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
FLAG-ZFP708 OE Embryonic Stem Cells (1)
tissue
mouse embryonic stem cells
antibody
-

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described {Guccione:2007dy}. Chromatin was fragmented using a BRANSON Digital Sonifier (#S540D) to 250-1000bp fragments, precleared and incubated with antibodies overnight. Antibody/chromatin complexes were incubated for 50% Protein-G Sepharose slurry and washed before elution/decrosslinking in 1% SDS and 0.1 M NaHCO3. DNA was column purified with QIAquick PCR purification Kit, Qiagen. ChIP DNA concentrations were measured with the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were prepared with the NEBNext Ultra II DNA Library Preparation Kit for Illumina (NEB), following manufacturer's instructions. PCR conditions were adjusted to starting material concentrations and final elution volumes were reduced. Libraries were quantified by Bioanalyzer (High Sensitivity DNA Kit, Agilent) and PCR (KAPA Library Quantification Kit for Illumina, Roche). ChIP-Seq libraries were pooled and sequenced on the NextSeq500, as a single end (76bp) run

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
42906568
Reads aligned (%)
98.0
Duplicates removed (%)
11.5
Number of peaks
306 (qval < 1E-05)

mm9

Number of total reads
42906568
Reads aligned (%)
97.8
Duplicates removed (%)
11.5
Number of peaks
281 (qval < 1E-05)

Base call quality data from DBCLS SRA