Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ELK3

Cell type

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

Attributes by original data submitter

Sample

source_name
HUVEC Cells
cell line
HUVEC cells (ATCC, CRL1730)
antibody
hELK3 2005 (in house)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and ELK3-DNA complexes were isolated with antibody. ChIP-seq libraries were prepared using Truseq ChIP-Seq Sample Prep Kit (Illumina, IP-202-1012) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 Poly Nucleotide Kinase . A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA ligase. The ligated products were enriched by PCR (30 sec at 98°C [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C), then size selected and purified using Agencourt AMPure XP beads (#A63881, Beckman). Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 7pM concentration and clusters were generated using the Cbot (Illumina, SY-301-2002 ) and sequenced on the Illumina Genome Hiseq2500 as single-end 50 base reads following Illumina’s instructions 

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
44875168
Reads aligned (%)
34.0
Duplicates removed (%)
63.6
Number of peaks
4222 (qval < 1E-05)

hg38

Number of total reads
44875168
Reads aligned (%)
35.7
Duplicates removed (%)
62.0
Number of peaks
4258 (qval < 1E-05)

Base call quality data from DBCLS SRA