5mC DNA methylation data (NimbleGen SeqCap Epi from ROCHE) include glioma tumor samples of WHO grade 2/3 IDH-WT (n = 4), grade 4 IDH-WT (n = 11) and four IDH-MUT samples (n = 3 G2/3; n = 1 G4 astrocytoma), obtained from the recently published glioma Atlas [27 (link)]. All four IDH-MUT samples were pooled together and hereafter are referred to as IDH-MUT. The methylomes of glioma Atlas cover millions of cytosines at a base pair resolution. Due to tumor-related DNA degradation, methylomes presented in glioma Atlas consist of over 10 million of cytosines per sample on average. Despite the limited number of tumor type specific samples, the number of covered DNA sites in glioma Atlas is a huge advantage in comparison to BeadChip panels such as Infinium® HumanMethylation450 or MethylationEPIC performed on larger patient cohorts.
Seqcap epi
Manufactured by Roche
Sourced in Switzerland, United States
The SeqCap Epi is a laboratory equipment product from Roche. It is designed to capture and enrich DNA regions associated with epigenetic modifications. The core function of the SeqCap Epi is to facilitate the targeted sequencing of genomic regions of interest related to epigenetic regulation.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq 2500 system, by Illumina (2 mentions)
Bioruptor pico instrument, by Diagenode (1 mentions)
Kapa hyper prep kit, by Roche (1 mentions)
4200 tapestation system, by Agilent Technologies (1 mentions)
Miseq instrument, by Illumina (1 mentions)
Kapa library quantification kit, by Roche (1 mentions)
Ez dna methylation lightning kit, by Zymo Research (1 mentions)
E220 focused ultrasonicator, by Covaris (1 mentions)
Miseq reagent kit v2, by Illumina (1 mentions)
Seqcap epi accessory kit, by Roche (1 mentions)
Ficoll density gradient, by Merck Group (1 mentions)
Wizard genomic dna purification kit, by Promega (1 mentions)
5 protocols using seqcap epi
1
DNA Methylation Profiling of Glioma
2
Canine Methylome Capture and Sequencing
3
Bisulfite-based DNA Methylation Sequencing
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Sequencing libraries consisted of 16–18 samples and were prepared according to the SeqCap Epi protocol (Roche, Basel, Switzerland) with KAPA HyperPrep Kit (Roche). Diagnostic whole-blood DNA from AML patients (800–1200 ng) was first mixed with the Bisulfite-conversion Control (unmethylated DNA from phage lambda) provided in the SeqCap Epi Accessory kit (Roche) and then fragmented either via E220 Focused ultrasonicator (Covaris, Woburn, MA, USA) or Bioruptor Pico instrument (Diagenode, Liège, Belgium) to get an average size of 200 bp. EZ DNA Methylation Lightning Kit (Zymo Research, Irvine, CA, USA) was used for the bisulfite conversion. Pooled samples from each library were hybridized for about 68 h with a custom set of probes (made by Roche Company). The final concentration of the libraries was measured using KAPA Library Quantification Kit (Roche), and the average size of the libraries’ fragments was assessed on 4200 TapeStation System (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced on a MiSeq instrument (Illumina, San Diego, CA, USA) using the MiSeq Reagent Kit v2 (300-cycles) (Illumina).
4
Mononuclear Cell Isolation and Methylation Sequencing
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For the enrichment of mononuclear cells, bone marrow samples were separated using a Ficoll density gradient (Sigma-Aldrich, St. Louis, MO, USA), and DNA from the lymphoblasts was purified using a Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA). MethylC-capture sequencing was performed as described previously [13 (link)]. Briefly, an amplified bisulfate-converted DNA fragment library was constructed using a SeqCap Epi enrichment system (Roche NimbleGen, Madison, WI, USA), and a HiSeq2500 system (Illumina, San Diego, CA, USA) was used for DNA sequencing.
5
Whole-Genome Methylation Sequencing using MCC-Seq
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A total of 44 DNA samples were used for MCC-Seq (Table 3 ). The concentration and integrity of DNA were detected by electrophoresis to confirm the quality. In MCC-Seq, a whole-genome methylation sequencing library is prepared with the qualified DNA samples, bisulfate-converted, and amplified, followed by a capture enriched for targeted bisulfite-converted DNA fragments. This process is achieved using the novel SeqCap Epi probe design platform developed by Roche NimbleGen. This platform enables the capture of double-stranded targets regardless of their methylated state via high-density tiling of probes [22 , 25 (link)]. Each capture was sequenced on a single lane of the 125 bp paired-end Illumina HiSeq2500 System (Supplementary Materials).
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