We used DiffBind version 1.12.0 with default EdgeR (3.8.3) option to identify peaks which were differentially bound between neutrophils and monocytes. For each cell type we used the six best quality samples and their peak sets for this analysis; PU.1: NS1509, NS1510, NS1511, NS1514, NS1516, NS1522, NS1463, NS1464, NS1554, NS1551, NS1437 and NS1490. C/EBPβ; NS1559, NS1565, NS1563, NS1558, NS1562, NS1566, NS585, NS743, NS791, NS729, NS717, and NS793. Quality control plots generated as part of this analysis include correlation between sample peak sets (Supplementary Fig. 5a) and PCA between samples using normalised counts within consensus peak set (Supplementary Fig. 5b). Differentially bound peaks were considered to those peaks present in at least three individuals with a minimum threefold difference (FDR < 0.05) in binding signal as cut off. The heat map visualisation of differentially bound regions Deeptools 2(Galaxy Version 3.3.2.0.1)72.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.