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
C2C12 cells
strain
CH3
cell line
C2C12
cell type
muscle
genotype/variation
overexpressing HA-tagged ZFP932
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were harvested, washed with Episerf, fixed in 2mL per 1x107 cells (10 min in 1% formaldehyde), quenched with glycine in 10mL (at 125 mM final), washed three times with PBS, and pelleted. Each pellet containing 1x107 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 1 mM EDTA, 0.1% SDS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65oC, RNAse A at 1µg/µL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 4x107, with Dynabeads (Protein G, ThermoFisher) in IP buffer (10 mM Tris at pH 8, 1 mM EDTA, 0.1% SDS, 150 mM NaCl, 10% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65oC, Proteinase K at 400ng/µL, overnight) and DNA was extracted. Single-end libraries were prepared and sequenced in 100bp reads runs according to Illumina instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
45182702
Reads aligned (%)
93.2
Duplicates removed (%)
23.0
Number of peaks
427 (qval < 1E-05)

mm9

Number of total reads
45182702
Reads aligned (%)
92.9
Duplicates removed (%)
23.0
Number of peaks
488 (qval < 1E-05)

Base call quality data from DBCLS SRA