Antigen

Antigen Class

Histone

Antigen

H3K4me1

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

ES cell line

developmental stage

Day 8 embryoid bodies

chip antibody

H3K4me1 (Abcam, ab8899, lot unknown)

strain

E14

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For ChIPSeq, lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen). For ChIPSeq, cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with anti-H3K27me1 (Millipore #07-448), anti-H3K27me2 (Cell signaling #9728S), anti-H3K27me3 (Cell signaling #9733S), anti-H3K4me1 (Abcam #ab8899), anti-H3K27ac (Abcam #4729). 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. For polyA RNA-Seq, Illumina protocol was followed.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

48904243

Reads aligned (%)

90.0

Duplicates removed (%)

65.0

Number of peaks

81632 (qval < 1E-05)

mm9

Number of total reads

48904243

Reads aligned (%)

89.9

Duplicates removed (%)

65.0

Number of peaks

83239 (qval < 1E-05)