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
CD4+ CD8+ Double Positive Thymocytes
cell type
CD4+ CD8+ Double Positive Thymocytes
chip antibody
input DNA
genotype
wild type
genetic background
C57BL\6 and 129 mixed

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [10 mM Tris-HCl, pH7.4, 800 mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X, 0.1% Sodium Deoxycholate, protease inhibitors]. Lysates were cleared by centrifugation and incubated with a mixture of RNaseA and proteinaseK for 2 hours at 37° and then 16 hours at 65° to reverse the cross-links. DNA was purified by phenol-chloroform extraction and 10ng was used with a Illumina ChIP-seq sample preparation according to the manufacturer instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
10286585
Reads aligned (%)
91.7
Duplicates removed (%)
7.8
Number of peaks
656 (qval < 1E-05)

mm9

Number of total reads
10286585
Reads aligned (%)
91.5
Duplicates removed (%)
8.1
Number of peaks
716 (qval < 1E-05)

Base call quality data from DBCLS SRA