{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["John Thomson"],"study_type":["methylation profiling by array"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-41397"],"description":["5-hmC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5hmC in both control mouse livers as well as in the livers of 91 day PB treated mice. 5hmC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events. 5-hmC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5hmC levels comparison of 5-hmC profiles in 5 control and 5 PB exposed mouse livers (dose: 91day PB)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - normal mouse liver tissue","Nucleic Acid Extraction - Genomic DNA (5hmC-IP - 2.5 M-5g in 450 M-5l TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100M-0C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 M-5l (10%) of denatured sample was removed and saved as input, and 45 M-5l of 10X IP buffer (100 mM Na-Phosphate pH 7.0 (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 M-5g of M-oM-^AM-!-5hmC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4M-oM-^BM-0C with gentle agitation overnight. Then, 40 M-5l of magnetic beads (DynabeadsM-. Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4M-oM-^BM-0C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 M-5l of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 M-5l of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 M-5l of proteinase K (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52M-oM-^BM-0C for 1.5 hr with constant shaking (M-bM-^IM-%800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquickM-oM-^CM-^R PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 M-5l dH2O. Inputs were also purified using a QIAquickM-oM-^CM-^R PCR Purification Kit and eluted in 40 M-5l dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlexM-. Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.","Sample Processing - genomic DNA extracted from mouse liver following 91 day exposed to Phenobarbital","Growth Protocol - PB exposed mouse liver tissue","Labeling - Amplification of DNA samples was carried out commercially by NimbleGen, Iceland (Cy5- (IP) or Cy3- (Input) labelled)","Hybridization - Labelled samples were applied commercially to a Nimblegen 2.1M Deluxe promoter array by Nimblegen, Iceland","Sample Processing - genomic DNA extracted from normal mouse liver"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Harri LempiM-CM-$inen","John Thomson"],"data_protocol":["Feature Extraction - Pair files normalised within arrays (loess), normalised between arrays (sclae normalisation), log2(IP/input)","Assay Data Transformation - ID_REF =  VALUE = Normalised data after normalised within arrays (loess) and between arrays (scale normalisation) resulting in log2(IP/input) scores for each probe","Image Adquisition - Arrays were scanned commercially by Nimblegen, Iceland"],"additional_accession":[]},"is_claimable":false,"name":"IP of 5-methylcytosine (5-hmC) enriched DNA fragments from control and PB treated mouse livers (91 day)","description":"5-hmC is an epigenetic modification of the DNA base cytosine with roles in gene silencing events, imprinting and X inactivation. Phenobarbital (PB) is a well studied non-genotoxic carcinogen with roles in epigenetic perturbation.  We profile 5hmC in both control mouse livers as well as in the livers of 91 day PB treated mice. 5hmC is largely found to reside in the bodies of active genes and promoter levels are perturbed upon PB induced gene activation events. 5-hmC is assocated with promoters fo silent genes. Upon PB exposire a handfull of genes are induced which reveal decreases in promoter 5hmC levels comparison of 5-hmC profiles in 5 control and 5 PB exposed mouse livers (dose: 91day PB)","dates":{"release":"2012-11-10T00:00:00Z","modification":"2023-08-25T01:00:19.801Z","creation":"2022-03-06T23:34:14.35Z"},"accession":"E-GEOD-41397","cross_references":{"GEO":["GSE41397"],"EFO":["EFO_0002759"]}}