Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ETV2

Cell type

Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA

Attributes by original data submitter

Sample

source_name
hDFs transduced with rtTA and tet-HA-ETV2
cell type
induced endothelial cells
stimulation
without doxycycline, day 7
chip antibody
anti-HA (901501, BioLegend)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde was added to culture medium at a final concentration of 1% and cells were incubated for 10 minutes at 37°C. Then glycine was added at a final concentration of 125 mM to the media, followed by washing with cold PBS containing protease inhibitors twice. The cells were harvested by scraping with Farnham lysis buffer (5 mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40) and collected by centrifugation. Cell lysates were resuspended with SDS lysis buffer and incubated for 10 minutes on ice. DNAs in lysates were sheared into 100 to 500 base pairs by sonication and sheared chromatin was purified by centrifugation (15000 x g, 4°C, 10 minutes). After calculation of DNA concentration, 1% of sheared chromatin was stored at -20°C as input. To precipitate chromatin, antibody against HA (901501, BioLegend) was added to the supernatant fraction and incubated overnight at 4°C. By incubation with Protein A Agarose/Salmon Sperm DNA for an hour, unbound DNA was removed, and HA-bound complex was collected. To reverse protein-DNA crosslinking, the solution and stored input were incubated with 5M NaCl for 4 hours at 65°C. Additionally, RNase A and Proteinase K were added and incubated for an hour at 45°C. DNAs were purified by PCR purification kit (Invitrogen). Purified DNAs were subjected to sequencing library preparation using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions. The chipped DNA was ligated with adaptors. Then, after purification, PCR reaction was done with adaptor-ligated DNA and index primer. High-throughput sequencing was performed as single-end 75-bp sequencing using NextSeq 500 (Illumina).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
21903772
Reads aligned (%)
40.7
Duplicates removed (%)
47.4
Number of peaks
1072 (qval < 1E-05)

hg38

Number of total reads
21903772
Reads aligned (%)
42.9
Duplicates removed (%)
45.4
Number of peaks
1398 (qval < 1E-05)

Base call quality data from DBCLS SRA