Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

Cell type

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

Attributes by original data submitter

Sample

source_name
H3K9me3 in differentiation medium
genotype/variation
Wild-type
cell type
human umbilical vein endothelial cells (HUVEC)
passages
P2
treatment
differentiation media (DM)
chip antibody
H3K9me7

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
24077911
Reads aligned (%)
91.7
Duplicates removed (%)
17.5
Number of peaks
1076 (qval < 1E-05)

hg19

Number of total reads
24077911
Reads aligned (%)
90.5
Duplicates removed (%)
19.1
Number of peaks
1079 (qval < 1E-05)

Base call quality data from DBCLS SRA