Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Muscle
Cell type
Skeletal muscle
NA
NA

Attributes by original data submitter

Sample

source_name
adult skeletal muscle
tissue
adult skeletal muscle
age
10 weeks
chip antibody
none
strain
BALB/c

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen tissues were pulverized in Covaris tissue TUBEs (Covaris 520001) using a chilled hammer on a cold metallic block, in dry ice. Powdered tissue was resuspended in PBS, cross-linked in 1% formaldehyde for 15 minutes. After blocking crosslink with 0.125M glycine for 5 minutes and washes with PBS plus protease and phosphatase inhibitors, pellet was resuspended in Farnham buffer (5 mM PIPES pH 8.0; 85 mM KCl; 0.5% NP-40) and briefly homogenized with a tissue homogenizer. Cells were subsequently lysed in RIPA buffer (1x PBS; 1% NP-40; 0.5% sodium deoxycholate; 0.1% SDS). 100mg of starting tissue was used for each antibody. Chromatin was sonicated to fragments length of approximately 0.5Kb and immunoprecipitated with 3.5µg of BRD4 antibody. Immunoprecipitation procedures were performed as in Proserpio et al., 2013. For ChIPSeq, 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
34751344
Reads aligned (%)
96.0
Duplicates removed (%)
13.3
Number of peaks
440 (qval < 1E-05)

mm9

Number of total reads
34751344
Reads aligned (%)
95.8
Duplicates removed (%)
13.4
Number of peaks
449 (qval < 1E-05)

Base call quality data from DBCLS SRA