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
myoblasts_input
cell line
C2C12
cell type
Growing C1C12 myoblasts
chromatin preparation method
Sonication
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Libraries were generated from input chromatin or ChIP enriched chromatin according to Illumina's standard protocol but using reagents from other companies: DNA end-repair was performed using the End-It DNA repair kit, Epicentre (cat:ER81050). A-overhang generation was performed uising Klenow from NED (cat: M0212). Adapter ligation was performede using the LigaFast kit from Promega (cat:M8225). LM-PCR was performed using Phusion DNA pol master mix from NEB (cat:F-531S). Very stringent quality controls were applied to the libraries: 1. Enrichment of a given site had to be preserved in the libraries in a manner comparable to the original ChIP. 10-12 positive and negative sites were tested for library preparation. 2. The total yield of the LM-PCR had to be ~500 ng. 3. The size distribution had to be centred around 350 bp for sonicated with a variation no larger than +/- 75 bp. Libraries that did not pass these criteria were considered substandard and were not used for sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
18876516
Reads aligned (%)
94.9
Duplicates removed (%)
15.7
Number of peaks
449 (qval < 1E-05)

mm9

Number of total reads
18876516
Reads aligned (%)
94.6
Duplicates removed (%)
15.7
Number of peaks
490 (qval < 1E-05)

Base call quality data from DBCLS SRA