Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Muscle
Cell type
C2C12
Primary Tissue
Skeletal Muscle
Tissue Diagnosis
NOS

Attributes by original data submitter

Sample

source_name
muscle
differentiation stage
myoblast (MB)
chip antibody
none
strain
C2C12

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIPSeq,cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Lysates were cleared from sonicated nuclei and used for immunoprecipitation For ChIRPseq, cells were cross-linked in 1% glutaraldehyde. Nuclei were sonicated and used for probe hybridization. For ATACseq, nucli were isolated and treated with Tn5 transpoase. For ChIPSeq, 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with NEBNext Ultra DNA library prep kit for Illumina (New England BioLabs) following the manufacturer's protocol. NEBNext Ultra II RNA library prep kit (New England BioLabs) was used to process RNA-Seq libraries following the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
37303654
Reads aligned (%)
97.8
Duplicates removed (%)
25.9
Number of peaks
498 (qval < 1E-05)

mm9

Number of total reads
37303654
Reads aligned (%)
97.6
Duplicates removed (%)
25.9
Number of peaks
527 (qval < 1E-05)

Base call quality data from DBCLS SRA