# epicypher knowledge base

> Knowledge base documentation for epicypher knowledge base.

## v1

- [CUT&RUN](https://support.epicypher.com/docs/cut-and-run.md)
- [Background and Resources](https://support.epicypher.com/docs/cut-and-run-background-and-resources.md)
- [Search CUT&RUN/Tag Publications](https://support.epicypher.com/docs/search-cut-run-tag-publications-3.md): Search published CUT&RUN and CUT&Tag studies by antibody target, cell type, tissue, species, and experimental conditions to guide assay design.
- [What is CUTANA™ CUT&RUN?](https://support.epicypher.com/docs/what-is-cut-and-run.md): Learn what CUT&RUN is, how it works, its advantages over ChIP-seq, and how it enables high-resolution chromatin profiling.
- [What is the difference between CUT&RUN and ChIP-seq?](https://support.epicypher.com/docs/run-vs-chip-seq.md): Compare CUT&RUN vs ChIP-seq, including workflow, cell input, sequencing depth, signal-to-noise, cost, and assay performance.
- [What are the 8 basic steps of CUT&RUN?](https://support.epicypher.com/docs/8-basic-steps-of-cut-and-run.md): Learn the 8 basic steps of the CUT&RUN workflow, from cell preparation and antibody binding to DNA purification and sequencing.
- [Where can I find the CUTANA™ CUT&RUN Protocol?](https://support.epicypher.com/docs/cutana-cut-and-run-protocol.md): Follow the CUTANA™ CUT&RUN protocol with step-by-step instructions for chromatin profiling, from sample prep to sequencing-ready DNA.
- [CUT&RUN Protocol Video](https://support.epicypher.com/docs/cut-and-run-protocol-video.md): Watch a step-by-step CUTANA™ CUT&RUN protocol video covering sample preparation, antibody binding, DNA release, and library preparation.
- [Where can I find CUT&RUN products?](https://support.epicypher.com/docs/cutana-cut-and-run-products.md): Follow the CUTANA™ CUT&RUN protocol for chromatin profiling, from sample preparation and antibody binding to sequencing-ready DNA.
- [Video library](https://support.epicypher.com/docs/video-library-cutana.md): Watch CUTANA™ videos covering CUT&RUN, CUT&Tag, protocols, workflows, best practices, troubleshooting, and epigenomics education.
- [CUT&RUN Optimization and Troubleshooting](https://support.epicypher.com/docs/assay-optimization-and-troubleshooting-cut-and-run.md)
- [What are Wash Buffer Enhancers? When and how should I use them?](https://support.epicypher.com/docs/how-do-i-know-whether-to-use-the-wash-buffer-enhancers.md): Learn when to use Wash Buffer Enhancers in CUT&RUN to improve antibody binding, reduce background, and optimize assay performance.
- [Optimizing E. coli Spike-in DNA concentration](https://support.epicypher.com/docs/optimizing-e-coli-spike-in-dna.md): Learn how to optimize E. coli spike-in DNA for CUT&RUN normalization to improve data quality, consistency, and sample comparison.
- [How to optimize CUT&RUN assays](https://support.epicypher.com/docs/how-to-optimize-cut-and-run-assays.md): Learn how to optimize CUT&RUN assays with best practices for sample prep, antibodies, digestion, library prep, and sequencing success.
- [Troubleshooting guidelines for CUT&RUN](https://support.epicypher.com/docs/troubleshooting-cut-and-run.md): Troubleshoot common CUT&RUN issues, including low yield, high background, poor enrichment, library quality, and sequencing results.
- [How many cells do I need for CUT&RUN?](https://support.epicypher.com/docs/number-cells-cut-and-run.md): Learn how many cells are recommended for CUT&RUN, minimum input requirements, and tips for optimizing low-input experiments.
- [How to optimize CUT&RUN for new targets, cell types, or low cell numbers](https://support.epicypher.com/docs/optimize-cut-and-run-targets-cells.md): Optimize CUT&RUN assays with best practices for sample preparation, antibodies, digestion, library prep, sequencing, and data quality.
- [What are signs of ConA bead damage?](https://support.epicypher.com/docs/cona-beads-damage.md): Learn how to prevent ConA bead damage during CUT&RUN and troubleshoot handling issues to improve sample recovery and assay results.
- [My ConA beads are clumpy - will this impact my yield?](https://support.epicypher.com/docs/cona-beads-sticky-cut-and-run.md): Learn why ConA beads become sticky during CUT&RUN and how to prevent clumping for improved sample handling and assay performance.
- [How do I prevent ConA beads from becoming sticky?](https://support.epicypher.com/docs/how-do-i-prevent-cona-beads-from-becoming-sticky.md): Learn how to prevent ConA beads from becoming sticky during CUT&RUN with tips for handling, washing, and maintaining bead performance.
- [Can I use qPCR or Bioanalyzer/TapeStation to evaluate raw CUT&RUN DNA?](https://support.epicypher.com/docs/qpcr-or-bioanalyzertapestation-to-evaluate-raw-cutrun-dna.md): Learn when to use qPCR or a Bioanalyzer/TapeStation to evaluate raw CUT&RUN DNA quality before library preparation and sequencing.
- [What should I do if I have low CUT&RUN yields?](https://support.epicypher.com/docs/what-should-i-do-if-i-have-low-cut-and-run-yields.md): Troubleshoot low CUT&RUN yields with tips for sample prep, antibody binding, digestion, DNA recovery, and library preparation.
- [My yields from the H3K4me3 positive control are low (i.e. below 5 ng), about the same as the IgG negative control. Did my experiment fail?](https://support.epicypher.com/docs/my-yields-from-the-positive-control-are-low-did-my-experiment-fail.md): Learn what low positive control yields mean in CUT&RUN, when to troubleshoot, and how to determine whether your experiment succeeded.
