Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
CD4 CD8 double positive cells
NA
NA

Attributes by original data submitter

Sample

source_name
DP T cells
strain
C57BL/6
tissue
Thymus
developmental stage
DP T cells
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed on ice in Lysis buffer (50 mM Hepes pH 7.9, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 140 mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25 % Triton, protease inhibitors and 5 mM sodium butyrate) in order to obtain nuclei, that were washed twice with washing buffer(10 mM Tris-Cl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 1x protease inhibitors, 5 mM sodium butyrate) and resuspended in shearing buffer(0.1% SDS, 1mM EDTA pH 8.0, 1x protease inhibitors, 5 mM sodium butyrate) . Then, chromatin was sheared in an average size of 200 bp using Covaris. Histones-DNA complexes were isolated using the H3K27Ac antibody. Libraries were prepared following standard procedures. Briefly, DNA was end repaired using the End Repair kit by Epicentre. A-tailing was performed using the large Klenow fragment enzyme by NEB.We used the TruSeq indexed adapters by Illumina. After adapter ligation DNA was PCR amplified for 10 cycles using Kapa HiFi DNA polymerase from Kapa Biosystems. Libraries were purified twice using Ampure Beads (Beckman Coulter) and subsequently were sequenced in an Illumina HiSeq 2000 instrument.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
27622618
Reads aligned (%)
97.8
Duplicates removed (%)
10.8
Number of peaks
442 (qval < 1E-05)

mm9

Number of total reads
27622618
Reads aligned (%)
97.5
Duplicates removed (%)
10.8
Number of peaks
502 (qval < 1E-05)

Base call quality data from DBCLS SRA