Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
embryoid bodies, UTX depleted, RA, input
cell line
v6.5
cell type
embryonic stem cells (ESCs)
genotype/variation
UTX knockout (UTX -/Y)
treatment
Retinoic acid (RA)
chip antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, cells were grown to log phase and fixed with 1% formaldehyde for 10 min at room temperature. The fixed cells were sonicated directly. Exactly 10% of the chromatin was used for the extraction of input DNA. For ChIP, 4 μg of antibodies, including anti-H3K4me3 or anti-H3K27me3 antibodies, was bound to protein A or protein G magnetic beads depending on the antibody origin. The ChIP-Seq libraries were constructed using the TruSeq DNA sample prep kit v2 (Illumina) according to the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
10983466
Reads aligned (%)
17.8
Duplicates removed (%)
31.1
Number of peaks
469 (qval < 1E-05)

mm9

Number of total reads
10983466
Reads aligned (%)
17.8
Duplicates removed (%)
31.3
Number of peaks
466 (qval < 1E-05)

Base call quality data from DBCLS SRA