Whole (WGBS)

DNA at the C5 position of plays a crucial role in gene expression and ch romatin remodelling, and perturbations in methylation patterns are implicated in the develop- ment of , neurodegenerative diseases, and neurological disorders. Therefore, the mapping of methylated bases (the methylome) is critical to understanding gene expression and other process- es subject to epigenetic regulation.

Novogene provides of bisulfite-converted DNA, as an effective method to identify individually methylated on a genome-wide scale. Methylome analysis is an in creasingly valuable research tool with a range of applications, including studies on gene regula- ti on, stem cell differentiation, embryogenesis, aging, cancer and other diseases, and phenotypic diversity andevolution in plants and animals.

Image by Christoph Bock (Max Planck Institute for Informatics) (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

The Novogene Advantage · Extensive experience: over 400 samples successfully sequenced ·Comprehensive data analysis: We use widely- accepted mainstream and a bioinformatics analysis team. software such as Bismark and a mature in-house pipeline for mapping, DMR analysis, functional analysis and data visualization. · Unsurpassed data quality: We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, exceeding Illumina’s o fficial guarantee of ≥ 75%.

Project Workflow Sample Library Data Quality Quality Quality SEQUENCING STRATEGY Control Control Control · 250 bp ~ 300 bp insert DNA library · Illumina platform, paired-end 150pb Library Sample Bioinformatics Construction with Preparation Sequencing Analysis DATA QUALITY GUARANTEE Bisulfite Treatment · Q30 ≥ 80% SAMPLE REQUIREMENTS TURNAROUND TIME RECOMMENDED SEQUENCING · DNA amount: ≥ 3 μg · 25 working days from verification of DEPTH sample quality (without data analysis) · DNA concentration: ≥ 50 ng/μl · ≥ 30X · Purity: OD260/280 = 0– 3 without · The data analysis turnaround is project- degradation or contamination dependent.

Analysis PiSequencingpeline Read Genomic Genome Chromosome GeFeaturesnome ChroDMRmosome DMP DMS Depth Coverage Features of C

Read Methylation Mapping Sequencing Clustering Coverage Density Rate Depth Di erential Analysis Bismark of C Methylation Analysis Methylation Alignment Level Analysis Analysis

DMRResult Raw Data Quality Motif DMR Annotation & Raw Data Alignment mC Calling Report Control Analysis Analysis Enrichment Analysis Functional Quality Control mC Calling Motif Analysis Correlation Analysis Analysis (DMR&DMP) Methylation Level PCA M-bias Control Analysis

Go KEGG Pearson PCA Analysis Pipeline Coecient Enrichment Enrichment Genome Chromosome Genomic Features

NOVOGENE (UK) COMPANY LTD. 25 Cambridge Science Park Tel: +44(0)1223 628750 Milton Road Eml: [email protected] Cambridge, CB4 0FW Web: www.novogene.com Follow us on United Kingdom China · China Hong Kong · Singapore · UK · USA LinkedIn Project Example The following study utilized Novogene’s expertise in WGBS.

Whole-Genome Analysis of 5-Hydroxymethylcytosine and 5-Methylcytosine at Base Resolution in the Human Brain Genome Biology, 15: R49 (2014).

Different forms of DNA methylation may differen- tially modulate gene expression and chromatin structure, with consequences for organ development and function. There is particular interest in the role of 5-hydroxymethylcytosine (hmC), which is abundant in some types of mammalian cells. In this study, genome-wide sites of hmC and 5-methylcytosine (mC) in the human brain were mapped to single-base resolution using, respectively, bisulfite sequencing and Tet-assisted bisulfite sequencing. Strand biases were observed with higher levels of hmC and mC associated, respectively, with the sense and antisene strand of gene bodies. Levels of hmC increased during develop - mental stages, with highest levels present in adult brains, and hydroxymethylation-enriched sites includ- ed actively transcribed regions and 5’ splicing sites at exon-intron boundaries, implying novel roles of hmC in regulating splicing and gene expression in the brain. Base-resolution hydroxymethylome and methylome in the human brain. (a) The percentages of hmCs or modCs in the adult or the fetal brain in the contexts of CG, CHH, and CHG. (b) Examples of the hmC, mC and total modification (hmC+mC) profiles are shown for a genomic region of 12 Mb on chromosome 4 as a scatterplot (upper panel) and for a 12Kb region surrounding the TSS of the TET2 gene as a bar chart. The green box indicates the CpG island located in the TET2 .

Novogene Data REPRESENTATIVE SAMPLES SHOWING DATA QUALITY OF NOVOGENE’ S WHOLE GENOME BISULFITE SEQUENCING:

BS Conversion Sample Name Raw Reads Raw Bases Clean Reads Clean Bases Error Rate Q20 Q30 GC Content Rate Sample1 750864918 112.63G 686418034 102.96G 0.03% 94.62% 86.52% 23.01% 99.29% Sample2 762188782 114.14G 618495260 92.61G 0.04% 94.35% 86.41% 21.08% 99.66% Sample3 789026912 118.35G 721080112 108.16G 0.02% 96.54% 90.63% 21.12% 99.66% Sample4 784535120 117.68G 760489944 114.07G 0.03% 92.81% 85.49% 20.70% 99.63%

EXAMPLES OF PUBLICATIONS USING NOVOGENE’S EXPERTISE

YJoeurarnalJournal TAitrleticle Single-base methylome analysis reveals dynamic epigenomic di erences associated with water 2Plant017 BiotechnologyPlant Biotec Journalhnolo 16.2(2018)gy Journal Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple Nature Genetics 49.7(2017) Lineage-specificdecit in app functionsle of TET1 in the postimplantation mouse embryo 2016 Developmental Cell N6-methyladenosine RNA modication regulates shoot stem cell fate in Arabidopsis Plant Physiology 171.3(2016) Analysis of chromatin regulators reveals specific features of rice DNA methylation pathways. 2016 Plant Physiology Analysis of chromatin regulators reveals specic features of rice DNA methylation pathways. 2Plant016 PhysiologyPlant Ph y171.3(2016)siology CooperationCooperati betweenon betw theee H3K27me3n the H3 Kchromatin27me3 markerchrom andati nnon-CG mark meer thylationand no inn- epigeneticCG meth regulation.ylation in epigenetic Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the 2014 Genome Biology human brain. 2012 Nature Communications. An atlas of DNA methylomes in porcine adipose and muscle tissues.