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| Status |
Public on Apr 30, 2024 |
| Title |
OC + Apiopaeonoside #3 |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Mus musculus |
| Characteristics |
tissue: Ovary
strain: Balb/c
Sex: Female
genotype: Wildtype
treatment: Apiopaeonoside
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| Treatment protocol |
Mice were randomly divided into groups of n=3 each. Aged mice(38-week-old) were orally administered either vehicle (distilled water containing 0.5% Dimethyl sulfoxide) or each of the 39 single compounds at a dose of 5mg/kg, five times a week for four weeks.
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| Growth protocol |
Thirty-eight-week-old Balb/c female mice were purchased from the Central Lab. Animal Inc.(Seoul, Korea). All mice were maintained on an ad libitum diet in a specific pathogen-free room under a 12-hour light-dark cycle. All mice handling and experimental procedures were approved by the Korea Institute of Oriental Medicine Institutional Animal Care and Use Committee (approval number 20-090).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Following compound administration for 4 weeks, to create a post-ovulatory state, mice were induced by intraperitoneal injection of 5 IU of pregnant mare serum gonadotropin (PMSG; HOR-272; Prospec, Rehovot, Israel), followed by an injection of 5 IU of human chorionic gonadotropin (hCG; HOR-250; Prospec) 48 hours later. Ovaries were removed from mice and weighed at 14h-16h post-hCG administration. The ovary was immediately preserved in liquid nitrogen for RNA sequencing. Each left ovary (n=3) of a post-ovulation mouse was immersed in 300ul TRIzol (Invitrogen, Carlsbad, CA, USA) and homogenized using a disposable grinder (Biomasher II; 890863; LMS Co., Tokyo, Japan).
Total RNA was isolated using Trizol reagent (Invitrogen). The quality of purity and integrity of the extracted RNA samples were analyzed using a NanoDrop ND-2000 Spectrophotometer (Thermo Inc., DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). RNA library was constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to 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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| Description |
Thirty-eight-week-old Balb/c female mice were orally administered single compound treatment at a dose of 5mg/kg, five times a week for four weeks.
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| Data processing |
Initial evaluation of the quality of raw RNA-seq fastq file was conducted utilizing FASTQC (v1.9).
The BBduk module within the bbmap toolkit (v38.95) was conducted with specific parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, and minlength=20 to eliminate adapter sequences and low-quality reads.
The cleaned reads were mapped to the mouse reference genome (build GRCm39) through the STAR aligner (v2.7.9a)
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) along with the gene structure file (GRCm39.104.gtf).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample
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| Submission date |
Apr 15, 2024 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Haeseung Lee |
| E-mail(s) |
haeseung@pusan.ac.kr
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| Organization name |
Pusan National University
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| Department |
College of Pharmacy
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| Street address |
63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu
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| City |
Busan |
| ZIP/Postal code |
46241 |
| Country |
South Korea |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE264002 |
Transcriptome profiling of ovaries in aged mice administered with individual ingredients of Samul-tang |
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| Relations |
| BioSample |
SAMN40977688 |
| SRA |
SRX24269518 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8208672_OC+C30-3.bbduk.STAR.RSEM.genes.results.gz |
1.1 Mb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
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