Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Others

Cell type

Mesenchymal stem cells

NA

NA

Sample

source_name

Bone marrow derived mesenchymal stem cells

antibody

H3K4me3 (Diagenode ,Mab-003)

differentiation-induction

Adipocyte 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

65041242

Reads aligned (%)

92.9

Duplicates removed (%)

39.4

Number of peaks

45306 (qval < 1E-05)

hg19

Number of total reads

65041242

Reads aligned (%)

92.5

Duplicates removed (%)

39.9

Number of peaks

45063 (qval < 1E-05)