Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZMYND8

Cell type

Cell type Class
Breast
Cell type
ZR-75-30
Primary Tissue
Breast
Site of Extraction
Ascites
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
ZR-75-30 cell
antibody
Bethyl, A302-090A
cell line
ZR-75-30
genotype
parental

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.1% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN). ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
4009730
Reads aligned (%)
92.1
Duplicates removed (%)
5.0
Number of peaks
253 (qval < 1E-05)

hg38

Number of total reads
4009730
Reads aligned (%)
92.7
Duplicates removed (%)
4.6
Number of peaks
250 (qval < 1E-05)

Base call quality data from DBCLS SRA