Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CEBPD

Cell type

Cell type Class
Cardiovascular
Cell type
HAEC
Primary Tissue
Aorta
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
human aortic endothelial cell
cell type
HAEC
passage
6 to 10
chip antibody
CEBPD, Santa Cruz #sc-636X
treatment
IL1b, 4h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, Cells were fixed with formaldehyde, lysates were sonicated, and complexes precipitated with antibody. For RNA-seq, RNA was extracted using the the Quick-RNA Micro Prep kit from ZymoResearch and poly-A selected. For ATAC-seq, nuclei were extracted with nuclear isolation buffer and DNA was size-selected for 125-175 bp fragments on a TBE gel For RNA-seq, cDNA was synthesized using the SuperScript III system from Invitrogen, followed by second strand synthesis, ds End Repair and UDG treatment to recover strand-specific libraries. Libraries were barcoded with BioO Nextflex adapters and amplified prior to sequencing. ChIP-seq libraries were synthesized similarly omiting the UDG treatment. ATAC-seq libraries were extracted from TBE gel, amplified, and sequenced.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
31834087
Reads aligned (%)
41.4
Duplicates removed (%)
57.2
Number of peaks
14173 (qval < 1E-05)

hg38

Number of total reads
31834087
Reads aligned (%)
43.1
Duplicates removed (%)
55.8
Number of peaks
14181 (qval < 1E-05)

Base call quality data from DBCLS SRA