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Series GSE109139 Query DataSets for GSE109139
Status Public on Jan 12, 2019
Title DNA IP for 5hmC modified CpGs in DNA of ESC derived hepatocyte like cells exposed to high energy substrates.
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary We report the application of antibody affinity DNA immunoprecipitation followed by proton sequencing to map 5'hydroxymethylcytosine profiles in DNA of ESC derived hepatocyte like cells exposed to high energy substrates.
Overall design Female H9 ESCs were maintained in mTeSR1 (Stem Cell Technologies, Cambridge UK) on matrigel (Corning, Tewksbury, USA) and differentiated into hepatocyte-like cells as previously described (Szkolnicka D, Curr Protoc Stem Cell Biol 2014;30:1G 5 1-12.). At day 20 of differentiation, cells were exposed to Sodium L-Lactate (L7022, Sigma, Gillingham, UK) 10mM, Sodium Pyruvate 1mM (Sigma, Dorset, UK) and Octanoic Acid (C2875, Sigma, Gillingham, UK) 2mM for 48 hours before harvesting. DNA was extracted using quigen DNAeasy kit. We carry out 5-hydroxymethylation DNA immunoprecipitation (hmeDIP) prior to sequencing Ion Proton P1 to report locus specific changes in 5hmC induced by LPO treatment.
Contributor(s) Lyall MJ, Thomson JP, Drake AJ, Hay D
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Submission date Jan 12, 2018
Last update date Mar 01, 2019
Contact name Marcus James Lyall
Organization name University of Edinburgh
Department University/British Heart Foundation Centre for Cardiovascular Science
Lab Drake Lab
Street address The Queen's Medical Research Institute, 47 Little France Crescent
City Edinburgh
State/province Lothian
ZIP/Postal code EH16 4T
Country United Kingdom
Platforms (1)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (12)
GSM2932779 control1
GSM2932780 control1 - input
GSM2932781 control2
BioProject PRJNA429758
SRA SRP129006

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Supplementary file Size Download File type/resource
GSE109139_RAW.tar 1.2 Gb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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