Epigenetics

9 months ago

You've prepared your epigenetic library for profiling histone marks. If you are not using the Zymo ChIP DNA Clean & Concentrator Kit for final elution, you may want to size select for your library region of interest using SPRI bead clean up. How much bead do you add relative to your volume of library? Because adapters for ...

9 months ago

One extraordinary presentation at "Ending Age-Related Diseases 2022 " was by Greg Fahy, on past and new clinical trials to regenerate the thymus - a gland which sadly shrinks in age, and is a key player in the immune system. The initial human clinical trial was named "TRIIM", at Stanford (2015-17), with notable results. ...

9 months ago

BAMBANKER Open to suggestions! This has worked incredibly well for me for both cell lines and FACS-purified cell populations from post-mortem human tissue. Will put in my manuscript reference as it becomes available. This has worked well for me for native ChIP-seq, CUT&Tag, and newer versions of CUT&Tag (to be updated by ...

9 months ago

Benchmarking CUT&Tag against ChIP-seq: https://www.biorxiv.org/content/10.1101/2022.03.30.486382v1 https://www.nature.com/articles/s41467-019-09982-5 Lovely blog post on CUT&Tag: https://www.activemotif.com/blog-cut-tag The improved sensitivity of CUT&Tag compared to ChIP-seq is due to the use of pA-Tn5 to streamline lib...

9 months ago

So many fascinating talks at the "Ending Age-Related Diseases 2022" conference that just came to a close! Where to start?!? Over recent years, it has been especially gratifying to see the maturing of the epigenetic clocks, sometimes referred to as "Horvath clocks" , after the UCLA professor Steve Horvath who pioneered the...

9 months ago

Use the cellenONE https://www.cellenion.com/products/cellenone-x1/ if you'd like an open platform for the single cell -omics of your choice (e.g. I used it to develop new single cell epigenetic and multiomic profiling methods). It has: nanoliter dispensing so you can save on reagents temperature/dew point controlled inter...

10 months ago

Want to perform ATAC-seq in the lab for genome wide mapping of open/accessible chromatin to find out which genes are likely expressed? This could be a good complement to RNA-seq of the same sample where you could potentially link upstream open chromatin confirmation to downstream gene expression. Here is some more informati...

10 months ago

Want to conduct genome wide profiling of histone marks and transcription binding, but don't have hundreds of thousands of cells needed for ChIP-seq? CUT&Tag may offer a solution, but because it is a relatively new method (since 2019), there lacked a framework for experimental design and analysis. This is where I step in: ht...

SPRI bead size selection guidance for histone marks

SPRI bead size selection guidance for histone marks

Restoring the function of the aging Thymus - clinical trials

Restoring the function of the aging Thymus - clinical trials

Best way to cryopreserve cells for chromatin assays

Best way to cryopreserve cells for chromatin assays

CUT&Tag is a recent method to profile epigenetic marks with reduced cell numbers and cost, but how does it compare to ChIP-seq?

CUT&Tag is a recent method to profile epigenetic marks with reduced cell numbers and cost, but how does it compare to ChIP-seq?

Horvath Epigenetic clocks : from the "Ending Age-Related Diseases 2022" conference

Horvath Epigenetic clocks : from the "Ending Age-Related Diseases 2022" conference

Open platform for accurate >95% recovery single cell -omics: cellenONE

Open platform for accurate >95% recovery single cell -omics: cellenONE

I used this protocol to attain high quality ATAC-seq data from FACS-purified human microglia

I used this protocol to attain high quality ATAC-seq data from FACS-purified human microglia

Framework for experimental design and analysis for low input/single cell chromatin profiling: CUT&Tag

Framework for experimental design and analysis for low input/single cell chromatin profiling: CUT&Tag