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Zymo-Seq Trio WGBS Library Kit
Cat # | Name | Size | Price | Quantity |
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Highlights
- Co-Detection of Genetic and Epigenetic Information: Seamlessly analyze both genomic data and DNA methylation in a single experiment, with the validated open-source bioinformatics tools and comprehensive step-by-step guides.
- True-End Fragment Analysis: Designed for optimal performance with small or degraded DNA fragments, including cell-free DNA (cfDNA) and FFPE-derived DNA, to capture the fragment’s true end.
- Accurate Methylation Detection: Achieve precise methylation calling with a direct ligation-based protocol that preserves native termini, ensuring accuracy in each DNA fragment analysis.
Documents
Product Description
Technical Specifications
Barcode Sequences | Please refer to the Documents Section. |
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Bisulfite Conversion | >99.5% of non-methylated cytosine residues are converted to uracil; >99.5% protection of methylated cytosines. |
Equipment Required | Thermal cycler(s) with temperature adjustable lids, microcentrifuge, magnetic stand. |
Hands-On Time | ~2 hours |
Input Quality | For optimal results, use at least minimum input of purified fragmented DNA with no RNA or gDNA contamination. Fragmented DNA can be concentrated using the DNA Clean & Concentrator (D4013) prior to processing. Input DNA can be suspended in water, DNA Elution Buffer, or TE buffer. |
Library Storage | Libraries eluted in DNA Elution Buffer (provided) may be stored at ≤ 4°C overnight or ≤ -20°C for long-term storage. |
Maximum Input | 10 ng |
Minimum Input | 5 ng |
Sample Input Material | Purified cell-free DNA (cfDNA), Sonicated FFPE DNA (average size of 300-600 bp), Sheared genomic DNA (average size of 300-600 bp) |
Sequencing Platform Compatibility | Libraries are compatible with all Illumina sequencing platforms. Recommended: NextSeq, NovaSeq. |
Total Processing Time | ~6 hours |
Resources
Q1: Can my input be lower than 5 ng?
It is possible to generate libraries with inputs lower than 5 ng; however, the quality of such libraries is not guaranteed. Typically, at lower inputs the percentage of adapter dimers increases in the final library. For best results, we recommend concentrating the sample input as much as possible to meet the 5 ng minimum input prior to using the kit. Samples can also be concentrated using a DNA Clean & Concentrator Kit and/or during the bisulfite conversion step by reusing the same column for clean-up.
Q2: Can my input be higher than 10 ng?
It is possible to generate libraries with inputs higher than 10 ng; however, the quality of such libraries is not guaranteed. For best results, we recommend diluting your sample down to meet the 10 ng maximum input.
Q3: My Adapter Ligation reagents were thawed more than 4 times, will my libraries be okay?
We recommend up to 4 freeze-thaw cycles for the Adapter Ligation Buffer 2 (orange cap), Adapter Ligation Buffer 3 (yellow cap), and the Adapter Ligation Master Mix (green cap). After 4 freeze-thaw cycles, the quality of the libraries may vary. We recommend making additional aliquots of these buffers upon first use as necessary to minimize the potential freeze-thaw cycles the reagents undergo. The Adapter Ligation Buffer 1 (red cap) is not as sensitive to freeze-thaw cycles and therefore is not affected by being thawed more than 4 times.
Q4: Are the Zymo-Seq UDI Primers included individual primers or pre-mixed primer sets?
Each tube/well contains a pre-mixed forward and reverse primer set that contain a unique i5 and i7 index, respectively. The concentration of each UDI primer pre-mix is 5 µM total (2.5 µM each primer).
Q5: What is the suggested read length and sequencing depth needed for WGBS libraries?
Libraries are suitable for any cycling number, but increased cycling numbers will require greater amounts of adapter trimming for the shorter library fragments. For most applications, 100 base paired-end (PE) reads are enough to generate substantial amounts of high-quality data for genome-wide coverage. The sequencing depth will be dependent on the genome size, genome coverage, and site coverage required. Generally, aiming for 10X coverage per CpG site is recommended.
Using 100 bp PE sequencing, we recommend at least 500 million reads for human WGBS at 10X CpG coverage, and at least 400 million reads for mouse WGBS at 10X CpG coverage.
Cat # | Name | Size | Price | |
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D5030-1 | Lightning Conversion Reagent | 1.5 ml | $28.40 | |
D5032-1 | Lightning Conversion Reagent | 15 ml | $168.10 | |
D5001-3 | M-Binding Buffer | 20 ml | $17.30 | |
D5002-3 | M-Binding Buffer | 80 ml | $47.00 | |
D5001-4 | M-Wash Buffer | 6 ml | $12.40 | |
D5002-4 | M-Wash Buffer | 24 ml | $30.90 | |
D5030-5 | L-Desulphonation Buffer | 10 ml | $18.50 | |
D5031-5 | L-Desulphonation Buffer | 40 ml | $51.90 | |
D3004-4-4 | DNA Elution Buffer | 4 ml | $11.30 | |
D3004-4-16 | DNA Elution Buffer | 16 ml | $20.40 | |
C1004-50 | Zymo-Spin IC Columns | 50 Pack | $60.00 | |
C1001-50 | Collection Tubes | 50 Pack | $17.00 | |
D4003-2-6 | DNA Wash Buffer (Concentrate) | 6 ml | $11.30 | |
D4003-2-24 | DNA Wash Buffer (Concentrate) | 24 ml | $37.40 | |
D5016 | E. coli Non-Methylated Genomic DNA | 5 µg/20 µl | $116.40 | |
D3008 | Zymo-Seq UDI Primer Set (Indexes 1-12) | 12 indexes | $200.90 | |
D3096 | Zymo-Seq UDI Primer Plate (Indexes 1-96) | 96 Indexes | $509.90 | |
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