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
Breast cancer cell line
cell line
MDA-MB-231
genotype
SATB1-depleted cells
chip antibody
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
14009220
Reads aligned (%)
99.0
Duplicates removed (%)
4.5
Number of peaks
25321 (qval < 1E-05)

hg19

Number of total reads
14009220
Reads aligned (%)
98.8
Duplicates removed (%)
4.5
Number of peaks
25284 (qval < 1E-05)

Base call quality data from DBCLS SRA