Di Hu
9 months ago

SPRI bead size selection guidance for histone marks

SPRI bead size selection guidance for histone marks

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 ...
GenomicsEpigeneticsNGS Library PreparationSequencingMagnetic BeadsGenomic DNA Library PreparationEpigenomicsQuality AssessmentSample PreparationDNA library preparation
Di Hu
9 months ago

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?

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...
GenomicsChIP-SequencingChromatinEpigenomicsEpigeneticsSequencingGenomic DNA Library PreparationDNA library preparationBenchmarkingDNA AmplificationPCRNext Generation Sequencing
Di Hu
9 months ago

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

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...
GenomicsNeuroscienceSingle Cell Genomics single-cell transcriptomes single-cell sorting single-cell RNA sequencing Genomic DNA Library PreparationNGS Library PreparationSequencingFACSFACS StainingBrainSpinal CordAntibody DetectionHumans
Di Hu
9 months ago

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

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

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...
Single Cell Isolation single-cell sorting single-cell RNA sequencing EpigeneticsGenomic DNA Library PreparationNGS Library PreparationSequencingCancerHealthy AgingGenomicsRoboticsSingle cell cloningSingle Cell Genomics
Di Hu
9 months ago

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

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...
GenomicsTranscriptomicsEpigenomicsSequencingSingle Cell GenomicsGenomic DNA Library PreparationNGS Library Preparation qPCR FACSBioanalyzerRNA-sequencing
Di Hu
10 months ago

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

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...
Aging Researchaged mousehumanised mouseGenomicsNeuroscienceEpigenomicsEpigeneticsGenomic DNA Library PreparationSequencing
Di Hu
10 months ago
Method

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

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...
GenomicsEpigeneticsSequencingGenomic DNA Library Preparation qPCR ChIP-Sequencing
Guy Rohkin
10 months ago
Method

Using the Illumina Nextera XT kit at 1/3 reagents

Using the Illumina Nextera XT kit at 1/3 reagents

In a genomics lab, if you need to work with really low input DNA samples you can use the Illumina Nextera XT kit. That being said, the kit is rather expensive and can be adapted to work perfectly fine by using 1/3 reagents for your reactions! You'll get pretty much the same results just make sure you keep the ratio of volum...
GenomicsGenetic EngineeringMolecular BiologyNGS Library PreparationGenomic DNA Library Preparation Nextera XT Illumina SequencingDNA Sequencing / Analysis SystemsAgilent Bioanalyzer 2100