|
| Status |
Public on Feb 23, 2014 |
| Title |
HAEC H3K9Me3 SAHA1 [ChIP-seq] |
| Sample type |
SRA |
| |
|
| Source name |
HAEC H3K9Me3 SAHA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary Human Aortic Endothelial Cells (HAECs)
passages: Passage 4-6
chip antibody: Anti-Histone H3 (tri methyl K9)
chip antibody vendor: Abcam
chip antibody cat. #: ab8898
chip antibody lot #: LOT#538581
|
| Treatment protocol |
HAEC were incubated for 12 hours with 500 nM SAHA.
|
| 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 |
After the incubation,HAECs were fixed for 10 minutes with 1% formaldehyde. Glycine (0.125 M) solution was then added for another 10 minutes. Cell pellets were resuspended in SDS lysis buffer containing protease inhibitors. Then cells were sonicated to shear chromatin and ChIP was performed using indicated above antibodies and DynaMag™-2 magnet (Invitrogen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
HAEC_H3K9Me3_SAHA1_FC046_2
processed data file: HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed, HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed
|
| 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 ChIP vs Input using MACS 1.4.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files comparing ChIP 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 |
| GSE54909 |
Vascular histone deacetylation by pharmacological HDAC inhibition [SAHA, ChIP-seq] |
|
| Relations |
| BioSample |
SAMN02640476 |
| SRA |
SRX469913 |
