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
Stat4WT
chip antibody
none
condition
IL12IL18
cell type
splenic NK cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Protein was cross-linked to DNA with 0.75% formaldehyde. Clarified supernatant from sonicated nuclei were applied to antibody-bound beads. After de-crosslinking and elution, DNA was isolated using Qiagen Gel Extraction Kit. Input samples were clarified supernatant that were not applied to antibody-bound beads. Immunoprecipitated DNA was quantified by Picogreen and size was evaluated on a HighSense BioAnalyzer chip. When possible, fragments between 100 and 600 bp were size selected and Illumina Hiseq libraries were prepared using the Kapa DNA library preparation chemistry (Kapa Biosystems) using 12-15 cycles of PCR. Adaptors were diluted 1/10 or 1/50 depending on the starting amount of material available. Barcoded libraries were run on Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina). An average of 57 million paired reads were generated per sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
49251701
Reads aligned (%)
97.9
Duplicates removed (%)
7.0
Number of peaks
207 (qval < 1E-05)

mm9

Number of total reads
49251701
Reads aligned (%)
97.8
Duplicates removed (%)
7.4
Number of peaks
200 (qval < 1E-05)

Base call quality data from DBCLS SRA