GeneAb™ GATA3

Bisulfite seq is a well know technology to detect DNA methylation and several technologies such as WGBS, RRBS, MeDIP-Seq, and MSBS are used for whole genome DNA methylation analysis. DNA methylation is important for regulation of cell development, differentiation and gene expression in molecular biology, genetics and epigenetics. Most methylated cytosines are found at CpG sites, and 70-80% of cytosines are methylated. The number of CpG sites in human genome is around 28 million, which is less than 1% of the genome compared with 4.4% expected.

Whole genome bisulfite sequencing (WGBS) is the most effective method of DNA methylation analysis. The only limitation is the sequencing cost is very high because the whole genome is sequenced including all the non-methylated regions.

Reduced Representation Bisulfite Sequencing (RRBS) is the reduced representation of a smaller fraction of the methylated CpG sites. RRBS combines restriction enzyme digestion and bisulfite sequencing, and enriches the sequencing for methylated CpG sites. It is an efficient technology for estimate the whole genome methylation patterns at the single base level. Although this allows a higher coverage depth and reduces the sequencing cost, the limitation is only 10% of the methylated CpG sites are covered.

Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq) is another whole genome enrichment technique used for selection of methylated DNA. Using antibodies against 5-methylcytosine, methylated DNA is enriched from whole genomic DNA via immunoprecipitation. 5-methylcytosine antibodies are incubated with fragmented genomic DNA and precipitated, followed by DNA purification and sequencing. There are several drawbacks of MeDIP-Seq: 1. Low resolution (150~200 bp) as opposed to the single base resolution; 2. Non-specific interaction due to antibody specificity and selectivity. 3. Bias towards hypermethylated regions.

The Methylation Specific Bisulfite Seq (MSBS) Library Prep Kit (illumina platform) was developed for construction of NGS libraries for methylated CpG sites using bisulfite treated DNA (20 ng – 500 ng) as input. The kit enriches methylated CpG regions, thus significantly reduce the sequencing cost. The kit estimates the whole genome methylation patterns at the single base level since it is based on a bisulfite-seq technology.

It is known that bisulfite treatment of completed NGS libraries causes tremendous damage to the libraries. By using bisulfite treated DNA as input, the kit overcomes the significant library loss due to the bisulfite conversion. The kit contains a mixture of PCR polymerases that have high-fidelity amplification and uracil tolerance which is ideal for bisulfite treated DNA.

Methylation Specific Bisulfite Seq Library Prep Kit Workflow

Three index types are available for the kit:

Non-index (Cat.# 30101): Libraries do not have index.

Index (Cat.# 30102): Each primer contains a unique barcode sequence of 6 bases to identify the individual library. Library multiplexing capacity is up to 48 samples. Index information can be downloaded here.

Unique dual index (Cat.# 30103): The multiplexing of bisulfite sequencing library is up to 96 samples with unique dual indexes. We used a Four-Base Difference Index System to generate indexes that have at least 4 bases different from each other in the 8-base index. The index primers remove NGS errors including index cross-contamination, index hopping, reads mis-assignment etc. Index information can be downloaded here.

Methylation Specific Bisulfite Seq advantages

• • • Enrichment of methylated CpG sites
    • Single-base resolution
    • Low cost for sequencing
    • Fast
      • Total time: 1.5 hours
      • Hands-on time: 10 minutes
    • Simple workflow
    • Bisulfite treated DNA as input: From 20 ng to 500 ng

MSBS Library Prep Kit enriches CpG sites

High methylation regions and low methylation regions in human genome.

High methylation region in human genome.

Low methylation region in human genome.

Sequencing setting: Single-end 35 cycles (Read 1, 35 bases) recommended
To maximize the methylated CpG enrichment, we recommend to sequence the MSBS libraries with single end 35 cycles (read1, 35 bases). This is because the enriched methylated CpG sites are mainly located around the beginning of read 1 sequences. Shorter single end reads tend to have better methylated CpG enrichment.