- [Experimental Controls and Success Metrics](https://support.epicypher.com/docs/controls-metrics-cut-and-run.md)
- [Summary of CUT&RUN quality control and success metrics](https://support.epicypher.com/docs/summary-of-cut-and-run-quality-control-and-success-metrics.md): Learn the key quality control metrics for CUT&RUN, including DNA yield, library quality, sequencing performance, and data analysis.
- [Why should I use an E. coli spike-in for CUT&RUN? How does it work?](https://support.epicypher.com/docs/why-should-i-use-an-e-coli-spike-in-for-cutrun.md): Learn why E. coli spike-in DNA is used in CUT&RUN for normalization, quality control, and accurate comparison between samples.
- [What are typical DNA yields from CUT&RUN?](https://support.epicypher.com/docs/cut-and-run-yields.md): Learn the expected DNA yields for CUT&RUN experiments and how yield varies by target, sample type, and overall assay performance.
- [What control antibodies and spike-ins should I use in CUT&RUN?](https://support.epicypher.com/docs/what-controls-should-i-use-cut-and-run.md): Learn which positive, negative, and spike-in controls to use for CUT&RUN to validate assay performance and interpret results.
- [How do I know ConA bead binding was successful?](https://support.epicypher.com/docs/cona-bead-binding-success-cut-and-run.md): Learn how to confirm successful ConA bead binding in CUT&RUN and optimize cell capture for reliable assay performance and results.
- [Sample Prep Protocols and Related FAQs](https://support.epicypher.com/docs/sample-prep-cut-and-run.md)
- [How to confirm high-quality sample prep in CUT&RUN](https://support.epicypher.com/docs/confirm-high-quality-sample-prep-cut-and-run.md): Learn how to assess CUT&RUN sample quality by evaluating cell viability, nuclei integrity, and preparation before starting the assay.
- [Standard CUT&RUN sample prep workflow](https://support.epicypher.com/docs/standard-cut-and-run-sample-prep-workflow.md): Follow the standard CUTANA™ sample preparation workflow, from cell collection and nuclei isolation to assay-ready samples for CUT&RUN and CUT&Tag.
- [How do I know if my cell sample is good enough for CUTANA™ assays?](https://support.epicypher.com/docs/cell-sample-good-enough-cut-and-run.md): Learn how to evaluate cell quality for CUT&RUN, including viability, morphology, integrity, and other factors that affect assay success.
- [Freeze/thawing cells](https://support.epicypher.com/docs/freeze-thawing-cells.md): How to prepare and use frozen, cryopreserved, freeze-thawed cells for CUT&RUN.
- [How should freeze/thawed cells look for CUTANA™ assays?](https://support.epicypher.com/docs/frozen-cells-sample-quality.md): Learn how to properly freeze and thaw cells for CUTANA™ CUT&RUN and CUT&Tag to preserve sample quality and maximize assay success.
- [Nuclei extraction protocol for CUTANA™ assays](https://support.epicypher.com/docs/nuclei-extraction-protocol-for-cutana-assays.md): Follow the CUTANA™ nuclei extraction protocol to isolate high-quality nuclei for CUT&RUN, CUT&Tag, and other chromatin profiling assays.
- [How should nuclei look for CUTANA™ assays?](https://support.epicypher.com/docs/how-should-nuclei-look-for-cutana.md): Learn how healthy nuclei should appear for CUTANA™ assays, including morphology, integrity, Trypan Blue staining, and quality indicators.
- [Optimizing cell permeabilization with Digitonin](https://support.epicypher.com/docs/optimizing-cell-permeabilization-with-digitonin.md): Learn how to optimize digitonin concentration for CUTANA™ CUT&RUN and CUT&Tag to improve permeabilization and assay performance.
- [Trypan blue staining protocol](https://support.epicypher.com/docs/trypan-blue-staining.md): Learn how to use Trypan Blue staining to assess cell viability and evaluate sample quality before CUTANA™ CUT&RUN and CUT&Tag assays.
- [Cross-linking cells for CUT&RUN](https://support.epicypher.com/docs/cross-linking-for-cut-and-run.md): Learn when to use cross-linking for CUT&RUN, recommended fixation conditions, protocol tips, and how to preserve assay performance.
- [Sample prep for adherent cells](https://support.epicypher.com/docs/sample-prep-for-adherent-cells.md): Learn how to prepare adherent cells for CUTANA™ CUT&RUN assays using enzymatic digestion or scraping while preserving cell quality
- [Search CUT&RUN/Tag Publications](https://support.epicypher.com/docs/search-cut-run-tag-publications-1.md): Search published CUT&RUN and CUT&Tag studies by antibody target, cell type, tissue, species, and experimental conditions to guide assay design.
- [Antibody Validation and FAQs](https://support.epicypher.com/docs/antibody-validation-cut-and-run.md)
- [Can I use my ChIP antibody for CUTANA™ assays?](https://support.epicypher.com/docs/can-i-use-my-chip-antibody-for-cutana-assays.md): Learn whether ChIP-validated antibodies work in CUTANA™ assays, why validation differs, and how to choose antibodies for best results.
- [How to validate antibodies for chromatin protein targets](https://support.epicypher.com/docs/cut-and-run-validate-a-chromatin-protein-antibody.md): Learn how to validate chromatin protein antibodies for CUT&RUN using positive controls, specificity testing, and sequencing results.
- [How to validate histone PTM antibodies](https://support.epicypher.com/docs/how-to-validate-histone-ptm-antibodies.md): Learn how to validate histone PTM antibodies for CUT&RUN by assessing specificity, controls, cross-reactivity, and sequencing results.
- [What CUT&RUN antibodies does EpiCypher offer?](https://support.epicypher.com/docs/what-cut-and-run-antibodies-does-epicypher-offer.md): Explore EpiCypher's CUT&RUN-validated antibodies for histone PTMs, transcription factors, chromatin proteins, and epitope tags.
- [Does CUT&RUN require adjustments for transcription factors or other chromatin proteins?](https://support.epicypher.com/docs/cut-and-run-adjust-for-protein-targets.md): Learn how to optimize CUT&RUN for histone modifications, transcription factors, and chromatin proteins with target-specific recommendations.
