Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

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
overexpression
KLF4
assay
ATAC

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ECs were washed twice with cold PBS, and nuclei were isolated by resuspending ~5000 cells in 50 uL cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40). The nuclear pellets were resuspended in 50 uL transposition buffer (Nextera DNA Library Preparation Kit and 22.5 uL nuclease free water, and then incubated at 37°C for 30 min. After incubation, the DNA samples were purified by the Qiagen MinElute PCR purification kit. Librariy preparation and Illumina sequencing were done by the IGM Genomics Core, University of California, San Diego.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
19428793
Reads aligned (%)
99.2
Duplicates removed (%)
60.9
Number of peaks
4420 (qval < 1E-05)

hg19

Number of total reads
19428793
Reads aligned (%)
99.1
Duplicates removed (%)
61.1
Number of peaks
4382 (qval < 1E-05)

Base call quality data from DBCLS SRA