Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4K4me3

Cell type

Cell type Class
Breast
Cell type
SK-BR-3
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
SKBr3
cell line
SKBr3
cell type
breast cancer epithelial cells
chip antibody
H4K4me3 (Abcam, ab1012)
treatment
control

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was isolated from the nuclei of formaldehyde cross-linked cells, sonicated and immunoprecipated with anti-H3K4me3 antibody. ChIP-Seq libraries were constructed from 10ng immunoprecipitated or original input chromatin using the ChIP-Seq Sample Prep Kit from Illumina, following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
21249937
Reads aligned (%)
99.5
Duplicates removed (%)
65.2
Number of peaks
18592 (qval < 1E-05)

hg19

Number of total reads
21249937
Reads aligned (%)
99.5
Duplicates removed (%)
65.5
Number of peaks
18587 (qval < 1E-05)

Base call quality data from DBCLS SRA