Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

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

Attributes by original data submitter

Sample

source_name
primary HUVEC cells
treatment
TNF-α (10ng/mL) 1hr
experiment
ChIP-seq
antibody
NF-κB p65 (Santa Cruz sc-372)
restriction enzyme
no

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).). ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).). Libraries were prepared according to Illumina's instruction or cited literatures.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
37597880
Reads aligned (%)
80.6
Duplicates removed (%)
10.1
Number of peaks
6022 (qval < 1E-05)

hg38

Number of total reads
37597880
Reads aligned (%)
82.5
Duplicates removed (%)
8.8
Number of peaks
6108 (qval < 1E-05)

Base call quality data from DBCLS SRA