Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AHR

Cell type

Cell type Class
Uterus
Cell type
T HESCs
Tissue
Uterus; Endometrium
Cell Type
Fibroblast
Disease
Non-Malignant Myomas

Attributes by original data submitter

Sample

source_name
decidual stromal cells
cell line
ATCC CRL-4003
treatment
control
chip antibody
Ah Receptor Antibody (H-211): sc-5579 (Santa Cruz, CA)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested, resuspended and chemically cross-linked in suspension by the addition of 1% fresh formaldehyde with 9 minutes incubation at room temperature on a rotator. Cross-linking was quenched and cells were harvested by centrifugation and washed twice in cold PBS. Nuclei were extracted and sonication was performed using a Misonix S4000 sonicator.  Fragment size between 200bp and 600bp was obtained and confirmed by gel electrophoresis and Bionalyzer.  DNA library preparation and high-throughput sequencing were performed on an Illumina Genome Analyzer II following the protocol recommended by Illumina with a 75bp readleght at the Yale Center for Genome Analysis.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
68806954
Reads aligned (%)
90.0
Duplicates removed (%)
7.8
Number of peaks
1570 (qval < 1E-05)

hg38

Number of total reads
68806954
Reads aligned (%)
93.0
Duplicates removed (%)
5.5
Number of peaks
2943 (qval < 1E-05)

Base call quality data from DBCLS SRA