Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CHD1

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.

Attributes by original data submitter

Sample

source_name
Fetal osteoblast
antibody
CHD1 (Bethyl ,A301-218A)
differentiation-induction
Undifferentiated

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

hg19

Number of total reads
39993269
Reads aligned (%)
82.6
Duplicates removed (%)
6.1
Number of peaks
1149 (qval < 1E-05)

hg38

Number of total reads
39993269
Reads aligned (%)
84.8
Duplicates removed (%)
4.5
Number of peaks
1162 (qval < 1E-05)

Base call quality data from DBCLS SRA