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
bone marrow
chip antibody
Input Control
strain
C57BL/6
cell type
primary whole bone marrow cells
genotype
C/EBPepsilon knock-out

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Magna ChIP™ A - Chromatin Immunoprecipitation Kit, Cat# 17-610 (EMD Millipore) Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Illumina Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
42743755
Reads aligned (%)
86.0
Duplicates removed (%)
20.5
Number of peaks
961 (qval < 1E-05)

mm9

Number of total reads
42743755
Reads aligned (%)
85.7
Duplicates removed (%)
20.4
Number of peaks
1082 (qval < 1E-05)

Base call quality data from DBCLS SRA