Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived mesendodermal cells
NA
NA

Attributes by original data submitter

Sample

source_name
hESC derived definitive endoderm cells
cell type
hESC derived definitive endoderm cells
chip antibody
H3K4me3 (abcam, ab8580)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For Chip-seq, Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. Antibodies were eluted from beads and formaldehyde cross-linking was reversed overnight by mild heating (65 °C), and chromatin was sequentially treated with RNase and Proteinase K before final column purification. Illumina sequencing libraries were generated using the TruSeq ChIP Sample Preparation Kit (Illumina). Briefly, 10 ng of ChIP-enriched DNA was end-repaired, 3’ adenylated, ligated with Illumina adapters, and amplified through 15 cycles of PCR amplification with Phusion High Fidelity DNA polymerase (Finnzymes) with primers directed against the adapters.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
37717885
Reads aligned (%)
93.8
Duplicates removed (%)
4.4
Number of peaks
18211 (qval < 1E-05)

hg19

Number of total reads
37717885
Reads aligned (%)
92.5
Duplicates removed (%)
6.2
Number of peaks
17978 (qval < 1E-05)

Base call quality data from DBCLS SRA