Product overview
High-resolution Epigenetic Profiling
Illuminate cell type-specific methylation signatures
Powerful Chemistry
Interrogate hundreds of thousands of CpG and CH sites per cell
Scalable Insights
Capture thousands of cells per run with seamless sample multiplexing
Target Enrichment Compatibility
Maximize your sequencing budget by focusing on specific regions of interest
Key advantages
True high-resolution epigenetics
Methylation is a heritable and stable epigenetic mark making it ideal for robust detection of epigenetic complexity in tissues. Detect single cell methylomes from thousands of cells with ease with our kitted solution, without hassle of complex, custom protocols or unvalidated reagents.
Discover cell type-specific methylation patterns
Most methylation data today is from bulk-level analysis. Break through the noise and unmask methylation patterns on a cell type-specific level.
Single cell analysis enables detection of differentially methylated regions specifically in cancer stem cells.
Focus on what matters most
Maximize your sequencing budget and expand the number of samples profiled by generating target-enriched libraries, without worrying about leaving important CpGs behind.
Target enrichment captures similar PBMC cell types as whole genome single cell methylation data with 75% fewer sequencing reads. Targeted single cell methylation library generated using Twist Human Methylome Target Enrichment panel.
Streamlined workflow
Massively parallelized single cell barcoding, the powerful technology behind Scale Bio's Single Cell Methylation Sequencing Kit, leverages the cell as the reaction compartment.
1. Fixation and nucleosome depletion: First, nuclei are fixed and nucleosomes depleted. Store for up to 4 weeks, or process right away.
2. First-level indexing: Fixed nuclei are distributed into 96-well plates for in situ tagmentation with a well-specific oligo index. After tagmentation, nuclei are pooled and distributed into a second 96-well plate.
3. Bisulfite conversion: Fixed nuclei undergo bisulfite conversion for detecting methylated cytosines. Unmethylated cytosines are converted to uracils, while methylated cytosines are protected from conversion.
4. Second-level indexing: A second well-specific oligo index is added via PCR, and sequencing adapters are also attached. The combination of the first and second level indices enable a unique cellular barcode for single cell analysis.
5. (Optional) Target enrichment: Using your panel of choice, enrich your libraries using hybridization capture.
6. Sequencing: ScaleBio libraries can be sequenced on several Illumina sequencing platforms, including NextSeq, NovaSeq, and NovaSeqX.
7. Data Analysis: Process raw sequencing data using our SeqSuite analysis pipeline, and easily perform cell calling and generate a single cell methylation matrix. Our tutorials for using secondary analysis software make it easy to go from data to insight.
Frequently asked questions
What types of samples have been demonstrated with the Single Cell Methylation Sequencing Kit?
Nuclei from primary tissues in fresh dissociated, snap-frozen, and OCT-embedded formats have been demonstrated in addition to PBMCs and cell lines.
How long can fixed samples be stored for?
Freshly fixed samples can be stored for up to 4 weeks before proceeding to the tagmentation step. Tagmented nuclei can be stored in the freezer for up to 6 months.
What data analysis solutions are provided with the Single Cell Methylation Kit?
A single cell methylation analysis pipeline is provided with the product to take you from raw sequencing outputs to a cell-methylation state matrix.
What sequencers is the kit compatible with?
We have tested compatibility on NextSeq 1000/2000, NovaSeq6000, and NovaSeqX.
Are there any publicly available data sets for methylation?
Yes, you can access our public data sets on the Datasets page.