Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Spleen
Cell type
Splenocytes
NA
NA

Attributes by original data submitter

Sample

source_name
Splenocytes
breed
C67BL/6
age
> 20 weeks
Sex
female
tissue
spleen
sorting strategy
B220+CD19+CD11c+CD11b+

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
RNA-seq:Total RNA was isolated using QIAGEN RNAeasy plus mini kit from FACS sorted FoB or ABC cells ATAC-seq: The nuclei of sorted DKO ABC or DKO Follicular B cells were prepared by incubation of cells with nuclear preparation buffer (0.30 M sucrose, 10 mM Tris, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM spermine, 0.5 mM spermidine and 2 mM 6AA) RNA-seq: Sequence-compatible libraries were prepared using Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library preparation at the Weil Cornell Epigenomics core. Quality of all RNA and library preparations were evaluated with BioAnalyser 2100 (Agilent) ATAC-seq: Sequencing libraries were constructed as discribed in PMID: 26083756 :Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17. PubMed PMID: 26083756; PubMed Central PMCID: PMC4685948.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
303193603
Reads aligned (%)
45.4
Duplicates removed (%)
43.2
Number of peaks
71154 (qval < 1E-05)

mm9

Number of total reads
303193603
Reads aligned (%)
45.3
Duplicates removed (%)
43.3
Number of peaks
71133 (qval < 1E-05)

Base call quality data from DBCLS SRA