Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Bone

Cell type

Chondrocytes

MeSH Description

Polymorphic cells that form cartilage.

Sample

source_name

CHON_H3K4me3

msc donor

2454e

cell type

differentiated chondrocytes

chip antibody

ChIP-seq grade polyclonal rabbit H3K4me3 (Diagenode, included in iDEAL Histone ChIP-seq kit cat. no. C01010050)

differentiation time point

14

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Chromatin from hMSCs and differentiated chondrocytes were extracted using the Diagenode iDeal histone ChIP-seq kit (Diagenode SA, Ougrée, Belgium). Extracted chromatin was sonicated using a Diagenode Bioruptor Standard or Bioruptor Pico to an average size of 200-500bp, using 15 sonication cycles (30s on/30s off). Replicate 1: Diagenode MicroPLEX v2 kit, replicate 2: NEBNext Ultra II kit (New England Biolabs, Hitchin, UK)

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

32248437

Reads aligned (%)

97.9

Duplicates removed (%)

4.4

Number of peaks

20132 (qval < 1E-05)

hg19

Number of total reads

32248437

Reads aligned (%)

97.2

Duplicates removed (%)

5.3

Number of peaks

20121 (qval < 1E-05)