- [What antibody should I use for CUT&RUN?](https://support.epicypher.com/docs/what-antibody-should-i-use-cut-and-run.md): Learn how to choose the best antibody for CUT&RUN, including validated antibodies, target selection, and antibody performance tips.
- [SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/snap-cutana-spike-ins.md)
- [What are SNAP-CUTANA™ Spike-ins? How do they work?](https://support.epicypher.com/docs/what-are-snap-cutana-spike-ins-cut-and-run.md): Learn what SNAP-CUTANA™ Spike-ins are, how they work in CUT&RUN, and how they improve assay validation, troubleshooting, and QC.
- [When to use SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/why-use-snap-cutana-cut-and-run.md): Learn why SNAP-CUTANA™ Spike-ins improve CUT&RUN by monitoring assay success, validating antibodies, and simplifying troubleshooting.
- [Analysis and expected results for SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/analyzing-snap-cutana-spike-in-controls-and-expected-results.md): Learn how to analyze SNAP-CUTANA™ Spike-in sequencing data, interpret expected results, and evaluate CUT&RUN and CUT&Tag assay success.
- [Determine assay success using SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/using-snap-cutana-spike-in-controls-to-determine-assay-success.md): Learn how SNAP-CUTANA™ Spike-ins determine CUT&RUN assay success by monitoring controls, specificity, background, and workflow performance.
- [Troubleshoot workflows using SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/using-snap-cutana-spike-ins-to-troubleshoot-workflows.md): Learn how to use SNAP-CUTANA™ Spike-ins to identify workflow issues, troubleshoot failed assays, and improve CUT&RUN and CUT&Tag results.
- [Validate histone PTM antibodies using SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/using-snap-cutana-spike-in-controls-for-histone-ptm-antibody-validation.md): Learn how SNAP-CUTANA™ Spike-ins validate histone PTM antibody specificity and identify off-target binding in CUT&RUN and CUT&Tag.
- [Sequencing and Data Analysis](https://support.epicypher.com/docs/sequencing-and-data-analysis-cut-and-run.md)
- [Sequencing metrics for CUT&RUN](https://support.epicypher.com/docs/cut-and-run-sequencing-metrics.md): Learn the expected CUT&RUN sequencing metrics, including read depth, alignment, duplication rates, controls, and assay QC benchmarks.
- [Analyzing CUT&RUN and CUT&Tag sequencing data](https://support.epicypher.com/docs/analyzing-cut-and-run-cut-and-tag-data.md): Learn how to analyze CUT&RUN and CUT&Tag data, including alignment, peak calling, normalization, visualization, and quality control.
- [How many reads do I need for the K-MetStat Panel?](https://support.epicypher.com/docs/how-many-reads-do-i-need-for-kmetstat.md): Learn how many sequencing reads the K-MetStat Panel requires for reliable spike-in analysis, normalization, and CUT&RUN quality control.
- [How many reads do I need for E. coli Spike-in DNA?](https://support.epicypher.com/docs/reads-for-e-coli-dna.md): Learn how many E. coli spike-in reads are needed for reliable CUT&RUN normalization and how to optimize spike-in DNA levels.
- [Normalizing to E. coli Spike-in DNA](https://support.epicypher.com/docs/normalizing-to-e-coli-spike-in-dna.md): Learn how to normalize CUT&RUN sequencing data using E. coli spike-in DNA for accurate sample comparison and quantitative analysis.
- [Considerations when sequencing low-concentration libraries](https://support.epicypher.com/docs/cut-and-run-sequence-low-concentration.md): Learn how to sequence low-concentration CUT&RUN libraries, improve library yields, and maximize sequencing success with limited DNA.
- [Do I need to sequence an input control?](https://support.epicypher.com/docs/do-i-need-to-sequence-an-input-control.md): Learn why CUT&RUN does not require an input control and which controls to sequence instead for accurate quality control and analysis.
- [Why is there high background in my sequencing data?](https://support.epicypher.com/docs/why-is-there-high-background-in-my-sequencing-data.md): Troubleshoot high background in CUT&RUN sequencing data by evaluating sample prep, antibodies, MNase digestion, library prep, and QC.
- [Why is there background in open chromatin in my sequencing data?](https://support.epicypher.com/docs/why-is-there-background-in-open-chromatin-in-my-sequencing-data.md): Learn why open chromatin background occurs in CUT&RUN sequencing data and how to reduce it by optimizing digestion and sequencing depth.
- [DIY Protocol](https://support.epicypher.com/docs/diy-protocol.md)
- [CUT&RUN DIY Protocol (Non-Kit Users)](https://support.epicypher.com/docs/cutrun-diy-protocol.md): Perform CUT&RUN without a commercial kit using this DIY protocol, Epicypher's reagent list, workflow, controls, and optimization recommendations.
