Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Plasma Cells
MeSH Description
Specialized forms of antibody-producing B-LYMPHOCYTES. They synthesize and secrete immunoglobulin. They are found only in lymphoid organs and at sites of immune responses and normally do not circulate in the blood or lymph. (Rosen et al., Dictionary of Immunology, 1989, p169 & Abbas et al., Cellular and Molecular Immunology, 2d ed, p20)

Attributes by original data submitter

Sample

source_name
bone marrow plasma cell (CD138+), Dnmt3-deficient
background/strain
B6;129S4-Dnmt3atm3.1Enl Dnmt3btm5.1Enl/Mmnc
genotype/variation
Cd19cre/wtDnmt3afl/flDnmt3bfl/fl
gender
female
tissue
bone marrow
cell type
bone marrow plasma cell (CD138+)

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
33240054
Reads aligned (%)
86.4
Duplicates removed (%)
52.6
Number of peaks
45703 (qval < 1E-05)

mm9

Number of total reads
33240054
Reads aligned (%)
86.3
Duplicates removed (%)
52.7
Number of peaks
45613 (qval < 1E-05)

Base call quality data from DBCLS SRA