Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
AT-3
NA
NA

Attributes by original data submitter

Sample

source_name
AT-3 mammary tumor cell line
cell line
AT-3 mammary tumor cell line
treatment
DMSO vehicle
culture media
DMEM-based media (supplemented with 10% FCS, 100U/mL penicillin, 100mg/mL streptomycin)
chip antibody
N/A
strain
C57BL/6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysate were isolated from formaldehyde cross-linked cells and sonicated to release the chromatin, then immunoprecipitated using relevant antibodies. For BRD4, RNA Polymerase II, IRF1, STAT1, H3K27Ac ChIP-Seq, indexed libraries were prepared using KAPA Hyper Prep Kit for Illumina platforms (Kapa Biosystems) and SeqCap Adapter Kit (Roche). For MYC ChIP-Seq, indexed libraries were prepared using Nugen Ovation Ultralow system (v2, Nugen protocol M01379v3).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
15051374
Reads aligned (%)
96.7
Duplicates removed (%)
9.2
Number of peaks
195 (qval < 1E-05)

mm9

Number of total reads
15051374
Reads aligned (%)
96.6
Duplicates removed (%)
9.3
Number of peaks
156 (qval < 1E-05)

Base call quality data from DBCLS SRA