- [CUT&RUN Library Prep Kit](https://support.epicypher.com/docs/cutrun-library-prep-kit.md)
- [Library Prep Kit Usage and Modifications](https://support.epicypher.com/docs/library-prep-kit-usage-and-modifications.md)
- [What instructions can I give my third party provider for library preparation and sequencing?](https://support.epicypher.com/docs/what-instructions-can-i-give-my-third-party-provider-for-library-preparation-and-sequencing.md)
- [Does this kit use UDI adapters?](https://support.epicypher.com/docs/does-this-kit-use-udi-adapters.md)
- [When should I remove adapter dimers? What protocol do you recommend?](https://support.epicypher.com/docs/when-should-i-remove-adapter-dimers.md)
- [Can I use this kit to prepare CUT&RUN libraries for transcription factors?](https://support.epicypher.com/docs/can-i-use-this-kit-to-prep-cutrun-libraries-for-transcription-factors.md)
- [Can I use other vendors' library prep kits?](https://support.epicypher.com/docs/can-i-use-other-vendors-library-prep-kits.md)
- [How do I confirm the quality of my CUT&RUN sequencing library?](https://support.epicypher.com/docs/confirm-quality-of-sequencing-library.md)
- [Input, Yield, and Amplification](https://support.epicypher.com/docs/input-yield-and-amplification.md)
- [Why are there no peaks in my Bioanalyzer/TapeStation results?](https://support.epicypher.com/docs/why-are-there-no-peaks-in-my-bioanalyzer-tapestation-results.md)
- [Preparing libraries from low CUT&RUN yields](https://support.epicypher.com/docs/cut-and-run-library-prep-low-yields.md)
- [Should I size select or fragment my CUT&RUN DNA before library prep?](https://support.epicypher.com/docs/should-i-size-select-or-fragment-my-cutrun-dna-before-library-prep.md)
- [Do I need to increase my PCR cycle number for low input DNA?](https://support.epicypher.com/docs/do-i-need-to-increase-my-pcr-cycle-number-for-low-input-dna.md)
- [What should I do if my library yields are low (less than 0.5 nM)?](https://support.epicypher.com/docs/what-should-i-do-if-my-library-yields-are-low-less-than-05-nm.md)
- [What yields are typical using this kit? What yields are required for Illumina® sequencing?](https://support.epicypher.com/docs/what-yields-are-typical-using-this-kit-what-is-required-for-illumina-sequencing.md)
- [Multiplexing and Indexing](https://support.epicypher.com/docs/multiplexing-and-indexing.md)
- [How do I make an equimolar pool for sequencing?](https://support.epicypher.com/docs/how-do-i-create-an-equimolar-pool.md)
- [Quality Control and Traces](https://support.epicypher.com/docs/quality-control-and-traces.md)
- [What do large DNA fragment sizes in Bioanalyzer/TapeStation mean?](https://support.epicypher.com/docs/what-do-large-dna-fragment-sizes-mean.md)
- [What do adapter dimers look like in CUT&RUN and how do I avoid them?](https://support.epicypher.com/docs/what-do-adapter-dimers-look-like-in-cut-and-run.md)
- [My library is enriched for fragments at ~150 bp. What does this mean?](https://support.epicypher.com/docs/my-library-is-enriched-for-fragments-at-150-bp.md)
- [CUT&Tag](https://support.epicypher.com/docs/cut-and-tag.md)
- [Background and Resources](https://support.epicypher.com/docs/cut-and-tag-background-and-resources.md)
- [What is CUTANA™ CUT&Tag?](https://support.epicypher.com/docs/what-is-cut-and-tag.md)
- [CUTANA™ CUT&Tag Protocol](https://support.epicypher.com/docs/cutana-cut-and-tag-protocol.md)
- [What are the basic steps of CUT&Tag?](https://support.epicypher.com/docs/basic-steps-of-cut-and-tag.md)
- [Where can I find CUT&Tag products?](https://support.epicypher.com/docs/cutana-cut-and-tag-products.md)
- [Video library](https://support.epicypher.com/docs/video-library-cut-and-tag.md): Watch CUTANA™ videos covering CUT&RUN, CUT&Tag, protocols, workflows, best practices, troubleshooting, and epigenomics education.
- [CUT&Tag Optimization and Troubleshooting](https://support.epicypher.com/docs/assay-optimization-and-troubleshooting-cut-and-tag.md)
- [How to optimize CUT&Tag assays](https://support.epicypher.com/docs/how-to-optimize-cut-and-tag.md)
- [Troubleshooting low CUT&Tag yields](https://support.epicypher.com/docs/troubleshooting-cut-and-tag-yields.md)
- [Troubleshooting CUT&Tag Sequencing Results](https://support.epicypher.com/docs/troubleshooting-cut-and-tag-sequencing.md)
- [How many cells do I need for CUT&Tag?](https://support.epicypher.com/docs/number-cells-cut-and-tag.md)
- [Why is there high background in my CUT&Tag sequencing data?](https://support.epicypher.com/docs/high-background-cut-and-tag.md)
- [When should I remove primer dimers? What protocol do you recommend?](https://support.epicypher.com/docs/primer-dimer-removal-questions.md)
- [My CUT&Tag library is enriched for fragments ~100 bp. What does this mean?](https://support.epicypher.com/docs/cut-and-tag-small-fragments.md)
- [What do primer dimers look like in CUT&Tag and how do I avoid them?](https://support.epicypher.com/docs/how-to-avoid-primer-dimers.md)
- [What do large DNA fragment sizes in Bioanalyzer/TapeStation mean in CUT&Tag?](https://support.epicypher.com/docs/large-fragments-cut-and-tag.md)
- [What are Wash Buffer Enhancers? When and how should I use them?](https://support.epicypher.com/docs/what-are-wash-buffer-enhancers-when-should-i-use-them.md): Learn when to use Wash Buffer Enhancers in CUT&RUN to improve antibody binding, reduce background, and optimize assay performance.
- [Experimental Controls and Success Metrics](https://support.epicypher.com/docs/controls-metrics-cut-and-tag.md)
- [Summary of CUT&Tag quality control and success metrics](https://support.epicypher.com/docs/summary-of-cut-and-tag-quality-control-and-success-metrics.md)
- [What control antibodies and spike-ins should I use in CUT&Tag?](https://support.epicypher.com/docs/what-controls-should-i-use-cut-and-tag.md)
- [How do I confirm the quality of my CUT&Tag sequencing library?](https://support.epicypher.com/docs/confirm-quality-of-cut-and-tag-library.md)
- [Sample Prep Protocols and Related FAQs](https://support.epicypher.com/docs/sample-prep-cut-and-tag.md)
- [How to confirm high-quality sample prep in CUT&Tag](https://support.epicypher.com/docs/confirm-high-quality-sample-prep-cut-and-tag.md)
- [How do I know if my cell sample is good enough for CUTANA™ assays?](https://support.epicypher.com/docs/cell-sample-good-enough-cut-and-tag.md)
- [Nuclei extraction protocol for CUTANA™ assays](https://support.epicypher.com/docs/nuclei-extraction-cut-and-tag.md)
- [How should nuclei look for CUTANA™ assays?](https://support.epicypher.com/docs/how-should-nuclei-look-cut-and-tag.md)
- [Freeze/thawing cells](https://support.epicypher.com/docs/freeze-thaw-cells-cut-and-tag.md): How to prepare and use frozen, cryopreserved, freeze-thawed cells for CUT&RUN.
