|
| Status |
Public on Feb 16, 2017 |
| Title |
DO Rep4 - Ames Prop1 Hom – 22 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 |
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.4L_df_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.DO-WTO.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv
|
| 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 |
| 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 |
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 |
|
| Relations |
| BioSample |
SAMN05950837 |
| SRA |
SRX2279672 |
