Understanding chromatin biology using high-throughput sequencing (2022)
Note: Until further notice, workshops will be taught online via Zoom. However, we anticipate returning to in-person teaching at some point in the near future.
Next workshop dates and times:
Tuesday, November 15th: 9:30 AM - 12PM
Friday, November 18th: 9:30 AM - 12PM
Tuesday, November 22nd: 9:30 AM - 12PM
Note: Registration will open about 3 weeks prior to the workshop dates, and the dates/times above may be updated at that time.
Description:
This 3-day hands-on workshop will begin with a basic introduction of concepts related to gene regulation followed by a description of three common approaches used to interrogate chromatin biology: ChIP-seq, CUT&RUN and ATAC-seq. This workshop will provide participants with important considerations for setting up a successful ChIP-seq/CUT&RUN/ATAC-seq experiment and describe the detailed workflow for analyzing ChIP-seq data. For each step of the workflow there will be additional information describing how parameters might change for CUT&RUN-seq and ATAC-seq. The workshop will instruct participants on how to efficiently manage and analyze high throughput sequencing data starting from sequence reads through to peak calling, using tools and software available on the HMS-RC's high performance compute cluster.
Prerequisites?
This is one of our advanced workshops, and requires registrants to have attended the following Basic workshop offered by our training team within the last 6-8 months:
If you have not taken the above workshop with us, but are already fluent with shell/bash and already use HMS-RC's O2 cluster, please do the following:
- Complete the registration first
- Then email us directly at hbctraining@hsph.harvard.edu with a description of your knowledge/experience.
Course requirements:
- Mandatory attendance for all three classes
- 2-3 hours of reading and exercises from selected lessons before each workshop session
- Active participation during discussion sessions
Instruction will be mostly learner-centric. Online classes will be focused on exercises and discussion. Please make sure you take this into account when you sign up for the workshop!
Who should attend?
Eligible* Harvard researchers who want to learn:
- How to design a good ChIP-seq/CUT&RUN/ATAC-seq experiment
- The analysis workflow starting with raw sequencing data (Illumina) through to identifying significantly enriched regions ("calling peaks")
- How to handle various file formats encountered with ChIP-seq (and related) analysis, using command-line tools such as bedtools and deepTools
Cost and Registration:
There is a non-refundable and non-transferable $50 registration fee for this advanced workshop.
We will be accepting 25-30 participants on a first-come, first-served basis:
If you are one of the first 25-30 eligible* registrants, you will receive an email with a link to pay the (non-refundable & non-transferable) $50 registration fee.**
If you are not among the first 25-30 eligible* registrants, you will be added to the waitlist and notified accordingly.
**NOTE: You will not have a reserved seat for this workshop until you pay the registration fee. Please make sure you pay within the time stated in that email, else you will lose your spot to someone on the waitlist.
Eligibility requirements:
* To be eligible to attend this workshop you should fulfill at least one of the following criteria:
- Harvard Medical School researcher in a lab on the Quad, with grants administered by Gordon Hall
- Harvard School of Dental Medicine researcher, with grants administered by Gordon Hall
- Graduate student at the Harvard Medical School
- Researcher affiliated with the Dana-Farber / Harvard Cancer Center (DF/HCC)
- Harvard researchers whose PIs are associated with the HSCI as Principal or Affiliated faculty
If you are unsure of your eligibility, please register anyways and we will get back to you.
Click here to register!
(Registration will open about 3 weeks prior to the workshop dates)
NOTE: We do * not * record our training sessions.
Questions?
Please contact us at hbctraining@hsph.harvard.edu with any questions.