- [How should freeze/thawed cells look for CUTANA™ assays?](https://support.epicypher.com/docs/frozen-cells-quality-cut-and-tag.md)
- [Trypan blue staining protocol](https://support.epicypher.com/docs/trypan-blue-staining-cut-and-tag.md): Learn how to use Trypan Blue staining to assess cell viability and evaluate sample quality before CUTANA™ CUT&RUN and CUT&Tag assays.
- [Optimizing cell permeabilization with Digitonin](https://support.epicypher.com/docs/optimizing-cell-permeabilization-cut-and-tag.md)
- [Cross-linking cells for CUT&Tag](https://support.epicypher.com/docs/cross-linking-cut-and-tag.md)
- [Sample prep for adherent cells](https://support.epicypher.com/docs/adherent-cells-cut-and-tag.md): Learn how to prepare adherent cells for CUTANA™ CUT&RUN assays using enzymatic digestion or scraping while preserving cell quality
- [Search CUT&RUN/Tag Publications](https://support.epicypher.com/docs/search-cut-run-tag-publications-2.md): Search published CUT&RUN and CUT&Tag studies by antibody target, cell type, tissue, species, and experimental conditions to guide assay design.
- [Antibody Validation and FAQs](https://support.epicypher.com/docs/antibody-validation-cut-and-tag.md)
- [How to validate histone PTM antibodies](https://support.epicypher.com/docs/validate-histone-ptm-antibodies-cut-and-tag.md)
- [Can I use my ChIP antibody for CUTANA™ assays?](https://support.epicypher.com/docs/can-i-use-my-chip-antibody-for-cut-and-tag.md)
- [What should I do if my antibody doesn't work in CUT&Tag?](https://support.epicypher.com/docs/antibody-failure-cut-and-tag.md)
- [What CUT&Tag antibodies does EpiCypher offer?](https://support.epicypher.com/docs/what-cut-and-tag-antibodies-does-epicypher-offer.md)
- [Can I map chromatin-associated proteins in CUT&Tag?](https://support.epicypher.com/docs/chromatin-associated-proteins-cut-and-tag.md)
- [What antibody should I use for CUT&Tag?](https://support.epicypher.com/docs/what-antibody-should-i-use-cut-and-tag.md)
- [SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/snap-cutana-spike-ins-cut-and-tag.md)
- [What are SNAP-CUTANA™ Spike-ins? How do they work?](https://support.epicypher.com/docs/what-are-snap-cutana-spike-ins-cut-and-tag.md)
- [When to use SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/why-use-snap-cutana-cut-and-tag.md)
- [Analysis and expected results for SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/analyzing-snap-cutana-spike-in-controls-and-results-cut-and-tag.md)
- [Determine assay success using SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/snap-cutana-controls-assay-success-cut-and-tag.md)
- [Troubleshoot workflows using SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/using-snap-cutana-spike-ins-to-troubleshoot-workflows-cut-and-tag.md)
- [Validate histone PTM antibodies using SNAP-CUTANA™ Spike-ins](https://support.epicypher.com/docs/snap-cutana-histone-ptm-antibody-validation-cut-and-tag.md)
- [Sequencing and Data Analysis](https://support.epicypher.com/docs/sequencing-and-data-analysis-cut-and-tag.md)
- [Sequencing metrics for CUT&Tag](https://support.epicypher.com/docs/cut-and-tag-sequencing-metrics.md)
- [Considerations when sequencing low-concentration CUT&Tag libraries](https://support.epicypher.com/docs/cut-and-tag-sequence-low-concentration.md)
- [Why do I have high read duplication rates in my CUT&Tag data?](https://support.epicypher.com/docs/high-read-duplicates-cut-and-tag.md)
- [How many sequencing reads are needed for CUT&Tag?](https://support.epicypher.com/docs/sequencing-reads-cut-and-tag.md)
- [Why is there background in open chromatin in my CUT&Tag data?](https://support.epicypher.com/docs/background-open-chromatin-cut-and-tag.md)
- [Are there adapter dimers in my CUT&Tag library?](https://support.epicypher.com/docs/adapter-dimers-cut-and-tag.md)
- [Can I use E. coli DNA for CUT&Tag sequencing normalization?](https://support.epicypher.com/docs/e-coli-dna-cut-and-tag.md)
- [Analyzing CUT&RUN and CUT&Tag sequencing data](https://support.epicypher.com/docs/analyzing-cut-and-tag.md)
- [DIY Protocol](https://support.epicypher.com/docs/diy-protocol-1.md)
- [CUT&Tag DIY Protocol (Non-Kit Users)](https://support.epicypher.com/docs/cuttag-diy-protocol.md)
- [ATAC-seq](https://support.epicypher.com/docs/atac-seq.md)
- [Sample Prep Protocols and Related FAQs](https://support.epicypher.com/docs/atac-seq-sample-prep.md)
- [What sample types are compatible with the CUTANA™ ATAC-seq Kit?](https://support.epicypher.com/docs/what-sample-types-are-compatible-with-the-cutana-atac-seq-kit.md)
- [How do I confirm high-quality sample preparation for ATAC-seq?](https://support.epicypher.com/docs/how-do-i-confirm-high-quality-sample-preparation-for-atac-seq.md)
- [How should I approach low-input ATAC-seq samples?](https://support.epicypher.com/docs/how-should-i-approach-low-input-atac-seq-samples.md)
- [Library QC, Sequencing, and Data Analysis](https://support.epicypher.com/docs/atac-seq-library-qc-sequencing-and-data-analysis.md)
- [Should I still sequence my sample if the TapeStation/Bioanalyzer trace looks suboptimal?](https://support.epicypher.com/docs/should-i-still-sequence-my-atac-seq-if-trace-looks-suboptimal.md)
- [How do I analyze CUTANA™ ATAC-seq data?](https://support.epicypher.com/docs/how-do-i-analyze-cutana-atac-seq-data.md)
- [Sequencing metrics for ATAC-seq](https://support.epicypher.com/docs/sequencing-metrics-for-atac-seq.md)
- [Why do I have high mitochondrial reads or duplicates in my ATAC-seq data? How can I troubleshoot?](https://support.epicypher.com/docs/why-do-i-have-low-high-mitochondrial-reads-duplicates-in-my-atac-seq-data.md)
