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 forChIP102.H3K36me3_siNS
cell line
C2C12
cell condition
myoblasts
library protocol
ChIP-seq

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Preparation of solubilized chromatin fraction and immunoprecipitation: Cell pellets were resuspended in buffer A (10 mM HEPES pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 1 mM dithiothreitol (DTT), and protease inhibitors (aprotinin, leupeptin, pepstatin A, and phenylmethyl sulphonyl fluoride)), supplemented with Triton X-100 (0.1%), and incubated on ice for 5 minutes. The nuclear pellet was separated from the cytoplasmic fraction, washed once with buffer A, and collected by centrifugation. Nuclei were lysed with buffer B (3 mM EDTA, 0.2 mM EGTA, 1 mM dithiothreitol (DTT), and protease inhibitors (aprotinin, leupeptin, pepstatin A, and phenylmethyl sulphonyl fluoride)). The solubilized chromatin fraction was separated from nucleoplasm by centrifugation at 2250 g for 4 minutes at 4°C, washed once with buffer B, and collected by centrifugation. For immunoprecipitations, the chromatin pellet was resuspended with binding buffer (20 mM Hepes pH7.9, 100 mM potassium chloride, 0.2 mM EDTA, 20% glycerol, 0.5 mM dithiothreitol (DTT), and 0.5mM AEBSF). 1 mg of protein was immunoprecipated, and antibody-protein A sepharose beads were washed three times with buffer (50 mM Hepes pH7.9, 250 mM sodium chloride, 5 mM EDTA, 0.50% NP-40, and 10% glycerol) prior to SDS–PAGE and immuno-blotting.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
52538852
Reads aligned (%)
97.7
Duplicates removed (%)
15.0
Number of peaks
626 (qval < 1E-05)

mm9

Number of total reads
52538852
Reads aligned (%)
97.4
Duplicates removed (%)
14.9
Number of peaks
698 (qval < 1E-05)

Base call quality data from DBCLS SRA