Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4ac

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_MLXDN-H4AC
cell line
C2C12
cell type
myoblasts
transduced with
MLX DN
chip antibody
Rabbit Anti-acetyl-histone H4
chip antibody vendor
Millipore

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-sequencing, libraries were prepared from 10 ng DNA using the NEB Next ChIP-Seq Library Prep Reagent Set for Illumina with NEB Next High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation; the Ampure size selection step prior to PCR was eliminated; the 72C extension step of the PCR was lengthened to 45 s. Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer) Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies) and Kapa Library Quantificaiton kit (Kapa Biosystems) or low pass sequencing on a MiSeq nano kit (Illumina). Fifty cycle single end sequencing was performed on an Illumlina HiSeq 2500 for DNA obtained from MLX-WT and MLX-DN samples immunoprecipitated for acetylated histone H4 with three replicates for each sample including input chromatin as control.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
36511754
Reads aligned (%)
99.5
Duplicates removed (%)
8.0
Number of peaks
8741 (qval < 1E-05)

mm9

Number of total reads
36511754
Reads aligned (%)
98.2
Duplicates removed (%)
8.5
Number of peaks
8947 (qval < 1E-05)

Base call quality data from DBCLS SRA