- [Summary of ATAC-seq quality control and success metrics](https://support.epicypher.com/docs/summary-of-atac-seq-quality-control-and-success-metrics.md)
- [Reagent Handling and Best Practices](https://support.epicypher.com/docs/reagent-handling-and-best-practices.md)
- [Can I use my own 1X PBS with the CUTANA™ ATAC-seq Kit?](https://support.epicypher.com/docs/can-i-use-my-own-1x-pbs-with-the-cutana-atac-seq-kit.md)
- [Can I use the CUTANA™ ATAC-seq Kit if I don’t have an 8-strip tube compatible thermomixer?](https://support.epicypher.com/docs/can-i-use-the-cutana-atac-seq-kit-if-i-dont-have-an-8-strip-tube.md)
- [How stable is CUTANA™ Tn5 Transposome? Will multiple freeze/thaws of from storage at -80ºC lead to lost activity? Should I aliquot the enzyme?](https://support.epicypher.com/docs/how-stable-is-cutana-tn5-transposome.md)
- [Do you have a recommended DIY ATAC-seq protocol if I’m only using CUTANA™ Tn5 Transposome?](https://support.epicypher.com/docs/do-you-have-recommended-diy-atac-seq-protocol.md)
- [What primers can I use with the CUTANA ATAC-seq Kit or Tn5 Transposome?](https://support.epicypher.com/docs/what-primers-can-i-use-with-the-cutana-atac-seq-kit-or-tn5-transposome.md)
- [Explore Fiber-seq](https://support.epicypher.com/docs/fiber-seq.md)
- [NEW! Shallow QC Sequencing for Fiber-seq](https://support.epicypher.com/docs/shallow-qc-sequencing-for-fiber-seq.md)
- [Can I check if my Fiber-seq labeling was done correctly before preparing an LRS library?](https://support.epicypher.com/docs/can-i-check-my-fiber-seq-labeling-was-done-correctly.md)
- [How do I analyze my Plasmidsaurus Fiber-seq QC sequencing data?](https://support.epicypher.com/docs/how-do-i-analyze-my-fiber-seq-qc-sequencing-data.md)
- [Can I use Plasmidsaurus QC-sequencing for non-human samples?](https://support.epicypher.com/docs/can-i-use-plasmidsaurus-qc-sequencing-for-non-human-samples.md)
- [My % 6mA (and other QC metrics) changed after deep sequencing. Did I do something wrong?](https://support.epicypher.com/docs/qc-metrics-changed-after-deep-sequencing.md)
- [How much DNA do I need to submit for QC sequencing?](https://support.epicypher.com/docs/how-much-dna-for-qc-sequencing.md)
- [Do you have any recommendations for full Fiber-seq sequencing?](https://support.epicypher.com/docs/recommendations-for-full-fiber-seq-sequencing.md)
- [If my final sequencing will be on PacBio, does QC on the Plasmidsaurus ONT device still reflect performance?](https://support.epicypher.com/docs/if-my-final-sequencing-will-be-on-pacbio-does-qc-on-plasmidsaurus-ont-device-sti.md)
- [What is Fiber-seq?](https://support.epicypher.com/docs/what-is-fiber-seq.md)
- [How does Fiber-seq work?](https://support.epicypher.com/docs/how-does-fiber-seq-work.md)
- [Where can I find the EpiCypher Fiber-seq protocol?](https://support.epicypher.com/docs/where-can-i-find-the-epicypher-fiber-seq-protocol.md)
- [What samples and cell types are compatible with Fiber-seq?](https://support.epicypher.com/docs/what-samples-and-cell-types-are-compatible-with-fiber-seq.md)
- [What do I need to purchase to start Fiber-seq?](https://support.epicypher.com/docs/what-do-i-need-to-purchase-to-start-fiber-seq.md)
- [Can Fiber-seq be used to study DNA-binding proteins?](https://support.epicypher.com/docs/can-fiber-seq-be-used-to-study-dna-binding-proteins.md)
- [Does Hia5 labeling affect sequencing quality?](https://support.epicypher.com/docs/does-hia5-affect-sequencing-quality.md)
- [What library prep kits and sequencing machines are compatible with Fiber-seq?](https://support.epicypher.com/docs/what-library-prep-and-sequencing-machines-are-compatible-with-fiber-seq.md)
- [What if my sample is from an organism without a reference genome?](https://support.epicypher.com/docs/what-if-my-sample-is-from-an-organism-without-a-reference-genome.md)
- [How do I analyze Fiber-seq data?](https://support.epicypher.com/docs/how-do-i-analyze-fiber-seq-data.md)
- [What are the real-world applications of Fiber-seq?](https://support.epicypher.com/docs/what-are-the-real-world-applications-of-fiber-seq.md)
- [How can I figure out the ideal Hia5 ratio for my project?](https://support.epicypher.com/docs/how-can-i-figure-out-the-ideal-hia5-ratio-for-my-project.md)
- [Nuclei extraction protocol for Fiber-seq](https://support.epicypher.com/docs/nuclei-extraction-protocol-for-fiber-seq.md)
- [meCUT&RUN](https://support.epicypher.com/docs/mecutrun.md)
- [Background and Resources](https://support.epicypher.com/docs/mecut-and-run-background-and-resources.md)
- [What is CUTANA™ meCUT&RUN?](https://support.epicypher.com/docs/what-is-mecutrun.md)
- [Which reagents are needed for meCUT&RUN?](https://support.epicypher.com/docs/generic-article-template-4.md)
- [meCUT&RUN FAQs](https://support.epicypher.com/docs/mecutrun-faqs.md)
- [How do I analyze meCUT&RUN data?](https://support.epicypher.com/docs/how-do-i-analyze-mecutrun-data.md)
- [What controls should I use in meCUT&RUN?](https://support.epicypher.com/docs/generic-article-template-1.md)
- [Can I do a cytosine conversion on meCUT&RUN DNA? What is meCUT&RUN-EM?](https://support.epicypher.com/docs/cytosine-conversion-mecutrun-em.md)
- [What type of methylation does meCUT&RUN detect?](https://support.epicypher.com/docs/generic-article-template-6.md)
- [CUTANA Sample Prep](https://support.epicypher.com/docs/cutana-sample-prep.md)
- [Start Here](https://support.epicypher.com/docs/sample-prep-start-here.md)
- [Search CUT&RUN/Tag Publications](https://support.epicypher.com/docs/search-cut-run-tag-publications.md): Search published CUT&RUN and CUT&Tag studies by antibody target, cell type, tissue, species, and experimental conditions to guide assay design.
