Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CASP3

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7 cells
cell line
MCF-7
modification
Stably transfected with Caspase-3 cDNA
tissue
Breast
treatment
Docetaxel
antibody
Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb from Cell Signaling, Ref: #9664, Batch: 0019

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinking, extraction and shearing of chromatin was performed by using the Truchip chromatin shearing reagent kit from 1,500,000 cells by following manufacturer protocol. Then, sheared chromatin was immunoprecipitated with different antibodies (anti-active Caspase-3 or control Immunoglobulin) by using the Active Motif's ChIP IT Kit by following manufacturer's instructions Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina. After library validation on a fragment analyzer, the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq device following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina MiSeq

hg19

Number of total reads
1911437
Reads aligned (%)
53.8
Duplicates removed (%)
0.9
Number of peaks
36 (qval < 1E-05)

hg38

Number of total reads
1911437
Reads aligned (%)
54.9
Duplicates removed (%)
0.8
Number of peaks
37 (qval < 1E-05)

Base call quality data from DBCLS SRA