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
Lin- BM derived Bcl11bKO cells
strain
C57BL6/J
cell type
DN3
treatment
Cultured on OP9DL1
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq; Ten million of BM-derived DN3 cells with 1% formaldehyde for 10 min. 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 ug per 10^7 cells of anti-H3K27Ac Abs (ab4729, Abcam) were hybridized to Dynabeads anti-Rabbit (Invitrogen) and added to the diluted chromatin complex. They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 ug/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
30557736
Reads aligned (%)
97.2
Duplicates removed (%)
15.0
Number of peaks
489 (qval < 1E-05)

mm9

Number of total reads
30557736
Reads aligned (%)
96.9
Duplicates removed (%)
14.9
Number of peaks
532 (qval < 1E-05)

Base call quality data from DBCLS SRA