Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
B cells
Sex
female
sorting markers
CFSE, CD138
strain
B6.SJL-Ptprca Pepcb/BoyJ (CD45.1)
stimulation
LPS
division
5
cd138
negative
cell type
adoptively transferred CD43- Splenic B cells

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Three days following LPS stimulation, CD45.1 transferred cells were magnetically enriched and 20,000 cells per sample were FACS sorted based on cellular division and CD138 status Cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed using the Illumina Nextera Kit by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
22413149
Reads aligned (%)
99.1
Duplicates removed (%)
60.0
Number of peaks
6839 (qval < 1E-05)

mm9

Number of total reads
22413149
Reads aligned (%)
99.0
Duplicates removed (%)
60.1
Number of peaks
6821 (qval < 1E-05)

Base call quality data from DBCLS SRA