Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TRIM28

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
MCF7 cells
cell line
MCF7
treatment
Control
antibody
TRIM28

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, MCF7 lysates with were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-seq, RNA was harvested using Trizol reagent from control, EZH2, and TRIM28 depleted MCF7 cells. RNA libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
44442792
Reads aligned (%)
85.7
Duplicates removed (%)
8.3
Number of peaks
1407 (qval < 1E-05)

hg38

Number of total reads
44442792
Reads aligned (%)
89.7
Duplicates removed (%)
5.7
Number of peaks
1882 (qval < 1E-05)

Base call quality data from DBCLS SRA