Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Bone Marrow Cells
MeSH Description
Cells contained in the bone marrow including fat cells (see ADIPOCYTES); STROMAL CELLS; MEGAKARYOCYTES; and the immediate precursors of most blood cells.

Attributes by original data submitter

Sample

source_name
Bcl11bKO_1%_input-seq
strain
C57BL6/J
cell type
Lin- BM derived Bcl11bKOcells
cultured on
OP9DL1

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 or Schd.adh.2c2 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. Six μg per 107 cells of anti-Bcl11b Abs (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)), anti-Chd4 (A301-081A), anti-Mta2 (sc-9447), anti-Hdac2 (ab12169), anti-Rest (12C11-1B11), anti-Ring1b (A302-869A), anti-LSD1 (ab17721) or anti-Runx1 (ab23980) were hybridized to Dynabeads anti-Rabbit, Dynabeads anti-Mouse or Dynabeads Protein A/G (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 μg/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. RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen). Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer's instructions. Libraries were 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
39543286
Reads aligned (%)
97.3
Duplicates removed (%)
24.1
Number of peaks
457 (qval < 1E-05)

mm9

Number of total reads
39543286
Reads aligned (%)
97.1
Duplicates removed (%)
24.0
Number of peaks
519 (qval < 1E-05)

Base call quality data from DBCLS SRA