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
ex vivo sorted naive B cells
cell type
ex vivo sorted naive B cells
strain
C57BL/6
genotype
WT
chip antibody
none

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Harvested spleens were processed and stained with antibodies. CD23+IgD+ cells were sorted on a BD FACsAria Fusion. 50,000 cells were used for library preparation. Cells were lysed, then treated with transposition mix (Nextera DNA Sample Preparation Kit) for 30 min at 37 degrees. Library fragments were amplified with 1x NEB Next PCR Master Mix and custom Nextera PCR primers. The number of cycles of PCR amplification was determined by q-PCR. 300-800 bps of libraries were selected using SPRI beads. Libraries were sequenced on a HiSeq 4000 system as paired-end reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
58700179
Reads aligned (%)
93.5
Duplicates removed (%)
41.4
Number of peaks
23899 (qval < 1E-05)

mm9

Number of total reads
58700179
Reads aligned (%)
93.4
Duplicates removed (%)
41.5
Number of peaks
24588 (qval < 1E-05)

Base call quality data from DBCLS SRA