Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Cardiovascular
Cell type
HUVEC
Primary Tissue
Umbilical Cord
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Human Umbilical Vein Endothelial Cells (HUVEC)
cell type
HUVEC
chip antibody
H3K27ac (Active Motif 39133)
treatment
CTRL
growth
flat (2D)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
To identify genome-wide localization of ETV2 in R-VEC, ChIP assays were performed with approximately 1x10e7 cells per experiment. Cells introduced with triple flagged ETV2 lentivirus were used for the ETV2 ChIP. Briefly, cells were crosslinked in 1% paraformaldehyde (PFA) for 10 min at 37°C, then quenched by 0.125M glycine. Chromatin was sheared using a Bioruptor (Diagenode) to create fragments of 200-400 bp, immunoprecipitated by 2–5 ug of antibody bound to 75 ml Dynabeads M-280 (Invitrogen) and incubated overnight at 4°C. Magnetic beads were washed and chromatin was eluted. The ChIP DNA was reverse-crosslinked and column-purified. To identify genome-wide localization of K4me3, K27me3, and K27ac modification, small-scale ChIP assays were performed with approximately 1x104 cells per experiment. Briefly, cells were washed once with nuclei extraction buffer (10 mM Tris-HCl pH 8.5, 2 mM EDTA, 140 mM NaCl, 5 mM MgCl2, 0.6% NP40, 1x EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride). The chromatin was fragmented for 5 min using MNase at 25 °C, diluted in ChIP buffer (10 mM Tris-HCl pH 8.0, 2 mM EDTA, 90 mM NaCl, 0.1% Triton X-100, 0.1% NaDOC, 1x EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride), and then immunoprecipitated with 1 ug of antibody bound to 10 ml Pierce Protein A/G Magnetic Beads (Invitrogen) and incubated overnight at 4°C. Magnetic beads were washed and chromatin was eluted. The ChIP DNA was reverse-crosslinked, purified by phenol chloroform, and precipitated by ethanol. ChIP samples were prepared for sequencing using KAPA Hyper Prep Kit.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
23165209
Reads aligned (%)
98.1
Duplicates removed (%)
24.6
Number of peaks
1591 (qval < 1E-05)

hg19

Number of total reads
23165209
Reads aligned (%)
97.4
Duplicates removed (%)
26.1
Number of peaks
1545 (qval < 1E-05)

Base call quality data from DBCLS SRA