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Sample GSM2363483 Query DataSets for GSM2363483
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 RNA was extracted by Rneasy Mini Kit (Quiagen)
Samples were sequenced in house on a single flow cell on the illumina NextSeq
Library strategy RNA-Seq
Library source genomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Cole.14L_N_young.RNA-seq
RNA sequencing of young (2 month) mice
Data processing Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to mm9 whole genome using Tophat with default settings
FPKM matrix was derived using Cufflinks suite using default settings
Differential expression quantified using DESeq2 (Bioconductor) following non-normalised read counting with Htseq (intersection-nonempty)
Genome_build: mm9
Supplementary_files_format_and_content: Summary files describe the results of DESeq2 differential expression analysis for core comparisons as well as FPKM matrix for all replicate created using Cufflinks suite.
Submission date Oct 28, 2016
Last update date May 15, 2019
Contact name Neil A Robertson
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 GPL19057
Series (2)
GSE89272 Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions (RNA-Seq)
GSE89275 Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions
BioSample SAMN05950827
SRA SRX2279682

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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