|
| Status |
Public on May 01, 2024 |
| Title |
CTRL_Male_3 |
| Sample type |
SRA |
| |
|
| Source name |
Gastrocnemius Muscle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Gastrocnemius Muscle
Sex: Male
treatment: untreated
treatment dose: drinking water
experimental batch: BATCH_2
|
| Treatment protocol |
Haenkenium extract was administered at the dosage of 0.5 mg/kg/day in drinking water. Mice treatment started at 20 months of age. HK extract was replaced and prepared fresh on a weekly basis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with TRIzol reagent (Sigma-Aldrich) and purified using the Direct-zol RNA MiniPrep Kit (Zymo Research) according to the manufacturer's protocol.
RNA integrity was checked with Agilent 2100 Bioanalyzer system. Protocol used was NEBNext rRNA depletion KIT. Sequencing of the libraries was performed using the NextSeq 500 with the NextSeq 500/550 High Output Kit v2 (75 cycles; Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
M1U_S12
|
| Data processing |
The overall quality of sequencing reads was evaluated using FastQC. Alignments to the reference mouse genome (GRCm38.p6) were performed using STAR (v.2.6.1c) in two-pass mode. Gene expression was quantified at the gene level by using the comprehensive annotations made available by Gencode (M25). Samples were adjusted for library size and normalized with the variance stabilizing transformation in the R statistical environment using DESeq2 (v1.28.1).
Assembly: GRCm38.p6
Supplementary files format and content: tab delimited raw count matrix, quantified at the gene level by using Gencode (M25 GTF-File) and STAR (v.2.6.1c)
|
| |
|
| Submission date |
Apr 26, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Marco Bolis |
| E-mail(s) |
marco.bolis@ior.usi.ch
|
| Organization name |
IOR Institute of Oncology Research
|
| Street address |
Via Francesco Chiesa
|
| City |
Bellinzona |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE266005 |
Targeting senescence induced by age or chemotherapy with a polyphenol-rich natural extract improves longevity and healthspan in mice |
|
| Relations |
| BioSample |
SAMN41096358 |
| SRA |
SRX24380136 |
