Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

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

Attributes by original data submitter

Sample

source_name
Definitive endoderm
cell line
CyT49
cell types
hESC derived definitive endoderm
antibody
H3K4me1, Abcam ab8895

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).  Libraries were prepared according to Illumina's instruction or cited literatures.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
33877753
Reads aligned (%)
97.9
Duplicates removed (%)
2.8
Number of peaks
34472 (qval < 1E-05)

hg19

Number of total reads
33877753
Reads aligned (%)
97.7
Duplicates removed (%)
3.2
Number of peaks
36488 (qval < 1E-05)

Base call quality data from DBCLS SRA