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

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

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

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