Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Breast
Cell type
3617
NA
NA

Attributes by original data submitter

Sample

source_name
3617-KOGR cells, stably integrated wild-type GFP-GR, Dex-treated, ATAC
cell line
3617-KOGR
cell type
mouse adenocarcinoma
stably expressing
wild-type GFP-GR
treatment
Dexamethasone
concentration
100 nM
time
1 h

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
For ChIP-seq, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with specified antibody. For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Nextera Tn5 Transposase from Nextera kit. For RNA-seq, RNA was extracted using the PureLink RNA mini kit. Libraries were prepared for sequencing using standard Illumina protocols. For ChIP-seq, Illumina TruSeq Chip Sample Prep Kit; for ATAC-seq, Illumina Nextera DNA Library Prep Kit; for RNA-seq, Illumina Stranded Total RNA.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
116283253
Reads aligned (%)
30.0
Duplicates removed (%)
28.4
Number of peaks
8717 (qval < 1E-05)

mm9

Number of total reads
116283253
Reads aligned (%)
30.0
Duplicates removed (%)
28.4
Number of peaks
8688 (qval < 1E-05)

Base call quality data from DBCLS SRA