Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZBTB17

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
MCF10A cells
cell line
MCF10A
tissue
mammary gland/breast
antibody
10E2 (anti-MIZ1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde. After a hypotonic lysis step, nuclei were resuspended in sonication buffer containing 0.1% SDS and 0.1% Na-deoxycholate and sonication was performed in a Branson sonifier. Anti-ER-a antibody (HC20, Santa Cruz) was coupled to Protein A-Dynabeads, 10E2 mouse anti-MIZ1 antibody was coupled to Protein G-Dynabeads (Invitrogen). Bound chromatin was eluted with 1% SDS and after decrosslinking DNA was purified with phenol-chloroform. ChIP DNA was end-repaired, A-tailed and ligated to Illumina adaptors using NEBNext ChIP-Seq Sample Preparation Kit. After size selection on an agarose gel and purification with a Qiagen gel extraction kit, PCR-amplification was performed. Library quality was tested with an Experion DNA Chip (BioRad) and quantified using a picogreen assay.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
13828820
Reads aligned (%)
91.4
Duplicates removed (%)
5.0
Number of peaks
1851 (qval < 1E-05)

hg38

Number of total reads
13828820
Reads aligned (%)
93.4
Duplicates removed (%)
3.8
Number of peaks
1746 (qval < 1E-05)

Base call quality data from DBCLS SRA