Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Uterus
Cell type
Endometrial stromal cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human endometrial stromal cells
tissue
Endometrial stromal cells
condition
induction with estradiol (10-8 M) and medroxyprogesterone acetate (10-6 M)
chip antibody
H3K4me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonication/enzymatic digested nuclei and histone-DNA complexes were isolated with antibody. The ChIP DNA and the Input DNA ends were repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase(PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3’ end. After ligation of the Solexa adaptor using TaKaRa ligation Mix (TaKaRa), the adaptor-ligated DNAs were amplified using Solexa PCR primers for 18 cycles, and the amplified library was isolated from an agarose gel. The samples were purified using the QIAquick MinElute kit (Qiagen) at each preparation step. The purified library was used for cluster generation and sequencing analysis using the Genome Analyzer GAIIx (Illumina).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
41250134
Reads aligned (%)
99.5
Duplicates removed (%)
60.2
Number of peaks
121 (qval < 1E-05)

hg19

Number of total reads
41250134
Reads aligned (%)
99.0
Duplicates removed (%)
60.9
Number of peaks
133 (qval < 1E-05)

Base call quality data from DBCLS SRA