Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
Splenic B cell
age
5 weeks old
Sex
male
treatment
10,000U IFNa
time point
48hr
strain
C57BL/6
antibody
Pol2 (Santa Cruz Biotechnology, N-20)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
B cells were negatively isolated using magnetic beads (EasySep Mouse B Cell Isolation Kit, STEMCELL Technologies). Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody conjugated to magnetic beads. Libraries were prepared according to a general protocol for ChIP-seq. Briefly, DNA was end-repaired using End-It DNA End-Repair Kit (Epicentre) followed by a single adenine nucleotide overhang attachment by Klenow fragment (Klenow Fragment 3'>5' exo-, New England Biolabs). The adaptor oligo mix was ligated by T4 DNA Ligase (LigaFast Rapid DNA Ligation System, Promega). Then the adapter ligated DNA was amplified by PCR employing NEBNext High-Fidelity 2X PCR Master Mix (NEB) and a set of indexed primers. Libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
5625853
Reads aligned (%)
98.2
Duplicates removed (%)
12.2
Number of peaks
2031 (qval < 1E-05)

mm9

Number of total reads
5625853
Reads aligned (%)
97.9
Duplicates removed (%)
12.5
Number of peaks
2049 (qval < 1E-05)

Base call quality data from DBCLS SRA