Bisulfite seq is a well know technology to detect DNA methylation and several technologies such as WGBS, RRBS, MeDIP-Seq, and MSBS are used for whole genome DNA methylation analysis. DNA methylation is important for regulation of cell development, differentiation and gene expression in molecular biology, genetics and epigenetics. Most methylated cytosines are found at CpG sites, and 70-80% of cytosines are methylated. The number of CpG sites in human genome is around 28 million, which is less than 1% of the genome compared with 4.4% expected.

Overview

• Isolate genomic DNA from animal tissues, cells, bodily fluids, viruses and swabs 
• Rapid and convenient spin column procedure 
• Purified DNA is of the highest quality and integrity for sensitive downstream applications including PCR, qPCR, genotyping, sequencing and more

This kit is designed for the rapid preparation of genomic DNA from various tissue samples, cultured cells, viruses, bodily fluids and swabs using a rapid spin column protocol. Purified DNA is of an excellent yield and quality, and is immediately ready for any downstream application including PCR, qPCR, genotyping, sequencing and more.  The protocol can be completed in approximately 80 minutes (including incubation time).

Details

Supporting Data

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Kit Specifications
Column Binding Capacity	25 µg
Average Yield:* HeLa Cells (1 x 106) Tissue (from 10 mg kidney)	8 µg 10 µg
Maximum Amount of Starting Material: Animal Tissues Cultured Cells Bodily Fluids (blood, saliva) Viral Suspension	20 mg 3 x 106 cells 150 µL 150 µL
Time to Complete 10 Purifications	80 minutes

* Yield will vary depending on the type of sample processed

Storage Conditions and Product Stability
The Proteinase K should be stored at -20°C upon arrival and after reconstitution. All other solutions should be kept tightly sealed and stored at room temperature. This kit is stable for 2 years after the date of shipment.

Component	Cat. 24700 (50 preps)	Cat. 24750 (100 preps)	Cat. 24770 (250 preps)
Digestion Buffer A	25 mL	2 x 25 mL	5 x 25 mL
Buffer SK	30 mL	2 x 30 mL	5 x 30 mL
Wash Solution A	18 mL	2 x 18 mL	5 x 18 mL
Elution Buffer B	30 mL	2 x 30 mL	5 x 30 mL
Proteinase K	12 mg	2 x 12 mg	5 x 12 mg
Spin Columns	50	100	250
Collection Tubes	50	100	250
Elution Tubes (1.7 mL)	50	100	250
Product Insert	1	1	1

Permagen’s 0.2 mL PCR / 1.5 mL Microcentrifuge tube separation rack is designed for labs with both PCR strip and 1.5 mL separation protocols. On the top, hold up to two of either 8 or 12 strips, or up to 24 individual tubes. Flip over and hold up to twelve 1.5 mL Microcentrifuge Tubes

Features include solid aluminum alloy design with hard coat finish for years of trouble-free use, rubber feet on both sides to help prevent slipping on work bench, less tippy than common plastic products, and fast separations using any magnetic bead

SKU #

MSR1224B

Features

• Aluminum alloy design for years of trouble-free use
• Fast magnetic bead separations
• Held to tighter tolerances for more consistent results
• Pulls beads to side of wells for easy tip tracking down opposite side
• Rubber feet to help prevent slippage
• Stable design
• Angled tube holes which allow the tubes to come close to magnets

Compatibility

• Most 1.5 mL Microcentrifuge tubes
• Some 2.0 mL Microcentrifuge tubes
• 8-strip PCR tubes
• 12-strip PCR tubes
• Individual PCR tubes 
• Any Magnetic Beads

Volumes

Maximum (PCR Tube)– .2 mL 

Minimum (PCR Tube)  – 10 µL 

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Maximum (1.5 mL Microcentrifuge) – 1.5 mL 

Minimum (1.5 mL Microcentrifuge Tube) – .5 mL

Permagen’s 0.2 mL PCR / 1.5 mL Microcentrifuge tube separation rack is designed for labs with both PCR strip and 1.5 mL separation protocols. On the top, hold up to two of either 8 or 12 strips, or up to 24 individual tubes. Flip over and hold up to twelve 1.5 mL Microcentrifuge Tubes