Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
BM derived Phase1 cells
strain
C57BL6/J
treatment
Cultured on OP9DL1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq; Five to ten million of Phase1 or Phase2 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%. The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco). Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power. Five g of anti-Rbpj mAbs (a mixture of 2.5 g of 5313 (CST) and 2.5 g of ab180588 (Abcam)) were pre-bound to Dynabeads anti-Rabbit Ig (Invitrogen) and then added to the diluted chromatin complexes in parallel aliquots. The samples were incubated overnight at 4 °C, then washed and eluted for 6 h at 65 °C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 g/ml proteinase K). Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
34115580
Reads aligned (%)
95.5
Duplicates removed (%)
25.6
Number of peaks
2179 (qval < 1E-05)

mm9

Number of total reads
34115580
Reads aligned (%)
95.2
Duplicates removed (%)
25.6
Number of peaks
2008 (qval < 1E-05)

Base call quality data from DBCLS SRA