Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
a human breast cancer cell line
origin
mammary gland/breast; derived from metastatic site: pleural effusion
disease
adenocarcinoma
antibody or sirna
N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, after fixation with 37% formaldehyde, nuclei was collected by sonication (Bioruptor, Diagenode). DNA-MAFF bound was immunoprecipitated with a MAFF-specific antibody. For RNA-seq, RNA was collected using a Rneasy kit (Qiagen) For ChIP-seq, libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix set for Illumina (NEB #E6240) and NEBNext Multiplex Oligos for Illumina (NEB #E7730S). For RNA-seq, libraries were prepared using Illumina's TruSeq RNA library prep kit v2. ChIP seq and RNA seq

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
32039288
Reads aligned (%)
98.8
Duplicates removed (%)
3.7
Number of peaks
1179 (qval < 1E-05)

hg19

Number of total reads
32039288
Reads aligned (%)
98.1
Duplicates removed (%)
5.5
Number of peaks
1264 (qval < 1E-05)

Base call quality data from DBCLS SRA