Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
Embryonic Stem Cells
cell line
D3 Embryonic Stem Cells
targeted protein
Halo-Sox2
purification of halotag fusion protein
Halo-Link Resin (Promega, Cat. # G1913, Lot # 31905004)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody or HaloLink Resin. Libraries were prepared according to "Rhee, H.S., and Pugh, B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419." with custom-made illumina adapters

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
105616953
Reads aligned (%)
64.6
Duplicates removed (%)
94.4
Number of peaks
2259 (qval < 1E-05)

mm9

Number of total reads
105616953
Reads aligned (%)
64.5
Duplicates removed (%)
94.5
Number of peaks
2264 (qval < 1E-05)

Base call quality data from DBCLS SRA