Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD2

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 cells
cell type
HUVEC (human umbilical endothelial cells)
passages
10
chip antibody
Smad2/3 (Cell Signaling 8685), Smad2/3 (R&D AF3797)
treatment
Treated with TGFB1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies. ChIP DNA samples was used in a 23.3 μl combined end repair and A-tailing reaction using a KAPA Hyper Prep Kit (Kapa Biosciences) for 30 minutes at 20°C followed by 30 minutes at 65°C. 10 μl of ligase buffer, 3.7 μl of Adapters and 3.3 μl ligase (KAPA Hyper Prep Kit) were added and incubated at 20°C for 4 hours. Double-stranded DNA fragments were purified from this reaction using KAPA Pure Beads (Kapa Biosciences) and eluted in 22 μl 10 mM Tris pH8.0. Libraries were generated by PCR and size-selected on a 2% E-Gel EX agarose gel (Invitrogen) and fragments between 150 and 400 bp were extracted using a QIAEX II Gel Extraction Kit (Qiagen) performed at room temperature.

Sequencing Platform

instrument_model
Illumina HiSeq X Ten

hg19

Number of total reads
65818903
Reads aligned (%)
23.1
Duplicates removed (%)
57.0
Number of peaks
4066 (qval < 1E-05)

hg38

Number of total reads
65818903
Reads aligned (%)
23.3
Duplicates removed (%)
56.9
Number of peaks
4089 (qval < 1E-05)

Base call quality data from DBCLS SRA