- [Should I use cells or nuclei?](https://support.epicypher.com/docs/should-i-use-cells-or-nuclei.md)
- [Should I clean up my nuclei? How do different nuclei cleanup options compare?](https://support.epicypher.com/docs/how-do-different-nuclei-cleanup-options-compare.md)
- [How to confirm high-quality sample prep in CUT&RUN](https://support.epicypher.com/docs/how-to-confirm-high-quality-sample-prep-in-cut-run.md): Learn how to assess CUT&RUN sample quality by evaluating cell viability, nuclei integrity, and preparation before starting the assay.
- [How should freeze/thawed cells look for CUTANA™ assays?](https://support.epicypher.com/docs/how-should-freeze-thawed-cells-look-for-cutana-assays.md): Learn how to properly freeze and thaw cells for CUTANA™ CUT&RUN and CUT&Tag to preserve sample quality and maximize assay success.
- [How should nuclei look for CUTANA™ assays?](https://support.epicypher.com/docs/how-should-nuclei-look-for-cutana-assays.md): Learn how healthy nuclei should appear for CUTANA™ assays, including morphology, integrity, Trypan Blue staining, and quality indicators.
- [Standard Protocols](https://support.epicypher.com/docs/standard-protocols.md)
- [Nuclei extraction protocol for Fiber-seq](https://support.epicypher.com/docs/nuclei-extraction-for-fiber-seq.md)
- [General Automated Tissue Dissociation Protocol](https://support.epicypher.com/docs/general-automated-tissue-dissociation-protocol.md)
- [General Manual Tissue Dissociation Protocol](https://support.epicypher.com/docs/general-manual-tissue-dissociation-protocol.md)
- [Are CUTANA assays compatible with cell sorting?](https://support.epicypher.com/docs/are-cutana-assays-compatible-with-cell-sorting.md)
- [How do I know if my cell sample is good enough for CUTANA™ assays?](https://support.epicypher.com/docs/how-do-i-know-if-my-cell-sample-is-good-enough-for-cutana-assays.md): Learn how to evaluate cell quality for CUT&RUN, including viability, morphology, integrity, and other factors that affect assay success.
- [Standard CUT&RUN sample prep workflow](https://support.epicypher.com/docs/standard-sample-prep-workflow-1.md): Follow the standard CUTANA™ sample preparation workflow, from cell collection and nuclei isolation to assay-ready samples for CUT&RUN and CUT&Tag.
- [Nuclei extraction protocol for CUTANA™ assays](https://support.epicypher.com/docs/nuclei-extraction-protocol-for-cutana-assays-1.md): Follow the CUTANA™ nuclei extraction protocol to isolate high-quality nuclei for CUT&RUN, CUT&Tag, and other chromatin profiling assays.
- [Freeze/thawing cells](https://support.epicypher.com/docs/freeze-thawing-cells-1.md): How to prepare and use frozen, cryopreserved, freeze-thawed cells for CUT&RUN.
- [Optimizing cell permeabilization with Digitonin](https://support.epicypher.com/docs/optimizing-cell-permeabilization-with-digitonin-1.md): Learn how to optimize digitonin concentration for CUTANA™ CUT&RUN and CUT&Tag to improve permeabilization and assay performance.
- [Trypan blue staining protocol](https://support.epicypher.com/docs/trypan-blue-staining-protocol.md): Learn how to use Trypan Blue staining to assess cell viability and evaluate sample quality before CUTANA™ CUT&RUN and CUT&Tag assays.
- [Cross-linking cells for CUT&RUN](https://support.epicypher.com/docs/cross-linking-cells-for-cut-run.md): Learn when to use cross-linking for CUT&RUN, recommended fixation conditions, protocol tips, and how to preserve assay performance.
