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Non-referenced genome assembly from epigenomic short-read data

Kaspi,A, Ziemann,M, Keating,ST, Khurana,I, Connor,T, Spolding,B, Cooper,A, Lazarus,R, Walder,K, Zimmet,P and El-Osta,A 2014, Non-referenced genome assembly from epigenomic short-read data, Epigenetics, vol. 9, no. 10, pp. 1329-1338, doi: 10.4161/15592294.2014.969610.

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Title Non-referenced genome assembly from epigenomic short-read data
Author(s) Kaspi,A
Ziemann,M
Keating,ST
Khurana,I
Connor,T
Spolding,B
Cooper,A
Lazarus,R
Walder,KORCID iD for Walder,K orcid.org/0000-0002-6758-4763
Zimmet,P
El-Osta,A
Journal name Epigenetics
Volume number 9
Issue number 10
Start page 1329
End page 1338
Total pages 11
Publisher Taylor & Francis
Place of publication New York, United States
Publication date 2014-12-01
ISSN 1559-2308
1559-2294
Keyword(s) ChIP-seq
ChIP-seq, immunoprecipitated chromatin sequencing
DMR, differentially methylated region
DNA methylation
High-throughput sequencing
MBD-seq
MBD-seq, methyl binding domain protein sequencing
MeDIP-seq; methylated DNA immunoprecipitation sequencing
Psammomys obesus
RNA-seq, RNA sequencing
de novo assembly
epigenomic integration
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Genetics & Heredity
INTRAUTERINE GROWTH-RETARDATION
GENETIC-VARIATION
PSAMMOMYS-OBESUS
SAND RAT
SEQ DATA
IDENTIFICATION
EXPOSURE
FAMINE
ALIGNMENT
Summary Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
Language eng
DOI 10.4161/15592294.2014.969610
Field of Research 110199 Medical Biochemistry and Metabolomics not elsewhere classified
Socio Economic Objective 970111 Expanding Knowledge in the Medical and Health Sciences
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2014, Taylor & Francis
Free to Read? Yes
Persistent URL http://hdl.handle.net/10536/DRO/DU:30070064

Document type: Journal Article
Collections: Faculty of Health
School of Medicine
Open Access Collection
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.