Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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.

Attributes by original data submitter

Sample

source_name
shSmyd5_EB
genotype/variation
Smyd5 depletion
cell type
embryoid body (EB)
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
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
29193626
Reads aligned (%)
97.6
Duplicates removed (%)
15.2
Number of peaks
458 (qval < 1E-05)

mm9

Number of total reads
29193626
Reads aligned (%)
97.3
Duplicates removed (%)
15.1
Number of peaks
529 (qval < 1E-05)

Base call quality data from DBCLS SRA