Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GRHL2

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
cell line
MCF7
cell type
breast
treatment
E2
chip antibody
GRHL2
time
30 min

Sequenced DNA Library

library_name
GSM6125883
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed for 10 minutes with 1.5% formaldehyde and quenched with 0.125M glycine. Nuclei were extracted from cell pellets and sonicated to shear DNA. DNA was immunoprecipitated using an anitbody against GRHL2 (Millipore Sigma, #HPA004820). DNA was purified after reverse-crosslinking using the Qiagen PCR purification kit (Qiagen, #28104). Libraries were constructed using the NEBNext Ultra II DNA Library Prep kit (#E7103) and NEBNext Multiplex Oligos for Illumina (#E6440) according to vendor instructions. Samples were sequenced by paired-end 150bp sequencing on an Illumina NovaSeq 6000 by the Next Generation Sequencing department at the UW-Madison Biotechnology Center.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
37897734
Reads aligned (%)
94.6
Duplicates removed (%)
15.1
Number of peaks
17276 (qval < 1E-05)

hg19

Number of total reads
37897734
Reads aligned (%)
93.9
Duplicates removed (%)
15.4
Number of peaks
16221 (qval < 1E-05)

Base call quality data from DBCLS SRA