Workshop Description (Intermediate Course)

This workshop aims to provide skills needed to address principles of the assay, quality assessment, sequencing depth, data processing and functional downstream analyses of ChIP-seq datasets. Students will have opportunities to practice hands-on with state-of-the-art analytical tools.

Workshop Materials

•Assay protocol
•Principles and theory
•Quality Control
•Data download from GEO (SRA toolkit)

•Alignment to human genome (Bowtie2)
•Peak calling (MACS)
•Genome browser viewing (IGB)
•Differential peak calling (HOMER)

•ChIP region annotation (CEAS)
•Peak overlap between datasets (SITEPRO/BEDtools)
•Integrative RNA-seq promoter analysis (CEAS)
•TF Motif discovery (HOMER)
•Gene assignment and gene ontology (GREAT)

For the workshop slides, please click below.

ChiP Slides

Technical Requirements

  • Attendees are required to have a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.


Dr. Nathan Zemke is currently a post-doc in the Lab of Professor Arnie Berk in the Microbiology, Immunology, & Molecular Genetics department at UCLA. He received his bachelor’s degree in molecular biology at UCSD. He earned his PhD from the Molecular Biology Interdepartmental program at UCLA researching the adenovirus oncoprotein e1a and its regulation of chromatin, innate immune responses, and differentiation. Email:



This was a great workshop that shows the various steps and options for representing and analyzing ChIP-seq data. The outline of the overall workshop made sense and provided me with a lot of information to try. Thanks!

He is a great instructor and very helpful with questions throughout the course.

I was glad that we went over QC methods and tools.

This is a good workshop for biologists to understand the analysis process of ChIP-seq data.

Workshop Details

Prerequisites: W1, & W2
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 15

Spring 2020 Dates

May 12, 13, and 14, 2020
1:30PM to 4:30PM