Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MB-231 cells
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody. Libraries were prepared using the ThruPlex DNA-seq kit from Rubicon Genomics using 20ng of ChIP DNA. Two unique tags were used. Two final pools were made. Each library was QC'ed using Qbit HS dsDNA kit for concentration and Agilent Bioanalyzer DNA HS chip for quality and fragment size. DNA was pooled based on qubit concentration, and qPCR was performed using Kappa Biosystems Illumina LIbrary Quant kit on the pool for nM concentration. DNA was then loaded onto an Illumina HiSeq 2500 50bp rapid run v2 flowcell.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
22933404
Reads aligned (%)
97.5
Duplicates removed (%)
2.6
Number of peaks
697 (qval < 1E-05)

hg19

Number of total reads
22933404
Reads aligned (%)
96.7
Duplicates removed (%)
4.0
Number of peaks
808 (qval < 1E-05)

Base call quality data from DBCLS SRA