Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA3

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7 breast cancer cell line
cell line
MCF7
replicate
1
chip antibody
GATA3 serum (generated in rabbits using recombinant 6x histidine tag-fused GATA3 full-length wild-type protein)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked, lysed and sonicated to generate 200 to 400 bp DNA fragments. Immunoprecipitation was performed with GATA3 serum generated in rabbits using recombinant 6x histidine tag-fused GATA3 full-length wild-type protein. ChIP DNA generated in 4-5 individual reactions was pooled to obtain 100ug. Libraries were constructed using TruSeq RNA Sample Preparation kit (Illumina, San Diego, CA, USA). The library was prepared following the manufacturer’s instructions, starting with the end repair step, and amplified with twelve PCR cycles.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
43328882
Reads aligned (%)
81.4
Duplicates removed (%)
6.1
Number of peaks
19804 (qval < 1E-05)

hg38

Number of total reads
43328882
Reads aligned (%)
83.2
Duplicates removed (%)
4.8
Number of peaks
19828 (qval < 1E-05)

Base call quality data from DBCLS SRA