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. Attached Files Name Description MIMEType Size Downloads Title Non-referenced genome assembly from epigenomic short-read data Author(s) Kaspi,A Ziemann,M Keating,ST Khurana,I Connor,T orcid.org/0000-0002-0700-1845 Spolding,B orcid.org/0000-0001-7453-4580 Cooper,A Lazarus,R 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 Persistent URL http://hdl.handle.net/10536/DRO/DU:30070064 Document type: Journal Article Collections: Faculty of Health School of Medicine Related Links Link Description Connect to Elements publication management system Go to link with your DU access privileges   Connect to published version Go to link with your DU access privileges   Author URL Go to link with your DU access privileges     Unless expressly stated otherwise, the copyright for items in DRO is owned by the author, with all rights reserved. Versions Version Filter Type Thu, 26 Feb 2015, 10:47:27 EST Wed, 04 Mar 2015, 13:07:09 EST Wed, 04 Mar 2015, 14:34:59 EST Wed, 04 Mar 2015, 14:49:10 EST Wed, 11 Mar 2015, 09:03:28 EST Wed, 11 Mar 2015, 09:05:38 EST Wed, 11 Mar 2015, 09:12:49 EST Thu, 19 Mar 2015, 09:31:01 EST Sat, 09 Nov 2019, 19:37:17 EST Sun, 24 Jul 2022, 01:37:12 EST Filtered Full Citation counts:   Cited 3 times in TR Web of Science Cited 3 times in Scopus Search Google Scholar Access Statistics: 646 Abstract Views, 2 File Downloads  -  Detailed Statistics Created: Wed, 04 Mar 2015, 13:07:09 EST