Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDKN1B

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-231-1833
cell line
derived from MDA-MB-231
cell type
cancer cells (a bone-tropic metastatic line)
tissue
breast
chip antibody
p27 (Cell Signaling; 3686S)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assay was preformed by ChIP-IT High Sensitivity kit (Active Motif; 53040). After cells were crosslinked with 1% formaldehyde, the cells were lysed and sonicated. For the immunoprecipitation, sonicated samples were incubated with anti-cJun (Cell Signaling; 9165s) and p27 (Cell Signaling; 3686s) antibodies for overnight at 4°C. After elution DNA, the quality was measured using Bioanalyzer DNA HS (Agilent Technologies). Libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit (NEB), and their quality was measured by High Sensitivity D1000 Screen Tape (Agilent Technologies). ChIP sequencing was performed on Illumina 75 cycles 400M reads.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
33943202
Reads aligned (%)
64.8
Duplicates removed (%)
31.5
Number of peaks
49022 (qval < 1E-05)

hg38

Number of total reads
33943202
Reads aligned (%)
65.1
Duplicates removed (%)
31.4
Number of peaks
49101 (qval < 1E-05)

Base call quality data from DBCLS SRA