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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 01, 2022 |
| Title |
OldControl_5 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
age: 19-21 weeks old
selection: Non-selected
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| Growth protocol |
The animals were maintained in a specific pathogen-free (SPF) environment with defined hygienic conditions at a temperature of 22.5±0.2°C, at least 40% humidity and a controlled light regime with a 12:12-h light-dark cycle. The mice were kept in Polysulfon-cages of 365 x 207 x 140 mm (H-Temp PSU, Type II L, Eurostandard, Tecniplast, Germany) and had free access to pellet concentrate and water. A standard breeding diet (SD) with 22% crude protein, 34% starch, 5% sugar, 4.5% crude fat, 3.9% crude fiber and 51.2% N free extracts (ssniff® M-Z autoclavable, Soest, Germany) were fed ad libitum.
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| Extracted molecule |
total RNA |
| Extraction protocol |
50 mg of tissues were homogenized in Trizol (Thermo Fisher; cat. no. 15596026) and processed according to the manufacturer’s instructions. RNA concentration and A260/280 ratio was measured with NanoDrop, followed by Bioanalyzer using RNA pico assay kit using manufacturer’s protocol.
rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) [NEB #E6310] and library preparation for RNA-sequencing was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina [NEB #E7760] following manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
02092019_78
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| Data processing |
Read mapping of mouse tissue samples to the mouse genome (GRCm38) and counting of reads mapped to genes were performed using STAR v2.5.3a (Dobin and Gingeras, 2015) using parameters --quantMode GeneCounts and providing annotation –sjdbGTFfile Mus_musculus.GRCm38.97.gtf. Aligned reads were filtered for unmapped, multimapped and ambiguous reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated text file: read counts per gene
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| Submission date |
May 07, 2020 |
| Last update date |
May 02, 2022 |
| Contact name |
Anuroop Venkateswaran Venkatasubramani |
| E-mail(s) |
a.venkateswaran@mdc-berlin.de
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| Organization name |
MDC-Berlin
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| Lab |
Ilaria Piazza
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| Street address |
Robert-Rössle-Straße 10
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| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE150073 |
Dietary intervention improves health metrics and life expectancy of the genetically obese Titan mouse |
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| Relations |
| BioSample |
SAMN14850422 |
| SRA |
SRX8288977 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4523023_02092019_78_GTGGCCTT.ReadsPerGene.out.tab.gz |
276.1 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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