Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZBTB17

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MD-231, G18 ChIP
cell line
MDA-MD-231
chip antibody
G18 (Santa Cruz, sc-5986)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using chloroform/phenol extraction. Libraries were constructed following manufacturer's instructions (NEB Next ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
15837713
Reads aligned (%)
60.1
Duplicates removed (%)
33.9
Number of peaks
7341 (qval < 1E-05)

hg38

Number of total reads
15837713
Reads aligned (%)
60.7
Duplicates removed (%)
33.5
Number of peaks
7317 (qval < 1E-05)

Base call quality data from DBCLS SRA