Antigen

Antigen Class

Bisulfite-Seq

Antigen

Bisulfite-Seq

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.

Sample

source_name

AL 5m BS-seq

strain

C3B6F1

gender

female

diet

control-fed (AL)

age

5 months

tissue

liver

Sequenced DNA Library

library_strategy

Bisulfite-Seq

library_source

GENOMIC

library_selection

RANDOM

library_construction_protocol

RNA-seq: RNA from 3 AL and 3 DR animals per time point was isolated from 30 mg of liver tissue using Trizol Reagent (ThermoFisher) according to the manufacturer’s instructions, followed by DNase treatment with the TURBO DNA-free Kit (ThermoFisher). RNA integrity was analyzed using the Agilent TapeStation System. BS-seq: DNA of 3 AL and 3 DR animals per timepoint was isolated from 30 mg of liver tissue using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA-seq: TruSeq RNA-seq library preparation was conducted as previously described (Sultan, et al., 2012) using 3 µg of total RNA as input and rRNA depletion. Barcoded libraries were sequenced with 2x40 mio, 100 bp paired-end reads on an Illumina HiSeq2500. BS-seq: Around 400 ng genomic DNA was used as input for BS-Seq library generation. DNA was sonicated, and end repair and A-tailing were performed using the NEB Next kit according to the manufacturers’ instructions. Illumina’s Early Access Methylation Adaptor Oligo Kit was used for adaptor ligation. Adaptor-ligated DNA was treated with sodium-bisulfite using the Imprint DNA Modification Kit from Sigma-Aldrich according to the manufacturer’s instructions for the one-step protocol. Bisulfite-treated DNA was amplified using PfuTurbo Cx Hotstart DNA Polymerase from Agilent Technologies with 14–18 cycles depending on input amount. Size selection was performed by gel extraction for DNA fragments between 200 bp and 250 bp, as adapted from (Seisenberger et al., 2012). Libraries of young samples were sequenced using the paired-end protocol. Old sample libraries were sequenced using single-end protocol and a subsequent re-run using a paired-end protocol to increase coverage.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

70538476

Reads aligned (%)

89.1

Coverage rate (×)

1.9

Number of hyper MRs

221380 (qval < 1E-05)

mm9

Number of total reads

70538476

Reads aligned (%)

90.2

Coverage rate (×)

2.0

Number of hyper MRs

220776 (qval < 1E-05)