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 negative cells
NA
NA

Attributes by original data submitter

Sample

source_name
WT_DN3_input
strain
C57BL/6
genotype/variation
wild-type
age
4-5 weeks
tissue
thymus
cell type
FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP protocol was adapted from the Millipore ChIP Assay Kit (17-295). Cells were cross-linked with 1% formaldehyde at 37°C for 10min in PBS/0.5% BSA and lysed in 1% Triton X-100, 50 mM MgCl2, 100 mM Tris-HCl ([pH 7.1), 11% sucrose, 1x PIC buffer. Pelleted nuclei were then lysed in 1% SDS lysis buffer and sonicated to 200-500 bp fragments using a Bioruptor 200 (Diagenode). Chromatin samples were incubated with the appropriate antibodies. DNA was purified using the iPure Kit (Diagenode). Libraries were prepared according to standard Illumina protocols, and were validated with the Agilent Bioanalyzer.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
12938090
Reads aligned (%)
98.2
Duplicates removed (%)
18.1
Number of peaks
529 (qval < 1E-05)

mm9

Number of total reads
12938090
Reads aligned (%)
98.0
Duplicates removed (%)
18.3
Number of peaks
575 (qval < 1E-05)

Base call quality data from DBCLS SRA