Intro

neuroscientist studying longevity | currently working on: single cell (epi)genomics methods development; epigenetic reprogramming; single cell multiomic human brain atlas

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Instrumentation

cellenONE mosquito 10x Chromium Controller Bio-Rad ddSEQ BD FACS Melody

Posts

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 ...
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 ...
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...
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...
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...
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...
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...
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...