Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
MDA-MB-231_UT Input
cell line/tissue
MDA-MB-231
cell type
Triple negative breast cancer cells
passages
3-6
treatment
none
chip antibody
input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with respective antibodies. Sequencing library preparation and reactions were conducted at City of Hope's Integrative Genomics Core. ChIP-seq libraries were made using Illumina Tru-Seq library preparation kit and multiplexing barcodes compatible with Illumina HiSeq 2500 technology. RMA-seq libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
52847588
Reads aligned (%)
93.0
Duplicates removed (%)
4.9
Number of peaks
1498 (qval < 1E-05)

hg19

Number of total reads
52847588
Reads aligned (%)
92.2
Duplicates removed (%)
6.9
Number of peaks
1445 (qval < 1E-05)

Base call quality data from DBCLS SRA