Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD2

Cell type

Cell type Class
Cardiovascular
Cell type
Aortic smooth muscle cells
NA
NA

Attributes by original data submitter

Sample

source_name
primary cells
cell type
HASMC (Human Aortic Smooth Muscle 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
14914365
Reads aligned (%)
112.9
Duplicates removed (%)
25.2
Number of peaks
337 (qval < 1E-05)

hg38

Number of total reads
14914365
Reads aligned (%)
115.3
Duplicates removed (%)
24.8
Number of peaks
600 (qval < 1E-05)

Base call quality data from DBCLS SRA