|
| Status |
Public on Dec 03, 2020 |
| Title |
IgG |
| 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 |
SAMN14060212 |
| SRA |
SRX7692812 |
