Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

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
1000nM JQ1+ 1ng/mL IFN-γ
culture media
DMEM-based media (supplemented with 10% FCS, 100U/mL penicillin, 100mg/mL streptomycin)
chip antibody
anti-RNA polymerase II (CTD4H8, Millipore)
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
15212374
Reads aligned (%)
92.5
Duplicates removed (%)
11.7
Number of peaks
7504 (qval < 1E-05)

mm9

Number of total reads
15212374
Reads aligned (%)
92.3
Duplicates removed (%)
11.8
Number of peaks
7474 (qval < 1E-05)

Base call quality data from DBCLS SRA