Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
Input in full medium
genotype/variation
Wild-type
cell type
human umbilical vein endothelial cells (HUVEC)
passages
P2
treatment
full medium (FM)
chip antibody
IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was isolated using Qiazol Lysis Reagent (#79306; Qiagen) and miRNeasy-kit (#217004; Qiagen) with additional DNase I (#79254; Qiagen) digestion according to the manufacturer's protocol. 1 μg of RNA from each sample was reverse-transcribed using random hexamer primed single-strand cDNA (10 min at 25 °C, 15 min at 42 °C, 5 min at 99 °C) by MMLV Reverse Transcriptase (#N8080018; Life technologies) as previously described. (Boeckel et al., 2011). For qPCR, cDNA was amplified using Fast SYBR Green Mastermix (#4385612 Life Technologies) on a ViiA7- Realtime qPCR System (Life Technologies). Expression level of mRNAs were normalized to RPLP0 which served as a housekeeping gene using the 2‑ΔCt method. 900ng of total RNA was used as input for whole transcriptome RNA-seq library preparation (TruSeq® Stranded Total RNA, Illumina) following low throughput protocol. Sequencing was performed on Illumina Nextseq 500 (Illumina) using V2 chemistry and 75bp single-end setup.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
18775095
Reads aligned (%)
82.5
Duplicates removed (%)
68.8
Number of peaks
382 (qval < 1E-05)

hg19

Number of total reads
18775095
Reads aligned (%)
82.2
Duplicates removed (%)
69.2
Number of peaks
388 (qval < 1E-05)

Base call quality data from DBCLS SRA