Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AHR

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
embryonic stem cells (ESC)
cell line
Mel1 ES cell line
treatment
TCDD
chip antibody
Ah Receptor Antibody (H-211) (Santa Cruz, catalog# sc-5579)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Human ESC cells were fixed using 1% formaldehyde for 10 min, and followed by 0.125 M glycine 5 min to stop the fixation. Then the cells were harvested, and DNA was fragmented to 300–500 bp by sonication with a microtip attached to Misonix 3000 sonicator. Immunoprecipitation was performed with 3 mg Dynabeads protein G (Life Technology) and AhR antibody overnight at 4C. Afterward, beads were washed, eluted, and reverse cross-linked. DNA was extracted by phenol/chloroform and precipitated. For ChIP-seq, 1 ng precipitated DNA or input was used to generate DNA library by use of Nextera XT DNA sample preparation Kit (Illumina) according to the manufacturer's instruction.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
208249103
Reads aligned (%)
118.4
Duplicates removed (%)
38.9
Number of peaks
4651 (qval < 1E-05)

hg38

Number of total reads
208249103
Reads aligned (%)
121.5
Duplicates removed (%)
38.0
Number of peaks
5582 (qval < 1E-05)

Base call quality data from DBCLS SRA