Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Arntl

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver
strain
C57B6/CR
age
22 months
genotype
WT
treatment
NR (~400 mg/kg)
treatment time point
6 months
collection time point
ZT20
chip antibody
BMAL1 (Bass Lab, Millipore ABE2599)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Liver was collected at the indicated time points and processed for ChIP-seq as previously published. Briefly, liver was fixed in disuccinimidyl glutarate (2mM in PBS + 1% DMSO, 30 min) and formaldehyde (1% in PBS, 10 min) prior to aliquoting and freezing at -80˚C. For BMAL1 (antibody produced in Bass Lab as in (43), Millipore ABE2599) and HSF1 (Cell Signaling 4356) ChIP-Seq, nucleii from a quarter of a liver were isolated in buffer (150 mM NaCl, 5 mM EDTA pH8, 50 mM Tris-HCl pH8, 0.35% NP-40) in the presence of protease inhibitors by needle, then sheared in 1% SDS buffer in a sonicator (diagenode) for 6 cycles 30on/30off at 4˚C. An aliquot for input samples was taken after shearing. Chromatin was diluted 1:10 in dilution buffer (.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 1.2 mM EDTA pH8, 1.67 mM Tris-HCl pH8), and immunoprecipitations with 15 µg of antibody were performed overnight at 4˚C, rotating. Secondary-conjugated, BSA-blocked paramagnetic beads were used to pull down protein/DNA complexes. Chromatin was de-crosslinked and purified by Qiagen MinElute column. Inputs were quantified by Qubit Fluorometer (Invitrogen) for each liver, and 2 ng of equimolar pools of the replicates per condition were processed into libraries. library prep with NEBNext Ultra II library prep kit. Libraries were size-selected to 200-600 bp on the Sage Pippin Prep prior to PCR amplification. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
15024823
Reads aligned (%)
95.3
Duplicates removed (%)
13.1
Number of peaks
3066 (qval < 1E-05)

mm9

Number of total reads
15024823
Reads aligned (%)
95.1
Duplicates removed (%)
13.2
Number of peaks
3054 (qval < 1E-05)

Base call quality data from DBCLS SRA