Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nr1d1

Cell type

Cell type Class
Muscle
Cell type
gastrocnemius
NA
NA

Attributes by original data submitter

Sample

source_name
gastrocnemius
tissue
gastrocnemius
strain
C57BL/6J
time
Zeitgeber Time 8
gender
male
genotype
Wild Type
chip antibody
Rev-erb⍺ (#23678 and #27401 produced by Ron Evans)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described (Uhlenhaut et al. 2012) with minor modifications. Briefly, around 300 mg of frozen muscle was homogenized, filtered through a 70µm cell strainer, and pellet fixed in 1% Formaldehyde. Nuclei were purified and chromatin sonicated to a 1-0.5 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies. Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
28990908
Reads aligned (%)
98.4
Duplicates removed (%)
23.8
Number of peaks
236 (qval < 1E-05)

mm9

Number of total reads
28990908
Reads aligned (%)
98.3
Duplicates removed (%)
23.7
Number of peaks
205 (qval < 1E-05)

Base call quality data from DBCLS SRA