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Sample GSM2363496 Query DataSets for GSM2363496
Status Public on Feb 16, 2017
Title DY Rep3 – Ames Prop1 Hom – 2 month
Sample type SRA
 
Source name Hepatocytes
Organism Mus musculus
Characteristics strain: Ames Dwarf
genotype: Prop1 Hom
Treatment protocol All mice were bred and maintained at the University of North Dakota Center for Biomedical Research under controlled conditions of photoperiod (12:12 h light/dark cycle) and temperature (22 -/+1 °C) and ad libitum access to food (Teklad #8640) and water. Animal procedures were reviewed and approved by the UND Institutional Animal Care and Use Committee. Liver tissue from male WT and Ames dwarf mice was collected at 2 and 22 months of age (n=4/genotype/age).
Growth protocol Ames dwarf mice were derived from a closed colony with a heterogeneous background (over 25 years) at the University of North Dakota. Dwarf mice were generated by mating either homozygous (df/df) or heterozygous (df/+) dwarf males with carrier females (df/+).
Extracted molecule genomic DNA
Extraction protocol DNA was extracted by Dneasy blood and tissue kit (Quiagen)
Libraries were prepared by BGI, Shenzhen. Briefly, DNA is fragmented and methylated adapters are ligated to DNA fragments. DNA is bisulphite treated and sequenced on Illumina platforms as per manufacturers instructions.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 4000
 
Description Bisulfite sequencing of young (2 month) mice
Data processing Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to mm9 whole genome using bismark v0.10.1 (bowtie2 v2.1.0) with directional setting and chunkmbs set to 256. Remaining default settings.
Multiple reads where both ends of the fragment align to the same genomic positions on the same strand were reduced to a single instance. Reads with more than 3 methylated cytosines in non-CpG contexts are discarded.
Reads are summarised on a per-CpG basis.
Genome_build: mm9
Supplementary_files_format_and_content: Summary files represent the number of reads supporting methylated/unmethylated bases at each CpG sequenced in that sample (Format is: chr <tab> position <tab> methylated reads <tab> unmethylated reads).
 
Submission date Oct 28, 2016
Last update date May 15, 2019
Contact name Neil A Robertson
E-mail(s) neil.alistair.robertson@hotmail.co.uk
Organization name University of Glasgow
Department Beatson Institute for Cancer Research
Lab Kristina Kirschner
Street address Switchback Road
City Glasgow
State/province Scotland
ZIP/Postal code G61 1BD
Country United Kingdom
 
Platform ID GPL21103
Series (2)
GSE89273 Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions (WGBS 1)
GSE89275 Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions
Relations
Reanalyzed by GSE120136
BioSample SAMN05950912
SRA SRX2279709

Supplementary file Size Download File type/resource
GSM2363496_Cole.11L_df_young.Rep3.CpG_context_aggregate.txt.gz 133.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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