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
Mouse Embryonic Stem Cells
strain
E14 [129 background]
treatment
Mouse ES cells routinely cultured in serum/LIF conditions
chip antibody
input DNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
In general, Flag ChIP followed the procedure described in Frank et al., 2001. Chromatin was fixed on 1% formaldehyde for 10 minutes and was sonicated on a bioruptor (Diagenode) to produce fragments of 100-500 bp. 500 μg of protein were used per ChIP with 10 μg of anti-Flag antibody (Sigma, catalog number F1804) and protein-bound fragments were retrieved with ProteinG-coupled magnetic Dynabeads (Invitrogen). Sequencing libraries were prepared using the NEBNext® UltraTM DNA Library Prep Kit and Multiplex Oligos (New England Biolabs) from 5 ng of DNA.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
24838647
Reads aligned (%)
97.6
Duplicates removed (%)
12.8
Number of peaks
464 (qval < 1E-05)

mm9

Number of total reads
24838647
Reads aligned (%)
97.4
Duplicates removed (%)
12.9
Number of peaks
498 (qval < 1E-05)

Base call quality data from DBCLS SRA