Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Muscle
Cell type
Skeletal muscle
NA
NA

Attributes by original data submitter

Sample

source_name
skeletal muscle - quadricep
strain
C57BL/6
genotype
PGC1-tg
tissue
skeletal muscle - quadricep

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Skeletal muscle was dissected and finely minced. ChIP-seq samples were subjected to cross linking in 1% formaldehyde for 30 minutes and quenched with glycine. Tissue was dounced to release nuclei. Nuclei were sonicated to shear the chromatin and subjected to immunoprecipitation. Precipitates were washed and DNA was purified by column (Qiagen Min-Elute). ATAC-seq samples were cryo-pulverized and 30mg of powdered tissue was subjected to transposase reaction as per Buenrostro et al 2013. ChIP-seq libraries were prepared with the KAPA Hyper Prep Kit (Kapa Biosciences). ATAC-seq libraries were prepared as per Beunrostro et al 2013.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
48735493
Reads aligned (%)
95.3
Duplicates removed (%)
44.6
Number of peaks
3308 (qval < 1E-05)

mm9

Number of total reads
48735493
Reads aligned (%)
95.3
Duplicates removed (%)
44.7
Number of peaks
3301 (qval < 1E-05)

Base call quality data from DBCLS SRA