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Sample GSM1326460 Query DataSets for GSM1326460
Status Public on Feb 23, 2014
Title HAEC CpG control1 [MBD-seq]
Sample type SRA
 
Source name HAEC CpG control
Organism Homo sapiens
Characteristics cell type: Primary Human Aortic Endothelial Cells (HAECs)
passages: Passage 4-6
treated with: none (control)
Treatment protocol HAEC were incubated for 12 hours with 500 nM TSA.
Growth protocol Primary HAECs (human aortic endothelial cells), purchased from Lonza (Walkersville, MD, USA), were cultured in EBM-2 medium (Lonza) containing EGM-2 growth factors and supplements (Lonza) and 10% fetal bovine serum (Gibco).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA derived from treated and controls HAECs was fragmented to 150-200bp by Diagnode sonicator and subjected to methylated DNA enrichment using MethylMiner Kit (Invitrogen, ME10035) in triplicate. Briefly, methylated DNA was captured from 500ng of fragmented genomic DNA via binding MBD2 protein coupled to magnetic Dynabeads, which was incubated for 1hr with rotation. The methylated fragments were then eluted in three distinct subpopulation using 0.6M, 1M and 2M salt elution buffers respectively (supplied in MethylMiner kit). Methylated DNA fragments, eluted with 2M salt buffer, were purified and selected for sequencing on the Illumina Genome Analyser.
Libraries were prepared according to the protocols described in the Illumina (San Diego, CA, US) ChIP-seq library preparation kit (cat# IP-102-1001).
 
Library strategy MBD-Seq
Library source genomic
Library selection MBD2 protein methyl-CpG binding domain
Instrument model Illumina Genome Analyzer IIx
 
Description HAEC_CpG_control1_FC057_2
Data processing Illumina pipeline 1.4 was used for base calling
Reads were aligned to the hg19 genome using bwa 0.5.9 with default parameters
A set of peaks were generated for each sample vs Input using MACS 1.4.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files comparing sample vs Input
 
Submission date Feb 12, 2014
Last update date May 15, 2019
Contact name Assam El-Osta
Organization name Baker Heart and Diabetes Institute
Lab Human Epigenetics
Street address 75 Commercial Road
City Melbourne
ZIP/Postal code 3004
Country Australia
 
Platform ID GPL10999
Series (2)
GSE37378 Vascular histone deacetylation by pharmacological HDAC inhibition
GSE54911 Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, MBD-seq]
Relations
BioSample SAMN02640488
SRA SRX469921

Supplementary file Size Download File type/resource
GSM1326460_CONTROL1_FC057_2_INPUT_FC047_1_methylminer_peaks.bed.gz 461.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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