ChIP-seq was done as previously described (Magnani et al. 2013 (link); Gallo et al. 2015 (link)) with some modifications. Antibodies used were anti-CTCF (Cell Signaling, #3418, Lot #1) and anti-H3K27ac (Active Motif, #39133, Lot# 31814008). ChIP-seq peaks were called using MACS2 callpeak (Zhang et al. 2008 (link)) on filtered alignments from BWA-MEM (Li and Durbin 2009 (link)). Superenhancer regions were then identified using ROSE (Lovén et al. 2013 (link); Whyte et al. 2013 (link)) on our H3K27ac data. See Supplemental Methods for the complete library generation protocol and analysis parameters.
Protocol detail
Chromatin Immunoprecipitation Sequencing Protocol
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization :
Other organizations : University of Calgary, Alberta Children's Hospital, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Hospital for Sick Children, SickKids Foundation, National Cancer Institute, BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Ontario Institute for Cancer Research
Top 5 similar protocols
Variable analysis
independent variables
- Antibodies used were anti-CTCF (Cell Signaling, #3418, Lot #1) and anti-H3K27ac (Active Motif, #39133, Lot# 31814008)
- ChIP-seq peaks
- ChIP-seq was done as previously described (Magnani et al. 2013; Gallo et al. 2015) with some modifications
- ChIP-seq peaks were called using MACS2 callpeak on filtered alignments from BWA-MEM
- Superenhancer regions were identified using ROSE on the H3K27ac data
- None specified
- None specified
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!