Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived chondrocytes
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic stem cell-derived chondrocytes - day 14
cell type
Chondrocytes
chip antibody
H3K4me3, Diagenode, C15410003-50

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed with about 10,000 cells per IP using Diagenode Low Cell ChIP kit (cat# C01010072 ) according to manufacturer's protocol. 1 µg of corresponding antibody from Diagenode was used per IP. ChIP-seq libraries wer constructed using Nugen's Ovation Ultralow DR Multiplex System 1-8 (cat# 0330-32) according to manufacturer's instructions. Library quality and concentration was assessed using Agilent Bioanalyzer 2100 and Qubit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
18524070
Reads aligned (%)
92.8
Duplicates removed (%)
57.5
Number of peaks
13503 (qval < 1E-05)

hg19

Number of total reads
18524070
Reads aligned (%)
92.3
Duplicates removed (%)
58.6
Number of peaks
13507 (qval < 1E-05)

Base call quality data from DBCLS SRA