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Series GSE110412 Query DataSets for GSE110412
Status Public on Feb 13, 2019
Title The bovine alveolar macrophage (bAM) DNA methylome is resilient to infection with Mycobacterium bovis
Organism Bos taurus
Experiment type Methylation profiling by high throughput sequencing
Summary Whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome (5-methylcytosine). The methylomes of bAM infected with M. bovis (n = 8) were compared to those of non-infected control bAM (n = 8) at 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed between control and infected bAM. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation = 33–66%). Gene ontology (GO) analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of two non-imprinted genes in the IM category, C1QB and IL2RA, confirmed the WGBS observation. This study is the first in cattle to examine genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model and provides evidence for intermediate promoter methylation in bAM.
 
Overall design Examination of CpG methylation in control and Mycobacterium bovis infected bovine macrophages, 24 hours post infection
 
Contributor(s) O'Doherty AM, Rue-Albrecht KC, Magee DA, Ahting S, Irwin RE, Hall TJ, Browne JA, Nalpas NC, Walsh CP, Gordon SV, Wojewodzic MW, MacHugh DE
Citation(s)
  • O'Doherty AM, Rue-Albrecht KC, Magee DA, Ahting S et al. The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. Sci Rep 2019 Feb 6;9(1):1510. PMID: 30728374
Submission date Feb 09, 2018
Last update date Feb 13, 2019
Contact name Thomas Hall
E-mail(s) tjhall1688@gmail.com
Phone 857168930
Organization name UCD
Department Vet sciences
Street address 2, Taney Grove
City Dublin
State/province Select One
ZIP/Postal code D14 KW14
Country Ireland
 
Platforms (1)
GPL19172 Illumina HiSeq 2500 (Bos taurus)
Samples (16)
GSM2990988 C1_Control
GSM2990989 C11_Control
GSM2990990 C12_Control
Relations
BioProject PRJNA433673
SRA SRP132590

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE110412_RAW.tar 3.4 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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