|
| Status |
Public on Feb 23, 2014 |
| Title |
HAEC CpG TSA3 [MBD-seq] |
| Sample type |
SRA |
| |
|
| Source name |
HAEC CpG TSA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary Human Aortic Endothelial Cells (HAECs)
passages: Passage 4-6
treated with: 500 nM TSA for 12hrs
|
| 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_TSA3_FC058_6
|
| 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 |
SAMN02640501 |
| SRA |
SRX469926 |
