Curated Sample Data


Genome
mm9
Antigen Class
Input control
Antigen
Input control
Cell type Class
Muscle
Cell type
gastrocnemius

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
gastrocnemius
tissue
gastrocnemius
strain
C57BL/6J
time
Zeitgeber Time 4
gender
male
genotype
Wild Type
chip antibody
input DNA

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described (Uhlenhaut et al. 2012) with minor modifications. Briefly, around 300 mg of frozen muscle was homogenized, filtered through a 70┬Ám cell strainer, and pellet fixed in 1% Formaldehyde. Nuclei were purified and chromatin sonicated to a 1-0.5 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies. Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

Platform Information


instrument_model
Illumina HiSeq 2500

External Database Query

Logs in read processing pipeline


Number of total reads
57977249
Reads aligned (%)
98.1
Duplicates removed (%)
12.8
Number of peaks
207 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA