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
genotype
WT
cell type
Mouse embryonic stem cells
chip antibody
NA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq for non-histone proteins (Dnttip1) was carried out with 5 x 10e7 cells and for histones with 2-2.5 x 10e7 mESCs, using a modified version of Lee et al., Nature Protocols, 2006. ChIP-seq Library Preparation and Sequencing:DNA was quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Libraries were prepared with the KAPA HyperPrep Library Kit (Roche, 07962363001) and analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067-4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067-5584, 5067-5585, 5067-5587, 5067-5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay. Single end 50 cycle sequencing was performed on a HiSeq 2500, HiSeq 4000, or NovaSeq 6000 System (all from Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
40652685
Reads aligned (%)
99.8
Duplicates removed (%)
6.5
Number of peaks
37 (qval < 1E-05)

mm9

Number of total reads
40652685
Reads aligned (%)
99.8
Duplicates removed (%)
6.6
Number of peaks
37 (qval < 1E-05)

Base call quality data from DBCLS SRA