Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
Natural Killer T-Cells
MeSH Description
A specific natural killer T-cell subtype that expresses an invariant T-cell receptor alpha-chain.

Attributes by original data submitter

Sample

source_name
ChIP-seq_H3K27Ac_NKT1
strain
C57BL/6
gender
female
age
5 weeks
tissue
thymus
cell type surface markers
NK1.1high, ICOSlow , CD27high, CCR6−
chip antibody
rabbit polyclonal Anti-Histone H3K27ac antibody
chip antibody vendor
Abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was performed as described in Seumois et al., Nat Immunol. 2014, PMID:24997565. Briefly: frozen cells were lysed in 120 μl of lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, 1 mM phenyl methane sulfonylfluoride, 20 mg/ml sodium butyrate, proteinase inhibitor cocktail; Sigma), and chromatin was sheared by sonication, using BioRuptorTM (Diagenode), to generate 100–500 bp DNA fragments. Chromatin was diluted in 1 ml of radioimmunoprecipitation assay (RIPA) buffer and immunoprecipitation was done overnight at 4 °C by incubating 1 μl of H3K27ac antibody (rabbit polyclonal IgG, lot# Gr167929-1, Abcam) pre-coated on 10 μl protein A coated magnetic beads (Invitrogen). Immunocomplexes were captured, washed, and ChIP DNA eluted as described previously. One ng of ChIP DNA was PCR amplified for 18 to 22 cycles using whole genome amplification (WGA) primers (WGA-SEQX, Sigma) following the manufacturer’s instructions. Approximately 100 ng amplified DNA was used for preparing a standard Illumina sequencing library (TruSeq® Nano DNA HT Sample Preparation Kit, Illumina). Whole Genome Amplification (MDA); Libraries were sequenced on the HiSeq2500 Illumina platform to obtain 50-bp single end reads (TruSeq® Rapid Kit, Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
12141335
Reads aligned (%)
84.8
Duplicates removed (%)
42.0
Number of peaks
3156 (qval < 1E-05)

mm9

Number of total reads
12141335
Reads aligned (%)
84.4
Duplicates removed (%)
42.0
Number of peaks
3141 (qval < 1E-05)

Base call quality data from DBCLS SRA