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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
E-mail(s) a.angeloni@garvan.org.au
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
Relations
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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