Sequencing

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

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

The 10x multiome kit allows you to link open chromatin (ATAC) and gene expression at single cell resolution https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expression?https%3A%2F%2Fwww.10xgenomics.com%2F%3Fsrc=search&utmmedium=search&utmsource=google&utmcampaign=sem-goog-2022-website-page-rag-pscmag...

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...

9 months ago

Simultaneous Profiling of Gene Expression and Chromatin Accessibility in Single Cells ATAC-RNA Joint Profiling Workflow Though this could work for any type of gDNA library, e.g. CUT&Tag for profiling histone marks and TF binding) Sorting and DSP Fixation Sort 50,000-100,000 cells into RPMI + 10% FBS Spin down 300g 5 min...

10 months ago

Fresh out of my lab notebook, this is how I conducted RNA-seq with success from human/mouse FACS-purified cells. If you're a new user, you may ask NEB for free trial kits for all reagents listed in this protocol! Purify RNA using Monarch® Total RNA Miniprep Kit (T2010) https://international.neb.com/products/t2010-monarch-t...

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

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?

FACS purification of target nuclei population for 10x multiome of human brain and spinal cord

FACS purification of target nuclei population for 10x multiome of human brain and spinal cord

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

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

Trick to capturing gene expression and epigenetics from the same cell – it's not rocket science, it's multiomics

Trick to capturing gene expression and epigenetics from the same cell – it's not rocket science, it's multiomics

Back to basics: how do I perform RNA-seq? Here's one way

Back to basics: how do I perform RNA-seq? Here's one way

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