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
input
cell type
differentiating C2C12 myoblasts
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with formaldehyde and disuccinimidyl glutarate. Cell lysates were subjected to two-step DNA fragmentation by a probe-type sonifier and a water bath sonifier, and chromatin-DNA complexes were pulled down using the specific antibody. Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end prep enzyme. After adapter ligation, DNA was PCR amplified with NEB Index primers for 8-10 cycles. The purified DNA was checked for quality on Agilent TapeStation instrument with an Agilent High Sensitivity D1000 kit. The library DNA was approximately 170–500 bp in length. Libraries ware quantified using quantitative real-time PCR with the Kapa Library Quantification Kit. Diluted library DNA was subjected NextSeq sequencers (Illumina) according to the manufacturer's protocols.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
73027780
Reads aligned (%)
82.3
Duplicates removed (%)
32.3
Number of peaks
69588 (qval < 1E-05)

mm9

Number of total reads
73027780
Reads aligned (%)
82.1
Duplicates removed (%)
32.3
Number of peaks
69489 (qval < 1E-05)

Base call quality data from DBCLS SRA