Antigen

Antigen Class

Unclassified

Antigen

Unclassified

Cell type

Cell type Class

Bone

Cell type

Osteoblasts

MeSH Description

Bone-forming cells which secrete an EXTRACELLULAR MATRIX. HYDROXYAPATITE crystals are then deposited into the matrix to form bone.

Sample

source_name

Fetal osteoblast

sirna treatment

siCHD1

differentiation-induction

Osteoblast differentiation

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were crosslinked for 10 minutes with 1% Formaldehyde in PBS or 1.42% formaldehyde for CHD1 ChIP. Chromatin extraction and subsequent steps were performed as described in Najafova et al. 2016. Briefly, nuclear extracts were incubated with 1 – 2 µg of antibody over night before precipitation with protein A or G sepharose beads. After washing the immunoprecipitated complexes the DNA was isolated via phenol-chloroform extraction. ChIP DNA library preparation was performed with the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer's instructions.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

18492946

Reads aligned (%)

97.0

Duplicates removed (%)

2.9

Number of peaks

717 (qval < 1E-05)

hg19

Number of total reads

18492946

Reads aligned (%)

96.2

Duplicates removed (%)

4.2

Number of peaks

860 (qval < 1E-05)