Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4K20me3

Cell type

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

Attributes by original data submitter

Sample

source_name
shSmyd5_mESC
cell type
mESC
cell line
R1 ES cell
protocol
shSmyd5
chip antibody
Anti-H4K20me3 antibody (Abcam; ab9053)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ES cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays. ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
30617975
Reads aligned (%)
77.0
Duplicates removed (%)
27.6
Number of peaks
2430 (qval < 1E-05)

mm9

Number of total reads
30617975
Reads aligned (%)
76.3
Duplicates removed (%)
27.3
Number of peaks
2306 (qval < 1E-05)

Base call quality data from DBCLS SRA