Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HDAC9

Cell type

Cell type Class
Cardiovascular
Cell type
Smooth muscle cells
NA
NA

Attributes by original data submitter

Sample

source_name
Wild type Smooth Muscle Cells
genotype/variation
Wild Type
cell type
Wild type Smooth Muscle Cells
chip antibody
HDAC9 (Abcom, ab59718)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Human wild-type or aneurysm (ACTA2R179H)10 smooth muscle cells (10 million) were fixed with 1% of formaldehyde at 37 C for 20 min, quenched with 125 mM glycine for 5 min (RT) and protein lysates were prepared using EpiTect ChIP kit according to the manufacturer's instructions (Qiagen, USA). Next, total protein lysates were sonicated to shear chromatin to an average length of 500–1,000 bp, followed by centrifugation for 10 minutes at max speed. Supernatants were collected into a 2 mL tube containing 6 μg of monoclonal antibody against HDAC9 (ab59718), BGR1 (ab110641), H3K27me3 (Abcam, ab4729) or IgG isotype control (ab171870) and 1 ml of lysis buffer supplemented with 1× of protease inhibitor cocktail (Roche Diagnostics), followed by incubation overnight (14 hours) at 4°C. Immunoprecipitates were analyzed using EpiTect ChIP kit according to the manufacturer's instructions (Qiagen). Then, ChIP-ed DNA was quantified and used for DNA-end repair (3'-dA) followed by PCR amplification and size selection (usually 100-400bp, including adaptor sequence). The, qualified libraries were used for HiSeq sequencing (Illumina HiSeq 50 SE sequencing).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
22805070
Reads aligned (%)
94.2
Duplicates removed (%)
19.5
Number of peaks
783 (qval < 1E-05)

hg19

Number of total reads
22805070
Reads aligned (%)
93.3
Duplicates removed (%)
21.3
Number of peaks
849 (qval < 1E-05)

Base call quality data from DBCLS SRA