Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Breast
Cell type
ZR-75-1
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

ENA first public
2019-01-18
ENA last update
2019-01-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA5207810
INSDC center alias
Kabara Cancer Research Institute
INSDC center name
Kabara Cancer Research Institute
INSDC first public
2019-01-18T17:02:25Z
INSDC last update
2019-01-08T17:31:39Z
INSDC status
public
Submitter Id
E-MTAB-7578:WT_FLAG
broker name
ArrayExpress
cell line
ZR-75-1
common name
human
developmental stage
adult
disease
invasive ductal carcinoma
individual
wild type GATA3
organism part
mammary gland
sample name
E-MTAB-7578:WT_FLAG
sex
female

Sequenced DNA Library

library_name
WT_FLAG_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approx 8 million adherent cells were crosslinked for 10 mins in 1% formaldehyde. Cross linking was stopped by adding glycine to 0.125M. Cells were lysed in Farnham Lysis Buffer, washed in PBS and nuclei were lysed with RIPA buffer. ZR75-1 cells were cultured in RPMI 1640 supplemented with 10% serum Cell lines were generated by retroviral transduction of ZR75-1 with vectors containing either GATA3 WT, 308 or 335 mutations. Samples were sonicated using a Diagenode XL Bioruptor to fragments of 200-400 bp. Chromatin immunoprecipitation was performed using anti-FLAG antibody bound to protein G magnetic dynabeads. DNA fragments recovered from chromatin immunoprecipitation were reapired using Klenow DNA polymerase, liganted to Illumina TruSeq adapters using T4 DNA ligase and size selected for DNA with adapters attached.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
42530545
Reads aligned (%)
97.4
Duplicates removed (%)
19.1
Number of peaks
32332 (qval < 1E-05)

hg19

Number of total reads
42530545
Reads aligned (%)
96.6
Duplicates removed (%)
20.2
Number of peaks
31856 (qval < 1E-05)

Base call quality data from DBCLS SRA