Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nbn

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
splenic B cells
tissue
spleen
cell type
B cells
strain
C57BL/6
chip antibody
anti-Nbs1 (Abcam, ab32074)
genotype
aid-/-

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
2 × 10e7 live cells were resuspended in SBSS and cross-linked with 1% formaldehyde for 5 min at 37°C. Cross-linking was quenched by addition of glycine to 125 mM and incubating for 5 min at room temperature. Cross-linked cells were sonicated on ice for twenty 10-sec bursts, cooling on ice for 15 sec between bursts. A total of 2 × 10e6 cell equivalents were used per ChIP. Lysates were incubated with the appropriate antibodies overnight at 4°C. Protein A or G Dynabeads (Invitrogen) were added to samples for 2 h,followed by washing with low-salt (150 mM NaCl), high-salt (500 mM NaCl), and LiCl salt buffers, and finally with TE. The complexes were then eluted overnight at 65°C in the presence of 1 mg/ml RNAse A (Sigma-Aldrich). The following day, the samples were incubated with 10 mg/ml proteinase K (Sigma-Aldrich) at 55 °C overnight. Following phenol:chloroform and chloroform extractions, DNA was precipitated using 1 mg/ml glycogen (Roche) and 95% ethanol overnight at −20°C. DNA fragments were made blunt using the END-IT DNA repair kit (Epicentre) and a 3'-dA overhang added using Exo-Minus Klenow DNA Polymerase (Epicentre). Illumina paired-end (PE) adapters were added using the Fast-Link DNA Ligation kit (Epicentre), and the fragments were amplified twice using Illumina PE primers and PfuUltra II Fusion HS DNA polymerase (Stratagene). Each round of PCR was followed by gel purification and sizing of the fragments.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
56002253
Reads aligned (%)
77.9
Duplicates removed (%)
54.2
Number of peaks
1451 (qval < 1E-05)

mm9

Number of total reads
56002253
Reads aligned (%)
77.5
Duplicates removed (%)
54.2
Number of peaks
1572 (qval < 1E-05)

Base call quality data from DBCLS SRA