Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse embryonic stem cells
chip antibody
H3(Active Motif, MABI 0301, 39763)
gender
male
genotype/variation
wild type

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
15 cm dishes were fixed in PBS containing 1% methanol-free formaldehyde for 8 min at RT. Chromatin was purified using Paro-washes as described in Baubec et al., Nature. Chromatin was fragmented using MNase as for the Drosophila ChIP protocol but digesting at 37C and adding SDS to 0.1% final concentration after addition of EDTA-containing buffer. Cleared chromatin was incubated for 6-8h with antibody, before addition of Protein A dynabeads for 1h. Beads were washed 3 x in RIPA, 1 x LiCl-DOC and 2 x in TE buffer. Chromatin was further processed according to standard procedures. NEB Next Ultra II

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
222966867
Reads aligned (%)
95.5
Duplicates removed (%)
20.0
Number of peaks
874 (qval < 1E-05)

mm9

Number of total reads
222966867
Reads aligned (%)
95.3
Duplicates removed (%)
20.1
Number of peaks
877 (qval < 1E-05)

Base call quality data from DBCLS SRA