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| Status |
Public on May 07, 2024 |
| Title |
Liver, seamglutide, rep1 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57BL/6N
genotype: WT
Sex: male
diet: low-protein
treatment: semaglutide
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| Treatment protocol |
Animals were either treated with vehicle solution (saline) or semaglutide (Novo Nordisk) at 30 nmol/kg of body weight, twice a week.
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| Growth protocol |
Animals were kept on a low-protein diet for 5 weeks after weaning (5% in kcal).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from liver using Nucleospin RNA kit (Macherey-Nagel, 740955.250), following manufacturer's instructions.
For each sample, mRNA purification, based on oligo dT-based mRNA isolation, was conducted with a starting material of 1µg of total RNA using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and following the manufacturer’s instructions. Then, single-indexed libraries were built using the CORALL Total RNA-Seq Library Prep Kit (Lexogen) and following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were then analyzed using a local pipeline derived from the one supported by Lexogen.
Adapter sequences were first removed using the Cutadapt package (version 3.5) and quality control of reads was performed using FastQC.
Read mapping was achieved with STAR (Spliced Transcripts Alignment to a Reference, version 2.7.11a) using the Mus musculus GRCm39 genome reference (Ensembl, release 110).
Umi_tools dedup (version 1.1.2) was conducted to UMI deduplication.
The mapped reads were then quantified by htseq-count (version 2.0.3) [34] allowing to generate a count table by sample.
Assembly: GRCm39 (Ensembl, release 110)
Supplementary files format and content: One tsv file for each sample containig raw counts
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| Submission date |
May 02, 2024 |
| Last update date |
May 07, 2024 |
| Contact name |
Filipe De Vadder |
| E-mail(s) |
filipe.de_vadder@ens-lyon.fr
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| Organization name |
Institut de Génomique Fonctionnelle, ENS de Lyon, CNRS UMR5242, Université Claude Bernard Lyon 1
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| Street address |
32-34 Avenue Tony Garnier
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| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE266477 |
Semaglutide interferes with postnatal growth in a diet-dependent manner |
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| Relations |
| BioSample |
SAMN41177350 |
| SRA |
SRX24437728 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8247929_Lib6_66_23_S6_R1_001.tsv.gz |
407.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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