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Sample GSM4523025 Query DataSets for GSM4523025
Status Public on May 01, 2022
Title YoungControl_2
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics tissue: Liver
age: 11 weeks old
selection: Non-selected
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description 02092019_04
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
 
Submission date May 07, 2020
Last update date May 02, 2022
Contact name Anuroop Venkateswaran Venkatasubramani
E-mail(s) anuroop.venkatasubramani@bmc.med.lmu.de
Phone 01774100976
Organization name Ludwig-Maximilian University of Munich
Department Molecular Biology
Lab Axel Imhof
Street address Großhadernerstr. 9
City Planegg-Martinsried
State/province Bavaria
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL18480
Series (1)
GSE150073 Dietary intervention improves health metrics and life expectancy of the genetically obese Titan mouse
Relations
BioSample SAMN14850420
SRA SRX8288979

Supplementary file Size Download File type/resource
GSM4523025_02092019_04_ACTGATAT.ReadsPerGene.out.tab.gz 276.1 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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