|
| Status |
Public on Feb 16, 2017 |
| Title |
WTY Rep2 – Ames Prop1 Het – 2 month |
| Sample type |
SRA |
| |
|
| Source name |
Hepatocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: Ames Dwarf
genotype: Prop1 Het
|
| 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 |
SAMN05950909 |
| SRA |
SRX2279712 |