- [Sample prep for adherent cells](https://support.epicypher.com/docs/sample-prep-for-adherent-cells-1.md): Learn how to prepare adherent cells for CUTANA™ CUT&RUN assays using enzymatic digestion or scraping while preserving cell quality
- [Cross-linking cells for CUT&Tag](https://support.epicypher.com/docs/cross-linking-cells-for-cut-tag.md)
- [Working with Tissue](https://support.epicypher.com/docs/working-with-tissue.md)
- [What are general guidelines for processing tissue for CUTANA assays?](https://support.epicypher.com/docs/what-are-general-guidelines-for-processing-tissue-for-cutana-assays.md)
- [What are tips for working with specific tissue types in CUTANA assays?](https://support.epicypher.com/docs/what-are-tips-for-specific-tissue-types-in-cutana-assays.md)
- [Can fluorescent markers be used for counting nuclei for CUTANA assays?](https://support.epicypher.com/docs/can-fluorescent-markers-be-used-for-counting-nuclei-for-cutana-assays.md)
- [Sample Prep Troubleshooting](https://support.epicypher.com/docs/sample-prep-troubleshooting.md)
- [What advice do you have for counting my cells/nuclei?](https://support.epicypher.com/docs/what-advice-do-you-have-for-counting-my-cells-nuclei.md)
- [Troubleshooting nuclei extraction in cell lines](https://support.epicypher.com/docs/troubleshooting-nuclei-extraction.md)
- [What should ConA beads look like?](https://support.epicypher.com/docs/what-should-cona-beads-look-like.md)
- [How should I deal with debris after cell/nuclei isolation?](https://support.epicypher.com/docs/how-should-i-deal-with-debris-after-cell-nuclei-isolation.md)
- [CUTANA Cloud](https://support.epicypher.com/docs/cutana-cloud.md)
- [General](https://support.epicypher.com/docs/cloud-general.md)
- [What is CUTANA Cloud?](https://support.epicypher.com/docs/what-is-cutana-cloud.md)
- [Does CUTANA Cloud eliminate the need for a bioinformatician?](https://support.epicypher.com/docs/does-cutana-cloud-eliminate-the-need-for-a-bioinformatician.md)
- [What is the Reaction Details Template?](https://support.epicypher.com/docs/what-is-the-reaction-details-template.md)
- [Do I need to be a bioinformatician to use CUTANA Cloud?](https://support.epicypher.com/docs/do-i-need-to-be-a-bioinformatician-to-use-cutana-cloud.md)
- [What types of sequencing files are compatible with CUTANA Cloud?](https://support.epicypher.com/docs/what-types-of-sequencing-are-compatible-with-cutana-cloud.md)
- [Why are multiple FASTQ files appearing with the same sample name?](https://support.epicypher.com/docs/why-are-two-multiple-fastq-files-appearing-with-the-same-sample-name.md)
- [Do I need to trim my FASTQ files?](https://support.epicypher.com/docs/do-i-need-to-trim-my-fastq-files.md)
- [How do I trim my FASTQ files?](https://support.epicypher.com/docs/how-do-i-trim-my-fastq-files.md)
- [How do I import FASTQ files?](https://support.epicypher.com/docs/how-do-i-import-fastq-files.md)
- [What is the difference between a FASTQ and a reaction?](https://support.epicypher.com/docs/what-is-the-difference-between-a-fastq-and-a-reaction.md)
- [What are Reaction Details?](https://support.epicypher.com/docs/what-are-reaction-details.md)
- [What is 'CUTANA Spike-In 2'?](https://support.epicypher.com/docs/what-is-cutana-spike-in-2.md)
- [Alignment](https://support.epicypher.com/docs/cloud-alignment.md)
- [What is Alignment?](https://support.epicypher.com/docs/what-is-alignment.md)
- [What is an Experiment?](https://support.epicypher.com/docs/what-is-an-experiment.md)
- [What does the CUTANA CUT&RUN/Tag pipeline do?](https://support.epicypher.com/docs/what-does-the-cutana-cutruntag-pipeline-do.md)
- [What is a Project?](https://support.epicypher.com/docs/what-is-a-project.md)
- [Can I run multiple alignments at the same time?](https://support.epicypher.com/docs/can-i-run-multiple-alignments-at-the-same-time.md)
- [How do I interpret the Alignment QC Report?](https://support.epicypher.com/docs/how-do-i-interpret-the-alignment-qc-report.md)
- [Where do I find the outputs of the Alignment pipeline?](https://support.epicypher.com/docs/where-do-i-find-the-outputs-of-the-alignment-pipeline.md)
- [Peak Calling](https://support.epicypher.com/docs/cloud-peak-calling.md)
- [What is Peak Calling?](https://support.epicypher.com/docs/what-is-peak-calling.md)
- [How do I decide if my data is good enough to call peaks?](https://support.epicypher.com/docs/how-do-i-decide-if-my-data-is-good-enough-to-call-peaks.md)
- [Can I call peaks on files from multiple alignments?](https://support.epicypher.com/docs/can-i-call-peaks-on-files-from-multiple-alignments.md)
- [How do I interpret the Peak Calling QC Report?](https://support.epicypher.com/docs/how-do-i-interpret-the-peak-calling-qc-report.md)
- [How do I determine if my peak calling worked?](https://support.epicypher.com/docs/how-do-i-determine-if-my-peak-calling-worked.md)
- [Can I call peaks on reactions aligned outside of CUTANA Cloud?](https://support.epicypher.com/docs/can-i-call-peaks-on-reactions-aligned-outside-of-cutana-cloud.md)
- [How many analysis credits does Peak Calling use?](https://support.epicypher.com/docs/how-many-analysis-credits-does-peak-calling-use.md)
- [Additional Analysis](https://support.epicypher.com/docs/cloud-additional-analysis.md)
- [How do I make publication-quality browser tracks?](https://support.epicypher.com/docs/how-do-i-make-publication-quality-browser-tracks.md)
- [How do I perform XYZ analysis?](https://support.epicypher.com/docs/how-do-i-perform-xyz-analysis.md)
- [Account Management](https://support.epicypher.com/docs/cloud-account-management.md)
- [What is a Billing Account?](https://support.epicypher.com/docs/what-is-a-billing-account.md)
- [Can a Billing Account or Project have more than one Admin?](https://support.epicypher.com/docs/can-a-billing-account-or-project-have-more-than-one-admin.md)
- [What is the difference between a Billing Account Admin and Member?](https://support.epicypher.com/docs/what-is-the-difference-between-a-billing-account-admin-and-member.md)
- [Is CUTANA Cloud GDPR compliant?](https://support.epicypher.com/docs/is-cutana-cloud-gdpr-compliant.md)
- [Nucleosomes](https://support.epicypher.com/docs/nucleosomes.md)
- [Nucleosome Quantification Method](https://support.epicypher.com/docs/nucleosome-quantification.md)