Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Smarcad1

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 type
Embryonic stem cells
strain
OCT4-deltaPE-GFP x C57BL/6
treatment
ES maintianence-feeder free
chip-antibody
ab67548(Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were scraped off dishes and collected by centrifuge. Cross-linked chromatin complexes were isolated from the Nuclei lysis buffer and then sonicated to obtain fragments in a size range between 350-500bp. H3R26Cit antibody (ab19847) were incubated with solubilized DNA fragments overnight at 4°C. Protein A/G agarose beads (Pierce, Rockford, IL) were used to capture the antibody-chromatin complex followed by washes and elution with 1% SDS. The DNA was recovered by reversing the cross-links with 20 mM NaCl at 65°C overnight. DNA was purified by QIAquick PCR Purification Kit (Qiagen 28106) and dissolving in a final volume of 30ul per immunoprecipitation. The Protocol of KAPA High-Throughput Library Preparation Kit (Cat. No. KK8234)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
90933185
Reads aligned (%)
96.2
Duplicates removed (%)
87.0
Number of peaks
11476 (qval < 1E-05)

mm9

Number of total reads
90933185
Reads aligned (%)
96.1
Duplicates removed (%)
87.0
Number of peaks
11495 (qval < 1E-05)

Base call quality data from DBCLS SRA