Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nipbl

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
NIPBL (Bethyl Laboratories, A301-779A, lot A301-779A-2)
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
50 million sorted CD4+ CD8+ DP thymocytes were fixed in 10% FCS DMEM media containing 1% formaldehyde. The cells were lysed and sonicated in [20 mM Tris-HCl, pH8, 150 mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X, protease inhibitors]. Lysates were cleared by centrifugation and NIPBL-DNA complexes were captured with 5 μg anti-NIPBL antibody (Bethyl, #A301-779A) and 25 μl Dynabeads. The captured DNA was eluted from the beads with a mixture of RnaseA, proteinaseK in [TE, 1% SDS] for 2 hours at 37° and then 16 hours at 65°. 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
57169235
Reads aligned (%)
82.7
Duplicates removed (%)
66.4
Number of peaks
19447 (qval < 1E-05)

mm9

Number of total reads
57169235
Reads aligned (%)
82.6
Duplicates removed (%)
66.5
Number of peaks
19778 (qval < 1E-05)

Base call quality data from DBCLS SRA