Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Natural killer cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse primary splenic NK cells
strain/background
C57BL/6
genotype/variation
WT
cell type
primary splenic NK cells
culture condition
ex vivo
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were chemically cross-linked by 1% formaldehyde. Lysates were made by sonication (10,000,000 cells/sample) and protein-DNA complexes isolated using the indicated antibodies. ChIP-seq: Single-end libraries were prepared for STAT5-bound fragments, along with un-precipitated input controls, using the NEBNext ChIP-Seq Library Prep kit for Illumina (New England Biolabs). Briefly, DNA fragments were end-repaired to generate phosphorylated blunt ends. These were then treated with Taq polymerase and dATP to generate 3-prime 'A' base overhangs for ligation to adapters containing complementary 'T' base overhangs. After ligation, DNA was PCR amplified for 15 cycles with indexed primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen). ChIP-seq: Indexed libraries were multiplexed and sequenced for 50 single read cycles on Illumina HiSeq 2000 or 2500 instruments according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
43044317
Reads aligned (%)
98.6
Duplicates removed (%)
40.4
Number of peaks
7822 (qval < 1E-05)

mm9

Number of total reads
43044317
Reads aligned (%)
98.5
Duplicates removed (%)
40.5
Number of peaks
7767 (qval < 1E-05)

Base call quality data from DBCLS SRA