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
splenic NK cells
genotype
WT
cell type
ex-vivo NK cells
condition
UNSTIM
replicate
1
chip antibody
none (H3K4me3 input)
experimentid
Project_05990

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA and proteins from sorted NK cells were cross-linked for 8 minutes at room temperature using 1% formaldehyde. Cross-linked cells incubated in cell lysis buffer (25 mM HEPES, 1.5 mM MgCl2, 10mM KCl, 0.1% NP-40, 1mM DTT, 1x proteinase inhibitor) and nuclei were isolated by centrifugation at 5400 rpm for 5.5 minutes. ChIP was performed using 1.5 μg of rabbit polyclonal anti-trimethyl-Histone H3 (Lys4) antibody (H3K4me3, Millipore, 07473) or 8 µg anti-Stat5 (#AF2168, R&D Systems) and Dynabeads Protein G (Invitrogen). Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Whenever possible, fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter catalog # A63882) and Illumina libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer's instructions with up to 10ng input DNA and 8-11 cycles of PCR. Barcoded libraries were run on a HiSeq 2500 in Rapid or High Output mode or a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq Rapid SBS Kit v2, HiSeq SBS Kit v4, or HiSeq 3000/4000 SBS Kit, respectively (Illumina). An average of 46 million paired reads were generated per sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
58675358
Reads aligned (%)
98.1
Duplicates removed (%)
10.7
Number of peaks
266 (qval < 1E-05)

mm9

Number of total reads
58675358
Reads aligned (%)
97.9
Duplicates removed (%)
11.3
Number of peaks
265 (qval < 1E-05)

Base call quality data from DBCLS SRA