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Sample GSM4301426 Query DataSets for GSM4301426
Status Public on Dec 03, 2020
Title Input LPO
Sample type SRA
 
Source name Hepatocyte-like cells
Organism Homo sapiens
Characteristics cell type: ES-derived hepatocyte-like cells
Treatment protocol At day 17 of differentiation, when cells had differentiated to mature hepatocyte-like cells, they were treated with a cocktail of lactate (10 mM), pyruvate (1 mM), and octanoate (2 mM) to stimulate intracellular lipid accumulation
Growth protocol Human ES cells were differentiated to hepatocyte-like cells, over the course of 17 days, as per the protocol from Wang, et al (2017), Defined and Scalable Generation of Hepatocyte-like Cells from Human Pluripotent Stem Cells
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from cells using the Monarch Genomic DNA Purification Kit from New England BioLabs
DNA libraries were prepared for sequencing using standard Illumina protocols
DNA immunoprecipitation sequencing
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Ion Torrent Proton
 
Data processing Bam files generated by IonTorrent Suite v5.2.0
Peaks were called using MACS2 v2.1
Differential peaks were identified using DiffBind
Peaks were annotated using Homer v4.8
Genome_build: hg19
 
Submission date Feb 07, 2020
Last update date Dec 03, 2020
Contact name Amanda J. Drake
E-mail(s) mandy.drake@ed.ac.uk
Organization name University of Edinburgh
Department Centre for Cardiovascular Science
Street address 47 Little France Crescent
City Edinburgh
ZIP/Postal code EH16 4TJ
Country United Kingdom
 
Platform ID GPL17303
Series (1)
GSE144955 Genome-wide mapping of 5-hydroxymethylcytosine enrichment in a novel model of 'NAFLD in a Dish'
Relations
BioSample SAMN14060210
SRA SRX7692814

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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