SRX4321991
GSM3231533: ATAC-seq Luminal Suz12-deleted 2; Mus musculus; ATAC-seq

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Breast
Cell type
Mammary epithelium organoid
NA
NA

Attributes by original data submitter

Sample

source_name
Mammary epithelium
background strain
C57BL/6
tissue
Mammary epithelium organoid
cell type from which organoid was derived
Luminal
genotype
Suz12-deleted

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Nuclei were isoluated from 50,000 cells using ATAC lysis buffer (10mM Tris-Cl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) DNA was tagmented using Illumina Tn5, PCR-amplifed and equimolar amounts sequenced.

Sequencing Platform

instrument_model
NextSeq 500

Where can I get the processing logs?

Read processing pipeline log

mm10

Number of total reads
64086549
Reads aligned (%)
52.7
Duplicates removed (%)
24.3
Number of peaks
18275 (qval < 1E-05)

mm9

Number of total reads
64086549
Reads aligned (%)
52.7
Duplicates removed (%)
24.3
Number of peaks
18258 (qval < 1E-05)

Base call quality data from DBCLS SRA