Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP63

Cell type

Cell type Class
Breast
Cell type
MCF10DCIS.com
Primary Tissue
Breast
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
Breast cancer cell line
cell line
MCFDCIS cells
antibody
p63 antibody (Santa Cruz, H129)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldhyde for 15 min. at room temperature, quenched with 0.125 M glycine, lysed with PIPES hypotonic buffer for 30 min and RIPA buffer for overnight at 4C. Samples were then sonicated using a Bioruptor Sonicator, pre-cleared with blocked sepharose beads and then incubated overnight with respective antibodies. Samples where then incubated with blocked beads for two hours, washed with ChIP wash buffers, incubated with ProteinaseK and RNAse then decrosslinked overnight at 65C. DNA was cleaned up using the Qiagen QiaQuick PCR Purification Kit (cat no. 28104). Library was constructed with KAPA HTP Library Prepartion kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
30893448
Reads aligned (%)
82.4
Duplicates removed (%)
9.7
Number of peaks
12167 (qval < 1E-05)

hg38

Number of total reads
30893448
Reads aligned (%)
83.4
Duplicates removed (%)
9.0
Number of peaks
12172 (qval < 1E-05)

Base call quality data from DBCLS SRA