Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

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
MDAMB231
cell line
MDAMB231
chip antibody
H3K4me1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For FAIRE, nuclei were extracted after the crosslinking step (1% formaldehyde in PBS) of intact cells, followed by re-suspension in SDS lysis buffer before sonication. FAIRE DNA samples were purified by phenol/chloroform extraction. Input DNA was also purified by phenol/chloroform extraction after the crosslinking was reversed. ChIP assays were performed in MDAMB231 as previously described (Jia et al, 2009). Libraries were prepared according to Illumina's instructions (refer to http://epigenome.usc.edu/services/nextgen/making_libraries.html)

Sequencing Platform

instrument_model
Illumina HiSeq 1000

hg38

Number of total reads
35164939
Reads aligned (%)
99.2
Duplicates removed (%)
2.8
Number of peaks
10933 (qval < 1E-05)

hg19

Number of total reads
35164939
Reads aligned (%)
98.7
Duplicates removed (%)
4.0
Number of peaks
11084 (qval < 1E-05)

Base call quality data from DBCLS SRA