Antigen

Antigen Class

ATAC-Seq

Antigen

ATAC-Seq

Cell type

Cell type Class

Pluripotent stem cell

Cell type

Embryoid Bodies

MeSH Description

Spontaneous aggregations of human embryonic stem cells that occur in vitro after culturing in a medium that lacks LEUKEMIC INHIBITORY FACTOR. The embryoid bodies can further differentiate into cells that represent different lineages.

Sample

source_name

Mouse KH2 cells

cell type

differentiated EBs

cell line

KH2

Sequenced DNA Library

library_strategy

ATAC-seq

library_source

GENOMIC

library_selection

other

library_construction_protocol

For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

5521196

Reads aligned (%)

80.5

Duplicates removed (%)

14.5

Number of peaks

2458 (qval < 1E-05)

mm9

Number of total reads

5521196

Reads aligned (%)

80.3

Duplicates removed (%)

14.6

Number of peaks

2468 (qval < 1E-05)