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Series GSE179673 Query DataSets for GSE179673
Status Public on Dec 03, 2021
Title Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling
Organism Danio rerio
Experiment type Methylation profiling by high throughput sequencing
Summary Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.
Overall design Nanopore sequencing (PromethION FLO-PRO002): 24hpf (n=20 embryos); Whole-genome bisulfite sequencing (WGBS): 24hpf (n=20 embryos)
Contributor(s) Angeloni A, Ferguson J, Bogdanovic O
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Submission date Jul 07, 2021
Last update date Dec 05, 2021
Contact name Allegra Angeloni
Organization name Garvan Institute of Medical Research
Department Genomics and Epigenetics Division
Street address 384 Victoria St Darlinghurst
City Sydney
State/province NSW
ZIP/Postal code 2010
Country Australia
Platforms (2)
GPL23085 HiSeq X Ten (Danio rerio)
GPL30372 PromethION (Danio rerio)
Samples (2)
GSM5426094 Sample 1_Wild-type zebrafish embryos 24 hours post-fertilisation
GSM5426095 Sample 2_Wild-type zebrafish embryos 24 hours post-fertilisation
BioProject PRJNA744528
SRA SRP327386

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Supplementary file Size Download File type/resource
GSE179673_RAW.tar 367.6 Mb (http)(custom) TAR (of BEDGRAPH, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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