Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Breast
Cell type
SUM 229PE
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
EpCAM/CD49f positive SUM229 breast carcinoma subpopulation
cell line
SUM229 breast carcinoma cell line, EpCAM/CD49f positive subpopulation
treatment
DMSO
time
24h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell lysates were sonicated resulting in an average chromatin fragment size of ~300 bp and immunoprecipiated with the indicated antibodies. All libraries were constructed using KAPA Hyper Prep kits with Illumina TruSeq adapters, 18 cycles of amplification and dual SPRI size selection post-amplification, except where indicated, whereby the libraries were constructed using DNA SMART ChIP Seq kit (Clontech) with dual SPRI size selection following 18 cycles of amplification. library preparation kit: KAPA Hyper Prep

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
42158998
Reads aligned (%)
100.0
Duplicates removed (%)
2.4
Number of peaks
1761 (qval < 1E-05)

hg19

Number of total reads
42158998
Reads aligned (%)
100.0
Duplicates removed (%)
3.8
Number of peaks
2942 (qval < 1E-05)

Base call quality data from DBCLS SRA