Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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 cells, H3K4me3 ChIP
cell line
SKBR3
cell type
Breast cancer cell line
treatment
Control
chip antibody
H3K4me3 (Abcam, ab8580, lot GR1902371-1 and GR224370-1)

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 antibody. ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
30925950
Reads aligned (%)
92.1
Duplicates removed (%)
24.1
Number of peaks
29213 (qval < 1E-05)

hg19

Number of total reads
30925950
Reads aligned (%)
91.8
Duplicates removed (%)
24.4
Number of peaks
29121 (qval < 1E-05)

Base call quality data from DBCLS SRA