Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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
MB231 cells, H3K4me3 ChIP
cell line
MB231
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
37903579
Reads aligned (%)
88.2
Duplicates removed (%)
11.7
Number of peaks
25141 (qval < 1E-05)

hg19

Number of total reads
37903579
Reads aligned (%)
87.9
Duplicates removed (%)
12.2
Number of peaks
25196 (qval < 1E-05)

Base call quality data from DBCLS SRA