Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCL9

Cell type

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

Attributes by original data submitter

Sample

source_name
DCIScom-NS
cell line
DCIS.com
cell type
breast cancer cell line
treatment
Non-scrambled control
chip antibody
BCL9 (Protein Tech 22947-I-AP)
biological replicate
2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and BCL9 and pSTAT3 were pulled down with 2ug antibody uisng ChIP-exo protocol. Details of the method can be found in a publication by H.S. Rhee and B.F. Pugh in Cell 2011, 147(6):1408-1419 titled “Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution"

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
29086546
Reads aligned (%)
125.2
Duplicates removed (%)
30.0
Number of peaks
784 (qval < 1E-05)

hg38

Number of total reads
29086546
Reads aligned (%)
126.3
Duplicates removed (%)
29.7
Number of peaks
863 (qval < 1E-05)

Base call quality data from DBCLS SRA