Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Naive B cells
NA
NA

Attributes by original data submitter

Sample

source_name
naïve B cell (B220+ Fas- GL7-), Dnmt3-sufficient
background/strain
B6;129S4-Dnmt3atm3.1Enl Dnmt3btm5.1Enl/Mmnc
genotype/variation
Cd19wt/wtDnmt3afl/flDnmt3bfl/fl
gender
male
tissue
lymph node
cell type
naive B cell (B220+ Fas- GL7-)

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were pelleted at 500g for 10 min and lysed in nuclei lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). Nuclei were pelleted at 500g for 30 min and tagmented with Tn5 (Illumina) for 60 min at 37°C prior to protein digestion with 2 mL 10 mg/mL Proteinase K at 40°C for 40 minutes. Libraries were size selected with SPRI beads (AMPure) prior to 12 rounds of PCR amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
17520040
Reads aligned (%)
83.2
Duplicates removed (%)
23.2
Number of peaks
28231 (qval < 1E-05)

mm9

Number of total reads
17520040
Reads aligned (%)
83.0
Duplicates removed (%)
23.3
Number of peaks
28143 (qval < 1E-05)

Base call quality data from DBCLS SRA