Filter All and make selections to match the image below.

  1. Press the Choose Signal Criteria button and make selections to match the following image. Press OK.

  1. Press Search. The search should yield 12 IP fragments.
  1. Press the Select and Show Results in IP Fragment Table tool (), located above the result table.
  1. In the Fragment Table, use the Quick-Filter tool to choose Show Only Selected IP Fragments.

  1. Click on Add/Manage Columns. In the IP Fragments section, choose Intersecting Genes, then >Add Column>, then OK.
  1. 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.

Congratulations on completing Tutorial 8. For a complete list of our other available tutorials, click here.

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